@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 vivo, in vitro, and multi-omics analyses. Earthworms efficiently accumulated 8:2 FTSA and biotransformed it into 11 distinct PFAS via α/β-oxidation mediated by metabolic enzymes, with trifluoroacetic acid (TFA) as the predominant metabolite. 8:2 FTSA induced significant oxidative stress, activated metabolic detoxification, and caused potential neurotoxic effects in earthworms. Furthermore, 8:2 FTSA exposure disrupted the microbial communities in the earthworm-soil system, with greater sensitivity observed in communities on the earthworm skin and in the soil compared to those in the gut. Predicted functional profiling further suggested that the gut microbiota may have greater potential for xenobiotic transformation, whereas the skin microbiota exhibited a host-dependent and low-activity phenotype. Raoultella ornithinolytica, isolated from earthworm gut and skin, transformed over 68% of 8:2 FTSA in 6 days via α/β-oxidation. Our findings advance the understanding of 8:2 FTSA interactions with the soil-earthworm system and provide a critical foundation for assessing its ecological risk in terrestrial environments.},
}
@article {pmid42082125,
year = {2026},
author = {Marzec-Grządziel, A and Borsuk, G},
title = {Between Host and Parasite: The Microbiome of Varroa destructor and Its Relationship with Honey Bees.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105617},
doi = {10.1016/j.dci.2026.105617},
pmid = {42082125},
issn = {1879-0089},
abstract = {The study of the microbiome of the mite Varroa destructor is crucial for understanding parasite-host interactions and their potential health implications for honey bees (Apis mellifera). The aim of this research was to characterize the microbial diversity of Varroa destructor populations collected from the body surface of honey bees and compare it with microbiome of Apis mellifera. DNA isolation was performed using standard methods, followed by next-generation sequencing (NGS) of the V3-V4 region of the 16S rRNA gene. The obtained bioinformatic data underwent taxonomic analysis, enabling the identification of dominant bacterial genera present in the Varroa and Apis mellifera microbiome. Results revealed significant microbial diversity, with dominance primarily by bacteria belonging to the families Acetobacteraceae, Morganellaceae, and Segniliparaceae. The identified bacteria may play a critical role in the pathogenicity of Varroa destructor, directly or indirectly affecting the health and condition of bees. These findings provide new insights into potential therapeutic and preventive targets for protecting bee colonies against the detrimental effects of Varroa mites.},
}
@article {pmid42082515,
year = {2026},
author = {Geng, Y and Zhang, J and Hu, Y and Tong, Q and Ye, Z and Yu, J and Tu, J and Wang, N and Zhang, HY and Liu, S and Jiang, Q and Yan, X and Wang, Y and Feng, Z},
title = {A manually curated pig gut microbiome dataset for precision feeding.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07238-8},
pmid = {42082515},
issn = {2052-4463},
support = {203-61022300002//the National Digital Animal Husbandry (Pig) Innovation Center Project/ ; },
abstract = {The gut microbiome of pigs is a complex microbial ecosystem critical to host health and agricultural productivity. While amplicon sequencing studies have expanded our understanding of this community, a lack of standardized data and metadata often hinders comparative analysis and data reuse. To address this challenge, we present the Pig Gut Microbiome Dataset (PGMD, version 1.0), a comprehensive resource developed through the systematic selection of publications, extensive manual curation of associated metadata, and standardized reprocessing of raw amplicon sequencing data. This initial release integrates 202 publications (encompassing 207 16S rRNA gene sequencing data BioProjects), comprising 12,336 samples, collected from 22 countries. The dataset encompasses 52 host species and 3,028 taxonomic groups. Samples are systematically categorized by research topics and host phenotypes, enabling users to explore microbial community composition, identify differentially abundant taxa across experimental conditions and phenotypes, investigate six core phenotype-associated microbial clades, and determine dominant taxa across four key growth stages. PGMD significantly enhances the standardization and integration of pig gut microbiome data, serving as a valuable resource for research towards precision feeding and improved animal health. All data in the dataset are hosted and available in figshare https://doi.org/10.6084/m9.figshare.25911745.v1.},
}
@article {pmid42082522,
year = {2026},
author = {Motger-Albertí, A and Gallardo-Nuell, L and Rosell-Díaz, M and Stefoglo, M and Pons, J and Garre-Olmo, J and Pérez-Brocal, V and Moya, A and Puig, J and Ramos, R and Mayneris-Perxachs, J and Fernández-Real, JM},
title = {Sex-specific microbial and tryptophan signatures of depression implicate archaeal methanogens and indole-3-acetic acid only in women.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00983-z},
pmid = {42082522},
issn = {2055-5008},
support = {PI20/01090//Instituto de Salud Carlos III/ ; PI15/01934//Instituto de Salud Carlos III/ ; CNS2023-144218//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2021 SGR 01263//Generalitat de Catalunya/ ; },
abstract = {Sex differences in mental health are often overlooked, yet gut microbiota-host metabolite interactions may contribute to sexual dimorphism in depression. In a population-based cohort, we investigated sex-specific links among plasma tryptophan metabolites, depressive symptoms (PHQ-9), and the gut microbiome, controlling for smoking, diet, alcohol, and physical activity. Women (N = 419) exhibited higher plasma indole-3-acetic acid (IAA) and picolinic acid (PA) concentrations, but lower trigonelline (TRIG) than men (N = 383). Machine learning models with SHAP explanations revealed that IAA and TRIG were positively associated, whereas PA was negatively associated with depression severity in women, whereas only kynurenic acid (KA) was inversely associated in men. In women, depression severity strongly correlated with methanogenic archaea, including Methanobrevibacter smithii, and microbial methane-production pathways. Methanobrevibacter and specifically M. smithii were negatively linked to genes for tryptophan, PA, and KA biosynthesis, but positively to genes for IAA and nicotinate/nicotinamide metabolism. Most microbial species associated with depression severity in women were predicted to produce IAA. These findings reveal pronounced sex-specific microbiome-metabolite interactions, highlighting potentially distinct microbial mechanisms shaping depression in men and women.},
}
@article {pmid42082767,
year = {2026},
author = {Lebeer, S and Goormachtig, S},
title = {Practical lessons from microbiome citizen-science projects.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42082767},
issn = {2058-5276},
support = {852600//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049022N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; S006424N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; VR 2016 2312 Doc.1521/4//Vlaams Instituut voor Biotechnologie (Flanders Institute for Biotechnology)/ ; },
}
@article {pmid42082772,
year = {2026},
author = {Alshareedah, I and Brunner, JD and Chain, PSG and Kumar, A},
title = {Significance and challenges in dissecting cancer-bacteriome interactions.},
journal = {BJC reports},
volume = {4},
number = {1},
pages = {},
pmid = {42082772},
issn = {2731-9377},
support = {20251143PRD1//Los Alamos National Laboratory/ ; },
abstract = {Cancer is the leading cause of death around the world. While some types of cancer have become manageable due to advancements in medicine, most cancers still lack available cures and treatments. Recent studies have shown that changes in the human microbiome, especially in the bacteriome, are associated with some cancers. Certain bacterial strains have been reported to promote the initiation and progression of cancer in humans. Other studies have used sequencing to observe changes in the bacteriome of healthy and cancer patients. However, studies that investigate the interactions between cancer cells and the complex bacteriome as a whole remain scarce. This is due to the absence of experimental methods to study the interactions between cancer cells and complex bacterial populations, which has delayed the progress in identifying cancer-causing and cancer-inhibiting bacteria, and in understanding the bacterial interactions and their influence on host cells. Here, we review approaches to studying cancer cell interactions with complex bacteriomes and suggest possible routes to overcome this problem, highlighting the need for interdisciplinary studies that may help advance this field. We speculate that a good understanding of cancer-bacteriome interactions may open the door to new lines of holistic bacteriotherapy for cancer that is otherwise unavailable.},
}
@article {pmid42083021,
year = {2026},
author = {Han, Y and Cui, J and Huang, X and Guo, P and Yang, S},
title = {Microbial inoculants with straw mediate degradation-level-specific changes in soil carbon cycling genes and microbial community.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00898-4},
pmid = {42083021},
issn = {2524-6372},
support = {2022YFD1500600//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Enhancing soil organic carbon (SOC) sequestration in degraded lands is critical for climate mitigation and sustainable agriculture. While straw amendment combined with microbial inoculants holds great promise, the underlying mechanisms governing its impact on soil microbiome and carbon cycling genes remain poorly understood.<br><br>RESULTS: Here, we employed metagenomic sequencing to analyze responses in soil carbon (C) cycling genes, microbial community structure, and functional profiles across three degradation levels (severely, moderately, and non-degraded) of cinnamon soils under straw application alone or in combination with microbial inoculants. Results showed that both straw and straw-microbial inoculants treatments significantly improved soil properties, with improvements in available nitrogen and microbial biomass carbon (severe degradation), SOC (moderate degradation), and available nutrients (non-degradation). The combined application notably reshaped microbial communities by enhancing bacterial alpha diversity while reducing fungal diversity, and strengthened the relationship of relevant key soil C genes in severely degraded soils. Soil pH exhibited significant positive correlations with soil C cycling genes. Key bacterial genera (Sphingomonas, Bradyrhizobium) showed strong associations with ABC transporters and glycoside hydrolases, and fungal genus (Chaetomium) linked to pyruvate and purine metabolism. Importantly, we observed degradation-level specificity: straw addition significantly increased the abundance of the amylase gene K01214 (encoding &#x3b1;-amylase for starch hydrolysis) in severely degraded soils, whereas the straw-inoculant combination enriched the chitinase gene K01207 (encoding chitinase for chitin hydrolysis) in moderately degraded soils.<br><br>CONCLUSIONS: Accordingly, we propose targeted application of straw with a customized chitinolytic-cellulolytic synthetic microbial community (1-5% of straw mass) to restore carbon cycling functions in degraded soils, while adopting optimized agronomic management to preserve microbiome stability in non-degraded soils. Our findings provide novel insights into microbial-mediated carbon cycling and a foundation for targeted soil restoration.},
}
@article {pmid42083054,
year = {2026},
author = {Todd, C and Rolshausen, PE},
title = {Microbial succession from nursery to vineyard highlights the role of beneficial and pathogenic microbes in young vineyard yield.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00905-8},
pmid = {42083054},
issn = {2524-6372},
abstract = {BACKGROUND: The grapevine microbiome plays a central role in shaping vineyard performance, yet the influence of nursery inherited microbes on vineyard establishment and early productivity remains poorly understood. Our goals were to study the endosphere and rhizosphere microbiome succession as grapevine transition from nursery to vineyard and determine in what capacity the endogenous microbiome from the nursery shapes vineyard outcomes.<br><br>RESULTS: We profiled, using amplicon-based sequencing, the fungal and bacterial communities across five bio-compartments (scion graft union, rootstock graft union, crown, roots, and rhizosphere) from two sets of grafted vines (Cabernet Sauvignon and Chardonnay grafted on 1103P rootstock) originating from two nurseries and followed their succession over three years after planting in a commercial vineyard. Nurseries produced vines with distinct endospheric microbiomes that converged overtime but that remained significantly different after three years. Microbial turnover occurred at a much faster pace in belowground (root and rhizosphere) compared to trunk compartments post-planting, with 15% of the initial microbes persisting in three-year-old vineyard. The fungal pathobiome partially inherited from nurseries and associated with vascular diseases of the trunk and root was also clearly distinct after three years. Yet, we did not observe typical disease symptoms development or vine death as we would expect, likely because vines were not under stress during the experimental timeframe. Vineyard yield was highly variable among clonal vines, and statistical modeling revealed that a narrow subset of amplicon sequence variants (ASVs) explained a large portion of this variance. Regression models using the top ten high-impact ASVs accounted for 51% and 60% of yield variation in trunk and belowground compartments, respectively. Notably, 16 of the 19 yield-associated ASVs originated from nurseries, underscoring the long-term influence of nursery-derived microbes on vineyard success.<br><br>CONCLUSION: These findings highlight the dual role of beneficial and pathogenic nursery microbiota in shaping grapevine performance. It also suggests that the nursery life stage could be leveraged to engineer the grapevine microbiome and improve vineyard resilience.},
}
@article {pmid42083059,
year = {2026},
author = {Diop, K and Benlaïfaoui, M and Hunter, S and Méndez-Salazar, EO and Hakozaki, T and Richard, C and Prifti, DK and Kourtian, S and Proulx-Rocray, F and Naimi, S and Ponce, M and Messaoudene, M and Cauchois, F and Belkaid, W and Bataille, V and Lee, K and Mihalcioiu, C and Watson, IR and Elkrief, A and Routy, B},
title = {Metagenomics and culturomics reveal the dual role of the gut microbiome in the development of immune-related toxicities and the efficacy of immune checkpoint inhibitors in cancer.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02419-4},
pmid = {42083059},
issn = {2049-2618},
support = {284894//Fonds de recherche du Qu&#xe9;bec/ ; },
abstract = {BACKGROUND: Despite their major impact on cancer treatment, immune checkpoint inhibitors (ICI) are frequently associated with immune-related adverse events (irAE). Growing evidence suggests that the occurrence of irAE may be correlated with enhanced ICI efficacy, although the underlying mechanisms remain unknown. Most studies investigating the role of the gut microbiome in oncology have relied on sequencing approaches, particularly shotgun metagenomics. Although microbiome profiling revealed strong associations between specific bacterial taxa and clinical outcomes, it has limitations, including an inability to detect low-abundance bacteria and to recover live cultivable bacteria. To overcome these limitations, we combined shotgun metagenomics and culturomics on fecal samples collected from patients with melanoma and non-small cell lung cancer (NSCLC), at baseline and at the onset of immune related (ir)-colitis.<br><br>RESULTS: We first validated across three independent cohorts of 589 patients with melanoma or NSCLC treated with ICI that grade&#x2009;&#x2265;&#x2009;2 irAE were associated with significantly longer overall survival (OS) and progression-free survival (PFS). Complementary analysis using shotgun metagenomics and culturomics revealed that patients who developed grade&#x2009;&#x2265;&#x2009;2 irAE had a lower alpha diversity compared to those who did not develop grade&#x2009;&#x2265;&#x2009;2 irAE. Metagenomics results showed enrichment of Ruminococcus gnavus and Streptococcus vestibularis at baseline in grade&#x2009;&#x2265;&#x2009;2 irAE patients, while Clostridium paraputrificum and Streptococcus spp. were isolated by culturomics from baseline stool samples from ir-colitis patients. Longitudinal analysis of paired stool samples revealed a shift in microbiome composition with enrichment of Paraclostridium bifermentans and Clostridium paraputrificum, lower lipopolysaccharide and higher flagellin concentrations at baseline compared with the time of ir-colitis. Fecal microbiome transplantation from a patient with ir-colitis into mice induced surrogate markers of colonic inflammation and enhanced the anti-tumor activity of combined anti-PD-1/CTLA-4. P. bifermentans isolated from this patient sample demonstrated direct epithelial barrier disruption in Caco-2 monolayers, characterized by decreased ZO-1 and Occludin&#xa0;immunofluorescence signal and increased TNF-&#x3b1; and IL-1&#x3b2; expression. Moreover, in the dextran sodium sulfate (DSS) colitis model, P. bifermentans worsened weight loss. In a separate tumor model, it amplified the anti-tumor effect of dual ICI. This beneficial effect was also&#xa0;maintained after treatment with P. bifermentans&#x2009;<&#x2009;3&#xa0;kDa filtered supernatant.<br><br>CONCLUSION: Altogether, our results suggest that P. bifermentans promotes subclinical colitis while increasing the efficacy of dual ICI. This provides a potential microbiome-derived link between irAE and improved anti-tumor responses. Video Abstract.},
}
@article {pmid42083117,
year = {2026},
author = {Helliwell, JA and Sciberras, P and Dosis, A and Burke, J and Chilton, CH and Wood, HM and Jayne, DG},
title = {Modulation of the gut microbiota as a novel strategy to prevent anastomotic leak after colorectal surgery: Systematic scoping review.},
journal = {Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland},
volume = {28},
number = {5},
pages = {e70472},
pmid = {42083117},
issn = {1463-1318},
mesh = {Humans ; *Anastomotic Leak/prevention &amp; control/microbiology ; *Gastrointestinal Microbiome/physiology/drug effects ; Probiotics/therapeutic use ; *Colorectal Surgery/adverse effects ; Fecal Microbiota Transplantation ; Animals ; Female ; Male ; },
abstract = {BACKGROUND: Anastomotic leak (AL) remains a major source of morbidity following colorectal surgery. Increasing evidence implicates the gut microbiome in the pathogenesis of AL, with certain microbial species disrupting tissue repair through collagen degradation. Perioperative modulation of the microbiome may offer a novel strategy to improve anastomotic healing. This scoping review aimed to map available evidence on microbiome-targeted interventions, synthesise mechanistic insights, and identify translation gaps in relation to anastomotic outcomes.<br><br>METHODS: A systematic scoping review was performed. MEDLINE, Embase and Cochrane Central Registry of Controlled Trials databases were searched from database inception to 5th August 2025. Studies were eligible if they investigated perioperative interventions that modulated the gut microbiome and evaluated anastomotic healing or leak rates. Both clinical and preclinical studies were included. A narrative synthesis was performed by charting key findings.<br><br>RESULTS: Of 4209 records screened, 27 studies met the inclusion criteria: 9 clinical and 18 preclinical. Interventions included bowel preparation, probiotics, synbiotics, arginine/omega-3 supplementation, dietary modification, faecal microbiota transplantation (FMT), phosphate, tranexamic acid, morphine and infliximab. Among clinical studies, only oral antibiotics combined with mechanical bowel preparation were associated with a significant reduction in leak rates. Preclinical studies showed interventions such as high-fibre diets, FMT, rectal tranexamic acid and phosphate supplementation improved anastomotic healing via enhanced microbial diversity, suppression of pathogenic organisms, or inhibition of collagenolytic activity.<br><br>CONCLUSION: This review highlights a range of microbiome-targeted interventions with potential to reduce AL. While clinical evidence remains limited, several preclinical strategies demonstrate promise and warrant evaluation in early-phase human trials.},
}
@article {pmid42083126,
year = {2026},
author = {Wu, F and Zhang, M and Wu, J and Wang, Z and Ma, Y and Dong, L and Cheng, L and Ji, T and Zheng, C and Ren, F and Fang, B},
title = {Aged Gut Microbiota Induces Mucosal Transcriptional Dysregulation, Impairing Immune Surveillance.},
journal = {Aging cell},
volume = {25},
number = {5},
pages = {e70533},
pmid = {42083126},
issn = {1474-9726},
support = {20240484606//Beijing Nova Program/ ; 241110110200//the Key Project of Henan Science and Technology Research and Development Plan/ ; FFHCI-2025061//the Cross-Innovation Open Project of Food Flavor and Health, Beijing Technology &amp; Business University/ ; //the 2115 Talent Development Program of China Agricultural University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Mice ; *Intestinal Mucosa/immunology/microbiology/metabolism ; *Aging/immunology ; Mice, Inbred C57BL ; *Immunologic Surveillance ; Male ; },
abstract = {Aging is associated with systemic immune remodeling and disease susceptibility, but its impact on intestinal mucosal immunity, particularly changes in M cells, remains largely unknown. This study aimed to investigate how aging alters intestinal mucosal immune phenotypes, specifically follicle-associated epithelial cells (FAE) and the gut microbiota, and to identify interconnected pathways that may be exploited to maintain intestinal immune function in the elderly. Using intestinal tissue from young and aged mice, this study assessed manifestations of intestinal epithelial aging, changes in immune cells in the lamina propria, and microbial composition. Aging was associated with increased expression of senescence-associated secretory phenotype (SASP) markers (IL-1β, TNF-α, p16) and decreased levels of tight junction proteins (Occludin, Tricellulin), suggesting epithelial barrier dysfunction. Aged mice exhibited decreased Naïve Th cells, increased Effector Th and Th17 subsets, and decreased fecal IgA. Microbiome analysis revealed enrichment of inflammatory bacteria, such as Desulfovibrio and Candidatus_Saccharimonas, and elevated dysbiosis indices. RNA sequencing of FAEs revealed 578 differentially expressed genes, including downregulation of Gp2 and Ccl28, indicating impaired M cell function. Association analysis between microbiome changes and mucosal immune aging revealed that enrichment of key inflammatory bacteria may contribute to impaired M cell function and dysregulated intestinal mucosal immunity. These findings reveal a multi-layered disruption of intestinal homeostasis during aging-comprising barrier function, immune imbalance, FAEs dysfunction, and shifts in specific microbial taxa -leading to increased susceptibility to pathogens. Targeting these age-related pathways may provide strategies for maintaining intestinal immunity in the elderly.},
}
@article {pmid42083308,
year = {2026},
author = {Thakur, BK and Choudhury, SR and Turpin, W and Martin, A},
title = {Gut microbiota and diet in colorectal cancer: Converging determinants of carcinogenesis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2664684},
doi = {10.1080/19490976.2026.2664684},
pmid = {42083308},
issn = {1949-0984},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/etiology/pathology/prevention &amp; control ; *Diet/adverse effects ; *Carcinogenesis ; *Gastrointestinal Microbiome ; Animals ; *Gastrointestinal Tract/microbiology ; *Bacteria/metabolism/genetics/classification ; },
abstract = {Diet and the gut microbiome are major, interdependent determinants of colorectal cancer (CRC) risk. This review discusses current evidence on how dietary patterns reshape microbial ecology, modulate microbial virulence, and alter host metabolic, inflammatory, and oncogenic pathways to influence colorectal carcinogenesis. We highlight key CRC-associated microbes, including pks[+] Escherichia coli, Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and Streptococcus gallolyticus, and discuss how diet governs their abundance, toxin production, and oncogenic potential. Mechanistic investigations into diet-microbe interactions reveal how pro-inflammatory, low-fiber Western-style diets foster mucosal inflammation, generation of reactive oxygen and nitrogen species, and genotoxic microbial niches, whereas fiber- and polyphenol-rich diets support protective commensals and production of anti-inflammatory metabolites. We also outline major challenges, including interindividual microbiome variability and limited translational models, and propose future directions for integrating dietary, microbial, and host-targeted strategies for CRC prevention and therapy.},
}
@article {pmid41851157,
year = {2026},
author = {Serventi, L and Huang, C and Hofmann, R},
title = {Exploring pea soaking water as alternative to synthetic fertilizer: growth and microbial analysis of pea and tomato plants.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41851157},
issn = {2045-2322},
abstract = {Synthetic fertilizers deplete soil microbiome. Organic fertilizers lack specific nutrients for plant growth. A fertilizer that delivers essential nutrients to plants without deteriorating soil is lacking. This study investigated the viability of using pea soaking water (PSW) as substitute for synthetic fertilizers to enhance the growth of pea and tomato plants. Traits included plant growth stages, shoot and root weight, estimated chlorophyll content, and soil microbial populations. Pea plants exhibited consistent growth stages and rates of development across treatments, whereas tomato plants displayed treatment-dependent growth variations and differences in rates of development. Synthetic fertilizer (NPK) and PSW treatments increased shoot weight and chlorophyll content in both pea and tomato plants, compared with their controls. Interestingly, PSW produced comparable shoot growth to synthetic fertilizer in both crops. Root weights were similar in response to both fertilizer treatments in tomato but only increased in response to synthetic fertilizer in pea plants. Soil microbial analysis highlighted differences in Lactobacillus amount with soil supporting pea plants having higher bacteria counts. Notably, Lactobacillus amounts were reduced by 48% in the synthetic fertilizer treatment, but not by PSW, compared with the control, for tomatoes only. These findings suggest that PSW is a potential alternative to synthetic fertilizer to sustainably support plant growth. Replacement of synthetic fertilizer with PSW could reduce the environmental impact of agriculture by promoting healthy soil microbiota and preventing eutrophication, as well as reducing reliance on fertilizers. Further research is needed to explore its effect on crop yield, and applicability across crop species, field, and environmental conditions.},
}
@article {pmid41851187,
year = {2026},
author = {Su, X and Jin, J and Huang, Y and Hou, H and Li, Z and Cao, C and Wang, X and Li, F and Deng, Z and Zhang, M},
title = {Tumor-suppressing multi-enterobacteria enhance the anti-PD-1/PD-L1 efficacy in microsatellite stable colorectal cancer.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41851187},
issn = {2045-2322},
support = {Y-HR2019-0295//Beijing Xisike Clinical Oncology Research Foundation/ ; 2024AFD426//Joint Fund Project for Innovation and Development of Hubei Provincial Natural Science Foundation/ ; },
abstract = {UNLABELLED: Gut microbiome plays a pivotal role in modulating immunotherapy responses in colorectal cancer (CRC) treatment. While individual enterobacteria have been identified as enhancers of anti-PD-1/anti-PD-L1 therapy, the synergistic effects of multiple probiotic strains remain insufficiently explored. In this study, we investigated the therapeutic potential of Tumor-Suppressing Multi-Enterobacteria (TSME), a consortium of nine beneficial intestinal probiotic strains, in enhancing anti-PD-1/anti-PD-L1 therapy for microsatellite stable (MSS) CRC. Using a tumor-bearing mouse and employing techniques including flow cytometry, immunohistochemistry, ELISA, and genomic sequencing, we found that TSME significantly improved the efficacy of immune checkpoint inhibitors (ICIs) by optimizing tumor immune and microbe microenvironment. Specifically, the addition of TSME increased CD8[+] T cell infiltration and reshaped cytokine profiles, including reducing pro-inflammatory cytokines (IL-17, IL-1β, IL-6, and TNF-α) while elevating anti-inflammatory factors (IFN-γ). Moreover, TSME significantly up-regulated key immune pathways, including TNF signaling, cytokine-cytokine receptor interaction, and JAK-STAT signaling. In addition, TSME restructured the gut microbiome, increasing the abundance of beneficial bacteria such as Akkermansia and Alistipes. These findings highlight the synergistic effect of the multi-strain probiotics in enhancing ICI efficacy. Well-formulated probiotic consortia offer a promising strategy for enhancing immunotherapy outcomes in MSS CRC and advancing broader implementation of microbiome-assisted precision oncology.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-44494-5.},
}
@article {pmid41877288,
year = {2026},
author = {Wei, G and Liu, M and Huang, L and Chen, C},
title = {Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41877288},
issn = {2524-4671},
support = {32272831//National Natural Science Foundation of China/ ; },
abstract = {UNLABELLED: Fungi are crucial components of the pig gut microbiome, influencing host immunity and metabolism. However, the investigation about gut fungi via metagenomic sequencing remains challenging due to analytical complexity. Here, we characterized pig gut fungal profiles using 750 metagenomes collected from public repositories and our previous datasets based on a comprehensive collection of fungal reference genomes, and revealed dynamic compositional changes of pig gut fungi from birth to market (7d, 14d, 21d, 28d, 35d, 70d, and 140d). Weaning significantly shaped the gut fungal community, affecting key fungi like Lachancea kluyveri and Kazachstania slooffiae. Inter-kingdom interaction analysis revealed significant correlations between fungi and bacteria, such as between L. kluyveri and Lactobacillus amylovorus (r = -0.48) and between K. slooffiae and Lactobacillus johnsonii (r = 0.75). We identified 87 diarrhea-associated fungal species at the significance threshold of LDA > 2.0 in three experimental piglet cohorts. In antibiotic-free piglets, fungal species from Saccharomyces and Aspergillus, some of which have been considered as potential probiotics, were enriched in healthy individuals, whereas in antibiotic-treated groups, Saccharomyces spp. and K. slooffiae were higher in diarrheal piglets. Notably, K. slooffiae were negatively correlated with the pathogen M. circinelloides, suggesting a protective role during gut dysbiosis. This study provides a foundation for developing fungal-based interventions to improve pig health.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00551-y.},
}
@article {pmid42071032,
year = {2026},
author = {Wang, H and Wang, F and Guo, Q and Zou, B and Li, P and Xu, X and He, J and Jiang, S and Yue, J},
title = {Dynamic changes in gut microbiota and discovery of prognostic biomarkers in locally advanced pancreatic cancer during chemoradiotherapy.},
journal = {Clinical and experimental medicine},
volume = {26},
number = {1},
pages = {},
pmid = {42071032},
issn = {1591-9528},
support = {82272753//National Natural Science Foundation of China/ ; ZF004//Collaborative Academic Innovation Project of Shandong Cancer Hospital/ ; },
abstract = {UNLABELLED: Pancreatic cancer has an exceptionally poor prognosis, with the majority of cases diagnosed at an advanced stage. Concurrent chemoradiotherapy (CCRT) remains the standard of care for locally advanced pancreatic cancer (LAPC); however, its therapeutic efficacy is limited. Emerging evidence suggests that the gut microbiota is an important modulator of cancer progression and treatment response. Nevertheless, the dynamic changes in the gut microbial ecosystem in LAPC patients undergoing CCRT remain poorly understood. This study aimed to characterize longitudinal alterations in the gut microbiota during CCRT, identify candidate microbiome-based prognostic markers, and explore their potential associations with host responses. This longitudinal study included 16 patients with LAPC. Fecal and peripheral blood samples were collected at three predefined time points: before CCRT initiation, during CCRT, and after CCRT completion. Gut microbiota composition and community structure were analyzed using 16 S rRNA sequencing targeting the V3–V4 region. Bioinformatic analyses were performed to assess taxonomic distribution, alpha and beta diversity, and microbial co-occurrence patterns. The prognostic relevance of microbial features was further evaluated using machine learning models integrating clinical parameters to predict overall survival. CCRT was associated with dynamic changes in specific microbial taxa across multiple taxonomic levels, with marked inter-individual heterogeneity in microbiota responses. In addition, microbial co-occurrence network complexity was reduced during treatment. Certain microbial taxa during CCRT showed associations with tumor-related serum biomarkers. Using integrated machine learning models, we identified candidate microbiota-based prognostic markers. In particular, Bifidobacterium and Bacteroides were associated with survival prediction, achieving areas under the receiver operating characteristic curve (AUC) of 0.833 and 0.722, respectively. CCRT is associated with longitudinal alterations in the gut microbiome of patients with LAPC, involving both compositional and structural changes. These findings suggest that microbiome dynamics may have potential value as exploratory prognostic indicators. However, given the limited sample size and observational design, further validation in larger cohorts and mechanistic studies are required before clinical application.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10238-026-02158-8.},
}
@article {pmid42075347,
year = {2026},
author = {Núñez-Muñoz, LA and Vargas-Hernández, BY and García-Sierra, MC and Calderón-Pérez, B and Xoconostle-Cázares, B and Ruiz-Medrano, R},
title = {Bacterial and Fungal Communities Associated with the Ectomycorrhizospheric Soil and Stem Endosphere of the Mycoheterotrophic Plant Monotropa uniflora.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081145},
pmid = {42075347},
issn = {2223-7747},
support = {CBF-2025-3383//Secretar&#xed;a de Ciencia Tecnolog&#xed;a e Innovaci&#xf3;n/ ; CF-2023-G-731//Secretar&#xed;a de Ciencia Tecnolog&#xed;a e Innovaci&#xf3;n/ ; },
abstract = {The mycoheterotrophic plant Monotropa uniflora relies on fungal symbionts for carbon and nutrient acquisition. However, its interactions with other microbial groups, beyond ectomycorrhizal fungi, remain unexplored. Here, we characterized bacterial and fungal communities associated with M. uniflora across two compartments: ectomycorrhizospheric soil linked to the mycorrhizal network and the surface-sterilized lower stem endosphere. Microbial community composition was assessed using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. Fungal richness was consistently higher in ectomycorrhizospheric soil than in the stem endosphere, whereas bacterial alpha diversity showed no consistent differences between compartments. Multivariate analyses suggested compartment-associated patterns in both bacterial and fungal community composition. Ectomycorrhizospheric soil was dominated by saprotrophic fungal taxa and bacterial groups with predicted metabolic potential, including taxa associated with iron, sulfur and nitrogen cycling. In contrast, the lower stem endosphere was enriched in bacterial taxa commonly associated with anaerobic and nitrogen-related metabolisms. Functional predictions further suggested an increase of carbon fixation-related pathways in rhizosphere-associated bacterial communities. Together, these results indicate that M. uniflora is associated with distinct and structured microbial assemblages across soil and internal plant compartments, highlighting the predicted functional potential of bacterial communities in nutrient- and carbon-related processes in mycoheterotrophic plant-soil systems alongside fungal partners.},
}
@article {pmid42075353,
year = {2026},
author = {Aleynova, OA and Ananev, AA and Nityagovsky, NN and Suprun, AR and Beresh, AA and Dubrovina, AS and Kiselev, KV},
title = {Ability of Different Bacteria from Grapevine to Colonize Arabidopsis thaliana Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081151},
pmid = {42075353},
issn = {2223-7747},
support = {22-74-10001-&#x41f;//the Russian Science Foundation/ ; },
abstract = {This study investigates the impact of inoculating seeds with bacterial endophytes isolated from Vitis amurensis Rupr. on endophytic community composition in Arabidopsis thaliana (L.) Heynh. Ten bacterial isolates of the genera Agrobacterium, Bacillus, Curtobacterium, Erwinia, Frondihabitans, Gordonia, Pantoea, Pseudomonas, Sphingomonas, and Xanthomonas were applied to seeds and some visible phenotypic effects were observed on plant growth after two weeks. High-throughput sequencing of 16S rRNA revealed that the native endophytic microbiome of A. thaliana was dominated by Gammaproteobacteria, Actinomycetes, Bacteroidia, and Alphaproteobacteria. The key families were Microscillaceae, Chitinophagaceae, Rhizobiaceae, Rhodanobacteraceae, Nocardioi-daceae, Nocardiaceae, Xanthomonadaceae, Devosiaceae, Microbacteriaceae, Crocinitomi-caceae, Pseudomonadaceae, Solimonadaceae, Comamonadaceae, Caulobacteraceae, and Micrococcaceae. Arabidopsis seed inoculation with Agrobacterium sp. R8SCh-B12, Curtobacterium sp. P7SA-B3, and Gordonia aichiensis P6PL2 significantly reduced alpha diversity (Shannon index) and altered beta diversity relative to controls, indicating strong community restructuring. These three isolates, along with Pseudomonas sp. R8SCh-B2, Sphingomonas sp. RA62c-B5, Xanthomonas sp. R7SCh-B6, and Bacillus velezensis AMR25, successfully colonized the plant tissues, as evidenced by significant increases in genus-specific amplicon sequence variants, ASVs (up to 17,820-fold for Curtobacterium sp. ASV33). In contrast, Pantoea sp. P7SCH-B5, Erwinia sp. R8SCh-B3, and Frondihabitans sp. RA62c-B2 failed to colonize A. thaliana, despite being applied to the seeds, suggesting the existence of mechanisms restraining colonization. These findings demonstrate that only a subset of grapevine-derived endophytes can effectively colonize A. thaliana, and that successful colonization correlates with significant shifts in the native microbiome, even in the absence of overt phenotypic changes. This emphasizes the importance of strain-specific compatibility in plant-endophyte interactions. Thus, we report the first descriptions of several novel endophytes that colonized Arabidopsis plants and establish a convenient model to investigate plant-bacterial interactions.},
}
@article {pmid42075357,
year = {2026},
author = {Sun, C and Ge, Z and Yang, X and Xie, X and Liang, X and Shen, L and Ren, J and Zhang, Y},
title = {Silicon Combined with Activated Carbon Enhances Salt Tolerance in Strawberry (Fragaria × ananassa) by Reinforcing Ion-Redox Homeostasis and Reshaping the Rhizosphere Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081154},
pmid = {42075357},
issn = {2223-7747},
support = {2021C02066-7//Crop New Variety Breeding of Zhejiang Province/ ; SY202304//the Local Science and Technology Cooperation Project of Zhejiang Academy of Agricultural Sciences/ ; 2025SNJF029//the Zhejiang "Sannong Jiufang" Science and Technology Collaboration Program/ ; 2023Z112//the Ningbo Municipal Major Special Project/ ; },
abstract = {Soil salinity severely constrains strawberry production by disrupting ion homeostasis and provoking oxidative injury. This study investigated whether soluble silicon (Si) and activated carbon (AC) act to enhance salt tolerance in strawberry (Fragaria × ananassa). Under NaCl stress, plants showed pronounced growth inhibition, increased Na[+] accumulation and a deteriorated K[+]/Na[+] balance, accompanied by elevated reactive oxygen species (ROS) and lipid peroxidation. In contrast, combined AC + Si treatment consistently provided the strongest protection, improving seedling vigor and survival. Relative to NaCl alone, AC + Si increased shoot and root fresh weight by 67.5% and 78.5%, reduced shoot Na[+] by 59.1%, and lowered shoot H2O2 and MDA by 62.6% and 66.5%, respectively, indicating marked improvement in ion-redox homeostasis. Beyond plant responses, AC-containing treatments alleviated salt-induced increases in soil electrical conductivity, coinciding with a clear restructuring of the rhizosphere bacterial community and enrichment of putatively beneficial taxa. Transcriptome profiling further supported coordinated reprogramming of ion transport, redox control and stress-responsive signaling pathways under the AC + Si regime. Collectively, the results indicated that Si and AC co-application enhances strawberry salt tolerance through an integrated soil-plant-microbiome mechanism that stabilizes ion homeostasis and reinforces redox homeostasis.},
}
@article {pmid42075461,
year = {2026},
author = {Rueda Foronda, JA and Ríos López, JS and Múnera Porras, LM and Pino Rodriguez, NJ},
title = {Climate Variability Under ENSO Reshapes the Coffea arabica Rhizosphere Microbiome While Preserving a Conserved Bacterial Core.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081259},
pmid = {42075461},
issn = {2223-7747},
support = {202143210//Universidad de Antioquia/ ; },
abstract = {Climate variability is a major driver of belowground microbial assembly, yet its effects on rhizosphere microbiomes in perennial crops remain insufficiently resolved. We investigated how macroclimatic oscillations associated with the El Niño-Southern Oscillation (ENSO) influence bacterial communities in the rhizosphere of Coffea arabica. Using 16S rRNA amplicon sequencing across five sampling campaigns covering El Niño, La Niña, and Neutral phases in the Colombian Andes, together with multivariate and variance-partitioning analyses, we quantified the relative contributions of climatic and edaphic factors to rhizosphere community structure. PERMANOVA across three dissimilarity metrics showed that the ENSO explained 11-17% of β-diversity, exceeding the contribution of intra-annual seasonality (6-12%). Ordination analyses indicated moderate compositional differentiation with considerable overlap among ENSO groups, consistent with gradual community turnover under contrasting hydroclimatic conditions. Rainfall and soil pH emerged as the main edaphic correlates of community composition, although their independent effects were no longer significant after accounting for the ENSO phase and season. Despite these shifts, the rhizosphere remained dominated by Acidobacteriota, Actinobacteriota, and Proteobacteria, and a prevalence-defined core microbiome (genera detected in ≥85% of samples) was maintained across climatic phases and seasons. These results indicate that, within the explained fraction of variation, macroclimatic variability contributed more to rhizosphere bacterial turnover than local edaphic heterogeneity, while a conserved prevalence-defined bacterial core may contribute to taxonomic stability in climate-sensitive coffee systems.},
}
@article {pmid42075467,
year = {2026},
author = {Tiwari, P and Park, KI},
title = {Plant-Associated Microbiomes: Crosstalk and Engineering to Improve Nutrient Use Efficiency (NUE) in Crops of Global Importance.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081265},
pmid = {42075467},
issn = {2223-7747},
abstract = {Global climate change is rapid and poses an alarming threat to agricultural production, significantly impacting economies. Modern agriculture has strongly emphasized improving nutrient availability in crops to address rising malnutrition and contribute to global food security. However, abiotic stresses, including warmer temperatures, drought, waterlogging stress, and elevated CO2, have critical direct and indirect effects on nutrient availability in plants. This systematic review was conducted in accordance with the PRISMA guidelines. The literature survey followed a time period of 2-5 months, during which the conceptualization, analysis, writing, and editing of the article were conducted. In the present era, it is essential to adopt measures to improve the nutritional value [enhance Nutrient Use Efficiency (NUE)] and nutrient management of plant-based foods. Plant-associated microbiomes have co-evolved with their plant counterparts and perform essential functions in nutrient acquisition, including microbial sensing and cross-talk with the plant host, nutrient uptake and sharing, and signaling mechanisms. In natural and agricultural ecosystems, plant microbiomes offer major opportunities and can be harnessed to sustainably supply essential plant nutrients and improve NUE in crops of global importance. Crop-associated microbiomes can be precisely tailored to achieve targeted outcomes, enhancing nutrient acquisition and utilization via microbiome engineering. However, bridging knowledge gaps, understanding microbial colonization, plant-microbiome dynamics, and adopting precise editing approaches are crucial to boost sustainable outcomes and crop productivity. By elucidating plant microbiome crosstalk and microbe-microbe signaling, a better understanding of microbe-mediated nutrient acquisition in plants can be achieved, defining key implications in global food security.},
}
@article {pmid42075560,
year = {2026},
author = {Cho, WS and Thillaichidambaram, M and Jeon, S and Kim, GR and Lee, SU and Lee, SH and Kim, YJ and Lee, ES and Kim, Y and Kang, D and Kim, SY},
title = {Lung Microbiome Dysbiosis in Pulmonary Fibrosis Induced by Multi-Walled Carbon Nanotubes and Bleomycin in Rats.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {4},
pages = {},
doi = {10.3390/medicina62040688},
pmid = {42075560},
issn = {1648-9144},
support = {This study was supported by the 2023 overseas training grant from Pusan National University Yangsan Hospital.//Pusan National University Yangsan Hospital./ ; },
mesh = {Animals ; *Pulmonary Fibrosis/microbiology/chemically induced/physiopathology/etiology ; *Bleomycin/adverse effects ; Rats, Wistar ; Rats ; *Dysbiosis/microbiology/etiology/physiopathology ; *Nanotubes, Carbon/adverse effects ; Female ; *Microbiota/drug effects ; *Lung/microbiology/physiopathology ; Bronchoalveolar Lavage Fluid/microbiology ; Disease Models, Animal ; RNA, Ribosomal, 16S ; },
abstract = {Background and objectives: Occupational and environmental inhalation exposures, including high-aspect-ratio carbon nanotubes, can trigger pulmonary fibrosis (PF). The relationship between exposure-specific fibrogenic pathways (granulomatous inflammation versus diffuse epithelial injury) and lung microbiome dysbiosis remains incompletely understood. We therefore compared lung microbiome alterations in rat PF models induced by multi-walled carbon nanotubes (MWCNTs) and bleomycin. Materials and Methods: Female Wistar rats received a single intratracheal instillation of vehicle, MWCNTs (750 μg/rat), or bleomycin (1 mg/rat). At day 28, fibrosis and inflammation were evaluated by histopathology and bronchoalveolar lavage fluid (BALF) profiling. Lung microbial communities were characterized by 16S rRNA gene sequencing (V3-V4). Seventeen lung samples passed stringent quality control and were analyzed (control n = 5; bleomycin n = 7; MWCNT n = 5). Results: Both agents induced PF with increased profibrotic signaling, but with distinct pathological signatures: MWCNTs produced localized granulomatous lesions and a robust neutrophilic response (25% of BALF cells), whereas bleomycin caused diffuse interstitial remodeling. Bleomycin increased microbial richness (alpha diversity; p < 0.05) and significantly shifted community structure (beta diversity; p < 0.05), while MWCNT exposure showed comparatively limited changes in global diversity. The relative abundance of Pseudogracilibacillus (including P. marinus) was higher in the bleomycin group than in controls, whereas Facklamia tabacinasalis and Corynebacterium maris were more abundant in the MWCNT group. Across samples, Proteobacteria abundance was inversely correlated with BALF TGF-β, MCP-1, and neutrophil proportion. At the species level, Pseudogracilibacillus marinus was positively correlated with BALF TGF-β, while Facklamia tabacinasalis and Corynebacterium maris were positively correlated with MCP-1, CINC-3, and neutrophil proportion (Spearman; p < 0.05). Conclusions: Mechanistically distinct fibrogenic exposures generate exposure-linked lung microbiome signatures that track with host inflammatory and profibrotic responses. These signatures may support biomarker development for environmentally and occupationally relevant PF and motivate longitudinal and functional studies to clarify causality.},
}
@article {pmid42075665,
year = {2026},
author = {Cazacu, SM and Streba, CT and Constantin, C and Ionele, CM and Rogoveanu, I and Popescu, AV and Florescu, MM},
title = {The Overlap Between Crohn's Disease and Intestinal Tuberculosis: A Never-Ending Story.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {4},
pages = {},
doi = {10.3390/medicina62040794},
pmid = {42075665},
issn = {1648-9144},
mesh = {Humans ; *Crohn Disease/diagnosis/physiopathology ; *Tuberculosis, Gastrointestinal/diagnosis/physiopathology ; Diagnosis, Differential ; },
abstract = {The prevalence of Crohn's disease has increased over the last few decades, even in developing countries, whereas that of intestinal tuberculosis has decreased, which places both diseases at an epidemiological crossroads. Crohn's disease and intestinal tuberculosis share many clinical, endoscopic, imaging, and pathological features, which sometimes make differential diagnosis very difficult; an accurate diagnosis is, however, very important since an erroneous treatment can worsen the evolution or delay proper therapy. The association between past TB infection and Crohn's disease can make the diagnosis especially hard. This review summarizes current data on specific features that allow differentiation between Crohn's disease and intestinal tuberculosis, paying particular attention to the microbiome, clinical signs, endoscopy, cross-sectional imaging, bacteriological, and immunological findings detailed. The importance of computerized models and scores for the differentiation is also detailed, because common features may make the differentiation based on a single criterion difficult.},
}
@article {pmid42075741,
year = {2026},
author = {Raut, N and Chaudhary, AA and Patil, H and Shidhaye, S and Khobragade, R and Umekar, M and Ali, MAM and Trivedi, R},
title = {Antimicrobial Consumption and Resistance Dynamics Across Healthcare Level: Global Evidence and Stewardship Implications.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040414},
pmid = {42075741},
issn = {2076-0817},
support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; },
mesh = {Humans ; *Antimicrobial Stewardship ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Bacterial ; Global Health ; Delivery of Health Care ; },
abstract = {BACKGROUND/OBJECTIVES: Antimicrobial resistance (AMR) is a critical global public health challenge driven by inappropriate and excessive antimicrobial use (AMU) across human, animal, and environmental sectors.<br><br>METHOD: This narrative review synthesizes recent evidence on antimicrobial utilization and resistance patterns. A structured search of PubMed, Scopus, and Web of Science was conducted for studies published between 2015 and 2025. Eligible sources included surveillance reports, registry-based analyses, and clinical studies. Data were qualitatively analyzed to identify key trends and regional variations.<br><br>RESULT: Marked geographical variation in AMR was observed. Carbapenem resistance in Escherichia coli remains low globally (2-3%) but is higher in Southeast Asia (17-18%) and India (~40%). Klebsiella pneumoniae shows consistently high resistance (>40% globally; ~54% in India), while Pseudomonas aeruginosa exhibits stable resistance levels (35-45%). Resistance prevalence increases from primary to tertiary care settings, reflecting greater antimicrobial exposure. Vulnerable populations-including pediatric, elderly, pregnant, and immunocompromised patients-face higher risks of antimicrobial exposure and adverse outcomes, including nephrotoxicity, hepatotoxicity, and microbiome disruption. WHO AWaRe data indicate a global shift toward increased use of Watch-category antibiotics. Stewardship interventions, such as audit and feedback, prescribing restrictions, rapid diagnostics, and decision support systems, effectively reduce inappropriate AMU.<br><br>CONCLUSIONS: Integrated, data-driven antimicrobial stewardship and robust surveillance systems are essential to mitigate the global burden of AMR.},
}
@article {pmid42075766,
year = {2026},
author = {Piloto-Sardiñas, E and Rodríguez, I and Santos, HA and Paulino, PG and Corona-González, B and Cabezas-Cruz, A},
title = {Ecological Frameworks of Pathogen-Pathogen and Pathogen-Microbiome Interactions Within the Tick Holobiont.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040440},
pmid = {42075766},
issn = {2076-0817},
mesh = {Animals ; *Ticks/microbiology ; *Microbiota ; *Host-Pathogen Interactions ; Symbiosis ; *Tick-Borne Diseases/microbiology ; },
abstract = {Ticks harbor complex microbial communities composed of symbionts, commensals, and tick-borne pathogens (TBPs). Together, these microorganisms form the tick holobiont. Within this system, the tick's physiological architecture structures microbial communities by distributing microorganisms across distinct tissues. This compartmentalization creates spatially distinct ecological niches, which in turn shape how microbial communities assemble and interact. In this review, we integrate ecological theory with current knowledge of tick microbiome research to examine how pathogen-pathogen and pathogen-microbiome interactions emerge within these tissue-structured microbial communities. We first outline how baseline ecological filters, including tick species, developmental stage, tissue identity, vertical transmission, and environmental context, shape the microbiome configuration through community assembly processes. We then examined how TBPs, as high-impact colonizers, can further modify microbial networks by altering host-mediated selective pressures, influencing interaction topology, and reshaping community stability. Based on these observations, we propose a dual selective pressure framework in which (i) baseline ecological structuring processes and (ii) pathogen-associated selective pressures interact to determine the microbial network configuration and functional outcomes within the tick holobiont. These interacting forces may drive shifts in diversity, modularity, keystone taxa emergence, and network resilience, ultimately influencing vector competence. This review frames the microbial communities within the tick holobiont as spatially structured ecological systems shaped by multilevel selective pressures. This conceptual foundation provides a coherent framework for understanding microbial interactions in arthropod vectors and highlights avenues for mechanistic research and microbiome-based strategies to mitigate tick-borne diseases.},
}
@article {pmid42075777,
year = {2026},
author = {Lagos, I and Pérez de Arce, E and Faggiani, I and D'Amico, F and Zilli, A and Furfaro, F and Massironi, S and Cicerone, C and Solitano, V and Parigi, TL and Peyrin-Biroulet, L and Danese, S and Allocca, M},
title = {The Role of Microbiota and Fecal Transplantation in Inflammatory Bowel Disease.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040451},
pmid = {42075777},
issn = {2076-0817},
mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/therapy/microbiology ; Crohn Disease/therapy/microbiology ; Colitis, Ulcerative/therapy/microbiology ; Feces/microbiology ; Treatment Outcome ; },
abstract = {Inflammatory bowel diseases (IBDs), including ulcerative colitis (UC) and Crohn's disease (CD), are consistently associated with alterations in gut microbial communities, although the extent and characteristics of these alterations vary across studies, supporting a potential role of the microbiota in disease pathogenesis and therapeutic modulation. We conducted a systematic review to synthesize current evidence on microbiota alterations in IBD and the clinical application of fecal microbiota transplantation (FMT). A total of 118 studies were included (76 focused on microbiota profiling and 42 evaluated FMT as therapy). Across heterogeneous study designs and microbial characterization methods, reduced microbial diversity was the most consistently reported alteration, generally more pronounced in CD than in UC. Depletion of Faecalibacterium prausnitzii-a key butyrate producer with anti-inflammatory properties-was commonly reported, often accompanied by functional impairment in short-chain fatty acid production. Microbial patterns were frequently associated with mucosal inflammation and varied across disease phenotypes; these patterns have been increasingly explored as predictors of treatment response and relapse, although mechanistic interpretation remains limited and causal relationships are difficult to establish. Evidence from randomized controlled trials suggests potential efficacy of FMT in UC, particularly with intensive or repeated protocols, whereas data in CD remain limited and heterogeneous, with signals of benefit often appearing transient. FMT was generally well tolerated, but long-term safety data remain scarce. Emerging multi-omic approaches are reshaping the field by integrating taxonomic and functional insights, with potential implications for risk stratification, diagnosis, prognosis, and therapeutic optimization. Further standardized, longitudinal, and mechanistically oriented studies are required to translate microbiome research into clinically actionable strategies in IBD.},
}
@article {pmid42075987,
year = {2026},
author = {Choińska, R and Nasiłowska, J and Wojtczak, A and Lewandowski, W and Świsłocka, R},
title = {Isoxanthohumol and Its Derivatives: Antioxidant Activity and Effects on the Gut Microbiota.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {8},
pages = {},
doi = {10.3390/molecules31081311},
pmid = {42075987},
issn = {1420-3049},
support = {2020/39/B/NZ9/01894//National Science Centre/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Xanthones/pharmacology/chemistry ; Humans ; *Antioxidants/pharmacology/chemistry ; Humulus/chemistry ; Animals ; Flavonoids/pharmacology/chemistry ; Propiophenones/chemistry/pharmacology ; Flavanones/chemistry/pharmacology/metabolism ; },
abstract = {Isoxanthohumol (IX) is a prenylated flavonoid derived from hop cones (Humulus lupulus) that is gaining increasing recognition for its potential biological effects. Despite numerous studies on its precursor, xanthohumol, studies on IX remain limited. Of particular interest is its metabolism, particularly its biotransformation by gut microbiota to 8-prenylnaringenin (8-PN), a potent phytoestrogen, which indicates the complex nature of its biological activity and potential health implications. This review summarizes the current state of knowledge on IX and its derivatives, covering their microbial metabolism, their impact on the gut microbiome, and the metabolic consequences of this conversion. Furthermore, it examines the relationship between the molecular structure of IX and its derivatives and their biological activity, highlighting existing research gaps and the need for further research on the safety and therapeutic potential of these compounds.},
}
@article {pmid42076028,
year = {2026},
author = {Karczmarzyk, A and Wojcieszyńska, D and Nowak, A and Smułek, W and Guzik, U},
title = {Berberine Toxicity Profile in Experimental Models as a Basis for Assessing Its Biological Safety.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {8},
pages = {},
doi = {10.3390/molecules31081350},
pmid = {42076028},
issn = {1420-3049},
mesh = {*Berberine/toxicity/pharmacology ; Oxidative Stress/drug effects ; Animals ; },
abstract = {Berberine, a natural alkaloid, is a substance widely used in natural medicine. However, there is a significant knowledge gap regarding the potential negative effects of higher environmental concentrations of berberine resulting from its use as a supplement. Therefore, the aim of this study was to assess its toxicity towards microorganisms and organisms from various trophic levels. The results indicate that berberine may influence the reorganization of bacterial membranes, thereby negatively impacting the environmental microbiome. However, oxidative cell damage, a phenomenon commonly described in the literature, was not demonstrated. At the concentrations used, berberine may even have a protective effect. The analysis of toxicity towards Tetrahymena, Selenastrum, and Heterocypris indicated a similar level of berberine toxicity across these organisms, suggesting that the toxic effect is not species-dependent and that the mechanism of toxicity is probably based on universal cellular mechanisms.},
}
@article {pmid42076046,
year = {2026},
author = {Toydemir, S and Merey, G},
title = {Biochemistry of Human Gut Microbiota: Related Diseases and Dietary Interactions.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {8},
pages = {},
doi = {10.3390/molecules31081369},
pmid = {42076046},
issn = {1420-3049},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology/metabolism ; *Diet ; Inflammatory Bowel Diseases/microbiology/metabolism ; Obesity/microbiology/metabolism ; },
abstract = {The human gut microbiota represents a complex and dynamic ecosystem of trillions of microorganisms that play a fundamental role in maintaining physiological homeostasis, regulating metabolism, and modulating the immune system. This narrative review explores the biochemical intricacies of the gut microbiome, focusing on the dominant phyla (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Fusobacteria) and their specific contributions to host health. A critical emphasis is placed on the metabolic outputs of these microorganisms, such as short-chain fatty acids (SCFAs) like butyrate, which serve as vital energy sources and anti-inflammatory signaling molecules. Conversely, the review examines how dysbiosis, the disruption of microbial balance, is mechanistically linked to the pathogenesis of diverse conditions, including obesity, diabetes mellitus, inflammatory bowel disease (IBD), and gout. Furthermore, it highlights the profound impact of dietary interventions on microbial architecture, notably, how non-digestible carbohydrates promote beneficial taxa and eubiosis, while high-fat and high-sugar diets drive metabolic endotoxemia and systemic inflammation. By synthesizing current knowledge on microbial biotransformations of proteins and polyphenols, this work underscores the bidirectional relationship between nutrition and the microbiome. Ultimately, understanding these biochemical interactions is essential for developing targeted probiotic, prebiotic, and nutritional strategies to prevent and manage chronic metabolic and inflammatory disorders.},
}
@article {pmid42076109,
year = {2026},
author = {Bharadwaj, R and Gaspar, C and Moeller, TD and Ward, D and Klempner, MS and Wang, Y and Cavacini, LA},
title = {Impact of Oral Pre-Exposure Secretory IgA Prophylactic Produced in Rice on Gut Microbiome Homeostasis.},
journal = {Pharmaceutics},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/pharmaceutics18040457},
pmid = {42076109},
issn = {1999-4923},
support = {MT21010.006//Naval Medical Research Command's Naval Advanced Medical Development Program/ ; W81XWH-21-2-0018//Combat Readiness - Medical Research Program/ ; INV-010709/GATES/Gates Foundation/United States ; },
abstract = {Background/Objectives: Enterotoxigenic Escherichia coli (ETEC) is a leading cause of diarrheal illness worldwide, resulting in approximately 380,000 deaths annually, with significant morbidity in children and travelers to endemic regions. ETEC infection begins with the attachment of the bacterium to the small intestine via filamentous colonization factors (CF), followed by the production of heat-labile (LT) and heat-stable (ST) toxins that induce watery diarrhea. Targeting CF to prevent ETEC attachment is challenging due to strain heterogeneity. Methods: In previous studies, we developed a class-switched human monoclonal antibody, 68-90, expressed as secretory IgA (SIgA) in rice for cost-effective and stable storage. Rice-produced SIgA exhibited comparable binding efficiency to CfaE, a component of CF, compared to CHO-produced SIgA in vitro. Results: In this work, we showed that oral administration of 68-90 SIgA to Aotus nancymaae did not alter gut microbiome distribution or show signs of systemic exposure. Conclusions: These findings suggest that oral delivery of ETEC-specific SIgA is safe and does not disrupt the gut microbial population, highlighting its potential as an effective and targeted therapeutic strategy.},
}
@article {pmid42076694,
year = {2026},
author = {Sahatsanon, K and Chaweewan, K and Sringarm, K and Arjin, C and Hnokaew, P and Satsook, A and Saman, P and Kim, HW and Patthararangsarith, P and Busayakanit, P and Adeyemi, KD and Sivapirunthep, P and Chaosap, C},
title = {Effects of Host-Specific Multi-Lactic Acid Bacterial Probiotics on Performance, Carcass Traits, Meat Quality, and Gut Microbiome in Fattening Pigs.},
journal = {Veterinary sciences},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/vetsci13040322},
pmid = {42076694},
issn = {2306-7381},
support = {KDS 2022/010//King Mongkut's Institute of Technology Ladkrabang/ ; No. 65-17 Sub Project No. 1//Thailand Institute of Scientific and Technological Research/ ; },
abstract = {This study evaluated the effects of a host-specific multi-lactic acid bacterial (MLAB) probiotic and sex on performance, carcass traits, meat quality, and gut microbiota in fattening pigs. Thirty-two crossbred pigs (10 ± 0.80 weeks; 23.43 ± 0.17 kg) were assigned to a 2 × 2 factorial design with diet (control or MLAB probiotics) and sex (barrow or female). The MLAB supplement consisted of seven lactic acid bacterial strains mixed in equal proportions (≈14.3% each)-Lactobacillus brevis, Lactobacillus reuteri, Weissella cibaria, Lactobacillus paraplantarum, Lactococcus lactis, Lactobacillus pentosus, and Pediococcus pentosaceus-administered at 1 × 10[9] CFU/kg feed for 12 weeks. MLAB probiotic supplementation reduced bone proportion while increasing skin and fat content (p < 0.05), with a treatment × sex interaction for loin eye area (p < 0.05). Meat quality improved in the MLAB group, showing higher ultimate pH and lower cooking loss (p < 0.05), indicating improved water-holding capacity. Female pigs exhibited higher early postmortem pH and protein content (p < 0.05). Microbiome analysis revealed increased abundances of Oxalobacteraceae and Paludibacteraceae and reduced Clostridium sensu stricto 6 (p < 0.05). These results suggest that host-adapted probiotics may support gut microbial balance and improve certain pork quality traits.},
}
@article {pmid42076708,
year = {2026},
author = {Yu, J and Dou, Z and Wang, C and Zhou, S and Shi, H and Zhang, H and Wang, H and Ma, N and Shen, X and Chang, G},
title = {Yeast Culture Enhances Production Performance in Late-Lactation Dairy Cows by Reshaping Rumen Microbiota and Metabolic Pathways.},
journal = {Veterinary sciences},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/vetsci13040336},
pmid = {42076708},
issn = {2306-7381},
support = {2022AAC02072//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; KYT2023004//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Yeast culture (YC), a complex functional feed additive containing fermentation metabolites, has demonstrated potential in dairy production systems. However, its mechanistic effects on rumen function and host metabolism in lactating dairy cattle warrant further investigation. This study evaluated the impacts of YC supplementation on production performance, systemic antioxidant status, and rumen function in late-lactation Holstein cows. Fourteen multiparous Holstein cows (body weight 655 ± 28 kg; days in milk 270.4 ± 1.6 d) were randomly allocated into two groups, a control group (CON, basal diet) and a YC-supplemented group (YC, basal diet + 50 g/d YC), in a 28-day feeding trial. YC supplementation significantly increased dry matter intake (p < 0.01), nutrient digestibility (p < 0.01 for DM, CP, EE, NDF, and ADF), and milk yield (p < 0.05) compared to CON. Systemic antioxidant capacity was enhanced, as evidenced by elevated serum superoxide dismutase activity (p < 0.01) and total antioxidant capacity (p < 0.05). Rumen fermentation was improved with higher concentrations of total volatile fatty acids (p < 0.01) and microbial protein (p < 0.01) and reduced ammonia nitrogen levels (p < 0.01). Macrogenomic analysis revealed a YC-mediated restructuring of the rumen microbiota, characterized by an increased relative abundance of Firmicutes and decreased Bacteroidota. Untargeted metabolomic profiling identified significant alterations in rumen metabolite profiles, with differential metabolites enriched in pyrimidine metabolism and vitamin digestion and absorption pathways. These results indicate that YC supplementation improves production performance in late-lactation dairy cows through multi-faceted mechanisms involving rumen microbial community modulation and metabolic pathway activation, ultimately enhancing nutrient utilization and metabolic efficiency.},
}
@article {pmid42076832,
year = {2026},
author = {Carracedo Lorenzo, Z and Rizaludin, MS and Wang, J and Berdaguer, R and Brito-López, C and Sánchez-Arcos, C and Garbeva, P and Pieterse, CMJ and Dicke, M and Testerink, C and Kloth, KJ and Karlova, R},
title = {Pseudomonas volatiles shape the root transcriptome and microbiome to promote plant growth under drought.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71203},
pmid = {42076832},
issn = {1469-8137},
support = {024.004.014//NWO Dutch Research Council (NWO/OCW)/ ; },
abstract = {Volatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and plants. While their potential as plant growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remain poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress Arabidopsis seedlings were exposed to VOCs emitted by Pseudomonas strains under control and osmotic stress conditions. Plant biomass and root architecture were evaluated. Root transcriptomics analysis was performed and validated using Arabidopsis mutants and metabolomics. Volatile organic compounds effects were also tested on soil-grown Brassica oleracea and on its rhizosphere microbiome. Pseudomonas VOCs promoted plant growth under both axenic and soil conditions in A. thaliana and in B. oleracea, and under control and drought conditions. Transcriptomics, metabolomics, and functional analysis revealed interactions between Pseudomonas VOCs, glucosinolates, and ABA signalling, as well as a positive association between VOC exposure and coumarin biosynthesis. VOC treatment also reshaped the rhizosphere microbiome under drought, leading to a community composition more similar to that of well-watered plants. Overall, Pseudomonas VOCs promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation.},
}
@article {pmid42076857,
year = {2026},
author = {Yang, Z and Zhou, W and Chen, P and Dai, Z and Feng, G and Limpens, E and Zhang, L},
title = {Phosphorus fertilizer forms orchestrate contrasting plant-microbe recruitment strategies in the rhizosphere of field grown wheat.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71231},
pmid = {42076857},
issn = {1469-8137},
support = {ZR2021MC042//Natural Science Foundation of Shandong Province/ ; 2024YFE0105000//National Key Research and Development Program of China/ ; PC2024B02003//Pinduoduo-China Agricultural University Research Fund/ ; 32130094//National Natural Science Foundation of China/ ; 42277112//National Natural Science Foundation of China/ ; },
abstract = {Plants engage in intricate interactions with rhizosphere microbes. These interactions are crucial for plant nutrient acquisition and productivity, but the mechanisms by which different nutrient forms shape rhizosphere microbes to enhance nutrient utilization under field conditions remain unclear. We investigated the rhizosphere bacterial communities of wheat and their functions across key growth stages in response to different phosphorus (P) fertilizer forms in a 4-yr field experiment, integrating 16S rRNA gene sequencing, metatranscriptomic sequencing, and soil chemical analyses. In the field, the three P fertilizer forms showed comparable P use efficiency (PUE) over 4 years. At the three-leaf stage, insoluble P fertilizer increased root-associated citrate concentrations, enriched carboxylate-associated bacteria (e.g. Bacillus, Solirubrobacter, and Nitrospira), and resulted in higher transcript abundance of genes involved in citrate metabolism and P acquisition. Polymeric P fertilizer enhanced soil phosphatase activity, increased root-associated succinate concentrations, and had higher transcript abundance of genes involved in succinate metabolism and complex polysaccharide degradation. Soluble P fertilizer increased soil available P and enriched Devosia, favored glycoprotein degradation, while showing a limited response to P mobilization processes. This study suggests that, under field conditions, different P fertilizer forms shape distinct rhizosphere bacterial communities to improve PUE by altering root-associated carboxylate release.},
}
@article {pmid42076882,
year = {2026},
author = {Hayashi, I and Sánchez-Pinillos, M and Toju, H},
title = {Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories.},
journal = {Ecology letters},
volume = {29},
number = {5},
pages = {e70388},
doi = {10.1111/ele.70388},
pmid = {42076882},
issn = {1461-0248},
support = {202302//Kyoto University CeLiSIS Program (23CeLiSIS-02)/ ; JPMJCR23N5//Core Research for Evolutional Science and Technology/ ; 24KJ1454//Japan Society for the Promotion of Science/ ; 202302//New Energy and Industrial Technology Development Organization/ ; JPMJFR2048//Fusion Oriented REsearch for disruptive Science and Technology/ ; },
mesh = {Stochastic Processes ; *Microbiota ; Ecosystem ; },
abstract = {Biological community dynamics arise from both deterministic and stochastic processes. While species' responses to environmental factors define attractors of community structure, stochasticity, particularly during early assembly, can redirect ecological trajectories. However, quantifying such roles of stochasticity in community assembly has remained challenging. We tracked community assembly in two multi-replicated experimental systems, each with four levels of founding community size, analysing > 3000 samples across four time points. Stronger initial stochasticity led to greater divergence of both population- and community-level consequences. Strikingly, conspicuous differentiation into alternative trajectories of community assembly occurred when the absolute number of founding prokaryotic cells was less than the order of 10[4]. Thus, quantitative differences in stochasticity produced qualitative differences in community fate. These results demonstrate that early stochastic events can have enduring impacts on ecological dynamics. Deeper quantitative insights into stochasticity will reorganise our views on biological invasions, agroecosystem microbiome management, and therapeutics of human-associated microbiomes.},
}
@article {pmid42077003,
year = {2026},
author = {Bukovac, J and Husain, M and Sapper, T and O'Dell, A and Bittoni, M and Gastier, H and Chebbi, A and Hockenhull, V and Dohar, Z and Moon, J and Tabung, F and Verschraegen, C and Wu, R and Kendra, K and Yang, Y and Volek, J and Spakowicz, D},
title = {How the Ketogenic Diet Shapes the Microbiome to Influence Cancer Immunotherapy Outcomes: An Exploration of Clinical Trials and Their Results.},
journal = {Nutrition and cancer},
volume = {},
number = {},
pages = {1-30},
doi = {10.1080/01635581.2026.2658807},
pmid = {42077003},
issn = {1532-7914},
abstract = {Ketogenic dietary interventions (KDIs) are increasingly explored as adjuncts in oncology due to their metabolic and immunomodulatory effects. One mechanism by which KDIs are expected to modulate the immune system is by altering the gut microbiome, which has been shown to affect treatment outcomes, particularly in the context of immunotherapies. This review synthesized findings from 43 clinical trials to evaluate the current landscape of KDIs in cancer care, with a focus on the gut microbiota and immunotherapy. Although 47% of identified trials are completed, none have yet published results combining KDIs with immunotherapy. Since 2020, however, there has been a significant increase in ongoing studies investigating this combination and incorporating microbiome endpoints. While KDIs may help shape an immunotherapy-permissive environment, further clinical evaluation is necessary to determine the full extent of KDIs on the microbiome. Future research should prioritize longitudinal microbiome profiling and standardized adherence reporting to clarify the therapeutic potential of KDIs as a metabolic adjuvant to immune checkpoint inhibitors.},
}
@article {pmid42077151,
year = {2026},
author = {Horner, KM and Corish, CA and Quinn, AM},
title = {Addressing Undernutrition in Older Adults with Plant-Based Products.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-31},
doi = {10.1017/S0029665126103000},
pmid = {42077151},
issn = {1475-2719},
abstract = {The aim of this review is to provide an overview of the evidence to date and several key considerations regarding addressing undernutrition in older adults with plant-based products. Undernutrition, resulting from inadequate protein and energy intake is common among older adults, and is associated with poor health and quality of life. Ensuring adequate protein and energy intake is a key component of strategies aiming to prevent and/or treat undernutrition. Increasing diversity of protein intake to include more sustainable plant-based sources is encouraged in the general population. However, to support healthy ageing, it is important to consider factors such as the impact of greater consumption of plant-based products on appetite and nutritional status, muscle protein synthesis and skeletal muscle mass. Although the literature in older adults is limited, the current evidence suggests no significant differences when comparing effects of plant to animal-based products/diets on a range of outcomes including appetite, nutritional status, longer-term muscle protein synthesis and muscle mass. Furthermore, there is evidence of improvements in nutritional status and muscle protein synthesis following plant protein supplementation compared to before supplementation or lower protein intakes. Therefore, greater intake of certain plant-based products could assist in enhancing sustainability of food systems and meeting nutritional requirements to prevent undernutrition. Among other factors, the plant protein source, the food matrix and presence of other nutrients need consideration. Further studies are needed in several areas, including investigating the effects of greater intake of plant-based products on the gut microbiome, and in the treatment of undernutrition.},
}
@article {pmid42077290,
year = {2026},
author = {Logan, AC and Mishra, P and Berryessa, CM and Caruso, GD and Hagenbeek, FA and Denson, TF and Robinson, JM and Prescott, SL},
title = {Challenging the prescientific frameworks of criminal justice: neurobiology and criminolytic interventions in the legalome era.},
journal = {Frontiers in psychology},
volume = {17},
number = {},
pages = {1791262},
pmid = {42077290},
issn = {1664-1078},
abstract = {Contemporary systems of criminal justice are rooted in prescientific folk psychology assumptions related to moral fiber, free will, agency, and near-universal levels of willpower. For instance, people often believe that morally "defective" people make voluntary choices, failing to utilize their own self-control capacities. Given the wide acceptance of such beliefs, they are considered "normative" within law, serving to underpin retributive punishment. However, rapid advances in biological sciences-aided by multi-omics technologies-have illuminated the ways in which brain architecture and current metabolic conditions can constrain agency and shape here-and-now decision-making. Here in this perspective article, we examine how these advances are placing the prescientific foundations of criminal justice systems under duress. Older single-gene and single neuroimage attempts at explaining criminal behavior are giving way to the legalome era. This describes a more holistic epoch in which the simultaneous integration of mass biological data (e.g., polygenetic, metabolic, microbiome, metabolomic, lipidomic, and other omics-derived information) can provide explanatory power to criminal behavior and vulnerability, and guide personalized approaches to prevention and treatment. Advances in behavioral epigenetics are revealing how genetic predispositions interact with the exposome to shape human behavior through dynamic, potentially modifiable mechanisms. Moreover, evidence suggests that the human microbiome acts as a dynamic interface between environment and brain, influencing behavior in ways that are relevant to vulnerability, impulse control, and decision-making. Promising criminolytic interventions range from nutritional and pharmaceutical approaches to cognitive-behavioral therapy and contemplative practices. The integration of biological evidence and science education, along with ethically guided neurointerventions, will be critical to more humane systems of judgement.},
}
@article {pmid42077435,
year = {2026},
author = {DiTulio, M and Navarro-Torres, CA},
title = {Clearance of multiple antibiotic-resistant coagulase-negative staphylococci is selectively associated with higher circulating α-melanocyte stimulating hormone in patients evaluated for chronic inflammatory response syndrome.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1728408},
pmid = {42077435},
issn = {1664-2392},
mesh = {Humans ; *alpha-MSH/blood ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Staphylococcus/drug effects/isolation &amp; purification ; Adult ; Biomarkers/blood ; *Staphylococcal Infections/blood/microbiology ; Coagulase/metabolism ; Aged ; Matrix Metalloproteinase 9/blood ; Anti-Bacterial Agents/therapeutic use ; Vasoactive Intestinal Peptide/blood ; Chronic Disease ; Drug Resistance, Bacterial ; },
abstract = {INTRODUCTION: Neuroimmune regulatory peptides play central roles in coordinating inflammatory, metabolic, and mucosal immune processes in humans. Among these, α-melanocyte stimulating hormone (α-MSH), a proopiomelanocortin-derived peptide, has been implicated in modulation of cytokine signaling, epithelial barrier function, and pain processing. However, determinants of circulating α-MSH levels in chronic inflammatory states remain incompletely characterized in human clinical populations. Persistent sinonasal colonization with multiple antibiotic-resistant coagulase-negative staphylococci (MARCoNS) has been reported in some cohorts presenting with environmentally associated multisystem illness, described in some clinical settings as Chronic Inflammatory Response Syndrome (CIRS). Yet its relationship to systemic neuroendocrine biomarkers has not been quantitatively examined.<br><br>METHODS: This retrospective observational cohort study examined whether follow-up MARCoNS culture status was associated with longitudinal trajectories of &#x3b1;-MSH, compared with two additional biomarkers commonly assessed in this population: matrix metallopeptidase-9 (MMP-9) and vasoactive intestinal polypeptide (VIP). A total of 188 adult patients evaluated within a CIRS-informed clinical framework at a single clinical site were included. Each participant contributed two timepoints of laboratory data for &#x3b1;-MSH, MMP-9, and VIP, along with MARCoNS culture results.<br><br>RESULTS: Across the full cohort, &#x3b1;-MSH increased by an estimated 10 pg/mL, MMP-9 decreased by 398 ng/mL, and VIP increased by 20 pg/mL between baseline and follow-up. Mixed-effects modeling revealed a significant timepoint-by-MARCoNS interaction for &#x3b1;-MSH, such that patients who were MARCoNS-negative at follow-up exhibited higher circulating &#x3b1;-MSH levels compared with those who remained positive. In contrast, no corresponding MARCoNS interaction was observed for VIP or MMP-9.<br><br>DISCUSSION: These findings provide quantitative evidence that follow-up MARCoNS culture status is selectively associated with &#x3b1;-MSH trajectories in this retrospective cohort, supporting further prospective investigation into potential links between persistent bacterial nasal colonization and neuroendocrine-immune biomarkers in multisystem chronic illness.},
}
@article {pmid42077489,
year = {2026},
author = {Islam, MZ and Pitta, DW and Niu, M},
title = {Breed-specific microbiomes drive differential responses to 3-nitrooxypropanol and Acacia mearnsii in dairy cows.},
journal = {JDS communications},
volume = {7},
number = {3},
pages = {332-338},
pmid = {42077489},
issn = {2666-9102},
abstract = {Methane (CH4) inhibitor 3-nitrooxypropanol (3-NOP) shows variable efficacy in Brown Swiss (BS) and Holstein (HF) cows, but the underlying mechanisms remain unclear. Rumination bolus, a proxy for rumen microbiota, combined with exhalomics (analysis of exhaled volatiles), offered a noninvasive approach to differentiate breed responses to CH4 mitigation strategies. We investigated whether differences in rumination bolus microbiota and exhaled VFA (eVFA) between BS and HF cows contribute to their responses to 3-NOP. Sixteen multiparous cows (8 BS, 8 HF) were studied in a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of 3-NOP (0 or 60 mg/kg of DM) and Acacia mearnsii tannin extract (TAN; 0% or 3% of DM). Rumination bolus samples collected 6 h postfeeding during the fourth period of the experiment were sequenced for full-length 16S rRNA sequences (PacBio Revio platform) to assess bacterial diversity, while exhaled samples from all 4 periods were analyzed for VFA using secondary electrospray ionization-MS. Microbial community shifts were analyzed using Bray-Curtis, unweighted, and weighted unique fraction metric (UniFrac) distances. Spearman correlations were performed between genus-level information and eVFA, CH4, hydrogen (H2), carbon dioxide (CO2), DMI, and milk yield between breeds. Supplementation of 3-NOP induced a modest but consistent shift in microbial composition, whereas TAN effects were minimal and inconsistent. Breed-specific differences were evident: BS harbored more Prevotella and Rikenellaceae, and HF were enriched in Succinivibrionaceae and Acetitomaculum. Under 3-NOP, HF genera aligned more strongly with propionate-producing pathways and showed stronger negative correlations with CH4, and BS genera remained more associated with acetate and butyrate proportions. Correlations with feed intake and milk yield were generally weak and inconsistent across genera. Overall, our results indicate that HF cows are more responsive to 3-NOP, likely redirecting spared H2 toward propionate-producing bacteria, and BS are more resilient to H2 fluxes and consequently less responsive to 3-NOP. Findings from this pilot study highlight the importance of host-microbiome interactions in evaluating and implementing enteric CH4 mitigation strategies in dairy cattle.},
}
@article {pmid42077491,
year = {2026},
author = {Navarro Marcos, C and de Evan, T and Gonzalez Recio, &#xd3; and Gutiérrez Rivas, M and Dolores Carro, M},
title = {Effects of feeding agroindustrial byproducts on rumen fermentation and microbiome of sheep.},
journal = {JDS communications},
volume = {7},
number = {3},
pages = {315-320},
pmid = {42077491},
issn = {2666-9102},
abstract = {The use of agroindustrial byproducts in ruminant nutrition is gaining increased attention because of economic and environmental benefits and their potential to enhance ruminal function and animal performance. However, the effect of these byproducts on ruminal microbiome and fermentation has been scarcely investigated. This study aimed to evaluate the effects of replacing conventional feeds with agroindustrial byproducts (18:18:8 mixture of corn dried distillers grains with solubles, dry citrus pulp, and exhausted olive cake) on the ruminal microbiome and fermentation parameters of sheep. Four rumen-fistulated Lacaune sheep were used in 2 experimental periods, receiving mixed diets composed of 50% alfalfa hay and 50% of either a control concentrate (CON diet) or a concentrate with agroindustrial byproducts (BYP diet). Ruminal samples were collected at 0, 3, and 6 h postfeeding to assess microbial composition and fermentation parameters. Diet significantly influenced the ruminal microbiome, but the effect of individual sheep was more pronounced than that of the diet. Sampling time also influenced the ruminal microbiome. The inclusion of agroindustrial byproducts in the concentrate did not significantly alter ruminal fermentation parameters. However, the BYP diet led to more steady ruminal fermentation, preventing large fluctuations in total VFA and ammonia concentrations, likely the result of a broader range of fermentable substrates present in the BYP concentrate and changes in ruminal microbiome. These results may indicate improved synchronization of nutrient availability for ruminal microorganisms. Overall, replacing conventional feed ingredients with agroindustrial byproducts promoted microbial diversity and improved ruminal fermentation, potentially leading to increased dairy ruminant performance.},
}
@article {pmid42077790,
year = {2026},
author = {Fan, X and Zhou, X and Wang, L and Zhang, X and Shen, Y and Xiao, Y and Wang, H and Deng, L and Xie, Y},
title = {Comparative Analysis of Gut Microbiomes in Parasitic Roundworms Reveals Phylogeny-Associated Community Structure and Functional Adaptation.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {},
pages = {2764696},
pmid = {42077790},
issn = {1865-1682},
mesh = {Animals ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Toxocara/microbiology ; Female ; Male ; *Ascaris/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Roundworm nematodes are globally distributed zoonotic parasites that inhabit the intestinal tract of various mammals. Although these parasites reside in the host's guts, their own intestinal ecosystems remain poorly understood. Recent evidence suggests that helminths may harbor distinct gut microbiomes that contribute to their physiology and host interactions, yet cross-species comparisons are lacking. Here, we performed full-length 16S rRNA sequencing to characterize and compare the gut microbiomes of four major roundworm species-Ascaris suum (As), Baylisascaris schroederi (Bs), Toxocara cati (Tc), and Toxocara vitulorum (Tv). Across 38 individual worms, we identified 359 bacterial taxa dominated by Enterobacteriaceae, with Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae forming a conserved core community. Despite this compositional similarity, beta-diversity and hierarchical clustering analyses revealed that microbial community structure was primarily determined by parasite phylogeny and roundworm sex, not host diet. Functional prediction using PICRUSt2 indicated clear species-specific enrichment in metabolic pathways, such as carbohydrate metabolism in Bs and xenobiotic metabolism in As, reflecting adaptive divergence of microbial functions. Collectively, these findings demonstrated that roundworm gut microbiomes exhibited taxonomic conservation but functional specialization, shaped by the evolutionary history of the parasites themselves. This study established a conceptual framework viewing the parasite as the primary host of its microbiome and provided new insights into the co-evolutionary relationships between helminths and their symbiotic bacteria.},
}
@article {pmid42077846,
year = {2026},
author = {Pinheiro, GL and Lin, NJ and Parratt, KH and Hines, I and Hack, HR and Servetas, SL and Iyer, H and Da Silva, SM},
title = {The Integration of Focused Ultrasonication, ddPCR, and Flow Cytometry Effectively Estimates Genome Copies per Cell and Enhances DNA Extraction Efficiency in Escherichia coli Samples.},
journal = {ACS omega},
volume = {11},
number = {16},
pages = {23885-23899},
pmid = {42077846},
issn = {2470-1343},
abstract = {Microbiology researchers rely on nucleic acid measurement techniques, such as the quantitative polymerase chain reaction (qPCR) and DNA sequencing, to address diverse scientific and practical challenges. These applications range from detecting microbial contaminants in regenerative medicine and biotherapeutic products to advancing waste remediation, pathogen detection, biosurveillance, and microbiome studies. A critical step in these techniques is DNA extraction, which involves breaking cells to release their DNA as the required input for downstream analyses. The efficiency of this process, known as DNA extraction efficiency (DEE), directly impacts the accuracy of quantitative measurements and, therefore, the interpretation of results. Unfortunately, most DNA extraction methods suffer from suboptimal efficiency that varies across microbial strains, potentially leading to inaccurate results. In this paper, we present a highly efficient DNA extraction protocol leveraging adaptive focused acoustics (AFA) technology to achieve a balance between cell lysis and DNA integrity. Using Escherichia coli as the model organism, the protocol delivers nearly 100% DEE, setting a benchmark for performance. A key innovation in this protocol is the integration of focused ultrasonication, droplet digital polymerase chain reaction (ddPCR), and flow cytometry to estimate genome copies and the corrected DNA extraction efficiency (cDEE), which accounts for the number of genome copies. The proposed protocol addresses the need for an accurate assessment of DEE and DNA quantification, as demonstrated here with E. coli, for various DNA-based techniques, including metagenomic analysis of complex microbial communities and the development of new DNA extraction protocols. This novel protocol addresses a longstanding limitation in microbiological research and has the potential to significantly enhance accuracy and reproducibility across various applications. While there is significant potential for applying this approach, the authors acknowledge that further studies using microorganisms with thicker cell walls will enhance the utility of this framework. However, the knowledge generated in this study can be readily applied and tailored to the specific objectives of individual research groups.},
}
@article {pmid42077904,
year = {2026},
author = {Nigam, AK and Falah, K and Momper, JD and Nigam, SK},
title = {Selectivity of OATs and OATPs for Endogenous Metabolites and Signaling Molecules In Vivo.},
journal = {ACS omega},
volume = {11},
number = {16},
pages = {24714-24724},
pmid = {42077904},
issn = {2470-1343},
abstract = {Organic anion transporters (OATs, SLC22) in the kidney and organic anion-transporting polypeptides (OATPs, SLCO) in the liver play crucial roles in the disposition of small molecule drugs that are organic anions. According to the Remote Sensing and Signaling Theory, these multispecific "drug" transporters are also central to crosstalk between the liver, kidney, and other organs via endogenous small molecules (e.g., metabolites, signaling molecules, gut microbiome products). These multispecific drug transporters govern access of small molecules with high informational content across multiple scales (organism to organelle). Previous chemoinformatic and machine learning methods have proven useful for identifying molecular properties of organic anion drugs that predispose them to handling by the OAT (renal) and the OATP (hepatic) transporters. This is important for understanding pharmacokinetics (ADME) in the context of chronic kidney disease (CKD) and liver disease. Given that OATs and OATPs are involved in many metabolic diseases, we sought to determine whether molecular properties could be identified for distinguishing OAT- versus OATP-interacting endogenous metabolites in vivo. This is essential for understanding endogenous small molecule communication between the kidney proximal tubule and hepatocytes in a larger Remote Sensing and Signaling System. We analyzed in vivo metabolomics data from OAT and OATP knockout mice, focusing on endogenous metabolites selective for OATs (e.g., OAT1 or SLC22A6; OAT3 or SLC22A8) vs OATPs (including the locus containing Oatp1b2, the closest homologue of human OATP1B1 or SLCO1B1 and OATP1B3 or SLCO1B3). Applying chemoinformatic methods to a data set of 210 metabolites based on knockout mouse metabolomics (92 OAT-selective, 118 OATP-selective), we identified a set of distinguishing molecular properties (e.g., MolLogP, RingCount, NumRotatableBonds). We then used machine learning approaches (e.g., Random Forest, Naive Bayes, Logistic Regression) to classify OAT vs OATP metabolites, achieving over 75% accuracy. These results support the view that transporter knockout mouse metabolomics can help define selectivity of SLC drug transporters for endogenous metabolites, signaling molecules, antioxidants, nutrients, and gut microbiome products. In the context of the Remote Sensing and Signaling Theory, we discuss the implications for understanding organ crosstalk and interorganismal communication as well as drug disposition, drug-metabolite interactions, and metabolite-based drug design.},
}
@article {pmid42077990,
year = {2026},
author = {Kijpornyongpan, T and Krasaesin, A and Chongcharoenkit, T and Rattanapornsompong, K and Truntipakorn, A and Bhuridej, P and Rodthongkum, N and Cho, SD and Porntaveetus, T},
title = {Microbial signatures of dental caries in the incarcerated elderly: a salivary microbiota study in a restricted environment.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2662787},
pmid = {42077990},
issn = {2000-2297},
abstract = {BACKGROUND: Dental caries is driven by microbial dysbiosis and influenced by diet and lifestyle. Incarcerated populations living under regulated regimens offer a unique model to study the oral microbiota in older adults by minimising environmental confounding variables.<br><br>OBJECTIVES: This study aimed to characterise the salivary microbiota of older incarcerated adults and identify bacterial taxa associated with caries status and severity.<br><br>DESIGN: Twenty-eight incarcerated men (aged&#x2009;&#x2265;&#x2009;50 years) were stratified into caries-active (CA) and caries-free (CF) groups (n&#x2009;=&#x2009;14 each). The salivary microbiota was profiled using 16S rRNA gene sequencing to assess diversity and differential taxonomic abundance.<br><br>RESULTS: CA subjects exhibited higher genus richness and beta-dispersion compared to CF controls. The CF group was enriched with Haemophilus parainfluenzae, Aggregatibacter sp. HMT-949 and Riemerella sp. HMT-322. Conversely, the CA group harboured elevated levels of Dialister invisus, Megasphaera micronuciformis, Prevotella intermedia, Selenomonas sputigena, Capnocytophaga ochracea and Gemella haemolysans. Furthermore, G. haemolysans, Solobacterium moorei and Streptococcus were positively correlated with caries severity, whereas Veillonella rogosae and Streptococcus koreensis and Peptostreptococcusexhibited negative correlation.<br><br>CONCLUSION: This study elucidates salivary dysbiotic signatures in older adults within a controlled environment. The identified bacterial profiles provide biomarkers for caries risk, underscoring the need for targeted oral health surveillance and preventative strategies in institutionalised populations.},
}
@article {pmid42078142,
year = {2026},
author = {Fu, M and Kang, Y and Zhou, J and Zhu, L and Wang, W and Lyu, T and Lin, L},
title = {Contrasting elevational patterns of soil and root-associated fungal communities highlight host-driven filtering in Quercus wutaishansea forests.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1825787},
pmid = {42078142},
issn = {1664-462X},
abstract = {The role of plant hosts in shaping root-associated microbial communities remains a central question in ecology, particularly in the face of changing environmental conditions. While considerable attention has been paid to soil microbial diversity, the interactive dynamics between plant individuals and soil microbial pool during root-associated fungi establishment across environmental gradients remain poorly understood. In this study, we explored the elevational variation in the diversity of soil and root-associated fungal communities of Quercus wutaishansea across ten elevational belts (1020 m-1770 m above sea level (asl)) on Dongling Mountain, Beijing, China. We found that root-associated fungal communities exhibited significantly increased alpha diversity with elevation (P < 0.05), whereas soil fungal communities showed no clear elevational trends (P > 0.05). Despite substantial variation in the soil fungal pool, the composition of root-associated fungal communities remained notably stable, suggesting a strong host filtering effect (P < 0.05). Compared with hump-shaped Sim and decreasing Morisita β-diversity of soil fungi as elevation increased (P < 0.05), the β-diversity of root-associated fungi did not exhibit a consistent elevational pattern nor mirror soil fungal β-diversity. These results suggest that, beyond environmental filtering, Q. wutaishansea plays an active role in shaping its root fungal community by selecting compatible fungal partners according to its physiological needs across altitudes. The findings reveal a significant and variable plant selectivity in the recruitment of microbiomes across different elevations, offering novel insights into plant-microbiome interactions within forest ecosystems in response to climate change.},
}
@article {pmid42078328,
year = {2026},
author = {Li, M and Wong, W and Xiong, H and Chen, K},
title = {16S rRNA gene sequencing-based preliminary study on the differences in the microbiota between children with rampant caries and those with arrested caries.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1693174},
pmid = {42078328},
issn = {2673-4842},
abstract = {OBJECTIVE: In clinical practice, arrested caries (AC) poses less harm to children than rampant caries (RC), as the development of caries is arrested. However, there is limited research on the microbiology of the two types of caries. This research study the differences in microbial profiles among AC, caries-free (CF)and RC patients.<br><br>METHODS: Thirty-six children aged 3-5 years were selected, grouped into AC, CF, and RC groups, with 12 children in each group. A total of 72 samples, including non-stimulated saliva and dental plaque, were collected. Microbial DNA was extracted, and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. Bioinformatics analysis was performed with QIIME2, and taxonomic classification was based on the SILVA database. Alpha and beta diversity were assessed, and the Kruskal-Wallis test (with Benjamini-Hochberg correction) was used to identify taxonomic abundance differences.<br><br>RESULTS: The &#x3b1;-diversity in plaque was significantly lower than in saliva. While the salivary microbiome showed minimal variation across different caries states, the plaque microbiome displayed distinct structural differences. At the taxonomic level, Bacteroidota and Prevotella were enriched in the RCP group, while Fusobacteriota and Leptotrichia were more abundant in the ACP and CFP groups, with Corynebacterium being most abundant in the arrested caries group. Differential abundance analysis identified five putative species-level biomarkers associated with specific clinical states in dental plaque.<br><br>CONCLUSION: This study suggests that different caries statuses are linked to distinct microbial profiles in dental plaque. The analysis revealed clear differences in microbial community structures across the three clinical groups, highlighting a potential connection between caries activity and plaque dysbiosis.},
}
@article {pmid42078366,
year = {2026},
author = {Sy, M and Ndiaye, T and Thakur, R and Gaye, A and Levine, ZC and Ngom, B and Bellavia, KL and Firer, D and Toure, M and Ndiaye, IM and Diedhiou, Y and Mbaye, AM and Gomis, JF and DeRuff, KC and Deme, AB and Ndiaye, M and Badiane, AS and Paye, MF and Sabeti, PC and Ndiaye, D and Siddle, KJ},
title = {Oral and plasma microbiome in the context of acute febrile illness.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.26351042},
pmid = {42078366},
abstract = {Emerging infectious diseases and antimicrobial resistance (AMR) have surfaced as two major public health threats over the past two decades. Consequently, integrative surveillance systems capable of detecting both emerging pathogens and resistance-carrying bacteria are crucial. With advances in next-generation sequencing, simultaneous detection of pathogens and AMR is increasingly feasible. In this study, we used short-read metatranscriptomics complemented by total 16S rRNA metagenomic long-read sequencing to analyze paired oral and plasma samples from a cohort of febrile individuals at two locations in Senegal. Oral microbiomes differed in community composition between locations, and reduced diversity and richness were significantly associated with high fever. We identified at least one known pathogen in 15.33 % (23/150) of samples, with Borrelia crocidurae as the most frequently detected pathogen. We detected both pathogenic and non-pathogenic viruses in oral (10/72) and plasma (09/78) samples. Finally, we observed a high frequency of genes associated with resistance and virulence: 10% of samples expressed at least one AMR gene (ARG), and 24% expressed virulence factor genes. Resistance to widely used beta-lactam antibiotics was the most prevalent. Our findings provide critical data on oral and plasma microbiomes in the context of acute febrile illness in Senegal while expanding understanding of circulating ARGs.},
}
@article {pmid42078518,
year = {2026},
author = {Batistel, F},
title = {Using gnotobiotic ruminants to dissect host-microbe interactions for sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771182},
pmid = {42078518},
issn = {1664-302X},
abstract = {Ruminant animals host one of the most complex gut microbial ecosystems, enabling the conversion of fibrous plant biomass into nutrient-dense foods such as meat and milk, which are essential for global food security. Over time, successive waves of research-from the initial recognition of microbes in the rumen, through anaerobic cultivation, to more recent multi-omics approaches-have progressively expanded our understanding of rumen microbial composition and its links to animal production and greenhouse gas emissions. Despite these advances, most insights into rumen microbial composition and traits of interest are based on associative or correlative evidence, and the host-derived mechanisms that actively shape rumen microbial composition and function remain poorly defined. Early gnotobiotic studies in ruminants demonstrated the value of maintaining animals under defined microbial conditions to dissect host-microbe interactions; however, this experimental capability has largely been lost from contemporary rumen research. This Perspective argues that revisiting gnotobiotic ruminant models is both timely and necessary for establishing causal mechanisms that govern host-microbe interactions in the rumen. Integrating gnotobiotic ruminant models is essential for establishing causal relationships between host biology and rumen microbial composition, thereby providing a foundation for biologically informed strategies that can enhance the sustainability of ruminant production systems.},
}
@article {pmid42078524,
year = {2026},
author = {Najnine, F and Guo, X and Cai, J},
title = {Lactobacillus salivarius GZPH2 reshapes hepatopancreatic microbiome structure and enhances immunometabolism in Litopenaeus vannamei under farm conditions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1762396},
pmid = {42078524},
issn = {1664-302X},
abstract = {INTRODUCTION: The hepatopancreas of Litopenaeus vannamei plays a central role in digestion, metabolism, mineral homeostasis, and immune defense; however, its strain-specific responsiveness to probiotics remains insufficiently characterized. This study aimed to elucidate the comparative effects of a single-strain probiotic (Lactobacillus salivarius GZPH2; HH) and a mixed-strain consortium (EM; TH) on hepatopancreatic function under tropical semi-intensive culture conditions.<br><br>METHODS: An integrated multi-omics approach, combining histology, mineral profiling, 16S/18S rRNA sequencing, and 4D data-independent acquisition (4D-DIA) proteomics, was applied to evaluate probiotic-induced changes after 90 days of feeding, with a non-supplemented group (WH) as control.<br><br>RESULTS: Both probiotics significantly improved growth, survival, and feed efficiency, increasing biomass by 26-27% relative to the control; however, distinct mechanistic responses were observed. HH enhanced hepatopancreatic regeneration by increasing embryonic (E) and fibrillar (F) cells while reducing blister-like (B) and resorptive (R) cells, alongside greater accumulation of Mg, Fe, Ca, and Se. It also promoted microbial evenness and enriched beneficial Alphaproteobacteria (e.g., Labrenzia, Tropicibacter) and fungal taxa (Candida-Lodderomyces clade). Proteomic analysis revealed upregulation of carbohydrate metabolism, calcium regulation, immune-related proteins, and antioxidant enzymes, including hemocyanin, crustin-like proteins, chitinase, and catalase. In contrast, TH maintained a storage-oriented morphology, exhibited lower mineral deposition and microbial diversity, was dominated by Bacillus, and preferentially enriched proteolytic enzymes and redox-related pathways.<br><br>DISCUSSION: These findings demonstrate that the single-strain probiotic GZPH2 induced a more regenerative, metabolically efficient, and immunologically robust hepatopancreatic state than the mixed consortium. These findings provide multi-omics evidence supporting strain-specific probiotic selection as a precision strategy to enhance shrimp health and sustainability in aquaculture.},
}
@article {pmid42078525,
year = {2026},
author = {Brahmbhatt, HD and Chavda, P and Vadee, D and Patel, AK and Bagatharia, S},
title = {Genome characterization and comparative genomics of Limosilactobacillus reuteri HDB isolated from the gut of an Indian infant.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780782},
pmid = {42078525},
issn = {1664-302X},
abstract = {Limosilactobacillus reuteri, formerly Lactobacillus reuteri, is a rod-shaped, Gram-positive, facultative anaerobe that colonizes the gastrointestinal tract of most vertebrates, including humans. We report the first isolation of L. reuteri strain HDB from the stool of a healthy Indian infant. Species assignment using the Type (Strain) Genome Server (TYGS) placed HDB within the L. reuteri clade, showing closest affinity to L. reuteri subspecies porcinus (dDDH 69.7%) yet clustering phylogenomically with L. reuteri DSM 17938. Hybrid de novo assembly (Illumina + Oxford Nanopore GridION MK1) generated a single circular 2,226,956 bp chromosome (GC 39.04%) encoding 2,160 CDS. Functional annotation identified genes involved in vitamin B12 biosynthesis, reuterin production, and probiotic functions, along with enriched carbohydrate and cofactor metabolic pathways. Comparative analysis with 59 L. reuteri genomes revealed a pangenome of 11,725 gene families, including 944 core gene families, 171 soft-core gene families, 1912 shell gene families, and 8698 cloud gene families, highlighting notable diversity. Core-genome phylogeny aligns HDB closely with the reference strain DSM 17938, confirming its identity as a human-associated lineage. dN/dS analysis indicated strong purifying selection across host niches, with no evidence of widespread positive selection. Genome-scale modeling predicts expanded carbohydrate flux in HDB against global references. The genetic background, along with its conserved metabolic features, suggests that HDB carries genomic characteristics commonly associated with human-derived L. reuteri strains. These observations support its consideration for further evaluation as a regionally sourced probiotic candidate. These conclusions are based on genomic and computational predictions and require experimental validation through adhesion, colonization, and safety studies.},
}
@article {pmid42078528,
year = {2026},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R and Han, Y},
title = {Identification of novel CRESS-DNA viruses in the human vaginal microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1790643},
pmid = {42078528},
issn = {1664-302X},
abstract = {INTRODUCTION: Circular replication-associated protein (Rep)-encoding single-stranded DNA (CRESS-DNA) viruses are widely distributed across diverse hosts and environments, yet their diversity within the human vaginal virome remains poorly characterized. This study aimed to investigate the presence, diversity, and evolutionary relationships of CRESS-DNA viruses in the human vaginal niche.<br><br>METHODS: Viral metagenomic sequencing was performed on 24 pooled vaginal swab libraries derived from women with and without vaginitis. After host sequence removal and quality control, de novo assembly and viral identification were conducted. Candidate viral genomes were curated based on genomic features, followed by functional annotation, phylogenetic analysis using Rep protein sequences, and genome-wide pairwise nucleotide identity comparisons.<br><br>RESULTS: A total of five CRESS-DNA viral genomes were identified, including four complete and one nearly complete circular genomes. All genomes exhibited canonical architectures, encoding Rep and Cap proteins and containing conserved HUH endonuclease and superfamily 3 helicase motifs. Phylogenetic analysis placed these viruses within the orders Rohanvirales, Ringavirales, Cirlivirales, and Cremevirales, representing multiple distinct evolutionary lineages. Genome-wide pairwise identity analysis showed that all identified viruses fell below established species- and genus-level thresholds, indicating that they represent novel taxa. Comparative analyses further revealed substantial divergence from known environmental and vertebrate-associated viruses.<br><br>DISCUSSION: These findings expand the known diversity of CRESS-DNA viruses in the human vaginal virome and highlight their broad evolutionary diversity. The detected viruses likely represent diverse ecological origins rather than stable host-specific infections, and no clear association with vaginitis was observed. This study provides new insights into the evolutionary landscape of CRESS-DNA viruses in the human reproductive tract and underscores the need for further investigation into their biological roles and potential health implications.},
}
@article {pmid42078532,
year = {2026},
author = {Padmanabhan, C and Puig, A},
title = {Editorial: Metagenomic insights into microbial communities in fruits and vegetable plants.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1844864},
pmid = {42078532},
issn = {1664-302X},
}
@article {pmid42078537,
year = {2026},
author = {Shen, T and Zhou, Y and Gao, J and Xiong, X and Chen, C},
title = {Gut microbiota regulates growth retardation in pigs through their metabolites of taurine and butyric acids.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1811659},
pmid = {42078537},
issn = {1664-302X},
abstract = {Growth retardation of piglets has always been observed in current pig production system. Here we defined these pigs as stunted pigs. Stunted pigs show normal feed intake, but exhibit extremely slow growth speed. This brings a big economic loss to pig industry. Many factors can lead to growth retardation, including gut microbiota which has been reported to play important roles in growth retardation of children. However, whether and which gut microbial taxa are associated with growth retardation of piglets are largely unknown. Here we used 16S rRNA gene and shotgun metagenomic sequencing to identify bacterial taxa associated with growth retardation in 126 pigs including stunted pigs and their pairwise littermates showing normal growth. We identified several Clostridium spp. significantly enriched in the gut of normal growing pigs, including Clostridium symbiosum which was the key biomarker distinguishing stunted pigs and normal growing pigs, while several Bacteroides spp. had higher abundances in stunted pigs. Clostridium spp. was significantly associated with the shifts of functional capacities of the gut microbiome between normal and stunted pigs, e.g., biosynthesis of unsaturated fatty acids. Untargeted serum metabolome analysis found that normal growing pigs had higher concentration of taurine in serum. Increased concentration of serum taurine was associated with increased abundance of Clostridium symbiosum. Furthermore, all metabolites having higher abundances in normal growing pigs were enriched in the pathway of taurine and hypotaurine metabolism. Short-chain fatty acids (SCFAs) analysis identified butyric acid having higher concentration in feces of normal growing pigs in both discovery and validation cohorts, and the changes in the abundances of Clostridium symbiosum was correlated with the shifts of the concentrations of fecal SCFAs. These results suggested that Clostridium spp., especially Clostridium symbiosum improved pig growth by increasing the concentrations of serum taurine and fecal butyric acid, and was an important biomarker associated with pig growth. This study provided important insights into the effect of the gut microbiome on pig growth retardation.},
}
@article {pmid42078551,
year = {2026},
author = {Yang, W and Ren, Q and Li, B},
title = {Case Report: Washed microbiota transplantation for the treatment of malnutrition with multidrug-resistant Klebsiella pneumoniae and Candida tropicalis coinfection in a child.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1809311},
pmid = {42078551},
issn = {2296-2360},
abstract = {BACKGROUND: Multidrug-resistant (MDR) Klebsiella pneumoniae and fungal coinfection in children with severe malnutrition are difficult to control with antibiotics alone. This report describes an 8-year-old boy whose pulmonary infection remained uncontrolled and whose nutritional status progressively deteriorated. Washed microbiota transplantation (WMT) was introduced as part of a multimodal salvage treatment strategy, after which the patient showed gradual improvement during continued antimicrobial therapy, respiratory support, and nutritional rehabilitation.<br><br>CASE PRESENTATION: We report the case of an 8-year-old boy with chronic malnutrition and recurrent severe pneumonia associated with an underlying central nervous system disorder. He developed recurrent respiratory failure and a persistent pulmonary infection caused by ESBL-producing MDR K. pneumoniae and Candida tropicalis. Despite broad-spectrum antimicrobial therapy, respiratory support, bronchoscopy/bronchoalveolar lavage, and enteral nutrition through a nasojejunal tube, infection control remained poor and nutritional status continued to deteriorate, complicated by sepsis and antibiotic-associated diarrhea. In this context, WMT was introduced through a nasojejunal tube as part of a multimodal salvage treatment strategy and was administered in two treatment courses. Thereafter, during continued antimicrobial treatment, respiratory support, and nutritional rehabilitation, the patient showed progressive clinical improvement, with subsequent negative sputum culture results, gradual radiographic resolution of pulmonary inflammation, weight gain from 14.0 to 22.5&#x2005;kg, and marked functional recovery.<br><br>CONCLUSION: This case suggests that, in severely malnourished children with refractory multidrug-resistant pulmonary bacterial and fungal infections, WMT may have potential adjunctive value as part of comprehensive management. However, because multiple interventions were implemented concurrently and no pre- and post-WMT microbiome sequencing was performed, the observed clinical improvement could not be attributed exclusively to WMT. Therefore, this case should be interpreted only as an exploratory clinical observation rather than confirmatory evidence, and future prospective studies under strict ethical oversight need to be conducted.},
}
@article {pmid42078569,
year = {2026},
author = {Oliveira, JS and Keim, KS and Evans, R and Kurasch, J and Jahansouz, C and Teigen, LM and Lin, AW},
title = {Capturing static and dynamic dietary patterns for human gut microbiome research: a conceptual framework.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2665578},
pmid = {42078569},
issn = {2993-3935},
abstract = {There is inconsistency in the evidence regarding the effects of food on the gut microbiome. These inconsistencies arise, in part, from substantial inter- and intraindividual variations in diet. The wide range of foods consumed directly influences substrate availability for the microbiota. By categorizing foods into broad groups and overlooking interactions among food constituents within individual foods, current dietary pattern approaches can obscure food-specific differences needed to understand dietary effects. Differences in habitual and occasional intake further complicate analyses since frequency of food consumption can produce different gut microbiota responses within the same individual. Flexible analytical approaches are needed to capture within-individual food intake frequency and food-specific effects. To address these challenges, this narrative review presents dietary pattern concepts that distinguish static (stable or consistent) and dynamic (fluctuating or episodic) intake of specific foods at the individual level. We performed a literature search in three databases, including Medline, CINAHL, and PsycINFO, to retrieve relevant articles that distinguish the concepts of "core foods" and "secondary foods" in population-level studies. We adapt these concepts to a microbiome context at the individual level and propose future directions for studies investigating the impact of diet on the gut microbiome.},
}
@article {pmid42078571,
year = {2026},
author = {Nakato, G and Inoue, H and Onawa, S and Furukawa, R and Obana, N and Tanaka, K and Agematu, H and Song, I and Inoue, J and Fukuda, S},
title = {Development of a monoclonal antibody-based approach for selective enrichment of target Bifidobacterium longum from a complex fecal community.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2663732},
pmid = {42078571},
issn = {2993-3935},
abstract = {Individual differences in gut microbiota composition highlight the need for methods capable of selectively enriching host-associated bacteria from complex microbial communities. Conventional cultivation approaches lack the precision required for targeted enrichment, limiting progress in personalized microbiome research. Here, we established a proof-of-concept monoclonal antibody-based strategy for the selective enrichment of a target gut bacterium. We generated a monoclonal antibody (8H2) exhibiting preferential reactivity toward the human-derived Bifidobacterium longum Jih1 and demonstrated that it selectively enriched viable Jih1 cells from a defined bacterial consortium and a human fecal sample. Proteomic and genetic analyses suggested that 8H2 recognizes glutamine synthetase (GS), an enzyme typically localized intracellularly, but detected on the surface of Jih1 cells. This surface association enables antibody binding and facilitates selective enrichment within complex microbial communities. These data support the feasibility of antibody-based, selective enrichment of viable bacteria and suggest potential applications for monitoring individual-associated bacteria in personalized nutrition and microbiome-based interventions.},
}
@article {pmid42064212,
year = {2026},
author = {Anshory, M and Strepis, N and Rosandy, MG and Pawestri, AR and Iskandar, A and Wulanda, IA and Setyowatie, L and David, NI and Malem, NR and Kalim, H and Nijsten, TEC and Nouwen, JL and Thio, HB},
title = {Skin microbiome variation in people living with HIV: associations with antiretroviral therapy and host factors.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1794878},
pmid = {42064212},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/drug therapy/microbiology ; *Skin/microbiology ; Male ; *Microbiota/drug effects ; Female ; Adult ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Indonesia ; *Anti-Retroviral Agents/therapeutic use ; DNA, Bacterial/genetics ; Skin Microbiome ; },
abstract = {INTRODUCTION: The skin microbiome plays a key role in cutaneous immunity and is shaped by host immune status. HIV infection is associated with immune dysfunction and dermatological disease, yet its impact on the skin microbiome and the modifying effect of antiretroviral therapy (ART) remain incompletely defined. This prospective observational study conducted in Indonesia aimed to characterize differences in skin microbiome composition across HIV status and ART exposure and relate these profiles to clinical parameters.<br><br>METHODS: Skin swabs were obtained from sebaceous (posterior neck) and dry (dorsal forearm) sites in HIV-ART-na&#xef;ve individuals, people living with HIV on ART, and HIV-negative controls, and analyzed using 16S rRNA gene sequencing. Microbial diversity and community structure were assessed using Bray-Curtis dissimilarity, PERMANOVA, and differential abundance testing with ANCOM-BC2, with multivariable models adjusting for demographic, clinical, behavioral, and anatomical factors and subgroup analyses by body mass index, skincare habits, and sampling site.<br><br>RESULTS: In total, 488 samples from 244 participants were analyzed. Both HIV groups showed significantly reduced alpha diversity compared with controls, and overall community composition differed by HIV status, although sampling site explained a larger proportion of variation. Across groups, the microbiome was dominated by Corynebacterium, Cutibacterium, Staphylococcus, and Streptococcus. Differential abundance analyses indicated targeted genus-level shifts rather than global dysbiosis, with ART-na&#xef;ve individuals showing the most consistent deviations, including increased Staphylococcus and reduced Streptococcus relative to controls, and partial attenuation among participants receiving ART. HIV-associated differences were observed within both sebaceous and dry sites, and HIV status remained independently associated with microbiome composition after adjustment.<br><br>CONCLUSIONS: These findings suggest that HIV infection is associated with subtle but consistent alterations in the skin microbiome within the context of strong site-specific skin microenvironments. Longitudinal studies integrating functional profiling and host markers of cutaneous barrier integrity and inflammation are needed to clarify their clinical implications.},
}
@article {pmid42064216,
year = {2026},
author = {Pang, S and Zhang, Z and Ma, Q and Liu, Y and Wang, S and Wang, J and Bi, Y},
title = {The gut-kidney microbiome-oxalate axis in calcium oxalate nephrolithiasis: mechanisms and microbiome-based interventions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1804800},
pmid = {42064216},
issn = {2235-2988},
mesh = {Humans ; *Nephrolithiasis/microbiology/therapy/metabolism ; *Gastrointestinal Microbiome/physiology ; *Calcium Oxalate/metabolism ; *Kidney/microbiology/metabolism ; Dysbiosis ; *Oxalates/metabolism ; Animals ; Hyperoxaluria ; },
abstract = {INTRODUCTION: Calcium oxalate nephrolithiasis is increasingly recognized as a disorder influencednot only by diet and host oxalate handling, but also by the gut-kidneymicrobiome axis. Emerging multi-omics studies suggest that disturbances inintestinal and urinary microbiota, together with altered microbial metabolites,may contribute to disrupted oxalate homeostasis, inflammatory signaling, epithelialinjury, and crystal retention.<br><br>METHODS: We performed a narrative, semi-structuredreview of PubMed, Embase, and Web of Science (2010-2025), focusing onoxalate metabolism, gut and urinary microbiota, and microbiome-targeted interventionsin nephrolithiasis, with emphasis on calcium oxalate stones. Human andexperimental studies examining microbial composition, microbial metabolites,host transport and genetic determinants, and nutritional or microbial therapieswere qualitatively synthesized.<br><br>RESULTS: Current evidence indicates that loss of oxalatedegradinggut bacteria and broader dysbiosis are associated with hyperoxaluriaand increased calcium oxalate stone risk, whereas microbiome-supportive dietarypatterns may be protective. Multi-omics analyses reveal coordinated alterationsacross stool, urine, and stone-associated microbiota, implicating pathways involvingshort-chain fatty acids, bile acids, and unconjugated bilirubin in oxalatehandling, inflammation, and lithogenesis. Nutritional modulation may favorablyinfluence this axis, while probiotics, synbiotics, and engineered livebiotherapeutics show encouraging preclinical results.<br><br>DISCUSSION: Fecal microbiota transplantationremains highly preliminary in this field, and overall human data remainlimited and heterogeneous. The gut-kidney microbiome-oxalate axis providesan integrative framework linking diet, host pathways, microbial metabolites, andmulti-site microbial communities to calcium oxalate nephrolithiasis, and may helpinform future microbiome-based prevention and adjunctive managementstrategies.},
}
@article {pmid42064333,
year = {2026},
author = {Reider, KE and Fannin, C and Hannah, KA and Gelona, AR and Anderson, C and Barnard-Kubow, K and Enke, RA},
title = {16S rRNA amplicon metabarcoding dataset from a retreating glacier forefield in the high tropical andes.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112758},
pmid = {42064333},
issn = {2352-3409},
abstract = {Glaciers are retreating rapidly worldwide, particularly at high elevations, changing the environments and habitats of microorganisms, plants, and animals drastically and leaving behind nutrient-poor sediment. We sought to explore seasonal, elevational, and soil age differences in microbial community diversity found in moraine deposits exposed by recent deglaciation and previously exposed during the Little Ice Age in the Cordillera Vilcanota of southeastern Peru. In the wet and dry seasons of 2023, JMU students and other researchers collected soil samples from 35 sites across a 2.5 square kilometer range in the Andes mountains. Each sample was assigned to the season collected, elevation of collection, and age of exposure. Total DNA was extracted from samples and the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq platform. The data were then processed and analyzed using the QIIME2 bioinformatics pipeline. This dataset will be useful to the field for studying ecological community and ecosystem formation in glacier forefields emerging from climate change.},
}
@article {pmid42064368,
year = {2026},
author = {Berbudi, A and Riswari, SF and Kwarteng, A},
title = {Helminth Infection, Gut Microbiome Alterations, and Their Impact on Pulmonary Tuberculosis Susceptibility.},
journal = {Journal of tropical medicine},
volume = {2026},
number = {},
pages = {3767562},
pmid = {42064368},
issn = {1687-9686},
abstract = {BACKGROUND: Helminth infections and pulmonary tuberculosis (TB) frequently coexist in low- and middle-income countries and interact through immune-mediated mechanisms that influence host susceptibility to Mycobacterium tuberculosis (Mtb). Beyond direct immunomodulation, increasing evidence indicates that helminth infections alter gut microbiome composition and microbial metabolite production, thereby shaping systemic and pulmonary immune responses through the gut-lung axis. Given the central role of the gut microbiome in regulating T-cell polarization, macrophage function, and inflammatory balance, microbiome-mediated pathways have emerged as a potential link between helminth infection and impaired host defense against pulmonary TB.<br><br>OBJECTIVES: This narrative review examines current evidence on how helminth-induced immunological changes and gut microbiome alterations, within the context of the gut-lung axis, may influence susceptibility to pulmonary TB.<br><br>METHODS: A narrative review approach was used to synthesize findings from experimental, observational, and clinical studies addressing helminth infection, gut microbiome dynamics, immune regulation, and TB.<br><br>RESULTS: Helminth infections are associated with Th2-skewed immune responses characterized by increased regulatory T-cell activity and anti-inflammatory cytokine production, which may attenuate Th1-mediated immunity essential for Mtb control. Helminths also modulate gut microbiome composition, with effects ranging from increased microbial diversity to dysbiosis, depending on helminth species and host context. These microbiome alterations may influence systemic immunity through microbial metabolites such as short-chain fatty acids (SCFAs). Importantly, SCFAs exhibit context-dependent effects, potentially supporting immune homeostasis while, under certain conditions, promoting regulatory pathways that may dampen protective antimycobacterial responses.<br><br>CONCLUSIONS: Current evidence suggests that helminth-associated immune modulation and gut microbiome alterations may influence pulmonary TB susceptibility, although most findings remain associative rather than causal. Further mechanistic and clinical studies are needed to clarify the role of the gut-lung axis in helminth-TB coinfection and to inform integrated disease management strategies in endemic regions.},
}
@article {pmid42064411,
year = {2026},
author = {Weiss, G and Voroshilina, E and Koranda, M and Blauensteiner, J and Schenk, M},
title = {Microbial signatures in follicular fluid and their association with fertilization success.},
journal = {Frontiers in reproductive health},
volume = {8},
number = {},
pages = {1773092},
pmid = {42064411},
issn = {2673-3153},
abstract = {BACKGROUND: Emerging evidence suggests that the upper female reproductive tract is not sterile and that microbial signals within follicular fluid (FF) may influence oocyte competence. However, previous studies have largely relied on pooled FF samples or dominant follicles, limiting insight into follicle-specific associations with fertilization outcomes.<br><br>METHODS: In this exploratory paired study, follicular fluid samples were collected from 24 women undergoing IVF/ICSI treatment. For each patient, two FF samples were analyzed individually: one associated with a fertilized oocyte, and one associated with an oocyte that failed fertilization. Bacterial DNA and total bacterial load (TBL) were assessed using quantitative real-time PCR targeting predefined microbial taxa.<br><br>RESULTS: Bacterial DNA above the predefined detection threshold was identified in 39.6% of all FF samples. Notably, within this exploratory cohort, FF samples associated with fertilization failure were more frequently TBL-positive compared with FF samples linked to successful fertilization (70.8% vs. 8.3%). Follicles from the same patient often differed in bacterial DNA presence, indicating substantial intra-individual variability. Several bacterial taxa, including Fannyhessea vaginae, Ureaplasma spp., and Lactobacillus spp., were more frequently detected in FF samples associated with failed fertilization; however, no individual taxon showed a consistent association with outcome across all samples.<br><br>CONCLUSION: In this paired follicle-level analysis, the absence of detectable bacterial DNA in follicular fluid was associated with fertilization outcome. These findings highlight follicle-level heterogeneity in microbial DNA detection and underscore the importance of follicle-specific analyses in reproductive microbiome research. Larger prospective studies are required to validate these observations and to clarify the biological mechanisms underlying follicular microbial signals.},
}
@article {pmid42064742,
year = {2026},
author = {Gordon, S and Evans, S and Kirven, K and Whisonant, M},
title = {Increased dietary iron alters taxonomic composition and function of zebrafish gut microbiome.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {42064742},
issn = {2578-9430},
abstract = {Gut microbiota are crucial to both gastrointestinal tract health and host well-being. Oral iron supplementation is commonly used, but knowledge of iron's impact on the gut microbiome is limited. Using Zebrafish (Danio rerio) as a model organism, we tested effects of increased dietary iron on gut taxonomic composition and function. Increased dietary iron significantly altered the zebrafish microbiome taxonomic composition and enriched physiological conditions of aerobic respiration. Mass spectrometry (GCMS and LCMS), utilized to measure primary metabolite and lipid levels, pointed to significant increases in amino acids under increased iron supplementation, but no significant change in lipid metabolite levels.},
}
@article {pmid42064815,
year = {2026},
author = {Li, J and Zhang, S and Zhang, Y and Wang, X and Zhuge, Y and Wu, Q and Zhao, Y and Gao, Q and Chen, R and Wang, Y and Jin, Q and Zhang, Y},
title = {Harnessing the gut microbiome for precision therapeutics in heart failure.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1781470},
pmid = {42064815},
issn = {1663-9812},
abstract = {Heart failure (HF) management remains challenging because patients often show large differences in how well treatments work and in how often adverse drug reactions occur. Traditional pharmacogenomics cannot fully explain these differences. Emerging evidence from pharmacomicrobiomics shows that the gut microbiome represents a previously underappreciated factor influencing drug responses. This review summarizes the two-way interactions between the gut microbiota and key HF drugs, including digoxin, angiotensin receptor-neprilysin inhibitors (ARNIs), ACE inhibitors (ACEIs), angiotensin receptor blockers (ARBs), β-blockers, sodium-glucose cotransporter 2 (SGLT2) inhibitors, mineralocorticoid receptor antagonists (MRAs), and diuretics. On the one hand, gut microbes can change drug effects because they can metabolize drugs and affect host physiological pathways. On the other hand, HF drugs can change the structure and function of the gut microbial community. This review also discusses how microbiome-related features may serve as biomarkers to support personalized treatment and how strategies such as dietary changes and microbiota-targeted therapies may improve clinical outcomes. Although evidence remains limited, and certain methods require further refinement, integrating microbiome insights into HF treatment may support more precise and individualized treatment strategies and help address current therapeutic limitations.},
}
@article {pmid42064906,
year = {2026},
author = {Nguyen, T and Woods, C and Liu, J and Wang, C and Lin, AL and Cheng, J},
title = {A multimodal AI model for modeling the genetic risk factor of Alzheimer's disease.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.13.26350803},
pmid = {42064906},
abstract = {The apolipoprotein E ε 4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), the most common form of dementia. APOE4 carriers exhibit cerebrovascular and metabolic dysfunction, structural brain alterations, and gut microbiome changes decades before the onset of clinical symptoms. Better understanding of the early manifestion of these physiological changes is critical for development of timely AD interventions and risk reduction protocols. Multi-modal datasets encompassing a wide range of APOE ε 4 and AD associated biomarkers provide a valuable opportunity to gain insight into the APOE4 phenotype; however, these datasets often present analytical challenges due to small sample sizes and high heterogeneity. Here, we propose a two-stage multimodal AI model (APOEFormer) that integrates blood metabolites, brain vascular and structural MRI, microbiome profiles, and other clinical and demographic data to predict APOE4 allele status. In the first stage, modality-specific encoders are used to generate initial representa-tions of input data modalities, which are aligned in a shared latent space via self-supervised contrastive learning during pretraining. The contrastive learning objective encourages learning of informative and consistent representations across modalities through leveraging cross-modality relationships. In the second stage, the pretrained representations are used as inputs to a multimodal transformer that integrates information across modalities to predict a key AD-risk genetic variant (APOE4). Across 10 independent experimental runs with different train-validation-test splits, APOEFormer predicts whether an individual carries an APOE4 allele with an average prediction accuracy of 75%, demonstrating robust performance under limited sample sizes. Post hoc perturbation analysis of the predictive model revealed valuable insights into the driving components of the APOE4 phenotype- including key blood biomarkers and brain regions strongly associated with APOE4.},
}
@article {pmid42065024,
year = {2026},
author = {Bharat, AA and Ali, O and Sahadeo, UM and Ramsubhag, A and Jayaraman, J},
title = {Preparation of a fermented Sargassum extract, microbial dynamics involved, and its effect on Capsicum annuum.},
journal = {3 Biotech},
volume = {16},
number = {5},
pages = {170},
pmid = {42065024},
issn = {2190-572X},
abstract = {UNLABELLED: The study explored Sargassum valorization through the production of a fermented extract for its application as a crop biostimulant. The dried and ground Sargassum (S. natans and S. fluitans) was subjected to anaerobic fermentation utilizing the endogenous microorganisms already present in the seaweed. During the fermentation process, samples were periodically taken (5, 15, 20, 27, 30, and 35) for 16S rRNA and ITS paired-end amplicon metataxonomics. Microbiome profiling revealed distinct temporal microbiome shifts over the 35 days of fermentation, with Firmicutes, Bacteroidota, and Nectriaceae emerging as the core microbiome. Furthermore, microbial network analysis identified Clostridiaceae, Sporolactobacillaceae, and Pirellulaceae as dominant bacterial families, while Gibberella and Aspergillus showed up as prevalent fungal genera. Beta-diversity analyses showed a significant shift in microbial composition on Day 35. Extracts were screened for their antimicrobial properties against plant pathogens (Xanthomonas campestris pv. vesicatoria and Alternaria solani), however results indicated no antimicrobial effect. Plant growth trials were conducted using Capsicum annuum L. plants and the extracts were applied as foliar application sprays at 0.5-1% v/v concentrations under greenhouse conditions. All parameters measured (chlorophyll content, root and shoot length, and root and shoot weights were all significantly greater than Control-treated plants. Chlorophyll content, root length, shoot length, fresh root and shoot weight, and dry root and shoot weight all had significant increases of up to 28.82%, 60.13%, 15.95%, 67.95%, 53.90%, 82.05%, and 95.86% respectively. The result of the study promotes the usage of fermented Sargassum extracts as an organic biostimulant and aligns with sustainable agricultural practices.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04811-1.},
}
@article {pmid42065141,
year = {2026},
author = {Talbott, S and Stephens, B and Talbott, J and Oddou, M and Fumiki, A},
title = {Effects of Lactiplantibacillus Plantarum KABP051 Probiotic on Body Composition, Microbiome and Mood in Healthy Overweight Adults.},
journal = {Journal of medicinal food},
volume = {},
number = {},
pages = {1096620X261448041},
doi = {10.1177/1096620X261448041},
pmid = {42065141},
issn = {1557-7600},
abstract = {Obesity and mental health disorders are among the greatest public health challenges of the 21st century. Interestingly, an altered microbiome profile has been associated with both conditions. The aim of this randomized, double-blind, placebo-controlled clinical trial was to evaluate the effects of dietary supplementation with a specific probiotic strain (Lactiplantibacillus plantarum KABP051) on body composition and gut microbiome balance, together with measures of mood state, in a population of healthy overweight subjects. Sixty healthy, moderately stressed, nondepressed and overweight or obese volunteers were supplemented for 12 weeks with probiotic (L. plantarum KABP051; 1 billion colony forming units/day) or placebo (microcrystalline cellulose). The KABP051 group experienced significantly greater improvements compared with placebo on body composition measurements, including a reduction in body weight and waist circumference, which decreased in 1.97 ± 0.77 (mean ± SE) kg and 2.15 ± 0.81 (mean ± SE) cm versus placebo at the end of the intervention (both P < .05, mixed model for repeated measures [MMRM] and post-hoc analysis). Microbiome composition improved in KABP051 group, with significant increase in the relative abundance of Lactiplantibacillus spp. versus placebo. Body fat percentage, profile of mood states fatigue, and confusion sub-scores showed a global trend toward improvement compared with placebo, with the change at 12 weeks being significant in the three measurements in post-hoc analysis (P = .015, P = .014, and P = .016, respectively). No serious adverse events were registered during the intervention period. These results suggest that a specific strain of probiotic bacteria (L. plantarum KABP051) may have both metabolic and psychobiotic effects and may be beneficial for enhancing weight loss and body composition, improving energy (less fatigue) and mood levels while embarking on a healthy lifestyle regimen. ClinicalTrials.gov identifier: NCT06808061.},
}
@article {pmid42065212,
year = {2026},
author = {Shen, Y and Wang, Z and Cheng, X and Tang, F and Rao, S and Zhang, D},
title = {Cluster analysis of research hotspots and trends in probiotics for constipation: A comprehensive bibliometric analysis (1977-2024).},
journal = {Medicine},
volume = {105},
number = {18},
pages = {e48338},
doi = {10.1097/MD.0000000000048338},
pmid = {42065212},
issn = {1536-5964},
support = {KS2201//Kunshan key R &amp; D program/ ; },
mesh = {*Probiotics/therapeutic use ; *Bibliometrics ; *Constipation/therapy/microbiology ; Humans ; Cluster Analysis ; *Biomedical Research/trends ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Probiotics are increasingly recognized as a promising therapeutic approach for managing constipation, sparking widespread interest in their effects on gastrointestinal health. This study conducts a cluster analysis to systematically map global research trends and hotspots in probiotics for constipation from 1977 to 2024.<br><br>METHODS: Relevant publications were retrieved from the Web of Science Core Collection. Bibliometric tools, including VOSviewer, CiteSpace, and R, were applied for cluster analysis, network visualization, and trend mapping.<br><br>RESULTS: A total of 519 publications were included in the analysis. China led in publication volume, while the United States demonstrated the highest academic influence. Key institutions, such as the University of California System and Harvard University, were identified as major contributors. High-impact journals, including Nutrients, World Journal of Gastroenterology, and Digestive Diseases and Sciences, played central roles in disseminating research. Quigley Eamonn M. M. indicated significant influence in the field. Cluster analysis of keywords revealed 6 principal research hotspots: microbial diversity and mechanisms, gut microbiota-host interaction and pathophysiology, dietary factors and microbiome analysis techniques, epidemiology, prevalence, and population health, clinical management and therapeutic efficacy, and clinical trials and study design. Citation burst analysis indicated a recent research focus shift toward mechanisms, personalized interventions, and gut microbiome modulation.<br><br>CONCLUSION: This bibliometric study based on cluster analysis identified 6 major research hotspots in probiotics for constipation, reflecting the evolving trends and collaborative networks of the field. These findings provide a comprehensive perspective on current research priorities and can guide future studies toward innovative and evidence-based clinical applications.},
}
@article {pmid42065376,
year = {2026},
author = {Bullard, BM and VanderVeen, BN and Cardaci, TD and McDonald, SJ and Bastian, AV and Willis, NB and Xu, M and Li, J and Pierre, JF and Hofseth, LJ and Fan, D and Murphy, EA},
title = {Panaxynol mitigates chemotherapy-induced intestinal mucositis by improving the colonic microenvironment in murine models.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00035.2026},
pmid = {42065376},
issn = {1522-1547},
support = {R01CA246809//HHS | NIH | National Cancer Institute (NCI)/ ; U01CA272977//HHS | NIH | National Cancer Institute (NCI)/ ; F31AT012589//HHS | NIH | National Center for Complementary and Integrative Health (OAM)/ ; R00CA27689//HHS | NIH | National Cancer Institute (NCI)/ ; F99CA294251//HHS | NIH | National Cancer Institute (NCI)/ ; P20GM155896//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32DK007665//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; T32CA244125//HHS | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Chemotherapy-induced mucositis (CIM) is a debilitating side-effect impacting as many as 90% of cancer patients undergoing treatment. Patients receiving 5-Fluorouracil (5FU), a first-line chemotherapeutic in colorectal cancer, experience significant gastrointestinal distress that perpetuates poor patient quality of life and reduces treatment tolerance, efficacy, and survival. Natural compounds have shown promise in improving CIM through their pleiotropic actions, including immune and mucosal regulation. We examined whether panaxynol, a bioactive compound isolated from American ginseng, can alleviate murine CIM symptomology and severity. Intestinal mucositis was induced in C57BL/6J male and female mice by 5 consecutive intraperitoneal injections of 5FU (35 mg/kg/day); PBS was used as the control. Vehicle or panaxynol (2.5 mg/kg/day) was administered via oral gavage every other day, starting on Day -1, for a total of 4 treatments. Panaxynol significantly improved overall mucositis symptomology, attenuated 5FU-induced cytopenia and anemia, ameliorated the 5FU-induced loss of goblet cells per crypt, suppressed pro-inflammatory immune cells in the colonic lamina propria, and altered microbial diversity and taxonomy. Sex differences were observed, with panaxynol exerting a stronger effect in males, significantly reducing the relative percentage of colonic macrophages and neutrophils. Panaxynol treatment was associated with sex-dependent alterations in gut microbial community structure and modulation of specific taxa, including Dubosiella and Bifidobacterium, alongside male-specific increases in Romboutsia and Alistipes; Akkermansia abundance was primarily influenced by 5FU treatment. These preclinical findings support the potential of panaxynol as a therapeutic candidate for the treatment of CIM and highlight the importance of considering sex as a biological variable.},
}
@article {pmid42065459,
year = {2026},
author = {Liu, M and Yang, Z and Liu, B and Cheng, H and Qin, J and Zhang, P and Tang, T and Peng, F and Yang, J and Wei, P and Su, H},
title = {Correction: Multi-omics reveals gut microbiome- and metabolome-specific responses to sugar alcohols.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo90033j},
pmid = {42065459},
issn = {2042-650X},
abstract = {Correction for 'Multi-omics reveals gut microbiome- and metabolome-specific responses to sugar alcohols' by Mengling Liu et al., Food Funct., 2026, https://doi.org/10.1039/D6FO00282J.},
}
@article {pmid42065740,
year = {2026},
author = {Mohsenzadeh, A and Mohammadi, A and Mohsenzadeh, H and Kamali, K and Moradi, M and Ebrahimi, N and Sheikhy, M and Zabet, AH and Mirheidari, H and Bavari, S and Elahi, R},
title = {The gut microbiota and kawasaki disease: exploring the role of microbial dysbiosis and metabolites in pathogenesis and therapeutics.},
journal = {European journal of pediatrics},
volume = {185},
number = {5},
pages = {},
pmid = {42065740},
issn = {1432-1076},
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/complications/therapy/microbiology ; Child ; },
abstract = {Kawasaki disease (KD) is an acute, immune-mediated medium-vessel vasculitis and the leading cause of acquired heart disease in children, yet its underlying etiology remains only partially defined. Emerging evidence implicates the gut microbiota as a key modulator of KD susceptibility, immune dysregulation, and therapeutic response. This narrative review aims to synthesise current insights linking gut microbial dysbiosis and microbial metabolites to the pathogenesis, clinical expression, and treatment of KD, and to explore microbiome-informed strategies with diagnostic and therapeutic potential. We conducted a comprehensive search of PubMed, Embase, Web of Science, and Google Scholar from database inception to April 2025 for English-language studies on Kawasaki disease and the gut microbiota, including terms related to microbiome, microbial dysbiosis, metabolites, pathogenesis, immunity, inflammation, and therapy. Reference lists of relevant articles and key reviews were also screened. Children with acute KD exhibit characteristic alterations in gut microbial composition, including an overrepresentation of Streptococcus species, depletion of short-chain fatty acid (SCFA)-producing taxa such as Faecalibacterium, Ruminococcus, and Roseburia, and a significant reduction in fecal butyrate. These changes have been associated with impaired intestinal barrier integrity, heightened NLRP3 inflammasome activation, and dysregulated cytokine signalling, contributing to systemic inflammation and vascular injury. Additional factors, such as antibiotic exposure and concurrent respiratory or oropharyngeal infections, can intensify dysbiosis and have been linked to resistance to intravenous immunoglobulin (IVIG) and an increased risk of coronary artery aneurysms. Conclusions: Gut microbial imbalance and metabolite disruption are likely associated with KD, potentially through interaction with host genetics and immune pathways. Microbiome-targeted approaches, including probiotics, dietary modulation, and metabolite-based therapies, hold promise for improving diagnostic precision, predicting treatment response, and guiding the development of targeted interventions in KD.},
}
@article {pmid42065823,
year = {2026},
author = {Esteban, DJ and Feeley, M and Goud, M and Abban-Demitrus, AM and Mishalani, L and Touchon, J and Czesak, ME},
title = {Alteration of the Microbiome is Associated with Changes in Mating and Locomotion in Callosobruchus Maculatus.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02783-6},
pmid = {42065823},
issn = {1432-184X},
abstract = {The seed beetle Callosobruchus maculatus is a model organism used to study environmental and genetic factors in the evolution of mating behaviors and life history traits. We sought to address the hypothesis that the microbiome of C. maculatus is associated with host life history traits and mating. To manipulate the microbiome, we developed a chemical treatment protocol to surface sterilize C. maculatus eggs and the food source on which they develop and examined the effect on microbial community structure, beetle life history traits, and mating behaviors including mate choice, and locomotion. Treatment eliminated culturable bacteria from the surface and altered the emerged adult beetle microbiome such that diversity was reduced and the community structure was altered. Treatment reduced survival of small male and female beetles; among the adults that did survive and emerge, females had higher fecundity compared to controls. We found that the treatment also affected mating behavior. Treated beetle pairs had a higher percentage of successful matings and a shorter mating latency period than control beetles. In mate choice tests in which a female was presented with either a treated or control male, females were more likely to mate with treated males. Finally, treated beetles exhibited increased locomotion. Treatment caused selective mortality of smaller individuals and reduced the diversity and altered the structure of the whole-body microbiome of the surviving adults. The treatment was also associated with enhanced mating behavior, increased fecundity and increased locomotion. These experiments revealed that treatment-induced perturbations in larvae result in altered adult behavior and life history traits that are associated with shifts in the beetle microbiome.},
}
@article {pmid42066053,
year = {2026},
author = {Rezaei, A and Habibabad, FS and Bina, S and Khoshnoud, MJ and Haghshenas, M and Rashedinia, M},
title = {Beyond antimicrobial efficacy: Complex interactions of sodium benzoate, potassium sorbate, and citrate alter the rat gut microbiome.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70703},
pmid = {42066053},
issn = {1097-0010},
support = {29466//Shiraz University of Medical Sciences/ ; },
abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a target of dietary food additives. Sodium benzoate (SB), potassium sorbate (PS), and citric acid (Cit) are widely used preservatives, yet their combined effects on the intestinal microbiota remain poorly understood. This study investigated the individual and combinatorial impacts of these three compounds on key bacterial populations in the rat gut.<br><br>METHODS AND RESULTS: Thirty-five adult male Sprague-Dawley rats received SB (500&#x2009;mg&#x2009;kg[-1] BW d[-1]), PS (300&#x2009;mg&#x2009;kg[-1] BW d[-1]), Cit (1200&#x2009;mg&#x2009;kg[-1] BW d[-1]), or their binary combinations in drinking water for 8&#x2009;weeks. Fecal samples were analysed by selective culture and quantitative real-time polymerase chain reaction (PCR). All treatments significantly reduced Lactobacillus abundance (P&#x2009;<&#x2009;0.05). Citrate alone and in combination with SB markedly increased Enterobacteriaceae (P&#x2009;<&#x2009;0.01), with the Cit&#x2009;+&#x2009;SB group showing the highest levels. Enterococcus populations were elevated in most treatment groups, particularly after Cit&#x2009;+&#x2009;SB exposure. Staphylococcus responses were context-dependent: increased by SB or PS alone, but suppressed by citrate-containing combinations. Combination effects were often non-additive, with citrate frequently overriding the antimicrobial action of benzoate or sorbate.<br><br>CONCLUSION: Chronic exposure to common preservatives at no-observed-adverse-effect level (NOAEL) induces significant, synergistic shifts in the gut microbiota, characterized by loss of beneficial Lactobacillus and expansion of potentially pro-inflammatory Enterobacteriaceae and Enterococcus. The unexpected promotion of Enterobacteriaceae by citrate reveals its role as an active ecological modulator. Our findings challenge the adequacy of single-additive safety assessments and support the inclusion of microbiome endpoints in regulatory toxicology. &#xa9; 2026 Society of Chemical Industry.},
}
@article {pmid42066227,
year = {2026},
author = {Ponte, AT and Liu, A and Acquah, KS and Balunas, MJ},
title = {The Complex Interplay between Botanical Supplements and the Human Gut Microbiome.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c01493},
pmid = {42066227},
issn = {1520-6025},
abstract = {Botanical supplements have been used for the prevention and treatment of human diseases since ancient times and remain important, widely consumed therapeutics. While they display promising efficacy across a broad spectrum of biological activities, poor oral bioavailability often limits their utility. Upon ingestion, these compounds may remain in the gastrointestinal tract prior to absorption, during which time they interact with gut microbiota. These interactions can significantly alter their bioavailability since microbial enzymes, known for their wide substrate specificity, are capable of readily transforming xenobiotics, often changing their biological activity as well as their bioavailability. Herein, we summarize the chemistry of microbial biotransformations of botanical supplements, highlighting key enzymatic transformations. The reciprocal interactions between four widely used botanical supplements and the human gut microbiome are outlined including green tea, açai, red wine, and mangosteen. Their microbial metabolism and modulation of human gut microbiota is discussed, highlighting the various enzymes and metabolites reported from relevant literature. Although the direct effect of microbiome bioconversion of botanical supplements is largely unexplored due to the complexity of both systems, this review provides a framework for research to determine the bidirectional effects of botanicals and gut microbiota on human health.},
}
@article {pmid42066401,
year = {2026},
author = {Wälchli, DL and Rathinavelu, S and Ackeret, J and Aquino, NJ and Beck, K and Janssen, DJ and Bürgmann, H},
title = {Ripples of resistance: Unveiling antimicrobial resistance dynamics along Switzerland's Aare river.},
journal = {Water research},
volume = {301},
number = {},
pages = {126005},
doi = {10.1016/j.watres.2026.126005},
pmid = {42066401},
issn = {1879-2448},
abstract = {The global spread of antimicrobial resistance (AMR) is a serious public health concern, driven by widespread antibiotic use and the global environmental circulation of antibiotic-resistant bacteria and resistance genes (ARGs). Wastewater treatment plants (WWTPs) are important sources of anthropogenic AMR entering large rivers, which serve as vital water resources but facilitate downstream dissemination. The drivers and dynamics of AMR propagation along river systems remain poorly understood. As Switzerland's longest and one of its largest rivers, the Aare, situated in the upper Rhine watershed, plays a central role in the 'water castle of Europe'. This study examines the impact of WWTP discharges, some receiving high loads of hospital effluent, on ARG distribution along the 288 km Aare river-continuum. Using quantitative PCR targeting 14 ARGs conferring resistance to eight antibiotic classes, combined with 16S rRNA gene amplicon sequencing, we conducted a high-resolution spatial survey to assess shifts in the riverine ARG content and microbiome. Concentrations of trace metals and nutrients were analyzed as tracers of anthropogenic inputs. Results revealed a progressive increase in ARG abundance downstream, driven by WWTP effluents enriched in ARGs. Effluents had 70-fold higher mean ARG concentrations than upstream waters, raising downstream levels up to 141-fold. Major tributaries such as the Reuss and Limmat sustained elevated ARG levels, while passage through lakes markedly reduced concentrations. This study provides the first detailed baseline for ARG prevalence along a large swiss river system, from pristine headwaters to pollution-affected lower reaches and insights into aquatic AMR dynamics and guidance for future monitoring.},
}
@article {pmid42066404,
year = {2026},
author = {Sitinjak, MC and Chen, JK and Lee, HJ and Chen, CM and Wang, CY},
title = {Antiviral effect of lactoferrin against infectious bronchitis virus (IBV) are associated with alterations in the gastrointestinal microbiome.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106995},
doi = {10.1016/j.psj.2026.106995},
pmid = {42066404},
issn = {1525-3171},
abstract = {Coronaviruses (CoVs) are an enveloped, polymorphic, positive-sense single-stranded RNA viruses. Currently, both humans and animals are threatened by CoVs, making them a major public health concern. Among the four genera of the family Coronaviridae, infectious bronchitis virus (IBV), which belongs to the genus Gammacoronavirus, continues to cause substantial economic losses in the poultry industry. Nephropathogenic IBV strains, including the Taiwan-I (TW-I) and Taiwan-II (TW-II) serotypes, are the most prevalent IBVs in Taiwan and China and have continued to spread and generate variants through mutation and genetic recombination. Because IBV can replicate in the epithelial cells of the trachea, lung, kidney, and intestine, this study investigated the dysbiosis of the ileal microbiota caused by IBV TW-I and TW-II serotypes. The reduced weight gain of chickens infected with IBV TW-I or TW-II was improved by lactoferrin (LF). The antiviral effects of LF included a significant reduction in viral loads in the ileum of infected chickens. Furthermore, the villus shedding, decreased villus height, increased crypt depth, and reduced number of goblet cells induced by IBV infection were markedly attenuated by LF. Alterations in the ileal microbiome were also observed following LF treatment. Regarding cytokine responses, the IBV-induced upregulation of TGF-β and IL-10 and the elevated infiltration of CD3[+] T cells in the ileum were reduced by LF, whereas the mRNA expression levels of IFN-γ, IL-2, and IL-4 were upregulated by LF. Moreover, the IBV-induced downregulation of MUC2, occludin, and ZO-1 in the ileum was reversed by LF. LF shifted the ileal microbiota toward homeostasis, regulated the immune response to facilitate viral clearance, and restored the intestinal barrier damaged by IBV TW-I and TW-II infection.},
}
@article {pmid42066496,
year = {2026},
author = {Río-López, R and Vourlaki, IT and Clavell-Sansalvador, A and Valdés, A and Padilla, L and García-Gil, LJ and Xifró, X and Ballester, M and Quintanilla, R and Ochoteco-Asensio, J and Prenafeta-Boldú, FX and Dalmau, A and Ramayo-Caldas, Y},
title = {Integrative metagenomic and metabolomic profiling identifies faecal biomarkers of prolonged social stress in pigs.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {5},
pages = {101823},
doi = {10.1016/j.animal.2026.101823},
pmid = {42066496},
issn = {1751-732X},
abstract = {Stressors significantly impact human and animal health, increasing the risk of physical and mental disorders, in part by affecting the gut-brain axis. Although a link between stress, alterations in gut microbial composition, and the serum metabolite profile has already been established in humans, multiomics studies integrating the faecal microbiome and untargeted metabolomics remain unavailable. The objectives of the present study were twofold: first, to identify microbial and metabolic signatures associated with prolonged stress, and second, to evaluate the potential of integrative multiomics approaches to predict key metabolites and discover non-invasive faecal biomarkers of stress in pigs (n = 60). Gut microbial profiles were obtained by shotgun metagenomic sequencing, while faecal metabolites were analysed by untargeted reverse-phase liquid chromatography quadrupole time of flight mass spectrometry, followed by partial least squares discriminant analysis. Metabolite prediction from microbial features was performed using the machine learning method based on neural ordinary differential equations. Eleven discriminant metabolites were identified. In the control group, neurotransmitters such as serotonin and metabolites such as 2-acetamidophenol and sinapine (which possess anti-inflammatory and antioxidant properties) were the most prominent. Conversely, the stressed group exhibited elevated levels of xanthosine, pyrimidine bases (thymine and uracil), n-octadecylamine, and N-α-acetyl-L-lysine. N-octadecylamine (r = 0.37) showed a positive, and serotonin (r = -0.32) a negative correlation with hair cortisol. The results revealed interspecific interactions that modulated microbial and metabolic shifts between the control and stressed pig groups. Feature selection further identified 64 microbial genes that improved classification accuracy between control and stressed pigs to 91.06% and enhanced the prediction of key metabolites, including serotonin and xanthosine. Overall, this integrative multiomics framework elucidates complex microbiome-metabolite interactions and identifies non-invasive biomarkers of prolonged stress-induced metabolic dysregulation, providing valuable insights for animal welfare and translational human health research.},
}
@article {pmid42066508,
year = {2026},
author = {Papadopoulos, GA and Giannenas, I and Lioliopoulou, S and Tassis, P and Papageorgiou, K and di Benedetto, M and van Hoeck, V},
title = {Effects of xylanase supplementation in low- and high-fiber diets on performance and fecal microbiota of lactating sows and their piglets.},
journal = {Research in veterinary science},
volume = {207},
number = {},
pages = {106216},
doi = {10.1016/j.rvsc.2026.106216},
pmid = {42066508},
issn = {1532-2661},
abstract = {The objective of this study was to evaluate the effect of xylanase supplementation in high- and low-fiber diets on the performance of lactating sows and their offspring. At d108 of gestation, 48 sows were assigned to four treatments in a 2 × 2 factorial design: a low-fiber control diet (LF; LF-Con; 12.43% NDF), LF supplemented with 45,000 U/kg xylanase (LF + XYL), a high-fiber control diet (HF; HF-Con; 13.93% NDF), and HF supplemented with xylanase (HF + XYL). Sow body weight (BW) and P2 backfat thickness were recorded at d108 of gestation and weaning. Average daily feed intake (ADFI) was recorded throughout lactation, and piglet BW was measured 24 h post-farrowing and at weaning. Results indicated that sows fed HF diets consumed more feed compared to LF sows (P = 0.003). Furthermore, xylanase supplementation significantly increased ADFI (P = 0.002), reduced lactation weight loss (P = 0.001), and attenuated backfat mobilization (P = 0.003) compared to unsupplemented controls. Regarding the fecal microbiota, HF diets increased the relative abundance of Prevotellaceae and Rikenellaceae. Notably, an increase in the butyrate-producing genus Roseburia (family Lachnospiraceae) was observed, likely driven by cross-feeding mechanisms. Xylanase supplementation reduced the relative abundance of Prevotellaceae, potentially by altering the availability of their preferred carbohydrate substrates. In conclusion, supplementing lactating sows with an endo-1,4-β-xylanase in both LF + XYL and HF + XYL diets, influenced sow energy balance, by elevating feed intake and reducing tissue mobilization, while simultaneously altering the fecal microbiome to a more beneficial, butyrate-producing composition, particularly when using fibrous feedstuffs.},
}
@article {pmid42066511,
year = {2026},
author = {Cha, HE and Seo, J and Cho, HS and Lee, JW and Jeon, AJ and Lim, SK},
title = {Temporal dynamics and stability of the human microbiome for forensic individual identification.},
journal = {Forensic science international. Genetics},
volume = {84},
number = {},
pages = {103519},
doi = {10.1016/j.fsigen.2026.103519},
pmid = {42066511},
issn = {1878-0326},
abstract = {The human microbiome is ubiquitous across nearly all body sites and exhibits biological characteristics that enable stable detection under diverse environmental conditions. Microbial DNA can be analyzed even when human DNA is present in trace amounts or is severely degraded, supporting its potential as a complementary approach to conventional DNA-based identification. However, systematic validation of whether the microbiome simultaneously maintains individual specificity and long-term stability remains limited. In this study, we conducted a longitudinal analysis of the microbiome from the scalp, cheek, hand, and saliva of five healthy Korean participants over a period of up to three years. Intra-individual temporal stability and inter-individual variability were evaluated across multiple temporal scales, ranging from daily to annual intervals. Microbial community dynamics were assessed using relative abundance analysis, beta diversity metrics, and the theta-YC similarity index. Individual identification performance was evaluated for each sampling source using an XGBoost-based machine learning approach. Skin sites and saliva represented distinct ecological niches, with intra-individual similarity exceeding inter-individual similarity across sampling sites and temporal intervals. Although transient community shifts were observed in frequently exposed sites such as the scalp and hand under the four-season climate of the Republic of Korea, individual-specific microbial signatures were maintained over time. The XGBoost-based identification models achieved high accuracy, particularly for saliva (93.3%) and cheek (92.9%) samples. These findings support the potential of the skin and saliva microbiome as complementary tools for individual identification, particularly in forensic contexts where conventional human DNA analysis is limited.},
}
@article {pmid42066541,
year = {2026},
author = {Li, L and Chi, Y and Kong, Y and Zheng, D and Shi, Z and Kang, X},
title = {Rapid species-level discrimination of pulmonary TB and NTM by metagenomic next-generation sequencing with concurrent respiratory microbiome profiling.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {1},
pages = {117442},
doi = {10.1016/j.diagmicrobio.2026.117442},
pmid = {42066541},
issn = {1879-0070},
abstract = {INTRODUCTION: Rapid discrimination between Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) remains clinically challenging, especially when conventional microbiological evidence is limited. Whether metagenomic next-generation sequencing (mNGS) can provide rapid species-level identification while simultaneously characterizing the respiratory microbiome remains to be systematically evaluated.<br><br>METHODS: Bronchoalveolar lavage fluid from 74 retrospectively enrolled patients with clinically diagnosed pulmonary mycobacterial disease (62 TB, 12 NTM-pulmonary disease (NTM-PD)) was analyzed by mNGS. Conventional test results were extracted from medical records. A supplementary assessment excluding mNGS from diagnostic review was additionally performed to reduce potential incorporation bias. Microbial diversity and between-group differences in the respiratory microbiota were evaluated.<br><br>RESULTS: In the clinically diagnosed cohort, mNGS was positive in 61/62 TB cases (98.4%) and 12/12 NTM-PD cases (100%). Mycobacterial cultures were negative in all tested patients in routine clinical practice. By comparison, AFB (8.82%, 3/34), T-SPOT.TB (71.43%, 10/14), and Xpert MTB/RIF (69.23%, 9/13) showed lower positivity among tested patients. In the supplementary assessment, 45/46 independently classified TB cases were mNGS-positive (97.8%). mNGS additionally detected non-mycobacterial pathogens in 62.16% (46/74) of patients, facilitating recognition of polymicrobial infection. Microbiome analysis revealed that the TB group showed relatively higher abundance of Streptococcus parasanguinis besides MTB, whereas NTM group was relatively enriched in opportunistic pathogens including Pseudomonas aeruginosa and Stenotrophomonas maltophilia.<br><br>CONCLUSION: In this retrospective real-world cohort, mNGS achieved rapid species-level discrimination of MTB and NTM with high positive detection rates, and simultaneously provided clinically relevant microbiome information, supporting its value as an adjunctive diagnostic tool for pulmonary mycobacterial infection.},
}
@article {pmid42066584,
year = {2026},
author = {Xu, Q and Wang, Q and Hou, D and Zhang, F and Zhang, C and Qi, B and Wei, M and Chen, J and Zha, Q and Qin, H and Song, Y and Wu, X},
title = {Cryptococcal pneumonia susceptibility in immunocompetent patients: Role of pseudomonas aeruginosa via IL-2/IL-12/IL-17 pathways.},
journal = {Journal of infection and public health},
volume = {19},
number = {6},
pages = {103230},
doi = {10.1016/j.jiph.2026.103230},
pmid = {42066584},
issn = {1876-035X},
abstract = {BACKGROUND: While pulmonary cryptococcosis affects immunocompromised patients, it also occurs in immunocompetent individuals. However, underlying mechanisms contributing to susceptibility in immunocompetent patients remain poorly understood.<br><br>METHODS: We enrolled 43 patients with pulmonary cryptococcosis, including 19 apparently immunocompetent patients (ICPC) and 24 immunocompromised patients (IMCPC), compared with community-acquired pneumonia (CAP) controls. Bronchoalveolar lavage fluid (BLAF) microbiota composition was analyzed using metagenomic next-generation sequencing. Peripheral blood immune parameters were measured, and correlation analyses were performed to identify potential associations. Publicly available single-cell transcriptomic datasets were analyzed to explore immune pathway alterations associated with chronic Pseudomonas infection.<br><br>RESULTS: ICPC patients were predominantly male, less likely to present with fever, and showed normal inflammatory markers compared to CAP controls. Despite normal reference ranges, ICPC patients demonstrated significantly reduced CD4&#x207a; T lymphocyte percentages&#xff0c;accompanied by elevated IL-2 and reduced IL-12p70 and IL-17A levels. BALF analysis revealed a significant enrichment of nonfermenting gram-negative bacteria: Ralstonia, Sphingomonas, Acinetobacter, Stenotrophomonas, Burkholderi and Pseudomonas, in ICPC patients&#xff0c;whereas no such alterations were observed in the IMCPC group. Correlation analyses demonstrated inverse relationships between the relative abundances of Stenotrophomonas and Pseudomonas abundance and CD4&#x202f;+&#x202f;T lymphocyte percentages and CD4&#x202f;+&#x202f;/CD8&#x202f;+&#x202f;ratios. Furthermore, single-cell transcriptomic analysis of chronic Pseudomonas infection showed enrichment of IL-2 signaling genes and suppression of IL-12 and IL-17A signaling pathways.<br><br>CONCLUSIONS: ICPC patients exhibit decreased peripheral CD4&#x202f;+&#x202f;T lymphocyte percentage with elevated IL-2 and reduced IL-12p70/IL-17A levels. The observed enrichment of specific bacterial taxa, particularly Pseudomonas species, and its inverse correlation with immune parameters suggest potential microbiome-immune interactions that may contribute to cryptococcal susceptibility.},
}
@article {pmid42066608,
year = {2026},
author = {Liao, X and Xie, C and Wang, L},
title = {Differential regulation of cadmium accumulation by root microbiomes in high- and low-Cd accumulating rice cultivars.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142256},
doi = {10.1016/j.jhazmat.2026.142256},
pmid = {42066608},
issn = {1873-3336},
abstract = {Cadmium (Cd) contamination threatens rice safety, and while low Cd-accumulating cultivars (LACs) offer a promising strategy, the mechanisms mediated by their root microbiome remain unclear. To address this gap, this study aimed to compare the rhizosphere and root endosphere bacterial communities of LACs and high Cd-accumulating cultivars (HACs) and to elucidate their roles in regulating Cd accumulation. A field experiment was conducted in Hengyang, China, to comparatively analyze the rhizosphere and root endosphere bacterial communities of LACs (CLiangYou755, ShenLiangYou5814, XiangWanXian-12) and HACs (MeiXiangZhan-2, YangDao-6, Changxianggu). Results confirmed that grain Cd content of LACs (0.14 ± 0.018 mg/kg) was significantly lower than that of HACs (0.23 ± 0.061 mg/kg). Critically, LACs rhizosphere exhibited significantly lower soil available Cd and higher pH compared to HACs, correlating with reduced Cd uptake. Physiological analysis indicated that LACs minimized Cd accumulation primarily by restricting root uptake and hindering root-to-shoot translocation. Microbiome profiling revealed that LACs assembled a potentially protective root microbial community. Specifically, their rhizosphere exhibited higher bacterial α-diversity and was enriched with taxa possessing potential Cd-immobilizing capabilities, such as Caldilinea and norank_f__norank_o__SJA-15, which were negatively correlated with soil available Cd and positively with pH. Within root endosphere, LACs specifically enriched key Cd translocation‑limiting taxa like Sideroxydans and specific operational taxonomic units (OTUs, e.g., OTU1619), collectively forming a microbial niche that further inhibits grains Cd accumulation. In contrast, HACs enriched taxa that may activate Cd, such as Bacillus and Geobacter in the rhizosphere, and were dominated by Anaerovorax in the root endosphere, exhibiting functional redundancy and assembly imbalance. In conclusion, this study elucidates that LACs mitigate grain Cd through a coordinated "rhizosphere co-shaping and root endosphere specific assembly" microbial strategy. These findings provide a crucial theoretical foundation for developing innovative, microbiome-based green technologies aimed at ensuring food security in contaminated regions.},
}
@article {pmid42066637,
year = {2026},
author = {Ioannou, S and Stern, E and Damas, OM},
title = {Personalizing nutrition therapy in inflammatory bowel disease: Practical applications and review of the latest studies.},
journal = {Current opinion in pharmacology},
volume = {88},
number = {},
pages = {102627},
doi = {10.1016/j.coph.2026.102627},
pmid = {42066637},
issn = {1471-4973},
abstract = {Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is a chronic condition influenced by genetic and environmental factors, including diet. Dietary interventions modulate IBD pathophysiology through microbiome reshaping, short-chain fatty acid production, and immune regulation. While pharmacologic therapies remain central, dietary interventions have emerged as evidence-based adjunctive strategies for inducing and maintaining remission. In UC, the Mediterranean diet (MED) demonstrates consistent improvements in clinical symptoms and inflammatory markers in mild-to-moderate disease, with emerging evidence supporting benefit in moderate-to-severe UC when combined with pharmacotherapy. The ulcerative colitis exclusion diet (UCED) shows preliminary promise, though larger trials are needed. For maintenance, anti-inflammatory whole-food patterns reduce fecal calprotectin and promote favorable microbiota shifts. In CD, exclusive enteral nutrition (EEN) remains the gold standard for induction, primarily in pediatric Crohn's disease, while the Crohn's disease exclusion diet (CDED) with partial enteral nutrition offers a well-tolerated food-based alternative. Notably, enteral nutrition combined with biologics enhances drug bioavailability and clinical outcomes. Across interventions, microbiome modulation, including increased SCFA-producing bacteria and enhanced microbial diversity, represents a unifying therapeutic mechanism. Future research priorities include trials with endoscopic endpoints, identification of predictive biomarkers, and development of precision nutrition approaches tailored to individual disease characteristics.},
}
@article {pmid42066640,
year = {2026},
author = {Sim, M and Hwang, GS and Shin, DM and Jeong, Y},
title = {Associations of solute carrier family 23 member 1 (SLC23A1) rs6596473 genetic variant with serum vitamin C status and gut microbial profiles in healthy adults: A cross-sectional study.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106669},
doi = {10.1016/j.clnu.2026.106669},
pmid = {42066640},
issn = {1532-1983},
abstract = {BACKGROUND &amp; AIMS: Solute carrier family 23 member 1 (SLC23A1) encodes sodium-dependent vitamin C transporter 1, which mediates intestinal vitamin C absorption. Although SLC23A1 variants are associated with vitamin C bioavailability, their relationship with gut microbiome remains unexplored. We aimed to investigate the associations of SLC23A1 polymorphism with serum vitamin C status and gut microbial profiles in healthy Korean adults.<br><br>METHODS: We genotyped the SLC23A1 rs6596473 polymorphism in 257 healthy individuals (20-39 years) and measured their serum vitamin C concentrations, which were categorized as optimal (&#x2265;50 &#x3bc;M) or suboptimal (<50 &#x3bc;M). Logistic regression analysis was used to evaluate the association between genotypes and suboptimal serum vitamin C status after adjusting for covariates. A subset of 43 participants with suboptimal serum vitamin C status underwent gut microbiota analysis and serum short-chain fatty acid (SCFA) measurements. Microbial profiles and SCFA concentrations were compared across the genotypes.<br><br>RESULTS: The genotype distributions were 92 CC, 131 CG, and 34 GG, with G as the minor allele. After covariate adjustment, GG carriers had higher odds of suboptimal serum vitamin C status than CC carriers (odds ratio = 2.65; p = 0.03). Among individuals with suboptimal serum vitamin C status, GG carriers (n = 7) exhibited distinct microbial community structures compared with CC (n = 13) and CG (n = 23) carriers, with elevated richness and evenness. GG carriers had higher abundances of Bifidobacterium (vs. CC, p < 0.01; vs. CG, p = 0.054) and Ruminococcaceae incertae sedis (all p < 0.05) compared with CC and CG carriers. In line with these microbial findings, GG carriers had higher propionate and butyrate concentrations than CC and CG carriers (all p < 0.05).<br><br>CONCLUSIONS: The SLC23A1 rs6596473 variant was associated with reduced vitamin C absorption into systemic circulation in the overall population; however, among individuals with suboptimal serum vitamin C status, it was associated with beneficial gut microbial profiles. Our findings suggest that this genetic variant in the vitamin C transporter has complex health effects that extend beyond circulating vitamin C levels to gut microbial ecology, supporting the use of genotype-informed nutritional approaches.<br><br>CLINICAL TRIAL REGISTRY: Clinical Research Information Services KCT0005074 (https://cris.nih.go.kr/cris/search/detailSearch.do?seq=16832&amp;status=5&amp;seq_group=16832&amp;search_page=M) and KCT0004276 (https://cris.nih.go.kr/cris/search/detailSearch.do?seq=14590&amp;status=5&amp;seq_group=14590&amp;search_page=M).},
}
@article {pmid42066682,
year = {2026},
author = {Su, C and Dong, B},
title = {A mendelian randomization study investigates the causal relationship between oral microbiome and cerebral aneurysm in East Asian population.},
journal = {Clinical neurology and neurosurgery},
volume = {267},
number = {},
pages = {109453},
doi = {10.1016/j.clineuro.2026.109453},
pmid = {42066682},
issn = {1872-6968},
abstract = {BACKGROUND: Growing evidence supports that oral microbiome play an essential role in the etiology of cerebral aneurysm.This study aimed to investigate the causal relationships between the oral microbiome and cerebral aneurysm in the East Asian population using Mendelian randomization (MR).<br><br>METHODS: Genetic summary data related to oral microbiota and cerebral aneurysm were collected from genome-wide association studies involving participants of East Asian descent. MR estimates were generated by conducting various analyses.Two-sample Mendelian randomization (MR) was utilized to compute the causal effects between the oral microbiome and cerebral aneurysm.<br><br>RESULTS: In the saliva group, we found causal relationships between 11 oral microbiotas and cerebral aneurysm,9 negative causal associations and 2 positive. In the tongue group, we found causal relationships between 15 oral microbiotas and cerebral aneurysm,9 negative causal associations and 6 positive.We found a causal relationship between cerebral aneurysm and Firmicutes (p&#x202f;=&#x202f;0.024, IVW), suggesting a bidirectional causal relationship between cerebral aneurysm and Firmicutes.<br><br>CONCLUSION: There may exist a potential correlation between oral microbiome and cerebral aneurysm within the East Asian population. The present study offers novel insights into the correlation between oral microbiome and cerebral aneurysms. Additional research is required to clarify the underlying mechanisms and validate our discoveries in diverse populations.},
}
@article {pmid42066822,
year = {2026},
author = {McMahan, RH and Evans, MR and Najarro, KM and Frank, DN and Basak, JM and Kovacs, EJ},
title = {Ethanol exacerbates post-burn neuroinflammation and gut-brain barrier dysfunction which are associated with microbiome changes.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2026.04.007},
pmid = {42066822},
issn = {1873-6823},
abstract = {BACKGROUND: Acute alcohol intoxication at the time of burn injury is associated with increased morbidity and worsened systemic inflammation. While the detrimental effects of ethanol on peripheral organs after burn injury are well established, its impact on neuroinflammation and the blood-brain barrier (BBB) integrity remains to be defined. We hypothesized that ethanol exposure prior to burn injury heightens neuroinflammation through disruption of intestinal and cerebrovascular barriers and alterations in the gut microbiome.<br><br>METHODS: Using a clinically relevant murine model, mice received acute ethanol exposure 30 minutes prior to burn injury. Brains were analyzed 24 hours later for inflammatory gene and protein expression. Microglial activation was determined by IBA-1 immunofluorescence and quantitative PCR of isolated microglia. Intestinal barrier dysfunction was evaluated by bacterial translocation to mesenteric lymph nodes (MLN) and serum lipopolysaccharide (LPS) levels. BBB permeability was assessed in brain tissue by albumin accumulation. Fecal microbiome composition was characterized by 16S rRNA gene sequencing.<br><br>RESULTS: Burn injury alone induced morphological evidence of reactivity, yet did not significantly increase brain pro-inflammatory cytokine transcription. In contrast, ethanol exposure prior to the burn injury elevated brain expression of Ccl2, Tnfa, and S100a8. Isolated microglia from the brains of mice given ethanol and burn injury exhibited enhanced expression of Ccl2 compared to burn alone. Ethanol exposure also resulted in an 8-fold increase in bacterial translocation to MLNs and a 5-fold increase in brain albumin levels, indicating exacerbated intestinal and BBB permeability. Microbiome analysis revealed expansion of Escherichia species in mice subjected to ethanol and burn injury, which positively correlated with brain S100a8 expression.<br><br>CONCLUSIONS: Ethanol exposure prior to burn injury potentiates neuroinflammation, enhances microglial pro-inflammatory reactivity, disrupts BBB integrity, and is associated with gut microbial dysbiosis. These findings implicate dysregulation of the gut-brain axis as a mechanistic contributor to worsened neuroinflammation in intoxicated burn injury and identify potential therapeutic targets to mitigate neurologic complications in this high-risk population.},
}
@article {pmid42066826,
year = {2026},
author = {Zhang, J and Li, H and Tan, J and Wu, J and Liu, Y and Huang, H and Jiang, J and Zeng, D and Xu, J},
title = {Polygonatum sibiricum polysaccharide alleviates irritable bowel syndrome via multidimensional phenotypic improvement and sex-specific gut microbiota modulation in mice.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121789},
doi = {10.1016/j.jep.2026.121789},
pmid = {42066826},
issn = {1872-7573},
abstract = {Polygonatum sibiricum polysaccharide (PSP), as a major bioactive component of P. sibiricum Delar. ex Redoute (Liliaceae, PS), holds great potential for treating irritable bowel syndrome (IBS). However, its therapeutic effects and mechanisms remain unknown.<br><br>AIM OF THIS STUDY: IBS is a prevalent functional gastrointestinal disorder. The limitation and adverse effects of current therapies highlight the need for novel strategies. This study aimed to optimize PSP extraction and evaluate the therapeutic effects of PSP on IBS model mice.<br><br>MATERIALS AND METHODS: Water-extraction and ethanol-precipitation were optimized via orthogonal experimental design to obtain PSP, which was purified via molecular sieve chromatography. PSP composition was characterized using 1-phenyl-3-methyl-5-pyrazolone precolumn-derivatization HPLC. PSP was administered to IBS model mice, which were evaluated via routine monitoring, blood tests, histopathology, microbiome analysis, network pharmacology and molecular docking.<br><br>RESULTS: Under optimal extraction conditions of a 1:15 g/ml solid-to-liquid ratio, 80&#xb0;C, and 150 W ultrasonic power for 120 min, 228.68 mg/g of PSP was obtained, which was mainly composed of six monosaccharides. PSP administration (200-600 mg/kg) significantly alleviated IBS symptoms by normalizing the faecal moisture content and blood indices, decreasing oxidative stress, reversing intestinal mucosal damage and microbiota homeostasis in a sex-based manner. Multiple targets, including DRD1, TRPV1 and HTR2, which theoretically had favourable binding energies with PSP and associated with PLA/PLC-ERK1/2-PKC signalling pathway, were predicted to involve in the therapeutic effects.<br><br>CONCLUSION: Subchronic PSP intervention promotes mouse recovery from IBS in a sex-specific manner. Putative targets and molecular pathways provide a theoretical direction for future validation.},
}
@article {pmid42066862,
year = {2026},
author = {Verdugo-Meza, A and Gill, SK and Godovannyi, A and Chiang, HM and Bosetti, S and Barnett, JA and Estaki, M and Ishida, R and Ye, J and Quin, C and Haskey, N and Mehain, H and Jafaripour, S and Josephson, JK and Ghesquiere, C and Copp, A and Usakiewicz, J and Adur, MK and Ghosh, S and Bergstrom, K and Sly, LM and Gibson, DL},
title = {Bioengineering a probiotic to bloom during colonic inflammation promotes reliable efficacy in translational models of colitis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.04.007},
pmid = {42066862},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Emerging insights into the gut microbiome have sparked interest in exploring microbial therapeutics for treating inflammatory bowel diseases (IBD). However, no microbial therapeutics have yet shown clinical efficacy for IBD. E. coli Nissle 1917 (EcN) while effective for maintenance of remission, is only marginally effective for treating active colitis. We postulated that EcN effectiveness is hindered by the inflamed intestine, which prevents colonization since EcN lacks stress-resistance mechanisms necessary to persist during colitis. To address this, we introduced a fitness advantage, the ttr operon, to EcN (EcN::ttr), enabling tetrathionate, a byproduct of intestinal inflammation, to be used as fuel. We hypothesized that EcN::ttr bioengineered to bloom during colitis would effectively treat colitis.<br><br>METHODS: We evaluated the efficacy of EcN::ttr in murine colitis: acute DSS and a chronic mucin 2-deficient model. To determine the role of IL-10 in EcN::ttr protection, we tested its efficacy in IL-10-deficient mice. Finally, we co-incubated EcN::ttr with human colonoids to understand its effect on barrier proteins.<br><br>RESULTS: EcN::ttr ameliorated colitis more effectively than EcN and 5-aminosalicylate. EcN::ttr bloomed during inflammation and promoted immunoregulatory responses reliant on IL-10 that limited leukocyte infiltration and decreased TNF-&#x3b1;[+] myeloid resident cells. EcN::ttr induced functional changes in the gut microbiome related to mucosal healing, increased butyric acid, reduced bacterial translocation, and improved ZO-1 organization.<br><br>CONCLUSIONS: We provide a proof-of concept study that bioengineering ttr into EcN unlocks a robust therapeutic effect during colitis. EcN::ttr may be a novel microbiome therapeutic for IBD due to its enhanced ability to successfully colonize the inflamed gut.},
}
@article {pmid42066875,
year = {2026},
author = {Liu, E and Huang, Y and Zhao, Z and Teng, T and Zhou, H and Liu, C and Liu, F},
title = {2-Hydroxyfluorene triggers a vicious cycle of oxidative stress and gut dysbiosis, leading to intestinal injury in the polychaete Perinereis aibuhitensis.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {},
number = {},
pages = {110556},
doi = {10.1016/j.cbpc.2026.110556},
pmid = {42066875},
issn = {1532-0456},
abstract = {Fluorene is biotransformed into the more toxic 2-hydroxyfluorene in the Perinereis aibuhitensis. However, the underlying toxicological mechanisms remain poorly defined. This study aims to decipher the mechanisms of intestinal injury in P. aibuhitensis under 2-hydroxyfluorene exposure. This study employed an integrated multi-endpoint approach to evaluate the dose-dependent effects of 2-hydroxyfluorene (0, 5, 50, and 500 μg/L) on P. aibuhitensis over a 28-day period. Results demonstrated that escalating concentrations triggered pronounced metabolic stress, indicating a shift in energy allocation toward detoxification and repair. Histopathological analysis identified the intestine as the primary target, showing mucosal necrosis and fragmented muscle fibers. These structural aberrations were mechanistically linked to sustained oxidative stress, which compromised intestinal permeability and paralyzed digestive and neurological functions. 16S rRNA sequencing further revealed that 2-hydroxyfluorene exposure reduced gut microbial diversity and the abundance of the beneficial genus, while promoting the abundance of the harmful genus. In conclusion, 2-hydroxyfluoreneinduces severe intestinal injury and metabolic dysfunction in P. aibuhitensis by initiating a vicious cycle: direct oxidative damage compromises gut barrier integrity, which in turn fosters dysbiosis microbiota. This dysbiosis characterized then likely exacerbates the initial host injury. This host-microbe interplay likely exacerbated the initial intestinal injury. These findings highlight the significant ecological risks posed by hydroxylated polycyclic aromatic hydrocarbon (PAH) metabolites to marine benthic invertebrates and underscore the crucial contribution of the gut microbiome in mediating environmental toxicity.},
}
@article {pmid42067083,
year = {2026},
author = {Yadav, AK and Naz, F and Singh, A and Sharma, S and Deka, J and Madhuri, M and Saini, C and Kumar, M and Kaur, P and Singh, TP and Ethayathulla, AS},
title = {Crystal structure of FtsZ from Acinetobacter baumannii and identification of a potential inhibitor targeting its GTPase domain.},
journal = {International journal of biological macromolecules},
volume = {364},
number = {},
pages = {152295},
doi = {10.1016/j.ijbiomac.2026.152295},
pmid = {42067083},
issn = {1879-0003},
abstract = {Acinetobacter baumannii is an opportunistic pathogen known for its extensive antibiotic resistance, posing a significant concern in healthcare settings. Given global concern over broad-spectrum antibiotic use and its impact on the human microbiome, targeting the bacterial cell-division protein Filamenting temperature-sensitive Z (FtsZ) is a promising strategy for developing new antibiotics, as this protein is essential for bacterial cell division. FtsZ polymerizes into filaments to form the Z-ring at the cell division site. This Z-ring orchestrates the recruitment of other crucial proteins in cytokinesis and cell wall synthesis, making it critical for bacterial viability. To target FtsZ from Acinetobacter baumannii (abFtsZ), we have elucidated the first crystal structures in the apo and GDP-bound state. The structural analysis revealed that the abFtsZ-GDP complex exists in a relaxed state conformation with weak inter-subunit interactions. The GTPase activity of abFtsZ showed a Vmax of 3.3 ± 0.4 nmolP/nmolFtsZ/min, and a Km of 2.3 mM. By virtual screening using the crystal structure of abFtsZ, we identified six potential inhibitors: Gossypin, Stafib-1, Tryphostin A51, Sangivamycin, Scutellarin, and Ellagic acid that target the GTP-binding pocket. These inhibitors exhibited high docking scores ranging from -10.2 to -8.4 kcal/mol and remained stable throughout the 500 ns MD simulation. These inhibitors can serve as lead molecules for the development of a new antibacterial agent.},
}
@article {pmid42067149,
year = {2026},
author = {Harlow, C and Mohamad, M and Bajaj, JS and Nibali, L and Banerjee, A and Patel, VC},
title = {Harnessing the oral microbiome in chronic liver disease: mechanisms, therapeutic modulation and translational frontiers.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2026.04.023},
pmid = {42067149},
issn = {1600-0641},
abstract = {Advanced chronic liver disease (ACLD) with cirrhosis is increasingly recognised as a condition shaped by the 'oral-gut-liver axis', in which dysbiosis within the oral microbiome contributes to systemic inflammation, infection, decompensation, and acute-on-chronic liver failure. Periodontal disease is highly prevalent in ACLD and is associated with endotoxaemia, immune dysfunction, and hepatic complications. The protected dental biofilm and keystone pathogens are key to the development of local and systemic inflammatory processes. The concept of "oralisation" of the gut microbiome further links oral dysbiosis to microbial translocation and hepatic injury. Recent advances in multi-omics, resistome profiling, and spatially resolved imaging have deepened insights into community function and host-microbial crosstalk, while salivary biomarker panels and microbial signatures across different aetiologies suggest potential tools for non-invasive diagnosis and risk stratification. Clinical priorities now lie along two paths which complement each other. The first is immediate implementation: embedding routine periodontal assessment and professional plaque removal within hepatology care; consistent advice on oral hygiene, fluoride use, diet, and smoking and alcohol cessation; careful review of proton-pump inhibitor use; and much closer coordination between hepatologists and dentists to facilitate indicated procedures. The second is innovation: development of precision microbiome-based interventional trials powered for hepatic outcomes, including targeted probiotics and postbiotics, biofilm-disrupting and quorum-quenching strategies, and phage or narrow-spectrum antimicrobial therapies supported by rapid diagnostics and robust antimicrobial stewardship. Integrating oral health into hepatology practice may represent a practical opportunity to reduce infection risk, delay decompensation, and improve survival and quality of life in people living with ACLD. This review aims to synthesise concepts around current understanding of the patho-biological mechanisms, analytical innovations, and therapeutic opportunities that define this evolving connection, as well as identify gaps in the knowledge base and propose avenues to harness and exploit the oral-gut-liver axis.},
}
@article {pmid42067484,
year = {2026},
author = {Roviello, G and Catalano, M and Gambale, E and Aquino, IG and Lai, E and Messina, C and Vascotto, IA and Rossi, V and Bimbatti, D and Erbetta, E and Messina, M and Mennitto, A and Rebuzzi, SE and Nasso, C and Mercinelli, C and Maiorano, BA and Fanelli, M and Sorarù, M and Scolari, F and Mela, MM and Galli, L and Salfi, A and Rizzo, M and Puglisi, S and Orlando, V and Fornarini, G and Rametta, A and Giannatempo, P and Cerbone, L and Buti, S and Doni, L and Pillozzi, S and Antonuzzo, L},
title = {Concomitant medications and survival outcomes in patients receiving avelumab maintenance for advanced urothelial carcinoma: sub analysis of Meet-URO 25 study.},
journal = {Clinical genitourinary cancer},
volume = {},
number = {},
pages = {102550},
doi = {10.1016/j.clgc.2026.102550},
pmid = {42067484},
issn = {1938-0682},
abstract = {BACKGROUND: Concomitant medications may impair immune checkpoint inhibitor (ICI) activity through modulation of the gut microbiome and systemic immunity. While a medication-based risk model (drug score) has been validated in pan-cancer cohorts, evidence in advanced urothelial carcinoma (aUC) remains limited. This study assessed the association between concomitant medications and survival in patients receiving avelumab maintenance in the Meet-URO 25 cohort.<br><br>METHODS: We retrospectively analyzed patients with aUC treated with avelumab maintenance in several Italian centers. The drug score assigned 1 point each for antibiotics and PPIs, and 2 points for corticosteroids &#x2265; 10 mg prednisone equivalent. Patients were classified as good (0), intermediate (1-2), or poor (3-4) risk. Progression-free survival (PFS) and overall survival (OS) were evaluated using Kaplan-Meier and Cox models.<br><br>RESULTS: Among 251 patients (median age 72; 82% male), use of interfering medications was low. Drug score distribution was 76.5% good, 21.9% intermediate, and 1.6% poor risk. Median PFS was 8.0, 3.9, and 2.9 months, respectively; median OS was 27.6, 14.0, and 3.4 months. Drug score, ECOG performance status, and bone metastases were independent prognostic factors.<br><br>CONCLUSIONS: The drug score showed significant prognostic value in aUC patients receiving avelumab maintenance, supporting its integration into risk stratification for ICI-treated UC.},
}
@article {pmid42067720,
year = {2026},
author = {Bindal, N and Mohanty, S},
title = {Neuroprotective role of Curcuma amada evidenced from pesticide-induced stressed Drosophila melanogaster: insights from RNAseq and gut microbiome analyses.},
journal = {Molecular genetics and genomics : MGG},
volume = {301},
number = {1},
pages = {},
pmid = {42067720},
issn = {1617-4623},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Drosophila melanogaster/drug effects/genetics ; *Curcuma/chemistry ; *Neuroprotective Agents/pharmacology ; *Pesticides/toxicity ; *Plant Extracts/pharmacology ; Oxidative Stress/drug effects ; RNA-Seq ; },
abstract = {Prolonged exposure to pesticides is linked to neurodegenerative disorders through mechanisms involving oxidative stress, inflammation, and neuronal signaling. Therapeutic plants may offer a promising and natural alternative for protecting against such damage. Hence, the present study aims to understand the role of Curcuma amada in mitigating pesticide-induced neurotoxicity and its molecular mechanism in Drosophila. The pesticidal stress was induced in Drosophila through oral feed of ethion and its action was confirmed through behavioural assay. The stressed flies were treated with C. amada rhizome and the effect of both ethion and ethion + C. amada was assessed through RNA profiling and gut microbiome analysis. Decrease in locomotory activity on exposure to ethion represents the induced neuronal stress and an increase was seen after C. amada was fed to the stressed flies. Many DEGs were identified through RNAseq results of stressed and C. amada treated which were further analysed using Cytoscape. In ethion and ethion + C. amada treated flies, the upregulated and downregulated genes were found to be associated with neuronal signal processing and mitochondrial function [MRPs, Dop2R, 5-HT1A, aminoacyl-tRNA synthetase (AARs), ND-B17]. A significant change in the gut microbial population (especially decrease in Lactiplantibacillus species) was observed in stressed flies. But the restoration of healthy bacterial population such as Lactiplantibacillus in C. amada treated flies evidencing the crucial role of gut microbiome in neuronal health. This study highlights the beneficial effects of C. amada from pesticidal stress which needs to be further researched to understand the underlying molecular mechanisms.},
}
@article {pmid42067885,
year = {2026},
author = {Cai, B and Zhang, L and Wu, Z and Wang, J and Wei, Y and Waseem, R and Zhang, M and Qi, D and Zhou, D and Zhao, Y and Li, K and Hu, H and Xie, J and Wang, W},
title = {Streptomyces-induced Glycerol-3-Phosphate enriches beneficial microbiota to enhance resistance against banana Fusarium wilt.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02409-6},
pmid = {42067885},
issn = {2049-2618},
support = {325RC849//Hainan Provincial Natural Science Foundation of China/ ; 322RC660//Hainan Provincial Natural Science Foundation of China/ ; 2024YFD1401101//Bingyu Cai, National Key Research and Development Program of China/ ; CARS-31//China Agriculture Research System/ ; NKLTCBCXTD27//the National Key Laboratory for Tropical Crop Breeding/ ; 1630052022006//Central Public-interest Scientific Institution Basal Research Fund/ ; 32202437//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4) is the causal agent of banana Fusarium wilt, a destructive soil-borne disease. Using antagonistic microorganisms, such as Streptomyces species, offers a promising strategy for controlling fungal diseases. However, their field application is limited by an incomplete understanding of microbe-plant-pathogen interactions.<br><br>RESULTS: This study shows that the marine-derived Streptomyces malaysiensis WHL7 exhibits strong antagonistic activity against multiple phytopathogenic fungi in vitro, particularly Foc TR4. In pot experiments using natural soil, WHL7 treatment significantly reduced the incidence of Fusarium wilt from 55% in the Foc TR4-inoculated control to 15%. No protective effect was observed in sterilized soil, indicating that its biocontrol efficacy depends on the indigenous microbial community. Integrated metabolomic analysis reveals that WHL7 stimulates the key root secretion of glycerol-3-phosphate (G3P). The compound enriches beneficial Bacillus and Pseudomonas species in the rhizosphere. Compared to the Foc TR4-treated group, exogenous application of G3P reduced Foc TR4 abundance by 73%, inhibited pathogenic infection, and consistently increased the populations of Bacillus and Pseudomonas. These enriched microbes were directly linked with reduced disease severity by inducing systemic ACQUIRED RESISTANCE OF plant.<br><br>CONCLUSIONS: While S. malaysiensis WHL7 directly suppresses Foc TR4 via antagonistic compounds in vitro, it controls disease in pot experiments indirectly by reshaping the rhizosphere microbiome. This restructuring induces host resistance through a g3p-mediated signaling pathway. the study highlights g3p-mediated priming as a sustainable strategy for managing soil-borne diseases. Video Abstract.},
}
@article {pmid42067956,
year = {2026},
author = {Shah, AH and Liu, Y and Armstrong, HK and Han, J and Goodlett, DR and Ravandi, A and Dhingra, S},
title = {Association of Fontan Circulation With Gut Microbiome Derived Straight and Branched Short Chain Fatty Acids.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70405},
pmid = {42067956},
issn = {1440-1746},
support = {//Department of Internal Medicine, University of Manitoba/ ; },
abstract = {BACKGROUND: Fontan circulation is associated with progressive multisystem dysfunction, yet its biochemical mechanisms are poorly understood. Gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs) and bile acids, shape cardiovascular health. We previously reported elevated secondary bile acids in Fontan patients, but their SCFA profile remains uncharacterized.<br><br>MATERIALS AND METHODS: Fontan patients and matched healthy subjects were evaluated by body composition, frailty, cardiopulmonary exercise testing, hemodynamics, and plasma SCFA quantification.<br><br>RESULTS: Twenty Fontan patients (25.5&#x2009;years [IQR: 22.8-30.3]; 35% women) and 20 healthy controls (30.0&#x2009;years [25.8-34.3]; 30% women) were enrolled. Compared to controls, Fontan patients exhibited elevated plasma levels of several SCFAs: propionic acid (1.84 [1.45-2.68] vs. 1.19 [1.07-1.49] &#x3bc;M; p&#x2009;=&#x2009;0.002), butyric acid (1.27 [0.90-1.71] vs. 0.75 [0.52-0.94] &#x3bc;M; p&#x2009;=&#x2009;0.002), valeric acid (0.25 [0.15-0.36] vs. 0.13 [0.11-0.16] &#x3bc;M; p&#x2009;< 0.001), and caproic acid (0.44 [0.35-0.67] vs. 0.25 [0.21-0.39] &#x3bc;M; p&#x2009;< 0.001). Acetic acid levels did not differ significantly between groups. Additionally, branched-chain SCFAs were elevated in Fontan patients: isobutyric acid (0.44 [0.32-0.68] vs. 0.26 [0.23-0.30] &#x3bc;M; p < 0.001) and 2-methylbutyric acid (0.38 [0.27-0.58] vs. 0.19 [0.15-0.25] &#x3bc;M; p < 0.001). Notably, caproic, isobutyric, and 2-methylbutyric acids showed strong correlations with key clinical and hemodynamic parameters. Furthermore, isobutyric and 2-methylbutyric acids were significantly correlated with dehydrolithocholic acid levels (R&#x2009;=&#x2009;0.67 and 0.54, respectively) and other bile acid components.<br><br>CONCLUSION: Fontan patients have elevated plasma straight and branched SCFAs linked to adverse clinical and hemodynamic profiles; further evaluation is warranted.},
}
@article {pmid42068031,
year = {2026},
author = {Chen, S and Feng, H and Wang, Y and Huang, J and Xu, S and Gong, Y and Liu, X and Ouyang, Y and Ye, Q and Zheng, D and Sun, K and Wang, A and Chen, Y},
title = {Intestinal epithelial Syndecan-1 maintains mucosal homeostasis in inflammatory bowel disease by enhancing Faecalibacterium prausnitzii biofilm formation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2665870},
doi = {10.1080/19490976.2026.2665870},
pmid = {42068031},
issn = {1949-0984},
mesh = {Animals ; *Syndecan-1/genetics/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Mice ; *Intestinal Mucosa/microbiology/metabolism ; Gastrointestinal Microbiome ; *Biofilms/growth &amp; development ; Mice, Knockout ; Humans ; *Faecalibacterium prausnitzii/physiology/genetics/growth &amp; development ; Mice, Inbred C57BL ; Homeostasis ; Disease Models, Animal ; Dextran Sulfate ; Colitis/microbiology/chemically induced ; Male ; Fecal Microbiota Transplantation ; },
abstract = {Despite the rising global incidence of inflammatory bowel disease (IBD), curative therapies remain unavailable. While our previous work implicated the intestinal proteoglycan Syndecan-1 (SDC1) in IBD-associated barrier dysfunction and inflammation, the underlying mechanism was unclear. This study aimed to elucidate how SDC1 maintains intestinal barrier integrity through interactions with the gut microbiome. In DSS-induced colitis, global knockout of Sdc1 (Sdc1[-/-]) exhibited exacerbated inflammatory infiltration and greater impairment of barrier structure and function than wild-type (WT). Formation of intestinal organoids was independent of genotype, indicating that Sdc1[-/-] does not impair barrier function via disrupting epithelial development. The heightened colitis susceptibility in Sdc1[-/-] mice was abolished in the antibiotic-treated pseudo-germ-free models, and transmissible to WT mice via fecal microbiota transplantation. Similar results were reproduced in a germ-free mouse model. Metagenomic sequencing identified Faecalibacterium prausnitzii as the most significantly depleted species upon Sdc1 knockout. In vitro, SDC1-attached glycosaminoglycans (heparan sulfate (HS) and chondroitin sulfate (CS)) but not the SDC1 core protein promoted F. prausnitzii growth. Prokaryotic transcriptome profiling indicated that HS/CS induces cobalamin biosynthesis in F. prausnitzii. The critical role of cobalamin as a mediator was confirmed, as its synthetic inhibition significantly diminished the growth-promoting effect of HS/CS. Mechanism studies showed that HS/CS enhanced biofilm formation in F. prausnitzii, thereby facilitating cobalamin biosynthesis. Oral administration of HS ameliorated DSS-induced colitis and promoted mucosal colonization of F. prausnitzii, independent of the host genotype. Finally, human IBD biopsies revealed a positive correlation between epithelial SDC1 and mucosal F. prausnitzii, as well as an inverse correlation with bacterial translocation and the number of LPS‑positive cells. Our study elucidates a novel mechanism in which the glycosaminoglycan chains of SDC1 promote F. prausnitzii colonization and growth through enhanced biofilm formation and cobalamin synthesis, thereby highlighting the therapeutic potential of HS for IBD and offering a new basis for host-directed microbiota regulation.},
}
@article {pmid42068047,
year = {2026},
author = {Shou, J and Fu, T},
title = {The gut microbiome-bile acid-FXR interplay: a pivotal axis in metabolic and gastrointestinal diseases.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2665890},
doi = {10.1080/19490976.2026.2665890},
pmid = {42068047},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bile Acids and Salts/metabolism ; *Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Signal Transduction ; Animals ; *Gastrointestinal Diseases/metabolism/microbiology ; Receptors, G-Protein-Coupled/metabolism/genetics ; *Metabolic Diseases/metabolism/microbiology ; Bacteria/metabolism/genetics/classification ; Gastrointestinal Tract/microbiology/metabolism ; },
abstract = {The gut microbiota is increasingly recognized as an essential metabolic "organ", involved not only in nutrient extraction and energy metabolism but also in generating diverse bioactive metabolites. Among these metabolites, bile acids (BAs) - initially synthesized in the liver - are substantially modified by bacterial enzymes in the gut, enabling them to engage various host signaling pathways. Notably, these BAs interact with critical host receptors, such as nuclear farnesoid X receptor (FXR) and G protein-coupled BA receptor 1 (TGR5), influencing numerous metabolic processes. Given the complexity and significance of BAs signaling between microbiota-host interactions, a comprehensive review of this interplay is essential. Here, we systematically explore the molecular mechanisms underlying the BA-microbiota axis, emphasizing its role in metabolic, gastrointestinal, and immune-related diseases, with a focus on the roles of FXR signaling pathways.},
}
@article {pmid42068399,
year = {2026},
author = {Allegrini, M and Villamil, MB and Zabaloy, MC},
title = {Anaerobic digestate fertilization reshapes the rhizosphere bacterial communities of Lolium perenne L. at compositional and predicted functional potential levels.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42068399},
issn = {1573-0972},
support = {PICT-2021-I-INVI-00467//Agencia Nacional de Promoci&#xf3;n de la Investigaci&#xf3;n, el Desarrollo Tecnol&#xf3;gico y la Innovaci&#xf3;n (Argentina)/ ; PICT-2020-02289//Agencia Nacional de Promoci&#xf3;n de la Investigaci&#xf3;n, el Desarrollo Tecnol&#xf3;gico y la Innovaci&#xf3;n (Argentina)/ ; award ILLU-802-978//United States Department of Agriculture, USDA-NIFA/ ; },
mesh = {*Rhizosphere ; *Lolium/microbiology ; *Fertilizers ; *Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Anaerobiosis ; *Microbiota/genetics ; Soil/chemistry ; Integrons/genetics ; Manure/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The effects of anaerobic digestates on soil microbial communities have received increasing attention due to their potential impacts on soil health and antibiotic resistance. To date, no integrated analysis of rhizosphere bacterial community structure, antibiotic resistance genes (ARGs), and mobile genetic elements has been conducted in digestate-treated perennial ryegrass (Lolium perenne L.). We analyzed rhizosphere bacterial communities of this pasture using metabarcoding to study the effects of a manure-derived digestate on community structure and predicted functions. We also explored the association between digestate-enriched taxa and explanatory variables, including the abundance of two ARGs, class 1 integrons, and IncP-1ε plasmids. The greenhouse study included an unfertilized control and three fertilization treatments: digestate, inorganic fertilizer, and combined fertilizer (digestate + inorganic fertilizer). The results indicated a significant effect of the fertilizer type on bacterial communities and a stimulation of predicted functions related to genetic information processing by digestate and its combination. Digestate application resulted in the greatest differentiation in bacterial community structure relative to the unfertilized control and shifted communities toward amplicon sequence variants (ASVs) positively associated with class 1 integrons. Differential abundance analysis identified three ASVs and three genera (Arenimonas, Algoriphagus and Novosphingobium) that were significantly enriched under digestate treatment, relative to both urea and the unfertilized control. Our results demonstrate that anaerobic digestate application alters bacterial community structure and highlight the need for further studies to elucidate the potential adaptive role of class 1 integrons in rhizosphere microbiomes following digestate fertilization, including their contribution to antibiotic resistance.},
}
@article {pmid42068426,
year = {2026},
author = {Wang, RQ and Elshafey, AE and Liu, ZT and Wen, B and Gao, JZ and Chen, ZZ},
title = {Gut microbiota and growth differentiation in koi carp with identification of a growth promoting Exiguobacterium sp. strain WY(Y)3.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42068426},
issn = {1573-0972},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Carps/growth &amp; development/microbiology ; *Probiotics/administration &amp; dosage ; Animal Feed/analysis/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; },
abstract = {Discovering specific microbial markers and probiotics related to rapid growth offers a route for developing targeted feed solutions. This study was conducted in two phases: Phase I: Using 16 S rRNA sequencing to characterize the intestinal landscape and to discover a significant taxonomic shift in koi (Cyprinus carpio) that grow fast (FG) and grow slow (SG). Phase II: A dietary intervention trial was implemented across four experimental cohorts: a negative control (NC) fed a basal diet and three treatment groups (C1, C2, and C3) supplemented with Exiguobacterium sp. strain WY(Y)3 at escalating concentrations of 1 × 10[6], 1 × 10[7], and 1 × 10[8] CFU/g, respectively. The FG fish (11.44 ± 0.61 cm; 20.81 ± 1.33 g) harbored markedly higher proportions of Cyanobacteriota, Actinobacteriota, Chloroflexota, and notably Exiguobacterium sp., alongside enhanced metabolic pathways related to secondary metabolite biosynthesis compared with the SG fish. A piscine-derived strain, Exiguobacterium sp. WY(Y)3, isolated from the FG, significantly improved growth performance when supplemented in feed, with the 1 × 10[6] CFU/g producing the best overall outcomes (WGR = 186.26 ± 1.07 and FCR = 1.437 ± 0.08), including higher gut microbial diversity and stability. Integrated microbiome and metabolomic analyses revealed that supplementation with Exiguobacterium enhances growth performance by reshaping gut microbial composition and regulating host energy metabolism. This includes the downregulation of fatty acid β-oxidation and pyruvate metabolism pathways, alongside the upregulation of bile acid synthesis and vitamin-associated pathways (p < 0.05). Collectively, dietary inclusion of 1 × 10[6] CFU/g of Exiguobacterium sp. WY(Y)3 effectively promotes growth through microbiota restructuring and metabolic optimization, supporting its potential as a probiotic in aquaculture nutrition.},
}
@article {pmid42068598,
year = {2026},
author = {Xu, M and Cheng, K and Cai, Z and Chen, G and Zhou, J},
title = {Metagenomic and metatranscriptomic insights into Ruegeria profundi-driven protective responses in coral holobionts against Vibrio coralliilyticus infection.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128530},
doi = {10.1016/j.micres.2026.128530},
pmid = {42068598},
issn = {1618-0623},
abstract = {In the context of climate-driven coral reef degradation, opportunistic pathogens such as Vibrio coralliilyticus are emerging as significant secondary threats, acting in synergy with thermal stress to accelerate coral bleaching and mortality. In this study, we investigated the role of Ruegeria profundi in mitigating V. coralliilyticus-induced bleaching. Specifically, the responses of coral holobiont members to pathogenic and probiotic influences were evaluated using metagenomics and metatranscriptomics. We found that the presence of V. coralliilyticus enhanced the metabolic potential of the coral-associated bacterial community, particularly regarding carbohydrate utilization and virulence. Conversely, R. profundi reduced the relative abundance of pathogenic Vibrio species by over 50% and broadly suppressed the expression of virulence genes within the coral-associated bacterial community, including a > 2-fold downregulation of genes involved in quorum sensing and flagellar assembly. Transcriptomic data indicated that immune-related genes in the host were upregulated, whereas photosynthesis-related genes in photosymbiotic microalgae were downregulated in response to V. coralliilyticus infection. R. profundi significantly promoted apoptosis resistance and antimicrobial peptide activity in the host and enhanced photosynthesis in photosymbiotic microalgae (p < 0.05). Furthermore, R. profundi significantly suppressed virulence gene expression in the coral-associated bacterial community (p < 0.05). Collectively, our results indicated that R. profundi orchestrates a tripartite defense mechanism involving the coral host, its associated bacterial community, and symbiotic microalgae, effectively mitigating pathogen-induced dysbiosis and bleaching. These findings have promising implications for microbiome-based strategies in coral reef restoration.},
}
@article {pmid42068622,
year = {2026},
author = {Ogbanga, N and Mickleburgh, HL and Nelson, A and Smith, D and Gocha, TP and Wescott, DJ and Procopio, N},
title = {Microbial decomposition in experimental single and mass graves: New insights on post-burial interval estimation.},
journal = {Forensic science international. Genetics},
volume = {84},
number = {},
pages = {103517},
doi = {10.1016/j.fsigen.2026.103517},
pmid = {42068622},
issn = {1878-0326},
abstract = {Soil microbiomes are increasingly recognized as valuable indicators in forensic investigations, but microbial dynamics in mass graves remain poorly understood. This study investigates differences in microbial succession between individual graves (IG) and mass graves (MG) with human body donors and evaluates the potential of soil microbiome data to predict post-burial interval (PBI). Using ASV-level assessment, we analysed soil samples collected over time from both grave types in a controlled decomposition experiment. At the final timepoint (M18), MG and IG soils exhibited significantly different microbial compositions, with specific taxa, some associated with specific decomposition stages, enriched in each context. A regression model trained on IG samples predicted PBI with a mean error of 2.68 months when adjusted for seasonal variation but performed poorly on MG samples (RMSE = 7.12 months), highlighting ecological complexity and reduced generalisability. These findings underscore the importance of studying MG-specific microbial processes and caution against applying models developed from single-body burials to mass grave contexts. As mass graves are encountered in humanitarian and criminal investigations and establishing the duration of burial can be an important component of forensic reconstruction, our findings highlight the value of further research into context-specific microbiome models and their integration alongside existing methods for detection and time estimation in complex burial environments.},
}
@article {pmid42068645,
year = {2026},
author = {Liu, J and Liu, M and Xu, Y and Wang, Z and Zhou, X and Sun, Q},
title = {Genetically predicted TTK inhibition and its association with reduced breast cancer risk: a two-step Mendelian randomization study of potential gut microbiome mediation.},
journal = {Clinics (Sao Paulo, Brazil)},
volume = {81},
number = {},
pages = {100961},
doi = {10.1016/j.clinsp.2026.100961},
pmid = {42068645},
issn = {1980-5322},
abstract = {BACKGROUND: BOS172722, a selective TTK inhibitor, shows promise for Breast Cancer (BC) treatment. The role of gut microbiota as a potential mediator in this process has not been established. This Mendelian Randomization (MR) study investigated the causal effect of TTK inhibition on BC and conducted an exploratory analysis of potential mediation by gut microbiota.<br><br>METHODS: A two-step, two-sample drug target MR analysis used IEU Open GWAS project datasets. The inverse-variance-weighted method estimated causal effects, with sensitivity tests confirming robustness. False Discovery Rate (FDR) correction was applied to analyses for all microbial taxa.<br><br>RESULTS: Genetically predicted TTK inhibition significantly reduced BC risk (OR = 0.667, 95 % CI 0.543-0.819; FDR-adjusted p < 0.001). In secondary analyses, initial uncorrected results indicated nominal associations between TTK inhibition and 20 gut microbial taxa, and between 6 taxa and BC risk. However, none of these microbiota-related associations remained statistically significant after FDR correction (all q-values >0.1). An exploratory mediation analysis on Genus Anaerostipes id.1991, which showed the strongest nominal signals (TTK inhibition on Anaerostipes: uncorrected p = 0.003; Anaerostipes on BC: uncorrected p = 0.025), was performed for hypothesis generation only; no statistically significant mediation was observed.<br><br>CONCLUSION: This study provides robust genetic evidence that TTK inhibition is causally associated with a decreased risk of breast cancer. The exploratory analysis of gut microbiota as a mediator did not yield statistically significant results after correction for multiple testing. The potential role of specific microbes, such as Genus Anaerostipes, remains inconclusive and requires further dedicated investigation.},
}
@article {pmid42068651,
year = {2026},
author = {Jia, J and Wang, S and Chen, Y and Li, H and Zheng, C and Deng, J and Zhao, F},
title = {Heavy metals, gastrointestinal polymer-related materials, and gut microbiome in an Indo-Pacific bottlenose dolphin (Tursiops aduncus) recovered from a fisheries bycatch-related event in the East China Sea.},
journal = {Ecotoxicology and environmental safety},
volume = {317},
number = {},
pages = {120191},
doi = {10.1016/j.ecoenv.2026.120191},
pmid = {42068651},
issn = {1090-2414},
abstract = {Incidental cetacean bycatch provides irreplaceable opportunities to investigate population dynamics, mortality, and health. This multidisciplinary study examined morphology, age, gut microbiome, heavy metals, and gastrointestinal polymer-related materials in an immature male Indo-Pacific bottlenose dolphin (Tursiops aduncus, 248 cm, 114 kg, 5 years) accidentally captured in the East China Sea. Morphometrics indicated excellent body condition (BCI = 0.506) and superior dorsal fin shape compared to captive individuals, highlighting the role of natural environments in development. The gut microbiome was dominated by Proteobacteria and Firmicutes, showing segment-specific variation. Heavy metals accumulated mainly as Cd in kidneys and Cu and Zn in liver, with overall levels lower than those in other Chinese marine regions. LDIR analysis indicated the presence of polymer-related materials in the gastrointestinal tract, including reported matches to polyamide and chlorinated polyethylene, which may be associated with fisheries activities. These findings provide critical baseline ecotoxicological data for the East China Sea and underscore the importance of standardized passive biomonitoring networks that transform bycatch events into valuable scientific and conservation resources.},
}
@article {pmid42068814,
year = {2026},
author = {Kanannejad, Z and Taylor, WR and Ghatee, MA and Mohkam, M},
title = {Microbial regulation of immune tolerance during embryonic implantation and pregnancy.},
journal = {Journal of reproductive immunology},
volume = {175},
number = {},
pages = {104898},
doi = {10.1016/j.jri.2026.104898},
pmid = {42068814},
issn = {1872-7603},
abstract = {Maternal immune tolerance is essential for successful embryo implantation and maintenance of pregnancy. The maternal microbiome, particularly in the gut, vagina, and possibly the placenta, has emerged as an important regulator of immune adaptation during gestation. Through continuous interaction with the maternal immune system, the microbiota influence key immune cell populations such as regulatory T cells, uterine natural killer cells, and dendritic cells. These cells promote a tolerogenic environment necessary for embryo acceptance and proper placental development. Microbial-derived metabolites, including short-chain fatty acids and tryptophan derivatives, play important roles in modulating cytokine production and immune cell differentiation. Disruption of microbial balance, or dysbiosis, has been associated with a range of pregnancy complications, including implantation failure, preeclampsia, gestational diabetes, and preterm birth. Additionally, the maternal microbiome may influence fetal immune development, with implications for the offspring's long-term health. Emerging translational research suggests that interventions targeting the maternal microbiota, such as probiotics, prebiotics, and fecal microbiota transplantation, may beneficially modulate immune responses during pregnancy. While these approaches are promising, variability in individual microbiome composition and immune responses underscores the need for personalized strategies. In summary, the maternal microbiome is a dynamic and influential factor in shaping immune tolerance during pregnancy. A deeper understanding of microbiota-immune interactions may pave the way for novel, microbiome-based therapies to enhance reproductive outcomes and promote maternal-fetal health.},
}
@article {pmid42068861,
year = {2026},
author = {Zhang, J and Wang, X and Wang, W and Cao, Y and Wang, G},
title = {Altered Salivary Microbiome and Increased Immune Markers in Mouth-Breathing Children: Implications for Oral Health.},
journal = {International dental journal},
volume = {76},
number = {4},
pages = {109580},
doi = {10.1016/j.identj.2026.109580},
pmid = {42068861},
issn = {1875-595X},
abstract = {OBJECTIVE: To investigate the impact of mouth breathing (MB) on the salivary microbiome in children by comparing the differences in biochemical indicators, immune proteins and microbial community structure between mouth-breathing children and nose-breathing children, as well as among mouth-breathing children with different malocclusion types.<br><br>METHODS: Saliva samples were collected from 30 mouth-breathing children (MB group) and 10 nose-breathing children (control group), aged 8 to 12, between August 2023 and August 2024. The MB group was further subdivided into Angle Class I, II and III malocclusion subgroups, with 10 cases each. Ion concentrations were measured using an automatic biochemical analyser, pH was determined using a pH metre, immune protein levels were assayed by enzyme-linked immunosorbent assay and the structure and diversity of the salivary microbiota were analysed using 16S rRNA high-throughput sequencing.<br><br>RESULTS: Compared with the control group, the MB group showed no significant difference in salivary pH (P > .05), but a significantly lower chloride ion (Cl&#x207b;) concentration (P < .05). Conversely, the concentrations of secretory immunoglobulin A (SIgA) and peroxiredoxin-5 (PRDX5) were significantly higher in the MB group (P < .05). No statistically significant differences in these indicators were observed among the different malocclusion subgroups. Spearman correlation analysis revealed a positive correlation between PRDX5 and SIgA concentrations (rs = 0.808, P < .001) and negative correlations between both PRDX5 and SIgA concentrations and Cl&#x207b; concentration (rs = -0.588 and -.600, respectively; P < .001) in the MB group. Microbiota analysis indicated that the species richness (Chao1 index) of the salivary microbiota was significantly higher in the MB group. At the genus level, the relative abundances of Dialister, Streptobacillus, Anaeroglobus and Scardovia were significantly increased in the MB group (P < .05).<br><br>CONCLUSION: MB alters the physicochemical properties of children's saliva, triggering an enhanced local immune response and a state of oxidative stress. This leads to dysbiosis of the salivary microbial community, characterised by a higher abundance of pathogenic bacteria associated with dental caries and periodontal disease and shows a correlation with pathogens linked to upper respiratory tract inflammation. These findings suggest that MB may impact oral and potentially systemic health by disrupting the oral microenvironment.},
}
@article {pmid42068873,
year = {2026},
author = {Luo, L and Wang, P and Xu, Y and Li, Z and Liu, Y and Liu, J and Cheng, YX},
title = {The paradox of potency: Insights into emergent mechanisms of Ganoderma lucidum's antitumor effects.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {156},
number = {},
pages = {158203},
doi = {10.1016/j.phymed.2026.158203},
pmid = {42068873},
issn = {1618-095X},
abstract = {BACKGROUND: An arms race between cancer cells and therapeutic pressure fuels drug resistance, immune evasion, and tumor heterogeneity, hindering therapy. Ganoderma lucidum (G. lucidum), a traditional Chinese medicine (TCM) with multitarget pharmacology, offers potential to address this complexity. However, the mechanistic basis of the emergent effects of its meroterpenoids remains unexplored.<br><br>PURPOSE: This study used G. lucidum meroterpenoids as a model to elucidate the mechanisms underlying emergent effects in TCM and to evaluate their therapeutic potential for overcoming tumor resistance and heterogeneity.<br><br>STUDY DESIGN: This study employed an integrative design combining phenotypic screening, in vitro cell-based assays, in vivo tumor xenograft models, and multiomics analyses to investigate the emergent antitumor mechanisms of G. lucidum meroterpenoids.<br><br>METHODS: Meroterpenoid and polysaccharide extracts were evaluated in vitro and in vivo for their effects on TNBC growth. Transcriptomic, metabolomic, and microbiome analyses were performed to explore systemic mechanisms. Phenotypic screening and transcriptome analyses were performed to characterize the synergistic (0 + 0 + 0&#x2026;>0) and potentiation (0 + 0 + 0&#x2026;+1 > 1) effects of the meroterpenoid combinations and to elucidate the underlying molecular mechanisms.<br><br>RESULTS: In MDA-MB-231 cells, the meroterpenoid extracts inhibited proliferation and migration by inducing ferroptosis and reprogramming inflammatory signaling. In a mouse tumor model, total meroterpenoid extracts suppressed tumor growth, enriched beneficial gut microbiota, and partially restored tumor-depleted serum lipids and amino acids. Cotreatment with G. lucidum polysaccharides accelerated the restoration of the microbiota and achieved more extensive metabolomic correction. Notably, a set of inert meroterpenoids, defined as those lacking phenotypic effects, exhibited emergent anticancer activity when combined with one another or with active compounds. These combinations acted through 0 + 0 + 0&#x2026;>0 synergy or 0 + 0 + 0&#x2026;+1 > 1 potentiation to inhibit proliferation and migration by overcoming drug resistance, reprogramming metabolism, and inducing ferroptosis. They also triggered cell cycle collapse and necroptosis.<br><br>CONCLUSION: This case study provides insights into how meroterpenoids, particularly combinations of inert meroterpenoids, drive the emergent pharmacological effects of G. lucidum and suggests a strategy to overcome drug resistance and tumor heterogeneity.},
}
@article {pmid42068885,
year = {2026},
author = {Ke, H and Zhang, X and Xamxidin, M and Zhang, C and Fei, M and Li, J and Zhan, L and Lan, J and Chen, Y},
title = {Microbial community divergence and environmental responses across multi-phase landfill environments.},
journal = {Waste management (New York, N.Y.)},
volume = {219},
number = {},
pages = {115578},
doi = {10.1016/j.wasman.2026.115578},
pmid = {42068885},
issn = {1879-2456},
abstract = {Municipal solid waste landfills are highly heterogeneous ecosystems comprising solid waste, leachate, and subsoils wherein complex microbial consortia regulate organic matter degradation and contaminant transformation. However, comprehensive insights into their microbiome structure across multi-phase and depth profiles and responses to environmental gradients remain scarce. This study presents a rare, multidimensional characterization of landfill microbiomes that integrates deep drilling (to 50 m), 16S rRNA gene sequencing, and biogeochemical pathway analysis. To quantify the extent of waste stabilization, a solid-phase stabilization index (β) is proposed to link degradation stages with microbial succession. This index indicates a clear transition from a Firmicutes-dominated rapid degradation phase (β < 0.58) to a Proteobacteria-dominated stabilization phase (β > 0.83). Spatially, the microbiomes exhibit distinct solid-liquid niche partitioning, as evidenced by the prevalence of biofilm formers (Advenella and Brevundimonas) on solid waste surfaces and specific enrichment of the thermophilic planktonic Defluviitoga in the surrounding leachate. At the critical waste-soil interface, leachate infiltration exerts strong environmental filtering that drives a pronounced enrichment of the dual-tolerant Ralstonia, which constitutes up to 46.49% of the community. Cu, Be, and Cd emerge as the key heavy metals driving the evolution of subsoil microorganisms. These findings collectively provide an integrated framework that advances the mechanistic understanding of waste stabilization and leachate-soil interactions, offering new insights for assessing landfill maturity and understanding pollution fronts.},
}
@article {pmid42068931,
year = {2026},
author = {Tsai, W and Zhu, F and Bar-Or, A and Bernstein, CN and Bonner, C and Graham, M and Marrie, RA and Mirza, AI and O'Mahony, J and Yeh, EA and Banwell, B and Waubant, E and Tremlett, H and , },
title = {The gut microbiome in pediatric-onset acquired demyelinating syndromes by myelin oligodendrocyte glycoprotein antibody status.},
journal = {Multiple sclerosis and related disorders},
volume = {110},
number = {},
pages = {107216},
doi = {10.1016/j.msard.2026.107216},
pmid = {42068931},
issn = {2211-0356},
abstract = {BACKGROUND: Alterations of the gut microbiome have been reported in central nervous system demyelinating diseases. While the gut microbiome in pediatric multiple sclerosis (MS) has been studied, the role of the gut microbiome in other pediatric-onset acquired demyelinating syndromes (ADS) remains unknown. We compared the gut microbiome composition between myelin oligodendrocyte glycoprotein antibody-positive (MOG+) and antibody-negative (MOG-) participants with pediatric-onset ADS.<br><br>METHODS: Participants aged &#x2264;21 years enrolled in the Canadian Pediatric Demyelinating Disease Network microbiome study (2015-2018) with a single episode or relapsing non-MS, non-neuromyelitis optica spectrum disease attacks of demyelination with symptom onset <18 years were included. Stool sample-derived DNA underwent 16S rRNA (V4) sequencing. Serum MOG-IgG antibodies were tested within 30 days of first attack onset. Alpha-diversity (Shannon, Margalef's index, Chao1) and beta-diversity (weighted UniFrac) were analysed. Phylum/genus-level taxa were assessed using negative binomial models with false discovery rate correction. Rate ratios were sex- and age-adjusted (aRR).<br><br>RESULTS: Forty-six participants (18 MOG+/28 MOG-) were included. Mean age at stool sample collection (MOG+/MOG-) was 14.7/17.2 years. Alpha-/beta-diversities did not differ between MOG+/MOG- participants (p > 0.3). At the phylum level, the relative abundance of Proteobacteria was lower in MOG+ than MOG- participants (aRR:0.22;95%CI:0.07-0.69;q = 0.03). At the genus level, the relative abundance of Escherichia/Shigella was lower in MOG+ than MOG- participants (aRR:0.01;95%CI:0.001-0.07;q = 0.001), CONCLUSIONS: While alpha/beta-diversities did not differ between MOG+/MOG- participants, taxa-level differences were observed. Our findings suggest that the gut microbiome composition may differ by MOG serostatus among pediatric-onset ADS participants. Future work is warranted, utilizing larger cohorts and longitudinal follow-up.},
}
@article {pmid42069117,
year = {2026},
author = {Makowska-Zawierucha, N and Trzebny, A and Mokracka, J and Bradley, JA},
title = {The high Arctic resistome: stress-response genes, virulence determinants, and microbial populations in human-impacted environments of Spitsbergen.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128242},
doi = {10.1016/j.envpol.2026.128242},
pmid = {42069117},
issn = {1873-6424},
abstract = {The high Arctic, particularly Spitsbergen, faces the combined challenges of climate change and other anthropogenic pressures - including waste and contaminant release from human activity - that influence microbial populations and the spread of antimicrobial resistance (AMR). This study presents a snapshot analysis of metagenomes from various environments across Spitsbergen, including untreated and treated wastewater outflows, fjords, and glacial ice cores, to explore the abundance of stress-response genes, including antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs), and virulence genes (VGs), alongside the compositions of the associated bacterial populations. We reveal varying levels of stress-response genes and VGs in environments exposed to differing levels of human influence. ARGs and MRGs dominate in raw sewage, while VGs are more prevalent in fjord waters receiving both raw sewage and effluent, indicating that specific environmental conditions favor different resistance and virulence traits. We detect high abundance of ARGs and VGs downstream of both untreated and treated wastewater. Our analyses indicate the presence of bacterial populations with resistance and virulence traits - including Enterobacteriaceae, Enterococcaceae, Bacillaceae, and Staphylococcaceae - in downstream ecosystems. While we do not directly assess effects on human health or ecosystem function, these observations point to potential ecological impacts in Arctic environments and highlight the importance of continued monitoring to understand and manage the possible effects of human activities and climate change.},
}
@article {pmid42069481,
year = {2026},
author = {Faherty-McGrath, LB and van Sinderen, D and Browne, HP},
title = {Developing spore-forming gut bacteria as model organisms.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.04.006},
pmid = {42069481},
issn = {1878-4380},
abstract = {Anaerobic gut bacteria have highly evolved functions that promote transmission between human hosts. These include resilient spores produced by many Bacillota (formerly Firmicutes) bacteria, which are tolerant to extended ambient oxygen exposure. Recent culturing and genomic studies have revealed the taxonomic diversity of gut spore-formers and their prevalence in human populations. However, due to a reliance on spore-forming model organisms that are not representative of commensal gut bacteria, we still have a limited understanding of gut microbiome-specific sporulation processes and their underlying genetics. In this opinion article, we outline a rational path for development of new model organisms derived from commensal spore-forming gut bacteria in order to obtain fundamental insights into sporulation and to provide a discovery platform for novel probiotic or microbiome-based therapeutic development.},
}
@article {pmid42069521,
year = {2026},
author = {Harriman, D and Ng, A and Bronowski, M and Yang, R and Dang, T and Sherwood, K and Nguan, C and Miller, A and Lange, D},
title = {Urobiome composition after renal transplantation: an exploratory study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05106-4},
pmid = {42069521},
issn = {1471-2180},
abstract = {BACKGROUND: The urobiome of renal transplant recipients is poorly defined. The purpose of this study was to investigate whether there are characteristic changes in the urobiome between pre- to post-transplant states, at varying degrees of post-transplant allograft function, and between those with acute T-cell mediated rejection (TCMR) versus a non-rejector cohort.<br><br>PATIENTS AND METHODS: 41 patients who consented to have urine stored in our transplant biobank were included in this study: 1) Rejectors (n&#x2009;=&#x2009;10 pts: 6 borderline, 1 Banff IA, 3 Banff IIA TCMR, mean age: 47.4&#x2009;&#xb1;&#x2009;12.4 yrs); 2) Women (n&#x2009;=&#x2009;16 pts; mean age: 49.3&#x2009;&#xb1;&#x2009;17.3 yrs); 3) Men (n&#x2009;=&#x2009;15 pts, mean age: 47.5&#x2009;&#xb1;&#x2009;17.2 yrs). Urine was collected via mid-stream clean-catch technique prior to transplant (n&#x2009;=&#x2009;21), at the time of TCMR (n&#x2009;=&#x2009;9; within 1&#xa0;month of transplant), 1-month (n&#x2009;=&#x2009;15), and 3-months post-transplant (n&#x2009;=&#x2009;38). Samples were processed and stored at -80 [Formula: see text] until 16S rRNA sequencing. Alpha diversity, beta diversity, and differential abundance analysis was performed.<br><br>RESULTS: The urobiome was altered post-transplant, with rejectors gaining Corynebacterium and Pseudomonas at time of rejection, and non-rejectors gaining Lactobacillus among other taxa. Within individuals, post-transplant urobiome composition was&#x2009;~&#x2009;75% dissimilar from pre-transplant (p&#x2009;<&#x2009;0.001). Urobiome composition differed by sex (p&#x2009;=&#x2009;0.002), but not by age. Differential abundance analysis based on 3-month post-transplant eGFR revealed consistent loss of Lactobacillus with decreased renal function.<br><br>CONCLUSIONS: Our results suggest that renal transplantation has a strong impact on individual urobiome composition, but not diversity, and microbial imbalance may be associated with acute rejection and post-transplant renal function. Our findings indicate a need for further research into the urobiome during renal transplantation to elucidate its potential as a biomarker of and/or contributor to post-transplant allograft health.},
}
@article {pmid42069543,
year = {2026},
author = {Tang, W and Wang, P and Jiang, T and Chen, N and Xue, M and Chen, Y and Pang, R and Zhang, J and Wang, R and Wang, Q and Chen, J and Ren, C and Huang, Y and Zhang, Z and Cheng, X},
title = {Multi-omics analysis reveals circadian disruption of rumen microbiota and serum metabolites in Tibetan sheep under transport stress.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05109-1},
pmid = {42069543},
issn = {1471-2180},
support = {CARS-38//the National Modern Meat Sheep Industry Technology System/ ; 32402701//Young Scientists Fund of the National Natural Science Foundation of China/ ; 2022-NK-134//the Science and Technology Program of Qinghai Province/ ; GXXT-2022-073//Anhui Provincial University Synergistic Innovation Project/ ; },
abstract = {BACKGROUND: Off-site fattening of Tibetan sheep is a key strategy to mitigate the effects of high-altitude grassland degradation and winter forage scarcity, promoting sustainable development in plateau animal husbandry. However, transport stress (TS) presents a significant challenge to realizing its benefits. The mechanism by which TS affects the health of Tibetan sheep by regulating rumen microbial and serum metabolite rhythmic changes remains unclear.<br><br>METHODS: This study selected six healthy male Tibetan sheep, aged seven months and of comparable body weight, for the transport experiment. Blood and rumen fluid samples were collected at four-hour intervals during 24-hour periods pre-transport (CON) and post-transport (TS) for serum indicators, serum metabolome, and rumen microbiome analyses.<br><br>RESULT: The results showed that TS significantly increased serum concentrations of cortisol (COR), melatonin (MT), lipopolysaccharide-binding protein (LBP), serum amyloid A (SAA), and non-esterified fatty acid (NEFA), while significantly decreasing glucose (GLU), total antioxidant capacity (T-AOC), and glutathione peroxidase (GPx) (P&#x2009;<&#x2009;0.05). Furthermore, the circadian rhythms of COR, MT, LBP, SAA, NEFA, and GPx were significantly disrupted (ADJ.P&#x2009;<&#x2009;0.05). TS reduced the proportion of rumen microbial circadian rhythms from 3.46% to 1.99%, with Prevotella, Butyrivibrio, and Ruminococcus losing their circadian rhythmicity in the TS phase (ADJ.P&#x2009;<&#x2009;0.05). Additionally, TS decreased the proportion of circadian rhythm-regulated serum metabolites from 51.74% to 29.51%. In the TS phase, rhythmically regulated metabolites, including 3',5'-cyclic AMP, fumarate, dopamine, glutathione, and angiotensin (1-7), were enriched in pathways such as oxidative phosphorylation, retinol metabolism, and tryptophan metabolism. Multi-omics analyses demonstrated significant correlations between Ruminococcus and energy metabolites (malic acid, 3',5'-cyclic AMP, fumarate, NEFA), and between Butyrivibrio, Anaeroplasma, and inflammatory/antioxidant markers (glutathione, SAA, LBP). In conclusion, this study reveals that TS induces a homeostatic imbalance in Tibetan sheep by disrupting the circadian rhythms of both the rumen microbiota and host metabolism. These findings provide a theoretical basis and molecular targets for developing interventions to alleviate TS in livestock.},
}
@article {pmid42069621,
year = {2026},
author = {Tandon, K and Hu, J and Ricci, F and Blackall, LL and Medina, M and Kühl, M and Verbruggen, H},
title = {RNA-seq sheds light on "who is doing what" in the coral Porites lutea.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02414-9},
pmid = {42069621},
issn = {2049-2618},
support = {DP200101613//Australian Research Council/ ; GBMF9206//Gordon and Betty Moore Foundation/ ; CEECIND:2023.06155//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
abstract = {BACKGROUND: The coral holobiont functions as a complex biogeochemical system, sustained by intricate metabolic exchanges between the host and its associated microbiome. While the taxonomic diversity of these communities is well documented, the specific metabolic roles and biogeochemical contributions of microorganisms across distinct coral compartments, particularly within the endolithic habitats, remain poorly understood. Using RNA-seq, we investigated the active microbiome of healthy stony coral Porites lutea, focusing on the coral tissue, the green endolithic algal layer (Ostreobium layer), and the deeper coral skeleton.<br><br>RESULTS: We identified distinct, metabolically active communities within these compartments and highlight substantial metabolic redundancy across carbon, nitrogen, and sulfur pathways. Our study provides the first transcriptomic evidence of Ostreobium's ability to transfer fixed carbon to other holobiont members and the coral host. We highlight the critical roles of diverse coral holobiont members in nutrient cycling and maintaining homeostasis through scavenging of reactive oxygen and nitrogen species.<br><br>CONCLUSIONS: This study provides a novel molecular-level understanding of the functional roles played by diverse coral holobiont members in their respective compartments and underscores that corals harbor distinct microbiomes with wide-ranging functions. Video Abstract.},
}
@article {pmid42069629,
year = {2026},
author = {Yinhang, W and Shuwen, H and Jing, Z and Min, F},
title = {Fungi and colorectal cancer: from dysregulation to clinical translation.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00835-3},
pmid = {42069629},
issn = {1757-4749},
support = {YXX2024-KF02-03//Fungal Infectious Diseases Innovation Center for Basic Research in Medicine of the Ministry of Education Open Research Project/ ; },
abstract = {Research on the gut microbiota has primarily focused on bacterial communities. However, the role of fungi-the second-largest eukaryotic component of the gut microbiome-in the development and progression of colorectal cancer (CRC) has been less extensively studied compared to bacteria. Recent studies have revealed significant fungal dysbiosis in the intestines of CRC patients, where the enrichment of specific pathogenic fungi (e.g., Aspergillus spp.) is closely associated with tumor progression, while the reduction of certain commensal fungi may weaken their protective effects. This fungal imbalance not only directly promotes tumorigenesis through carcinogenic mechanisms but also indirectly accelerates CRC progression by reshaping the bacteria-fungi interaction network and the host immune microenvironment. This article reviews the structural alterations of fungal communities in CRC, the changing patterns of specific fungal species, the relationship between fungal dysbiosis and clinicopathological features, the potential molecular mechanisms of fungi in CRC pathogenesis, the significance of cross-kingdom microbial interactions, as well as the potential diagnostic and therapeutic applications of fungi in CRC and the challenges and prospects of novel fungal-modulating therapeutic strategies.},
}
@article {pmid42069657,
year = {2026},
author = {de Oliveira Andrade, F and Staley, C and Jin, L and Ozgul-Onal, M and McDermott, M and Kenanoglu, S and de Oliveira, KA and Verma, V and Hilakivi-Clarke, L},
title = {Gut microbiome modulates breast cancer risk in socially isolated mice.},
journal = {Breast cancer research : BCR},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13058-026-02292-x},
pmid = {42069657},
issn = {1465-542X},
abstract = {BACKGROUND: Breast cancer risk and mortality are associated with disrupted gut microbiome functions which in turn can affect tumor immune responses. One source of disruption could be stress. Social isolation (SI) stress consistently increases breast cancer risk and mortality in preclinical models and women, but whether SI promotes mammary tumor growth by affecting gut microbiome has not been studied.<br><br>METHODS: We investigated if increased E0771 mammary tumorigenesis in SI female C57BL/6 mice was associated with changes in their gut microbiome by treating mice with an antibiotic mix that suppresses bacterial abundance and by performing fecal microbiota transplantation (FMT) from SI or group-housed (GH) donors to GH host. The effect of SI on anti-tumor CD8&#x2009;+&#x2009;T and immunosuppressive Foxp3&#x2009;+&#x2009;Treg cells was also studied.<br><br>RESULTS: Fecal bacteria that were present at different abundances between GH and SI mice were short chain fatty acid (SCFA) producers, and the most consistent change across three replicate studies was decreased fecal abundance of Akkermansia genus in SI mice. In addition, fecal propionic acid levels were reduced in SI mice, compared with GH mice, in agreement with Akkermansia being propionic acid producer. SI reduced the activation of CD8&#x2009;+&#x2009;T cells systemically and in the tumor microenvironment, while the levels and activation of immunosuppressive Foxp3 Tregs were increased. Antibiotic treatment reversed increased mammary tumorigenesis and immunosuppression in SI mice but did not affect GH mice. Further, FMT from SI donors increased tumor growth in GH host, compared with FMT from GH donor.<br><br>CONCLUSION: Gut dysbiosis caused by SI may be driving their increased mammary tumorigenesis, potentially through gut dysbiosis induced immunosuppression.},
}
@article {pmid42069663,
year = {2026},
author = {Yin, C and Osborne, SL and Lehman, RM},
title = {Legacy effects of cover cropping and crop phase on soybean health and associated rhizosphere microbiome in corn-soybean rotation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00899-3},
pmid = {42069663},
issn = {2524-6372},
abstract = {BACKGROUND: Crop diversification through crop rotation or cover cropping is widely recognized as an important strategy to improve agroecosystem sustainability, enhance soil health, and suppress soilborne diseases. Rotating crops or introducing cover crops can disrupt pathogen life cycles, improve nutrient cycling, and promote beneficial microbes. However, the outcomes of diversification practices are often complex, influenced by soil type, crops, and pathogen pressures. Evaluating how cover crops and crop phase affect crop soilborne diseases and root-associated microbiome is critical for designing resilient cropping systems.<br><br>RESULTS: This study evaluated the legacy effects of cover crops and crop phase on soybean root diseases and root-associated microbiome. Soybean plants were grown in soils collected from a corn-soybean rotation field experiment with and without cover crops, and then challenged with either Fusarium graminearum inoculum or soybean cyst nematode (SCN) in the growth chamber. Soils with a cover crop history significantly reduced F. graminearum-induced root rot, but had a limited impact on SCN, indicating divergent disease responses. Microbial profiling revealed that F. graminearum inoculum strongly reshaped bacterial communities, reducing Shannon diversity and enriching fast-growing copiotrophic taxa, including Bacteroidota genera (Pedobacter, Chitinophaga, Flavobacterium, and Mucilaginibacter) and Proteobacteria genera (Dyella, Pseudomonas, Rhizobium, and Paraburkholderia) regardless of cover crops. In contrast, SCN infection increased bacterial Shannon diversity in soybean-phase soils regardless of cover crops but decreased fungal Shannon diversity in soybean soils without cover crops, highlighting pathogen-specific microbial shifts. Cover cropping enhanced microbial heterogeneity under both pathogen pressures, enriching microbial taxa potentially involved in nutrient cycling (Chitinophaga and Mucilaginibacter), antagonism (Flavobacterium, Streptomyces, Pseudonocardia, and Nocardioides), and competitive interactions (Paraburkholderia). Correlation analyses further linked specific bacterial and fungal genera with disease suppression.<br><br>CONCLUSIONS: Soilborne pathogens and cropping practices exerted interconnected, pathogen- and crop-specific effects on root microbial communities. Cover cropping offers a promising strategy to enhance microbial-mediated disease resilience in soybean systems, providing ecological insights into microbiome-driven plant health.},
}
@article {pmid42069868,
year = {2026},
author = {Müller, K and Gillard, J and Typas, A and Knopp, M and Goemans, CV},
title = {Antibiotic-induced gut microbiome dysbiosis: risks and strategies for mitigation.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {42069868},
issn = {1460-2075},
support = {10002165//SNF/ ; TMSGI3_226334/1//SNSF Starting Grant/ ; 2019-00666//Swedish Research Council/ ; },
abstract = {The discovery of antibiotics and their subsequent therapeutic use revolutionized our ability to treat once deadly infectious diseases, and antibiotics have become one of the most commonly prescribed drug classes. Unfortunately, these compounds not only target pathogenic strains, but also non-pathogenic bacteria that fulfill important functions for the human host. As such, antibiotic treatment can cause severe collateral damage, resulting in dysbiosis, for example, in the human gut microbiome. Given the immense importance of the gut microbiome for human health, antibiotic-induced dysbiosis can cause a variety of detrimental health outcomes. In addition, antibiotic (over-)use causes selection of antibiotic-resistant strains, and the human gut microbiome has become a major reservoir for resistance determinants that can transfer to pathogenic isolates and cause hard-to-treat infections. In this review, we describe various adverse effects that antibiotic use has on the human gut microbiome, how we can approach this problem experimentally, and discuss pathways to mitigate antibiotic-induced collateral damage.},
}
@article {pmid42069941,
year = {2026},
author = {Singh, A and Bhattacharjee, S and Singh, Y and Kostova, I},
title = {Parabiotics as Next-Generation Microbiome Therapeutics: Insights into Mechanisms, Evidence, and Therapeutic Potential.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
pmid = {42069941},
issn = {1432-0991},
mesh = {Humans ; *Prebiotics/administration &amp; dosage ; Animals ; *Gastrointestinal Microbiome/drug effects ; Probiotics ; *Microbiota ; },
abstract = {Parabiotics (also termed paraprobiotics) are defined as non-viable microbial cells or their components, including peptidoglycans, teichoic acids, surface proteins, that confer health benefits without requiring viability which distinguishes them from traditional probiotics. Their non-viable nature eliminates risks such as microbial translocation, bacteremia, and sepsis, making them suitable for vulnerable populations including immunocompromised, critically ill, paediatric and elderly individuals. In addition, parabiotic exhibit improved thermal stability, extended shelf life, and easier incorporation into functional foods, nutraceuticals, and pharmaceutical formulations without cold-chain requirements. Mechanistically, parabiotics retain immunomodulatory, anti-inflammatory and have barrier-enhancing activities through interactions with host pattern recognition receptors, including Toll-like receptors, modulation of cytokine responses, and reinforcement of gut epithelial integrity. Preclinical and clinical studies support their therapeutic potential such as in case of heat-killed Lactobacillus acidophilus LB (L. acidophilus) has shown efficiency in managing acute paediatric diarrhoea, while heat-inactivated Lacticaseibacillus paracasei PS23 (Lcb. paracasei) has demonstrated improvements in muscle strength and inflammatory markers, including reduced C-reactive protein and interleukin-6 and increased interlukin-10 in elderly individuals. Similarly, inactivated Lactiplantibacillus plantarum (Lpb. plantarum) and Bifidobacterium strains have been associated with benefits in irritable bowel syndrome, atopic dermatitis, respiratory infections, visceral fat reduction, and antibiotic-associated dysbiosis. Synergistic combinations with prebiotics, postbiotics and related bioactives further enhance therapeutic outcomes in inflammatory, metabolic and infectious conditions. Advances in metagenomics, next-generation sequencing, proteomics, metabolomics, CRISPR-Cas systems, and synthetic biology are accelerating strain characterization, functional evaluation, and scalable production. Despite ongoing challenges in standardization and regulated harmonization, parabiotics represent a safe and effective approach for microbiome-targeted interventions. This review synthesizes current evidence on their therapeutic applications, technological advancements, and translational potential, highlighting their role in precision health and next-generation functional nutrition.},
}
@article {pmid42070004,
year = {2026},
author = {Alum, EU and Uti, DE and Paul-Chima Ugwu, O and Okon, MB and Aggad, WS and Almohaimeed, HM and Bainsal, N and Shukla, SK and Ealla, KKR},
title = {Medicinal Plants and the Gastrointestinal Microbiota in Chronic Diseases Modulation: A Structured Mechanistic and Translational Review.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
pmid = {42070004},
issn = {1432-0991},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Plants, Medicinal/chemistry ; Chronic Disease ; Phytochemicals/pharmacology ; Dysbiosis ; Animals ; },
abstract = {The gut microbiome supports digestion, immunity, and metabolism; its imbalance (dysbiosis) drives inflammation and metabolic dysfunction, contributing to chronic diseases such as diabetes, cardiovascular disease, inflammatory bowel disease, and autoimmune disorders. Medicinal plants provide a wide range of phytochemicals (such as polyphenols, flavonoids, alkaloids, saponins), which reach the colon and undergo two-sided interactions with microbes in the gut, acting as potential microbiome modulators and substrates of biotransformation into bioactive metabolites. This structured narrative review synthesises evidence from peer-reviewed studies indexed in PubMed, Scopus, and Web of Science over the last 10 years on the role of medicinal plants in microbiome-mediated chronic disease modulation. This literature is organised into three mechanistic axes: (i) perturbations, defined here as measurable shifts in microbial diversity or taxonomic composition relative to a baseline or healthy reference state, together with beneficial taxa enrichment; (ii) alterations in microbial metabolite output, especially short-chain fatty acids (SCFAs) and other immunometabolic mediators; and (iii) downstream host metabolic and immune signalling. Rather than broad descriptive summaries, the literature is organised using an axis-based mechanistic framework, highlighting key translational constraints such as botanical heterogeneity, dose/formulation variability, and inconsistent microbiome endpoint standardisation, that must be addressed to strengthen human evidence and clinical relevance. Illustrative microbiome-mediated processes involve botanicals such as turmeric (curcumin), ginseng (ginsenosides), and green tea (catechins), though evidence strength varies by study design. Future progress requires standardised phytochemical characterisation, microbiome-stratified trials, and integration of multi-omics with artificial intelligence analytics to enhance mechanistic insight, identify responders, and enable personalised plant-based microbiome therapies.},
}
@article {pmid42070114,
year = {2026},
author = {Davids, M and Herrema, H and K Groen, A and Galenkamp, H and Zwinderman, A and Palmu, J and Havulinna, A and Niiranen, T and Knight, R and Acherman, Y and Franken, R and Verheij, J and Dukas, M and , and Bajaj, J and Llorente, C and Schnabl, B and Nieuwdorp, M and Meijnikman, A},
title = {Lactic acid bacteria and endogenous ethanol mediate proton pump inhibitor-associated MASLD: a multicohort cross-sectional mediation analysis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2664712},
doi = {10.1080/19490976.2026.2664712},
pmid = {42070114},
issn = {1949-0984},
mesh = {Humans ; *Proton Pump Inhibitors/adverse effects ; Cross-Sectional Studies ; Male ; Female ; *Ethanol/metabolism ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; Adult ; *Lactobacillales/metabolism/classification/genetics/isolation &amp; purification ; *Fatty Liver/microbiology/chemically induced/metabolism ; Cohort Studies ; Mediation Analysis ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Aged ; },
abstract = {BACKGROUND &amp; AIMS: Proton pump inhibitor (PPI) use has been associated with metabolic dysfunction associated with steatotic liver disease (MASLD) in multiple studies. While the association is confounded by various risk factors, such as BMI and age, a potential mediating factor of the microbiome has been suggested. In this study, we aimed to identify bacterial clades with the highest mediating potential and evaluate the serially mediated path through microbially derived endogenous ethanol.<br><br>METHODS: Microbiome mediation analysis of PPI use and MASLD was conducted in two cohorts. In a bariatric surgery cohort (n&#x2009;=&#x2009;122), liver biopsy-proven steatosis grade and postprandial ethanol concentrations were used as outcomes. In the HELIUS cohort (n&#x2009;=&#x2009;2440), a general population cohort study, mediation was performed using the Fatty Liver Index (FLI) score. The strongest associations were validated in the FINRISK cohort (n&#x2009;=&#x2009;7066).<br><br>RESULTS: Several bacterial taxa, which are predominantly found in the small intestine, showed a potential role in mediating the effects of PPIs on MASLD, postprandial ethanol levels, and FLI score. The Lactobacillales order showed the strongest mediating potential across the outcomes tested in both discovery cohorts. A notable serial mediation pathway was identified, linking PPI use to MASLD via Lactobacillales abundance and postprandial plasma ethanol concentrations. The mediating role of Lactobacillales in the association between PPI use and FLI scores was confirmed in the final study cohort.<br><br>CONCLUSIONS: Data from multiple cross-sectional cohort studies support a mediating potential of the microbiome in the association between PPI use and hepatic steatosis, independent of alcohol consumption. The effect of PPIs on MASLD appears to be mediated mainly by increased lactic acid bacteria abundance, and is potentially, in part, serially mediated by endogenous ethanol production.},
}
@article {pmid42070249,
year = {2026},
author = {Afshar, Y and Rezaei, N},
title = {The Silent Link: Exploring the Impact of Periodontal Diseases on Head and Neck Carcinogenesis.},
journal = {Clinical and experimental dental research},
volume = {12},
number = {3},
pages = {e70341},
pmid = {42070249},
issn = {2057-4347},
mesh = {Humans ; *Head and Neck Neoplasms/microbiology/etiology/immunology/pathology ; *Squamous Cell Carcinoma of Head and Neck/microbiology/immunology/etiology/pathology ; Microbiota ; *Carcinogenesis ; *Dysbiosis/microbiology/complications ; Tumor Microenvironment ; *Periodontal Diseases/microbiology/complications ; *Periodontitis/microbiology/complications ; Fusobacterium nucleatum ; Epigenesis, Genetic ; },
abstract = {OBJECTIVES: Oral dysbiosis can accelerate the progression of head and neck squamous cell carcinoma (HNSCC) by fostering a pro-inflammatory, immunosuppressive, and metabolically altered environment. This narrative review examines the relationships between periodontitis-associated bacteria and HNSCC, focusing on their impact on oncogenic pathways, immune modulation, and epigenetic alterations.<br><br>MATERIALS AND METHODS: A comprehensive search of PubMed and Google Scholar was conducted up to January 28, 2026, without time limitations, using all relevant keywords related to HNSCC, head and neck cancers, periodontitis, and the oral microbiome.<br><br>RESULTS: Key periodontitis-associated bacteria, including&#x202f;Fusobacterium nucleatum, Porphyromonas gingivalis, Capnocytophaga gingivalis, and&#x202f;Prevotella intermedia, may play a vital role in HNSCC. These bacteria stimulate several oncogenic pathways, including Wnt/&#x3b2;-catenin, NF-&#x3ba;B, and PI3K/Akt, enabling HNSCC to evade immune responses, trigger epithelial-to-mesenchymal transition and angiogenesis, and encourage cell proliferation and stemness. Furthermore, microbial interactions within the tumor microenvironment significantly impact treatment resistance, particularly in the context of immune checkpoint inhibitor therapy.<br><br>CONCLUSIONS: Incorporating periodontal screening, microbiome profiling, and bacterial-targeted therapies into oncology could enhance treatment outcomes for HNSCC. Future research should investigate CRISPR-based microbial interventions, targeted epigenetic therapies, and microbiome-driven precision oncology strategies.},
}
@article {pmid42070584,
year = {2026},
author = {Nasseh, N and Tahergorabi, M},
title = {Pesticides and the microbial world: a review of disturbance, resilience, and the road to recovery.},
journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/03601234.2026.2648405},
pmid = {42070584},
issn = {1532-4109},
abstract = {Pesticides are widely used tools in modern crop production, yet their impacts on soil ecosystems are often context-dependent and not fully quantified. Over several decades, research has shown that pesticides and their metabolites can alter the diversity, structure, and functional capacity of soil microbial communities, with effects that may be either inhibitory or stimulatory depending on the context. However, their long-term influence on microbial resilience and recovery remains insufficiently understood. This review synthesizes current knowledge by integrating microbial ecology, soil chemistry, and environmental toxicology, with a focus on how pesticides alter microbial community composition and enzyme-mediated nutrient cycling. Particular attention is given to key soil enzymes, such as dehydrogenases, ureases, and phosphatases, which serve as sensitive, though sometimes limited, indicators of soil disturbance, and recovery. Furthermore, the review emphasizes how soil physicochemical properties, contamination history, and management practices collectively modulate microbial responses to pesticide exposure. By bringing these perspectives together, this synthesis offers a conceptual framework for interpreting pesticide-microbe interactions and provides a foundation for monitoring soil health and guiding sustainable pest management strategies that maintain agricultural productivity while preserving soil vitality.},
}
@article {pmid42070604,
year = {2026},
author = {Ma, Y and Wang, Q and Liu, L and Jia, J},
title = {Integrated microbiome and untargeted metabolomics analyses reveal the mechanism by which Haematococcus pluvialis polysaccharide alleviates obesity.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152354},
doi = {10.1016/j.ijbiomac.2026.152354},
pmid = {42070604},
issn = {1879-0003},
abstract = {Haematococcus pluvialis is a microalga with substantial nutritional and medicinal value. This study aimed to investigate the anti-obesity efficacy of Haematococcus pluvialis polysaccharide (HP) in high-fat diet (HFD)-induced obese mice. Structural characterization revealed that HP was mainly composed of glucose, rhamnose, arabinose, galactose, fructose, xylose, galacturonic acid, and glucuronic acid, with molar ratios of 74.14%, 0.87%, 2.98%, 3.19%, 0.88%, 17.05%, 0.05%, and 0.90%, respectively. Its molecular weight was 1.363 × 10[4] Da. Results from animal experiments showed that HP significantly suppressed body weight gain in HFD-fed obese mice and exerted beneficial anti-obesity effects. Furthermore, HP effectively alleviated HFD-induced abnormalities in glycolipid metabolism, systemic inflammation, and fat fat accumulation in the liver and epididymal adipose tissue. High-throughput fecal 16S rRNA gene sequencing revealed that HP corrected HFD-induced gut microbial dysbiosis, significantly modulating the structure and diversity of the gut microbiota in mice. HP notably increased the relative abundance of beneficial genera, including Bacteroides, Allobaculum, Dorea, and Butyricicoccus. Untargeted metabolomic analysis further demonstrated that HP markedly upregulated the relative levels of gut microbiota-associated metabolites such as indole and sulfated cholic acid. These changes directly affected metabolic pathways closely linked to glycolipid homeostasis, including bile acid metabolism and tryptophan metabolism. Therefore, Haematococcus pluvialis polysaccharide could serve as a promising anti-obesity bioactive compound for intervening metabolic disorders in obese individuals.},
}
@article {pmid42070645,
year = {2026},
author = {Farah, H and Polatova, D and Rizaev, J and Mhdy, FA and Muhammad, FA and Maharana, L and Bainsal, N and Singh, R},
title = {Overcoming Conditional Immune Resistance in MSS and pMMR Colorectal Cancer: A Sequential Gating Framework for Immunotherapy.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105353},
doi = {10.1016/j.critrevonc.2026.105353},
pmid = {42070645},
issn = {1879-0461},
abstract = {Microsatellite stable and mismatch repair proficient colorectal cancer (CRC) represents the largest population of patients exposed to immune checkpoint inhibitors, yet remains largely refractory to these therapies. Resistance is commonly attributed to low tumor mutational burden or limited neoantigenicity. However, this explanation is insufficient in light of accumulating clinical, transcriptional, and spatial profiling data demonstrating the presence of immune cells, antigen expression, and inducible immune signaling in a substantial fraction of MSS tumors. In this Review, we propose that immunotherapy failure in MSS and pMMR CRC reflects a hierarchical immune gating problem rather than intrinsic immune indifference. We outline a sequential model in which immune priming, physical access of effector cells to tumor epithelial compartments, and suppression by stromal, myeloid, and metabolic programs constitute ordered and rate-limiting steps that must be relieved before immune checkpoint blockade can exert clinical activity. This framework reconciles decades of negative clinical trials with emerging conditional successes observed using epigenetic priming, stromal and vascular remodeling, myeloid reprogramming, and microbiome-modulating strategies. By reframing resistance as a dynamically enforced and therapeutically tractable immune state, this Review provides a decision shaping framework for rational combination therapy, treatment sequencing, and biomarker guided immunotherapy development in MSS and pMMR CRC.},
}
@article {pmid42070688,
year = {2026},
author = {Shurigin, V and Lu, X and Khan, AR and Muhammad, M and Ullah, I and Egamberdieva, D and Yu, Y and Li, L},
title = {Unveiling the Plant Growth-Promoting and Antifungal Potential of Melissa officinalis Endophytes: the Integrative Culture-Dependent and Metagenomic Approaches.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {113182},
doi = {10.1016/j.plantsci.2026.113182},
pmid = {42070688},
issn = {1873-2259},
abstract = {Endophytic bacteria play a central role in plant health, yet their diversity and functions in medicinal plants remain poorly characterized. In this study, we integrated high-throughput sequencing, culture-based isolation, functional assays, and greenhouse validation to characterize the endophytic microbiome of Melissa officinalis L. High-throughput sequencing revealed 347 species with strong tissue-specific structuring. Paucibacter and Pseudomonas genera related to phylum Pseudomonadota dominated in all plant tissues. Nineteen culture-dependent strains representing Pseudomonas, Microbacterium, Plantibacter, Agreia, and Kocuria demonstrated various plant growth-promoting traits, including phosphate solubilization, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-related compounds (IRC) production, siderophore secretion, and hydrolytic enzyme activities (chitinase, protease, and lipase). Pseudomonas fluorescens XIEG-4RS14 showed antifungal activity against Fusarium graminearum (50%) and F. moniliforme (37%), P. marginalis XIEG-4RS15 showed 100 and 62%, P. baetica XIEG-4RS18 showed 28 and 42%, P. fluorescens XIEG-4RS32 showed 45 and 39%, and P. rhodesiae XIEG-4RS37 showed 58 and 27% respectively. Greenhouse assays demonstrated that strains Pseudomonas fluorescens XIEG-4RS14, P. fluorescens XIEG-4RS32, P. taetrolens XIEG-4RS19, and P. poae XIEG-4RS27 increased wheat root and shoot dry weight by up to 113% to 60% respectively. These findings revealed that M. officinalis harbors highly cooperative and functionally effective endophytes with strong potential as next-generation bioinoculants for sustainable crop production.},
}
@article {pmid42070697,
year = {2026},
author = {Margarita, E and Ianiro, G},
title = {Gut microbiome interactions can predict health and disease states.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.04.023},
pmid = {42070697},
issn = {1528-0012},
}
@article {pmid42070832,
year = {2026},
author = {Yang, S and Chu, Y and Liu, Z and Zhang, C and Yu, Y and Wang, J},
title = {Synergistic improvement of phytoremediation efficiency of arsenic-contaminated soil with Sedum lineare by phosphate-solubilizing strain P-1 and 2,4-epibrassinolide.},
journal = {Journal of environmental sciences (China)},
volume = {164},
number = {},
pages = {394-406},
doi = {10.1016/j.jes.2025.10.017},
pmid = {42070832},
issn = {1001-0742},
mesh = {*Soil Pollutants/metabolism/analysis ; Biodegradation, Environmental ; *Arsenic/metabolism/analysis ; *Brassinosteroids/metabolism ; *Sedum/metabolism/physiology ; *Steroids, Heterocyclic/metabolism ; Phosphates/metabolism ; Soil/chemistry ; Rhizosphere ; Soil Microbiology ; },
abstract = {Phytoremediation of arsenic (As)-contaminated soils is often hindered by As toxicity, low bioavailability, and the limited growth rate and biomass of remediator plants. To address this, we investigated the synergistic effects of 24-epibrassinolide (EBR) and the phosphate-solubilizing strain P-1 on enhancing As phytoremediation efficiency using Sedum lineare-a stress-tolerant species. Our results demonstrated that both individual and combined applications significantly improved S. lineare's physiological performance, alleviating As-induced growth inhibition. The EBR+P-1 co-treatment exhibited the strongest effects, increasing biomasses (shoot and root dry weight by 66. 7 % and 62.5 %, respectively) and total As accumulation (97.3 %) compared to the control. This treatment also enhanced antioxidant enzyme activities (superoxide dismutase and catalase), reduced oxidative stress markers (reactive oxygen species and malondialdehyde), and decreased bioavailable As in soil. Partial Least Squares Path Modeling identified antioxidant defense and nutrient uptake as key drivers of As tolerance. Crucially, EBR application uniquely restructured the rhizosphere microbiome, enriching stress-tolerant (Flavobacterium) and metal-mobilizing taxa (Patescibacteria), which correlated with improved soil enzyme activities (alkaline phosphatase, sucrase) and contributed significantly to plant resilience and As mobilization. These findings demonstrate that the combined use of EBR and strain P-1, leveraging novel microbiome engineering, offers a highly effective strategy for enhancing S. lineare-based As phytoremediation. It provides a practical approach for the sustainable remediation of moderately to heavily As-contaminated soils, especially in mining-affected or industrial wasteland areas.},
}
@article {pmid42070848,
year = {2026},
author = {Hu, X and Wu, Y and Tang, Y and Liu, W and Tan, H and Luo, G},
title = {Water biofloc microorganism enhance shrimp resistance to microplastics.},
journal = {Journal of environmental sciences (China)},
volume = {164},
number = {},
pages = {559-571},
doi = {10.1016/j.jes.2025.07.024},
pmid = {42070848},
issn = {1001-0742},
mesh = {Animals ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Penaeidae/physiology ; Aquaculture ; },
abstract = {Microorganisms play a crucial role in modifying the physical-chemical properties and ecotoxicological effects of microplastics (MPs) in aquatic ecosystems. However, existing studies have not been conducted in actual aquaculture environments, which are typically enriched with a variety of microorganisms. To address this, we have investigated the potential of water biofloc to mitigate MPs contamination in Litopenaeus vannamei aquaculture systems. Here, shrimps were subjected to varying concentrations of MPs in clean water and biofloc water. Results showed that clean water group displayed significantly lower survival rate (65.28 % ± 8.67 %) and diminished immune enzymes (i.e., lysozyme and polyphenol oxidase) activities compared to the water biofloc treatment (p < 0.05). Significant differences were observed in the activities of digestive enzymes, antioxidant enzymes and Na[+]/K[+]-ATPase in the clear water and biofloc water treatments (p < 0.05). Notably, biofloc treatments maintained consistent proximate composition and enzymatic activities (p < 0.05), while demonstrating remarkable microbial community stability between aqueous and intestinal habitats that proved resilient to MPs exposure. However, biofloc microorganisms significantly reduced shrimp astaxanthin content (49.24 %), leading to declines in pigmentation, water-holding capacity, and muscle adhesiveness. These findings offer a theoretical foundation for assessing MPs-related risks in aquaculture and advancing ecologically sustainable shrimp farming. In addition, our study provides practical insights for promoting cleaner and more sustainable aquaculture practices.},
}
@article {pmid42070864,
year = {2026},
author = {Wang, L and Wang, H and Xue, X and Gao, C and Yan, Y},
title = {High-lipid diets exacerbate copper-induced hepatointestinal toxicity in yellow catfish (Pelteobagrus fulvidraco) via gut microbiota dysbiosis.},
journal = {Journal of environmental sciences (China)},
volume = {164},
number = {},
pages = {729-740},
doi = {10.1016/j.jes.2025.07.020},
pmid = {42070864},
issn = {1001-0742},
mesh = {Animals ; *Catfishes ; *Gastrointestinal Microbiome/drug effects ; *Copper/toxicity ; *Dysbiosis/chemically induced/veterinary ; *Water Pollutants, Chemical/toxicity ; *Diet/veterinary ; Liver/drug effects ; Animal Feed/analysis ; Oxidative Stress ; },
abstract = {Copper (Cu)-contained chemicals and high-lipid diets are commonly applied in aquaculture, both of them are capable of negatively affecting fish health via complicated mechanisms, yet their microbiota-mediated interactions remain unclear. This study investigated their combined effects on yellow catfish (Pelteobagrus fulvidraco). A control (Con), high-lipid (HL), and HL + antibiotics (HLA, deplete intestinal microbiota) diets were fed fish for nine weeks, and half fish underwent acute Cu exposure (0.8 mg/L) during week nine (assigned as ConCu, HLCu, and HLACu, respectively). Results showed the HL feeding impaired growth but not Cu exposure. The HL and HLA groups showed exacerbated hepatic vacuolization, oxidative stress (reduced antioxidant enzymes, elevated malondialdehyde (MDA), and inflammation (upregulated tnfα, il1β, and nfκb expression). Cu exposure worsened these effects in all groups, further reducing intestinal villus length and tight junction genes (zo1 and occludin) expression while activating mitogen-activated protein kinase (MAPK)-related inflammation. Hepatic Cu accumulation followed HLACu > HLCu > ConCu (P < 0.05), linked to upregulated Cu transporters (ctr1 and ctr2) and metallothionein (mt2) expression. Microbiota analysis revealed high-lipid diet and Cu exposure caused microbiota dysbiosis, reducing Plesiomonas and Pseudomonas abundances, which amplified copper toxicity. This study demonstrates that high-lipid diets intensify Cu-induced hepatointestinal toxicity via oxidative and inflammatory pathways and microbiota dysbiosis, highlighting microbiome-driven Cu metabolism as a key mechanism in fish toxicity.},
}
@article {pmid42071136,
year = {2026},
author = {Gupta, AK},
title = {Malignant Fungating Wounds in Advanced Cancer: Pathophysiology, Odor Control, and Dignity-Centered Management.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42071136},
issn = {1534-6269},
mesh = {Humans ; *Odorants/prevention &amp; control ; *Neoplasms/complications/pathology/physiopathology ; *Wounds and Injuries/therapy/etiology/physiopathology ; Quality of Life ; Palliative Care ; Wound Healing ; },
abstract = {PURPOSE OF REVIEW: Malignant fungating wounds (MFWs) represent a profoundly distressing complication of advanced cancer, affecting an estimated 5-10% of patients with solid tumors and imposing a disproportionate burden on quality of life, caregiver wellbeing, and therapeutic engagement. Despite their clinical significance, MFWs remain a systematically neglected domain within oncology and palliative medicine. Existing literature addresses wound odor, wound myiasis, and dignity-related dimensions as isolated topics; a unified clinical framework integrating these three domains from both biological and ethical perspectives has been conspicuously absent. This review was designed to address that gap. The review introduces and applies a triple-framework approach to MFW management: (1) a Biological Dimension encompassing anaerobic microbial metabolism and volatile organic compound (VOC) generation; (2) a Clinical Dimension operationalizing evidence-based strategies for odor control and wound myiasis management; and (3) an Ethical Dimension centering dignity-conserving care as an indispensable component of oncologic wound management. This tripartite integration constitutes the primary conceptual contribution of this article.<br><br>RECENT FINDINGS: Wound microbiome profiling using 16S rRNA sequencing has identified anaerobic genera including Bacteroides, Prevotella, Peptostreptococcus, and Fusobacterium as principal contributors to the VOC profile responsible for MFW malodor, providing a mechanistic basis for targeted antimicrobial therapy. Biofilm-forming organisms, particularly Pseudomonas aeruginosa and Staphylococcus aureus, create recalcitrant wound environments that resist conventional topical therapies. Topical metronidazole remains the most robustly supported intervention for odor control, with emerging evidence for cadexomer iodine and Manuka honey as biofilm-disrupting adjuncts. Wound myiasis, increasingly reported in tropical and resource-limited settings, benefits from stepwise management combining mechanical debridement, larval asphyxiation techniques, and systemic ivermectin for severe cases. Electronic nose (e-nose) technology and volatile compound analysis represent emerging diagnostic tools for objective odor quantification. Palliative radiotherapy-using hypofractionated regimens such as 20 Gy in 5 fractions or single-fraction schedules in frail patients-offers biologically rational tumor cytoreduction with sustained improvement in odor and exudate. Community-based palliative care models, particularly those adapted for India and sub-Saharan Africa, demonstrate that dignified, evidence-informed MFW care is achievable within low-resource frameworks using trained community health workers and locally compounded or accessible wound care agents. Malignant fungating wounds demand a comprehensive, dignity-centered clinical response that is simultaneously evidence-based, culturally sensitive, and globally implementable. This review synthesizes the pathophysiology, evidence base, and ethical imperatives of MFW care into a unified clinical framework, providing oncologists and palliative care teams with practical algorithms for odor management and myiasis control, and reinforcing the imperative for equitable access to palliative wound care worldwide.},
}
@article {pmid42071142,
year = {2026},
author = {Praveen, A and Nair, T and Singha, B and Murmu, S and Padmanarayana, M and Upadhyay, A and Soni, Y and Soni, V},
title = {Metabolomics: Fundamentals, Methods, Analysis, Limits, and Recommendations.},
journal = {Advances in experimental medicine and biology},
volume = {1504},
number = {},
pages = {119-144},
pmid = {42071142},
issn = {0065-2598},
mesh = {*Metabolomics/methods/standards ; Humans ; Animals ; Mass Spectrometry/methods ; Magnetic Resonance Spectroscopy/methods ; *Metabolome ; Reproducibility of Results ; },
abstract = {Metabolomics has emerged as a powerful discipline for characterizing the small molecules that define cellular physiology, environmental responses, and disease states. As technologies advance, researchers face an expanding landscape of analytical platforms, data-processing strategies, and integrative approaches that require clear guidance for effective application. This chapter was written to provide a comprehensive and accessible resource for students, clinicians, and researchers entering or advancing in the field. We outline the fundamentals of metabolomics, describe major analytical methodologies-including MS, NMR, chromatography, and imaging-and summarize key considerations for experimental design, data preprocessing, statistical analysis, and functional interpretation. We also address current challenges related to metabolite identification, reproducibility, and multi-omic integration, and highlight emerging innovations such as stable-isotope tracing, spatial metabolomics, and AI-driven analytics. Together, these elements offer a detailed roadmap for conducting robust, reproducible, and insightful metabolomic studies.},
}
@article {pmid42071154,
year = {2026},
author = {Balestrini, R and Bevilacqua, I and Campa, M and Chitarra, W and Favaretto, F and Guaschino, M and Moffa, L and Narduzzo, A and Nerva, L and Niero, M and Paradiso, G and Rossetto, A and Spada, A and Villano, F and Zizzamia, E},
title = {A Journey into Plant-Microbe Interactions: From Lab to Field for a Sustainable Agriculture.},
journal = {Advances in experimental medicine and biology},
volume = {1504},
number = {},
pages = {373-386},
pmid = {42071154},
issn = {0065-2598},
mesh = {*Agriculture/methods ; *Plants/microbiology/virology ; *Crops, Agricultural/microbiology/growth &amp; development ; *Fungi ; Symbiosis ; Bacteria ; },
abstract = {The relationship between plants and microorganisms has ancient roots. However, only recently we have begun to appreciate the true complexity of the holobiont and its intricate interactions. Fungi, bacteria and viruses residing within or around plants play a crucial role in enhancing their resilience to biotic and abiotic stressful factors. The impact of these interactions is not limited to stress resilience but are strictly correlated with the plant's life cycle. The recognition of specific effects on plant growth and resilience has driven research towards utilizing microorganisms as sustainable solutions for agricultural challenges. The application of selected microorganisms, combined with the development of SynCom consortia, marks the beginning of a promising strategy for achieving sustainability in agriculture. This chapter explores the hidden world of plant-associated microorganisms, emphasizing their diverse beneficial impacts and providing evidence to support their potential applications in modern agriculture.},
}
@article {pmid42071828,
year = {2026},
author = {Liang, Q and Zeng, T},
title = {Disentangling causal relationships linking the oral microbiome, metabolism, inflammation, and dental caries via Mendelian randomization.},
journal = {Medicine},
volume = {105},
number = {17},
pages = {e48263},
doi = {10.1097/MD.0000000000048263},
pmid = {42071828},
issn = {1536-5964},
support = {20257524//Health Research Project of Hunan Provincial Health Commission/ ; kzd2501059//Changsha Municipal Science and Technology Bureau/ ; },
mesh = {Humans ; Mendelian Randomization Analysis ; *Dental Caries/microbiology/genetics/metabolism ; *Microbiota/genetics ; Genome-Wide Association Study ; *Inflammation/genetics/microbiology ; *Mouth/microbiology ; },
abstract = {Dental caries is a major global health burden. While observational studies suggest links between the oral microbiome, metabolism, inflammation, and caries, causal relationships remain unclear due to confounding and reverse causation. This study aimed to systematically dissect both the causal roles and the interplay between these factors in caries etiology. We employed a two-sample Mendelian randomization (MR) framework using large-scale genome-wide association study summary statistics. Univariable MR was used to assess the direct causal effects of oral microbial taxa, circulating metabolites, and inflammatory proteins on caries risk. Multivariable MR and 2-step MR were subsequently applied to perform mediation analysis and disentangle complex causal pathways. Effect sizes are reported as odds ratios (ORs) with 95% confidence intervals (CIs). Univariable MR identified protective causal effects of the genera Haemophilus (OR = 0.965, 95% CI: 0.937-0.994) and Rothia (OR = 0.965, 95% CI: 0.934-0.996) on caries risk. Genetically predicted higher levels of N4-acetylcytidine and pyrraline were associated with increased risk, whereas eicosapentaenoate showed a protective effect. The inflammatory proteins C-X-C motif chemokine 11 and signaling lymphocytic activation molecule family member 1 were causally associated with higher caries risk. Crucially, mediation analysis revealed that the protective effect of Haemophilus was partly mediated through its influence on circulating gamma-glutamylthreonine and X-11483 (an untargeted metabolomics feature ID). Our findings provide robust causal evidence for an integrated oral microbiome-metabolism-inflammation axis in caries etiology. These results highlight novel biomarkers for risk stratification and potential therapeutic targets, offering a scientific basis for developing more effective preventive strategies against this prevalent disease.},
}
@article {pmid42071909,
year = {2026},
author = {Corrigan, A and Stockdale, S and Mackenzie, AM and Wilkinson, RG and Warren, H and Taylor-Pickard, J and Murphy, R},
title = {Rumen Microbiome Development in Lambs Following Maternal and Early-Life Prebiotic Mannan-Rich Fraction (MRF) Supplementation.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/ani16081137},
pmid = {42071909},
issn = {2076-2615},
support = {NA//Alltech (Ireland)/ ; },
abstract = {The early-life rumen microbiome is highly dynamic, shaped by dietary transitions and maternal influences. Several dietary additives have been studied during the pre- and post-weaning periods to improve animal welfare, growth performance, and farming efficiencies. This study investigated microbial community assembly and growth performance of lambs provided with a mannan-rich fraction (MRF) supplement, either through maternal supplementation, directly, or via a combination of both. Using metagenomic sequencing and gas chromatography, we found differences in rumen microbial alpha and beta diversity related to both sampling time point and MRF supplementation (p < 0.05). At week 8, lamb microbiomes showed greater variance in their Shannon alpha diversity, with direct MRF supplementation only to the lamb resulting in a significantly greater diversity (p < 0.05). At week 20, combined maternal and lamb supplementation resulted in the highest Shannon diversity and was different compared to all other groups (p < 0.05). Beta diversity analyses combined with differential abundance analyses revealed that microbial community structures are driven by both diet and time, with maternal MRF supplementation associated with enrichment of taxa involved in carbohydrate fermentation and succinate metabolism, including Succiniclasticum ruminis, Succinovibrio dextrinosolvens, and Fibrobacter succinogenes. Generalized linear modeling identified significant associations between microbial alpha diversity metrics and total volatile fatty acids in lambs, particularly butyrate and valerate. Furthermore, at week 8, there was a significant positive correlation between alpha diversity metrics and propionate and valerate. In this study, lambs receiving MRF through maternal and direct supplementation had the highest growth performance, measured as the median average daily gains (kg) and final weights (kg) of lambs. These findings suggest that MRF supplementation, especially when provided both maternally and directly, may influence the lamb rumen microbiome and alter its metabolic potential with potential implications for optimizing early-life nutrition strategies in ruminant production systems.},
}
@article {pmid42072006,
year = {2026},
author = {Szőke, Z and Gashi, N and Dávid, P and Fauszt, P and Mikolás, M and Szilágyi-Tolnai, E and Szilágyi, E and Bíróné Molnár, P and Pesti-Asbóth, G and Homoki, JR and Kovács-Forgács, I and Gál, F and Stündl, L and Remenyik, J and Paholcsek, M},
title = {Comparative Analysis of Gut Microbiome Composition and Blood Lipid Profiles in Intensively Reared Broiler Chickens and Ducks.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/ani16081240},
pmid = {42072006},
issn = {2076-2615},
abstract = {This study investigated phase-dependent changes in gut microbiome composition, predicted functional potential, and lipid metabolism in intensively reared broiler chickens and ducks across the starter, grower, and finisher phases (from day-old to 42 days of age), over six production cycles (four chicken and two duck cycles), using 16S rRNA sequencing and blood lipids profiling. A total of 70 pooled manure samples were collected (46 from chickens and 24 from ducks), along with 34 blood samples (22 from chickens and 12 from ducks), all obtained under standard production conditions. Microbial diversity remained stable across growth phases within each species, whereas clear interspecies differences were observed (p < 0.01). Microbiome maturation involved a shift from early facultative and environmentally associated taxa during the starter phase (day-old to 14 days of age), including Acinetobacter (p < 0.01) and Enterococcus (p < 0.001), toward a more stable, host-adapted community. At the level of predicted functional pathways, shifts between growth phases were more pronounced in ducks. Predicted gene-level profiles showed phase-specific differentiation in chickens, with starter-associated genes linked to core carbon and nitrogen metabolism and finisher-associated genes related to structural and transport functions, whereas ducks exhibited a more balanced reorganization involving carbohydrate, energy, and nitrogen metabolism. Host lipid profiles between adjacent growth phases showed dynamic shifts in ducks (p < 0.05). These species-specific lipid patterns were mirrored by microbiome-lipid associations, as demonstrated by correlation analyses between dominant bacterial genera and blood lipid parameters, revealing more coordinated relationships in chickens and more heterogeneous patterns in ducks. Overall, these findings demonstrate species-specific organization of gut microbiome changes and their integration with blood lipid profiles under intensive production conditions.},
}
@article {pmid42072023,
year = {2026},
author = {Yildirim, EA and Finageev, E and Sokolova, K and Patiukova, N and Shubina, M and Belikova, A and Korochkina, E},
title = {Microbial Landscape of Bull (Bos taurus) Ejaculate: Assessment of Diversity and Link to Fertility.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/ani16081257},
pmid = {42072023},
issn = {2076-2615},
support = {25-76-10066//Russian Science Foundation/ ; },
abstract = {The composition of the sperm microbiome in bulls (Bos taurus) may influence reproductive function. This study aimed to examine the taxonomic composition of the sperm microbiome in bulls to establish its possible link with semen quality. The study investigated the composition of the sperm microbiome of 21 Holstein bulls with varying sperm quality, including subfertile animals. The quality of sperm was assessed using standard methods. Analysis of the microbial community of the semen was performed using targeted next-generation sequencing (NGS). The data indicated significant species richness of microorganisms in the semen of the studied bulls. At least 15 different bacterial phyla were identified in the semen samples. Significant differences in the microbiome composition were revealed in samples of different sperm quality groups. Higher relative abundance of Actinobacteriota (from 1.9 ± 0.12% to 14.1 ± 1.02%) was observed in bulls with excellent semen quality. Bacteroides fragilis was detected in 75% of samples of low-quality sperm. At the same time, the analysis revealed individual differences in the microbial composition of samples. Our results indicate a link between the microbiome composition and qualitative indicators of the sperm of bulls. This suggests that the identified taxonomic markers may serve as additional bioindicators for assessing fertility in males.},
}
@article {pmid42072313,
year = {2026},
author = {Alamri, A and Almutairi, AK and AlSinan, F and Alramadhan, A and Aldehalan, F and Almutairi, H and Alghuraybi, M and AlHarbi, NM and Alghannam, SF and Alotaibi, SS and AlOmary, M and AlKhater, S},
title = {Functional and Resistome Profiling of Paediatric Airway Microbiota in Asthma Using Shotgun Metagenomics.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040772},
pmid = {42072313},
issn = {2227-9059},
support = {IF-2020-016-CAMS//This work was funded by the Deputyship for Research &amp; Innovation, Ministry of Education in Saudi Arabia (IF-2020-016-CAMS) and approved by the deanship of scientific research (DSR) at Imam Abdulrahman bin Faisal University (IAU)./ ; },
abstract = {Background/Objectives: Asthma affects millions of patients worldwide and impacts their quality of life, particularly among children. Colonisation or an imbalance within natural resident microbiota may drive inflammatory responses in asthma; antibiotic resistance genes (ARGs) have also been investigated in asthma microbiome studies. However, research on the association between airway microbiota and ARGs remains limited. Therefore, we elucidated functional-level characterisation at the level of ARGs, virulence factors, and active pathways among a paediatric asthma cohort relative to a healthy control. Methods: Overall, 29 children with asthma and 20 control subjects were enrolled, and 3 swabs (2 nasal and 1 oropharyngeal) were obtained from each participant. Genomic DNA was extracted and sent for shotgun sequencing, after which bioinformatic analysis was conducted to remove human reads and analyse the microbiota pattern in the samples. The abundance of antibiotic resistance genes was evaluated along with the distribution of virulence genetic markers. Functional investigation of the most prevalent metabolic pathways was also performed. Results: Upper airway microbiome functional capacity varied by anatomical location, with oropharyngeal communities exhibiting greater metabolic breadth than nasal communities, suggesting the sample source to be the dominant factor shaping gene content, pathway profiles, and community structure. Asthma-related functional differences were modest, and no biological pathways remained significant following false discovery rate correction. Enrichment of antimicrobial resistance genes was observed, particularly those conferring resistance to β-lactams, macrolides, and tetracyclines. Conclusions: Different anatomical niches exhibit differential activities, and further exploration in this direction could aid in the development of diagnostic and therapeutic biomarkers for asthma.},
}
@article {pmid42072321,
year = {2026},
author = {Jordan, MD and Agarwal, L and Sodhi, CP},
title = {Beyond the Gut: Necrotizing Enterocolitis as a Gut-Brain Axis Disorder of Neurodevelopment.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040780},
pmid = {42072321},
issn = {2227-9059},
abstract = {Necrotizing enterocolitis (NEC) is a major cause of illness and death in preterm infants and is increasingly linked to long-term neurodevelopmental issues among survivors. Usually seen as a gastrointestinal disease, NEC is rarely viewed from a brain-centered perspective. In this Perspective, we suggest that NEC should be understood as a disorder of the gut-brain axis affecting neurodevelopment. We combine clinical and experimental evidence showing that intestinal inflammation, microbial imbalance, epithelial barrier failure, and systemic immune activation during NEC all contribute to the disruption of early brain development. We contend that neurodevelopmental damage is a key feature of NEC rather than just a secondary effect of prematurity. Recognizing NEC as a gut-brain axis disorder is crucial for research models, treatment approaches, and assessing long-term outcomes in affected infants.},
}
@article {pmid42072339,
year = {2026},
author = {Almajdi, A and Shehab, M},
title = {From Conventional Therapy to Precision Medicine in Inflammatory Bowel Disease: A State-of-the-Art Review.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040798},
pmid = {42072339},
issn = {2227-9059},
abstract = {Background/Objectives: Inflammatory bowel disease (IBD) management has evolved from conventional therapies to advanced biologics and targeted small molecules; however, clinical practice often relies on empirical treatment sequencing rather than individualized approaches. The heterogeneity of IBD phenotypes, variable treatment responses, and expanding therapeutic options necessitate a shift toward precision medicine. This review aims to synthesize current evidence on personalizing IBD therapy and provide an implementation framework for clinical practice. Methods: A narrative review was conducted encompassing peer-reviewed literature, recent network meta-analyses, and clinical guidelines. Evidence was gathered on treat-to-target strategies, therapeutic drug monitoring (TDM), clinical decision support systems, artificial intelligence applications, multi-omics platforms (genomics, transcriptomics, microbiome, metabolomics), advanced imaging modalities, and special populations including pediatric patients and pregnant women. Results: Treat-to-target strategies incorporating endoscopic and biochemical endpoints improve long-term outcomes when individualized to patient-disease factors. TDM-guided optimization enhances biologic efficacy and reduces immunogenicity. Emerging AI tools and multi-omics platforms show promise in predicting treatment response and patient stratification. Network meta-analyses provide comparative effectiveness estimates guiding advanced therapy selection in both Crohn's disease and ulcerative colitis. Implementation of precision medicine frameworks remains constrained by regulatory, economic, and technical barriers. Conclusions: Personalizing IBD therapy through integration of precision medicine tools, patient-specific factors, and comparative effectiveness data represents the future of IBD management. Overcoming implementation barriers through standardized frameworks and multidisciplinary collaboration is essential to translate these advances into routine clinical practice.},
}
@article {pmid42072347,
year = {2026},
author = {Dinkov, B and Pendicheva-Duhlenska, D},
title = {The Interplay Between GLP-1-Based Therapies, the Gut Microbiome, and MASLD/MASH in Type 2 Diabetes Mellitus: A Narrative Review.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040806},
pmid = {42072347},
issn = {2227-9059},
support = {Project &#x2116; BG-RRP-2.004-0003//Medical university-Pleven, Bulgaria, European Union-NextGenerationEU/ ; },
abstract = {GLP-1-based drugs are approved for the treatment of type 2 diabetes mellitus (T2DM) and obesity. Metabolic dysfunction-associated steatotic liver disease (MASLD) affects more than 60% of patients with T2DM, and the gut microbiome plays a critical role in its pathogenesis. The gut-liver axis represents a key mechanistic link between dysbiosis and hepatic steatosis. A narrative literature review was conducted using PubMed, Scopus, and ClinicalTrials.gov (2015-2026). Search terms included "GLP-1 receptor agonist," "microbiome," "MASLD," "MASH," "NAFLD," "NASH," "liraglutide," "semaglutide," "tirzepatide," "dulaglutide," and "exenatide." Of 363 identified articles, 330 were excluded due to duplication or non-relevant study design; 33 studies (18 preclinical, 15 clinical) were included. In preclinical models, liraglutide demonstrated normalization of the Firmicutes/Bacteroidetes ratio and increased Bifidobacterium and Lactobacillus spp., while tirzepatide significantly reduced hepatic steatosis and increased Akkermansia abundance in diabetic mice. Semaglutide improved gut barrier integrity, increased Alloprevotella and Alistipes, and ameliorated MASLD in murine models. In clinical studies, tirzepatide achieved MASH resolution in 44-62% of patients in the phase 2 SYNERGY-NASH trial. In August 2025, the FDA approved semaglutide for MASH with fibrosis based on the Phase 3 ESSENCE trial. A recent longitudinal study in T2DM patients showed that baseline microbiome composition predicted glycemic response to semaglutide, without significant changes in microbiome diversity. In conclusion, GLP-1-based therapies demonstrate consistent preclinical associations with gut microbiome modulation and reduction in hepatic steatosis. Baseline microbiome composition has been suggested as a potential predictor of treatment response, supporting a personalized approach to MASLD management and warranting future clinical studies.},
}
@article {pmid42072380,
year = {2026},
author = {Beresescu, FG and Ion, RM and Crisan, AS and Bors, A},
title = {Microbial Shifts After Sleeve Gastrectomy: The Gut-Oral Axis, Periodontal Outcomes, and Competing Oral Risks.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040838},
pmid = {42072380},
issn = {2227-9059},
support = {Research Grant Number 511/2/17.01.2022.//This work was supported by the George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, Romania, Research Grant Number 511/2/17.01.2022./ ; },
abstract = {Background: Severe obesity is associated with chronic low-grade inflammation, dysglycemia, and higher periodontitis risk. Sleeve gastrectomy (SG) is now a dominant bariatric procedure and reliably improves weight and metabolic status yet reported oral and periodontal trajectories after surgery remain heterogeneous. Objective: To synthesize SG-centered evidence on periodontal outcomes, oral and gut microbiome remodeling, and mechanistic pathways that may link postoperative physiology to the gut-oral axis. Methods: We conducted a structured narrative review guided by SANRA principles using targeted searches of PubMed/MEDLINE, Web of Science, Scopus, and Embase, complemented by citation chaining of key reviews and mechanistic anchor papers; evidence was organized into clinical, oral microbiome, gut microbiome, and mechanistic gut-oral axis streams and interpreted with a pragmatic evidence hierarchy. Results: Small prospective SG cohorts suggest bleeding on probing (BOP), gingival indices, and sometimes probing depth (PD) may improve in some patients, particularly alongside weight loss, improved glycemic control, and lower systemic inflammatory burden, whereas clinical attachment level (CAL) and longer-term structural trajectories remain mixed; mixed-procedure syntheses also report early deterioration in some settings. Oral microbiome findings after bariatric surgery are site- and time-dependent, and salivary signals do not necessarily mirror subgingival plaque, whereas gut microbiome remodeling and bile acid signaling changes are more consistently reported and provide plausible but indirect mediator candidates. At the same time, reflux, vomiting, salivary changes, diet patterning, medications, and periodontal care can modify or counteract potential periodontal benefits and may increase competing risks such as caries or erosive tooth wear. Conclusions: The SG-gut-oral axis-periodontal pathway is a biologically plausible working hypothesis rather than a proven causal pathway in humans. The present evidence for any periodontal benefit relies mainly on small observational cohorts and is most credibly demonstrated for inflammatory, not structural, endpoints.},
}
@article {pmid42072400,
year = {2026},
author = {Lin, Y and Lu, P and Ding, Q and Liu, M},
title = {Current Perspectives on the Inflammatory Bowel Disease Pathogenesis of Microbiota and the Gut-Brain Axis, and Emerging Therapeutics.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040859},
pmid = {42072400},
issn = {2227-9059},
abstract = {The pathogenesis of inflammatory bowel disease (IBD) is driven by an interplay among intestinal dysbiosis and aberrant mucosal immune responses. This review centers on the microbiota as a pivotal pathogenic hub, systematically dissecting how three hallmark features of dysbiosis-reduced microbial alpha diversity, depletion of immunomodulatory commensals, and expansion of pro-inflammatory pathobionts-collectively compromise epithelial barrier function, promote bacterial translocation, and sustain chronic mucosal inflammation. We further integrate emerging evidence implicating bidirectional gut-brain axis communication in amplifying both peripheral inflammation and central nervous system (CNS)-mediated behavioral comorbidities. Building on this mechanistic framework, we critically evaluate next-generation microbiota-targeted interventions: standardized fecal microbiota transplantation (FMT), rationally designed live biotherapeutic products (LBPs), precision phage cocktails targeting defined pathobionts, and microbiome-informed dietary strategies. Collectively, these approaches represent a paradigm shift-from broad-spectrum immunosuppression toward mechanism-guided, ecosystem-level modulation-thereby advancing the goal of precision medicine in IBD.},
}
@article {pmid42072403,
year = {2026},
author = {Shajahan, SR and Hamid, N and Okunsai, B and Shari, N and Ramli, MDC},
title = {Microbiota-Gut-Brain Axis in Alzheimer's Disease: Linking Oxidative Stress, Mitochondrial Dysfunction and Amyloid Pathology-A Systematic Review.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040860},
pmid = {42072403},
issn = {2227-9059},
abstract = {Background: Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder characterized by amyloid-β aggregation, tau hyperphosphorylation, oxidative stress, and mitochondrial dysfunction. Emerging evidence indicates that the gut microbiota plays a critical role in modulating neuroinflammatory, and metabolic pathways involved in AD pathogenesis through the microbiota-gut-brain axis. Objective: This systematic review aims to comprehensively evaluate the role of the microbiota-gut-brain axis in Alzheimer's disease, with a particular focus on its mechanistic links to oxidative stress, mitochondrial dysfunction, and amyloid pathology, as well as its therapeutic potential. Methodology: A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science databases, focusing on studies evaluating gut microbiota composition, metabolomic changes, oxidative stress markers, mitochondrial activity, and therapeutic interventions in AD models and patients. Results: Altered gut microbial composition in AD is associated with increased pro-inflammatory taxa (Escherichia-Shigella, Bacteroides) and depletion of short-chain fatty acid (SCFA) producing bacteria (Faecalibacterium, Roseburia). Dysbiosis contributes to systemic inflammation, disrupted intestinal permeability, and microglial activation, leading to oxidative damage and mitochondrial impairment in neurons. Preclinical and clinical studies indicate that probiotics, prebiotics, and fecal microbiota transplantation can restore redox balance, reduce neuroinflammation, and improve cognitive outcomes. Multi-omics and AI-based models are emerging as tools for identifying microbiome-derived biomarkers for early AD detection. Conclusion: The gut microbiota-mitochondria-oxidative stress axis represents a promising therapeutic target in Alzheimer's disease. Future research should focus on longitudinal human studies, standardized microbial profiling, and personalized microbiome-based interventions to translate these mechanistic insights into clinical benefit.},
}
@article {pmid42072412,
year = {2026},
author = {Vidal, A and Kilian, AY and Vinayahalingam, V and Zagrapan, B and Pape, J and Karrer, T and von Wolff, M},
title = {The Role of Endometrial Microbiota in the Pathogenesis of Chronic Endometritis: A Systematic Review and Meta-Analysis.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040871},
pmid = {42072412},
issn = {2227-9059},
support = {//Institute Biochimique SA, Lugano, Switzerland/ ; },
abstract = {Background: Chronic endometritis (CE) is a subtle, often asymptomatic endometrial inflammation marked by CD138[+] plasma cell infiltration and linked to recurrent implantation failure (RIF), recurrent pregnancy loss (RPL), and unexplained infertility. Emerging evidence implicates endometrial microbiome dysbiosis in CE. Objective: To systematically review and conduct meta-analysis on the association between CE and endometrial microbiome alterations and their reproductive implications. Methods: We searched MEDLINE, Embase, Web of Science, Scopus, Cochrane CENTRAL, and Google Scholar for studies diagnosing CE via CD138 immunostaining, assessing microbiota with molecular techniques. Data extraction, quality assessment, and meta-analysis were performed. Results: Twenty-two studies including 4022 women were analyzed. CE was associated with reduced prevalence of Lactobacillus-dominated microbiota and increased detection of non-Lactobacillus species, particularly Streptococcus spp., Enterococcus spp., Escherichia coli, Staphylococcus spp., Ureaplasma spp., and Gardnerella vaginalis. In the meta-analysis (2947 women), Enterococcus spp. and Ureaplasma spp. were significantly more prevalent in women with CE, whereas Streptococcus spp., E. coli, Staphylococcus spp. and G. vaginalis showed non-significant trends. Only E. coli and Streptococcus spp. showed significant heterogeneity between-studies. Conclusions: CE is linked to microbial dysbiosis with reduced Lactobacillus dominance and enrichment of potentially pathogenic taxa, notably Enterococcus and Ureaplasma spp. These findings suggest that the endometrial microbiome contributes to chronic inflammation and adverse reproductive outcomes, yet heterogeneity and limited evidence call for standardized diagnostics and robust trials before clinical implementation.},
}
@article {pmid42072451,
year = {2026},
author = {Triantafillidis, JK},
title = {The Paradoxical Role of Pyroptosis in Gastrointestinal Cancers: From Molecular Mechanisms to Therapeutic Horizons.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040911},
pmid = {42072451},
issn = {2227-9059},
abstract = {Pyroptosis, a gasdermin-mediated and highly immunogenic form of regulated cell death, has surfaced as a critical determinant in the progression and therapeutic landscape of gastrointestinal (GI) cancers. Unlike non-inflammatory apoptotic pathways, pyroptosis involves the assembly of inflammasome complexes and the subsequent activation of caspases, leading to the cleavage of gasdermin proteins and the formation of transmembrane pores. It contributes to tumor suppression via immunogenic cell death and activation of antitumor immunity but may also promote tumor progression through chronic inflammation and remodeling of the tumor microenvironment. In this comprehensive review, we delineated the molecular architecture of pyroptotic signaling within the GI tract, highlighting the "double-edged sword" nature of this process. We further evaluated its role in the pathogenesis of GI cancers and in emerging translational strategies, including the pharmacological modulation of gasdermins and microbiome-based interventions, aiming to integrate pyroptosis induction into current immunotherapeutic frameworks.},
}
@article {pmid42072464,
year = {2026},
author = {Mejía-Muñoz, A and Cedillo Monter, J and Saldívar-Cerón, HI and Escobedo, G and Leon-Cabrera, S},
title = {Sucralose and the Gut-Immune Axis: Emerging Evidence Linking Dysbiosis, Barrier Alterations, and Implications for Colitis and Colorectal Cancer Immunotherapy.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040917},
pmid = {42072464},
issn = {2227-9059},
support = {CIKAS-FICDTEM-25-014//Consejo Mexiquense de Ciencia y Tecnolog&#xed;a/ ; PAPIIT IN201724//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT IA201725//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; },
abstract = {Sucralose is one of the most widely used non-nutritive sweeteners and has long been considered metabolically inert and safe within established acceptable daily intake levels. However, emerging evidence suggests that chronic exposure to sucralose may alter gut microbial composition, epithelial barrier function, mucosal inflammation, and immune responses. This review examines current experimental and clinical evidence on the effects of sucralose on the gut-immune axis, with particular attention to its potential implications for colitis and colorectal cancer (CRC). Preclinical studies indicate that sucralose may reduce beneficial short-chain fatty acid-producing taxa, alter microbial metabolic pathways, disrupt epithelial barrier-related molecules, and promote inflammatory and immune changes associated with colitis severity and inflammation-driven tumorigenesis. Experimental evidence also suggests that sucralose may impair CD8[+] T-cell fitness and reduce responsiveness to immune checkpoint inhibitors through microbiome-dependent mechanisms involving altered arginine and citrulline metabolism. Human studies further indicate that sucralose can modify gut and oral microbiome composition and influence metabolic responses, although these effects appear heterogeneous and context-dependent. Overall, the current literature suggests that sucralose may act as a modifier of microbiome-immune interactions in susceptible settings, but most mechanistic evidence remains preclinical, and human data are still insufficient to establish causality. These findings highlight the need for prospective studies to determine whether sucralose-associated microbial and immune alterations translate into clinically meaningful effects in colitis, CRC, and immunotherapy response.},
}
@article {pmid42073016,
year = {2026},
author = {Quansah, M and David, MA and Martins, R and El-Omar, E and Aliberti, SM and Capunzo, M and Jensen, SO and Tayebi, M},
title = {Correction: Quansah et al. The Beneficial Effects of Lactobacillus Strains on Gut Microbiome in Alzheimer's Disease: A Systematic Review. Healthcare 2025, 13, 74.},
journal = {Healthcare (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/healthcare14080974},
pmid = {42073016},
issn = {2227-9032},
abstract = {In the original publication [...].},
}
@article {pmid42073058,
year = {2026},
author = {Benninga, MA and Schäfer, KH and Piloquet, H and Stanton, C},
title = {The Gut in Early Life-Postnatal Challenges.},
journal = {Children (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/children13040480},
pmid = {42073058},
issn = {2227-9067},
abstract = {The neonatal development period from the time of birth can be considered the period of greatest physiological changes throughout the human lifespan. These changes are partly due to dietary or environmental factors and are also modulated by genetic, neuronal, and humoral influences. The focus of research is increasingly on the microbial colonization of the neonatal intestine, since the establishment of a healthy, symbiotic newborn microbiota not only corresponds closely with nutrient metabolism, immune functions, and growth, but also with the brain as part of the so-called "gut-brain axis". At the same time, a critical time window of opportunity opens up for the early infant microbiota, which is accessible to modulating approaches in favor of normal infant development. Although the definition of "normal" microbiota in infants still remains challenging, the microbiota of infants delivered at term can be discussed as the gold standard-provided they were exclusively breastfed and have not been exposed to antibiotics. Advances in sequencing technologies now also allow us to identify and characterize the microbiota at the strain level and to provide the scientific rationale for new approaches to modulate the early-life microbiome in a more targeted and personalized way-applicable also for formula-fed children who cannot be supplied with human milk. This review addresses the challenges associated with the "healthy" development of a newborn during the first weeks and months of life and discusses potentially modifiable external factors in light of the requirements for the establishment of a functional gut microbiota, gastrointestinal system, and gut-brain axis.},
}
@article {pmid42073216,
year = {2026},
author = {Guo, Y and Shi, RQ and Dechakhamphu, A and Zhao, M and Zheng, JS and Siriamornpun, S},
title = {Effects of Cricket Powder Supplementation on Gut Microbiota in High-Fat Diet-Fed Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/foods15081328},
pmid = {42073216},
issn = {2304-8158},
support = {//Mahasarakham University/ ; },
abstract = {The gut microbiota plays an important role in host physiology and is highly influenced by dietary factors. This study aimed to investigate the effects of cricket powder (CP) supplementation on gut microbiota composition in high-fat diet-fed C57BL/6J mice. Male C57BL/6J mice were fed a normal diet or a high-fat diet. Mice fed the high-fat diet were administered low, medium, or high doses of CP by gavage. Serum lipid levels and liver-related biochemical indicators were measured, and gut microbiota composition was analyzed using 16S rRNA gene sequencing. We found that CP supplementation significantly (p < 0.05) altered gut microbiota diversity and community structure, with differences observed among CP doses. Alpha diversity indices were significantly reduced after the intervention (p < 0.05). Beta diversity analysis showed no significant separation among groups before the intervention, whereas a clear separation in gut microbiota structure was observed after the intervention. Correlation analysis further revealed that beneficial bacterial genera, including Lactobacillus, Bifidobacterium, and Akkermansia, were negatively associated with lipid-related parameters. Overall, these findings suggest that CP supplementation can modulate gut microbiota composition under high-fat dietary conditions, indicating its potential role in metabolic regulation.},
}
@article {pmid42073222,
year = {2026},
author = {Li, M and Wang, X and Ma, L and Huang, K and Tong, T},
title = {Comparative Microbiota and Metabolite Profiles of Undried and Dried Typica Luwak (Civet) Coffee Beans.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/foods15081334},
pmid = {42073222},
issn = {2304-8158},
support = {7222249//Beijing Natural Science Foundation/ ; 2025bskj09//2025 Baoshan Municipal Science and Technology Program/ ; },
abstract = {Kopi Luwak (civet coffee), produced from coffee beans recovered from the feces of the Asian palm civet, is among the most expensive specialty coffees worldwide for its unique sensory characteristics. In this study, a multi-omics strategy was employed to elucidate the impact of drying on the microbial community structure and metabolic profiles of Typica Kopi Luwak beans. Drying induced pronounced shifts in the microbial composition, with a significant enrichment of Sphingobacterium and depletion of Streptococcus at the genus level. Concurrently, drying resulted in substantial metabolic remodeling, characterized by increased levels of prenol lipids, fatty acyls, carboxylic acids and derivatives, steroids and steroid derivatives, and organooxygen compounds, accompanied by a marked reduction in flavonoids. KEGG pathway analysis indicated that both altered microbial taxa and metabolites were associated with lipid metabolism, carbohydrate metabolism, amino acid metabolism, and the biosynthesis of other secondary metabolites. Correlation network analysis further revealed the associations between key microbial genera and specific classes of differential metabolites. Collectively, these findings suggest the potential role of post-excretion sun-drying in shaping the microbiome and metabolome of Typica Kopi Luwak beans, offering a scientific basis for controlled or in vitro fermentation strategies to produce coffees with reproducible quality attributes.},
}
@article {pmid42073322,
year = {2026},
author = {Li, J and Yan, Q and Du, B and Feng, G},
title = {An Integrated Review of Pesticides and Antibiotics in Agricultural Environments: Occurrence, Cross-Media Transport, and Plant Uptake.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/foods15081436},
pmid = {42073322},
issn = {2304-8158},
support = {LZ26D010004//Key Project of Natural Science Foundation of Zhejiang Province/ ; },
abstract = {With the continuing intensification of modern agriculture, pesticides and antibiotics are extensively used to control pests and diseases, but their improper use and indirect inputs have resulted in widespread contamination of agricultural environments and food products. This review synthesizes how these contaminants enter agroecosystems, their occurrence across soils, waters and agricultural products, and the processes that redistribute residues across air-water-soil interfaces and into the soil-plant continuum. We summarize cross-media transport pathways (e.g., runoff/leaching, volatilization-deposition and irrigation-driven redistribution) and relate environmental exposure to plant uptake using a harmonized indicator set, including the bioconcentration factor (BCF), translocation factor (TF), octanol-water partition coefficient (log Kow) and soil organic carbon-water partition coefficient (Koc). We further discuss key determinants of crop accumulation, including compound-specific properties, soil characteristics and plant physiological traits, and highlight how these factors jointly shape residue profiles in edible tissues. Finally, we outline research priorities for source reduction, standardized multi-matrix surveillance, fate-to-uptake modeling, and microbiome-enabled remediation strategies to support pollution control, food safety and public health.},
}
@article {pmid42073328,
year = {2026},
author = {Indio, V and Mekonnen, YT and Oliveri, C and Rubboli, S and Candela, M and Seguino, A and Serraino, A and De Cesare, A},
title = {Reducing Antimicrobial Resistance in Poultry Carcasses Extends Beyond Farm-Level Interventions.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/foods15081440},
pmid = {42073328},
issn = {2304-8158},
support = {Horizon 2020 "Controlling Microbiomes Circulations for Better Food Systems" (CIRCLES) no. 818290.//European Union/ ; },
abstract = {The aim of this study was to assess how raising chickens without the use of antimicrobials affects the microbiome of poultry carcasses. A total of 151 caeca and neck skin samples from chickens raised without antimicrobials were collected in the same slaughterhouse and submitted to shotgun metagenomic sequencing. Caeca were dominated by Bacillota and Bacteroidota, while carcasses by Pseudomonadota. The caeca microbiome was enriched in genes related to a proliferating and metabolically active microbial community. Carcass-associated microbiomes were enriched in functional genes linked to adaptation to nutritionally limited and oxidative environments. A significantly higher cumulative antimicrobial resistance gene abundance was detected in carcasses compared to caeca. Specifically, carcasses exhibited approximately 1.5 times more AMR genes, reflecting an increase of nearly 49%. While caeca showed enrichment of resistance determinants associated with Gram-positive anaerobic gut commensals, carcasses were characterized by a predominance of multidrug efflux systems and clinically relevant β-lactam resistance genes, commonly associated with environmental and opportunistic Gram-negative bacteria. In carcasses, carbapenem-associated genes, such as OXA-58-like and CphA, were detected. However, these genes have not been associated with carbapenemase-producing Enterobacterales. Overall, the findings of this study indicate that reducing antimicrobial resistance in food animal production systems extends beyond farm-level intervention. At present, the benefits of the interventions aimed at reducing antimicrobial resistance at farm level seem to be compromised during the post-harvest stages.},
}
@article {pmid42073376,
year = {2026},
author = {Aleynova, OA and Ananev, AA and Nityagovsky, NN and Kiselev, KV},
title = {The Influence of Wild Grapevine Endophytes on the Growth of the Model Plant Arabidopsis thaliana (L.) Heynh.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040566},
pmid = {42073376},
issn = {2075-1729},
support = {22-74-10001-&#x41f;//Russian Science Foundation/ ; },
abstract = {We have evaluated the growth characteristics of the model plant Arabidopsis thaliana after inoculation of A. thaliana seeds with the most common endophytes of wild grapevine Vitis amurensis Rupr., namely bacteria Rhizobium (syn. Agrobacterium) sp., Bacillus velezensis, Curtobacterium sp, Erwinia sp., Gordonia aichiensis, Pantoea sp., Pseudomonas sp., Sphingomonas sp., Xanthomonas sp., and the fungi Biscogniauxia sp., Cladosporium sp., Didymella sp., Exobasidium sp., Penicillium sp., Pestalotiopsis sp, and Xylaria sp. A positive effect on plant growth was observed in A. thaliana following seed inoculation with endophytic fungi (Xylaria sp., Didymella sp., and Exobasidium sp.) and bacteria (Gordonia aichiensis and Sphingomonas sp.). The inoculation with the fungi Xylaria sp., Didymella sp., Exobasidium sp., and Penicillium sp. significantly increased seed production in A. thaliana by 2.5-5-fold. The analysis of the phytohormone-regulating gene transcription in A. thaliana plants following inoculation with the grapevine endophytic microorganisms suggests that plant growth was enhanced through transcriptional changes in individual genes of hormone biosynthetic pathways. Consequently, endophytic bacteria and fungi from V. amurensis may serve as potential natural growth stimulators for agricultural plants.},
}
@article {pmid42073418,
year = {2026},
author = {Mahimkar, S and Thompson, JM and Blackwood, CB and Watts, SW and Restini, CB},
title = {Presence and Variability of the Microbiome in Perivascular Adipose Tissue: A Whole-Genome Sequencing Study in Dahl SS Rats.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040609},
pmid = {42073418},
issn = {2075-1729},
support = {NHLBI P01HL152951//NHI/ ; (#2025_PAT-FIRE_001//Foundry for Innovative Research and Education Program (FIRE)/ ; },
abstract = {Background: Perivascular adipose tissue (PVAT) contains adipocytes and a stromal-vascular fraction with immune cells that modulate the adjacent vasculature. The presence of immune cells in PVAT of vascular beds is poorly understood-are they resident or recruited? We propose a novel resident microbiome present in PVAT, given the immune-rich stromal environment. Hypothesis: We hypothesized the existence of distinct bacterial and viral communities in healthy PVAT compared to non-PVAT adipose tissues. Methods: PVAT samples from thoracic and abdominal aorta, mesenteric resistance arteries, non-PVAT tissues (subscapular brown adipose tissue, retroperitoneal white adipose tissue), and fecal samples were collected one year apart from male Dahl SS rats, split into two cohorts (2023 and 2024, n = 3 each). Whole-genome shotgun sequencing (CosmosID) and 16S rRNA gene analysis assessed microbial relative abundance. Results: PVAT harbored bacterial and viral sequences, and species composition varied significantly between cohorts. Bacterial and viral fecal samples showed lower variability. Conclusions: PVAT microbiome differed dramatically from the fecal microbiome, with temporal influences on bacterial and viral diversity, marking the first such report. Despite inherent limitations, these findings establish the potential of PVAT microbiota in vascular biology and immune modulation, paving the development of microbiome-targeted drugs to address vascular dysfunctions.},
}
@article {pmid42073437,
year = {2026},
author = {Wasiak, J and Oszajca, KA and Szemraj, J and Witusik-Perkowska, M},
title = {Postbiotics as Emerging Strategy Targeting Obesity- and Aging-Related Breast Cancer-Prospects in Prophylaxis and Therapy.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040628},
pmid = {42073437},
issn = {2075-1729},
abstract = {Aging and obesity accompanied with hormonal disequilibrium represent critical, inter-related risk factors for breast cancer, significantly influencing disease incidence, progression, and therapeutic outcomes. This review aims to elucidate the multifaceted biological mechanisms linking obesity and aging to breast carcinogenesis, with a particular focus on the emerging therapeutic and preventive potential of postbiotics as molecules targeting cellular events important for cancer growth and responsiveness. Despite continuous advancement, breast cancer therapy still poses several challenges, such as treatment-induced acquired resistance, which is boosted by the inflammatory phenotype of senescent cancerous cells, as well as undesired side effects resulting from the destruction of normal cells. Such a complex background of breast carcinogenesis and oncotherapy resistance opens avenues to search for new preventive approaches and adjunctive treatment regimens. Postbiotics demonstrate a variety of benefits due to their selective antineoplastic activity, as well as the cytoprotective potential associated with antioxidant, anti-inflammatory and anti-senescent properties. Pleiotropic effects of postbiotics make them a promising tool for counteracting cellular and physiological disturbances that favor breast cancer development, including age- and obesity-related factors. They are prospective adjunctive agents in oncotherapy, albeit their efficacy and safety need to be thoroughly evaluated in clinical studies prior to implementation in routine treatment modes.},
}
@article {pmid42073447,
year = {2026},
author = {Sufaru, IG and Burlea, SL and Martu, MA and Solomon, SM and Laza, MG and Pasarin, L and Luca, EO and Martu, I},
title = {Periodontitis Severity and Subgingival Microbiome Variation in Postmenopausal Women: A Stratified Case-Control Study.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040637},
pmid = {42073447},
issn = {2075-1729},
abstract = {BACKGROUND: This study aimed to determine whether osteoporosis is associated with differences in the subgingival microbiome of postmenopausal women, stratified by periodontitis stage.<br><br>METHODS: In this observational, stratified case-control study, 166 postmenopausal women were assigned to six strata defined by bone status (osteoporosis vs. normal BMD) and periodontal category (no periodontitis, Stage I-II, Stage III-IV). Standardized pooled subgingival samples were profiled by 16S rRNA gene sequencing. Community structure was evaluated using Bray-Curtis dissimilarity and tested with PERMANOVA (9999 permutations) and prespecified contrasts comparing osteoporosis versus normal BMD within each periodontal category (Holm adjustment). Alpha diversity (Shannon) was assessed using two-way ANOVA.<br><br>RESULTS: Periodontal category was strongly associated with community structure (PERMANOVA R[2] = 0.514, pseudo-F = 86.681, p < 0.0001), whereas bone status (R[2] = 0.004, p = 0.178) and the bone status &#xd7; periodontal category interaction (R[2] = 0.007, p = 0.294) were not. None of the three prespecified within-category contrasts reached significance after Holm adjustment. Shannon diversity differed by periodontal category (p = 1.93 &#xd7; 10[-24]) but not by bone status (p = 0.200), with similar distributions between osteoporosis and normal BMD within each periodontal category.<br><br>CONCLUSIONS: In postmenopausal women, periodontitis severity dominates variation in the subgingival microbiome, and osteoporosis does not confer an additional community-level or taxonomic signature when periodontal status is held constant. Longitudinal and multi-omic studies incorporating host-response biomarkers and therapy exposures are warranted to clarify whether osteoporosis influences periodontal susceptibility and progression primarily through host-mediated mechanisms.},
}
@article {pmid42073451,
year = {2026},
author = {Cerreto, M and Maestri, M and Pallozzi, M and Cerrito, L and Stella, L and Ianiro, G and Gasbarrini, A and Ponziani, FR},
title = {Gut Microbiota Biomarkers in Patients with Hepatocellular Carcinoma in the Era of Immune Checkpoint Inhibitors.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040641},
pmid = {42073451},
issn = {2075-1729},
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the therapeutic landscape for hepatocellular carcinoma (HCC); however, a considerable proportion of patients do not achieve durable clinical benefits. This highlights the need for reliable predictive biomarkers, which are currently lacking. The accumulated evidence supports a relevant role of the gut-liver axis in modulating immunotherapy outcomes, and several studies have identified distinct microbial features associated with either responders or non-responders. Responders to immunotherapy frequently present with higher microbial diversity and enrichment of beneficial taxa, whereas the expansion of pro-inflammatory and pathogenic bacteria has been associated with primary resistance and increased treatment-related toxicity in non-responders. However, the available findings remain heterogeneous across cohorts, likely owing to differences in geography, diet, liver disease etiology, treatment regimens, and microbiome analytical methods. Machine-learning models integrating metagenomic and metabolomic data have shown encouraging results in defining microbial signatures associated with treatment outcomes, although variability among cohorts currently limits their clinical applicability and generalizability. Beyond microbial taxonomic composition, microbiota-derived metabolites-such as short-chain fatty acids, bile acids, inosine, and tryptophan catabolites-appear to play a crucial role in shaping the tumor microenvironment and host immune responses, thus representing additional candidate biomarkers, also due to the relative ease of their measurement. Finally, microbiota-targeted interventions are emerging as potential strategies to enhance immunotherapy efficacy. Overall, the gut microbiome and its metabolic activity represent promising tools, albeit still under investigation, for patient stratification and personalized management in HCC treated with ICIs. Therefore, this review aims to summarize and critically discuss the current evidence on gut microbiota-derived biomarkers of response and resistance to ICIs in HCC, with particular focus on microbial composition, microbiota-related metabolites, and emerging microbiome-based therapeutic strategies. This narrative review provides an updated overview of the role of gut microbiota as both a biomarker and a therapeutic target in patients with hepatocellular carcinoma (HCC) receiving immune checkpoint inhibitor (ICI) therapy.},
}
@article {pmid42073454,
year = {2026},
author = {Abdolmohammadi, P and Aali, M and Lehmann, C},
title = {Cytokine Toxicity and Bacterial Dysbiosis in Chemotherapy- and/or Radiotherapy-Induced Oral Mucositis: Pathophysiological Mechanisms and Therapeutic Interventions.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040644},
pmid = {42073454},
issn = {2075-1729},
abstract = {Chemotherapy- and/or radiotherapy-induced oral mucositis (CRIOM) is a common complication in patients with head and neck cancer, driven largely by excessive proinflammatory cytokine signalling and treatment-associated bacterial dysbiosis. This narrative review synthesizes current mechanistic evidence and summarizes emerging therapeutic strategies targeting these pathways. Research indicates that elevated levels of IL-1β, IL-6, TNF, iNOS, and nitric oxide amplify tissue injury and ulceration, while disruption of oral and gut microbial communities, characterized by loss of beneficial commensals and enrichment of pathogenic taxa, further exacerbates mucosal inflammation. Anti-inflammatory agents, including pentoxifylline, atorvastatin, trans-caryophyllene, azilsartan, recombinant human IL-11, and low-level laser therapy have been shown in preclinical models to reduce cytokine levels and promote mucosal healing. Similarly, microbiome-targeted approaches, such as oral microbiota transplantation and multi-strain probiotic formulations, have demonstrated potential in restoring microbial balance and attenuating CRIOM severity, with current evidence including both preclinical and clinical studies. Overall, current findings highlight cytokine toxicity and dysbiosis as synergistic drivers of CRIOM and support anti-inflammatory and microbiome-modulating strategies as promising adjunctive approaches; however, further well-designed clinical studies are required to validate their efficacy and guide clinical translation.},
}
@article {pmid42073476,
year = {2026},
author = {Ichim, C and Boicean, A and Mihaila, R and Todor, SB and Anderco, P and Birlutiu, V},
title = {Effect of Fecal Microbiota Transplantation on Arterial Stiffness in Alcohol-Related Liver Cirrhosis: A Prospective Pilot Study.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040668},
pmid = {42073476},
issn = {2075-1729},
abstract = {BACKGROUND: Alcohol-related liver disease is frequently associated with systemic vascular dysfunction and increased arterial stiffness. This may contribute to adverse clinical outcomes. Modulation of the gut microbiota through fecal microbiota transplantation (FMT) has emerged as a potential therapeutic strategy in liver cirrhosis, but its influence on vascular stiffness in humans remains insufficiently characterized.<br><br>METHODS: This prospective study evaluated arterial stiffness in patients with alcohol-related liver cirrhosis undergoing FMT. A control group received standard care. Vascular stiffness was assessed non-invasively using an oscillometric arteriograph based on pulse wave analysis. Measurements were performed at baseline and at one and three months after FMT under standardized conditions. The main indices assessed included aortic pulse wave velocity, augmentation index, ejection duration and return time. Direct microbiome sequencing and metabolomic profiling were not performed.<br><br>RESULTS: At baseline, the study and control groups had comparable vascular stiffness profiles. Only minor differences in selected hemodynamic parameters were observed. At one month after intervention, no statistically significant differences in arterial stiffness indices were observed between groups. Longitudinal analysis within the FMT group also showed no significant changes in direct markers of arterial stiffness across the three-month follow-up period. A non-significant tendency toward reduced ejection duration was noted.<br><br>CONCLUSIONS: In patients with advanced alcohol-related liver cirrhosis, FMT did not produce measurable short-term improvements in arterial stiffness. These findings suggest that short-term vascular effects of microbiota modulation may be difficult to detect in patients with advanced alcohol-related liver cirrhosis. Larger studies including earlier-stage patients, longer follow-up and direct microbiome and metabolomic assessment are needed to clarify potential vascular effects of FMT.},
}
@article {pmid42073497,
year = {2026},
author = {Carraturo, F and Salamone, M and Annunziata, M and Di Brizzi, EV and Giorgio, CM and Petrillo, A and Fedi, L and Maione, A and Guida, M and Galdiero, E},
title = {Preliminary Characterization of Skin Microbiota and Mycobiota in Atopic Dermatitis by Metagenomic and Culture-Based Analyses.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040690},
pmid = {42073497},
issn = {2075-1729},
support = {PRIN2022//European Union-Next Generation EU location/ ; 2022HC3FRM//Serum metabolomics in atopic dermatitis (MetabAD)/ ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease influenced by several factors, including immune system imbalance, impairment of the epidermal barrier, and alterations in the composition of the gut and skin bacterial and fungal microbiota. This study combines metagenomic sequencing and culture-based methods to explore the impact of probiotic supplementation on the cutaneous microbiota and mycobiota of AD patients. Twenty-five adults diagnosed with AD were enrolled, and skin swabs were analyzed to characterize microbial diversity and load. Culturomic analyses identified 42 bacterial and 6 fungal species, confirming Staphylococcus aureus and Candida parapsilosis as predominant taxa. High-throughput sequencing revealed Staphylococcus spp. and Malassezia spp. as dominant genera, with notable interindividual variability. While probiotic use did not significantly influence bacterial diversity, it was associated with higher richness and evenness in fungal communities, as shown by alpha and beta diversity metrics. Malassezia restricta was more prevalent among probiotic users, whereas Candida parapsilosis and Rhodotorula mucilaginosa were enriched in non-users. These findings indicate an association between probiotic use and differences in the composition and diversity of the skin mycobiota compared with the bacterial microbiota, suggesting that fungal communities may be more responsive to probiotic-associated factors. Integrating metagenomic and culturomic approaches offers valuable insights into the complex interactions among host factors, microbial communities, and probiotic use in AD, paving the way for targeted microbiome-based therapeutic strategies.},
}
@article {pmid42073499,
year = {2026},
author = {Kollár, B and Biathová, S and Klobučníková, K and Turčáni, P and Rádiková, &#x17d; and Žitňanová, I and Argalášová, &#x13d; and Šiarnik, P},
title = {Effects of Positive Airway Pressure Therapy on Cognitive Function in Patients with Obstructive Sleep Apnea: A Prospective Observational Study Protocol.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040692},
pmid = {42073499},
issn = {2075-1729},
support = {VEGA 1/0075/25//Slovak Academy of Sciences/ ; VEGA 1/0022/23//Slovak Academy of Sciences/ ; VEGA 2/0163/26//Slovak Academy of Sciences/ ; APVV-23-0028//Slovak Research and Development Agency/ ; },
abstract = {Obstructive sleep apnea (OSA) is the most common sleep-related breathing disorder and is increasingly recognized as a contributor to cognitive decline and a potential risk factor for neurodegeneration. Previous studies have also identified various associated comorbidities such as vascular dysfunction, metabolic alterations, and neuroinflammatory changes. Positive airway pressure (PAP) therapy has been associated with cognitive improvement in some studies, but its long-term effects on cognitive function remain uncertain. This study employs a prospective, observational, longitudinal cohort design to examine longitudinal associations between disease severity, PAP therapy and cognition. Additionally, we aim to examine the relationships between cognitive dysfunction, brain structure and associated OSA-related risk factors. A total of 100 eligible participants with mild to severe OSA will be recruited. All participants will undergo comprehensive assessments at baseline and after 12 months, including neurological, pulmonary, and ear, nose and throat clinical examinations, polysomnography, neuropsychological testing, brain magnetic resonance imaging with volumetry, anthropometric measurements, blood and saliva sampling for the assessment of the selected laboratory parameters, gut microbiome analysis, and evaluation of endothelial function and baroreflex sensitivity. This study may improve understanding of how PAP therapy and OSA-related pathophysiological processes influence cognitive outcomes.},
}
@article {pmid42073545,
year = {2026},
author = {Zhu, Z and Yang, Y and Pan, L and Ma, L and Fang, L},
title = {Gut Microbiota Metabolic Reprogramming Drives Endocrine and Immune Resistance in Hormone-Dependent Cancers.},
journal = {Cancers},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/cancers18081218},
pmid = {42073545},
issn = {2072-6694},
support = {2024ZD0533500//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; GZY-KJS-ZJ-2026-108//Joint TCM Science &amp; Technology Projects of National Demonstration Zones for Comprehensive TCM Reform/ ; 82274020//National Natural Science Foundation of China/ ; 82304608//National Natural Science Foundation of China/ ; 82504903//National Natural Science Foundation of China/ ; LQ23H310002//Zhejiang Provincial Natural Science Foundation/ ; },
abstract = {The gut microbiota, acting as a critical extrinsic endocrine organ, is profoundly involved in the pathological evolution and therapeutic response of hormone-dependent malignancies. This review elucidates the core mechanisms governing the microbiota, endocrine, and immune triple-axis. Multi-omic and biochemical evidence demonstrates that microbial metabolic networks, comprising the estrobolome, androbolome, and progestobolome/corticobolome, rely on enzymatic systems such as β-glucuronidases (GUS) and steroid-17,20-desmolases to execute hormone deconjugation and structural modification, thereby modulating systemic steroid exposure. Concurrently, microbe-derived metabolites, such as secondary bile acids and purine derivatives, act as inter-kingdom messengers. These metabolites remodel the tumor immune microenvironment by antagonizing hormone receptors and activating specific signaling axes, such as the Inosine-A2AR pathway. By modulating localized immune cells like effector T cells and myeloid cells, they play a pivotal role in tumor immune evasion. Furthermore, pharmacomicrobiomics reveals a bidirectional regulation between anti-tumor agents and the gut microbiota, where endocrine and immunotherapeutic drugs can induce microbial dysbiosis, while specific gut taxa contribute to primary or acquired resistance by enzymatically inactivating drugs (e.g., reductive inactivation of Enzalutamide) or providing hormonal precursors through bypass pathways. Facing translational challenges, such as real-world microbiome complexity and the colonization resistance of indigenous flora, we propose treating the human body as a unified host-microbe holobiont system. Future research should leverage gnotobiotic models and genetic causal inference to establish functional causality. These efforts will facilitate the development of precision tools, including ubiquitin-proteasome system (UPS) modulators, microbial enzyme inhibitors, and engineered live biotherapeutics. Collectively, these systems biology strategies offer a robust framework for overcoming therapeutic resistance in hormone-dependent malignancies.},
}
@article {pmid42073547,
year = {2026},
author = {Pérez-Campos Mayoral, E and Pérez-Campos Mayoral, L and Hernández-Huerta, MT and Cabrera-Fuentes, HA and Jarquín-González, EE and Martínez-Ruiz, H and Martínez-Cruz, M and Romero-Diaz, C and Avendaño-Villegas, ME and Mayoral-Andrade, G and Lastre-Domínguez, CM and Zenteno, E and Pina-Canseco, MDS and Olivera González, PI and Martínez-Martínez, L and Santiago-Luna, BR and Vázquez-Pérez, J and Cruz-Pérez, AP and Palmero-Alcántara, D and Santiago-Ramírez, TS and Briones-Guerash, E and Ramírez-Davila, AA and Ruiz-Rosado, JD and Pérez-Campos, E},
title = {Microbial Genomic Consortia in Prostate Cancer: Mechanistic Signaling, the Gut-Prostate Axis, and Translational Perspectives.},
journal = {Cancers},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/cancers18081219},
pmid = {42073547},
issn = {2072-6694},
abstract = {Background: Prostate cancer (PCa) arises from complex interactions among host genetics, androgen signaling, and microbial communities. Emerging genomic evidence supports the presence of microbial consortia within prostate tissue, suggesting that microbial genes, metabolites, and host-microbe interactions may contribute to chronic inflammation, oncogenic signaling, and therapeutic resistance. Methods: We conducted a narrative review using targeted searches of PubMed and Google Scholar for studies published between 2020 and 2025, complemented by selected mechanistic reports published in March 2026. Human studies and experimental research providing mechanistic insights into prostate models were prioritized. Due to the heterogeneous methodologies, evidence was synthesized qualitatively, with an emphasis on genomic and signaling perspectives. Results: Low-biomass microbial DNA is consistently detected in prostate tissue. Proteomic analyses of Corpora amylacea suggest a "fossil record" of past infections through sequestered microbial DNA and antimicrobial proteins, potentially priming tissue for long-term carcinogenic processes, although contamination remains a key limitation. Recurrent bacterial and viral signals, including Cutibacterium acnes, Escherichia coli, Pseudomonas, Acinetobacter, human papillomavirus, Epstein-Barr virus, and cytomegalovirus, appear to converge on a restricted set of tumor-relevant pathways, including TLR-NF-κB, MAPK, PI3K/AKT/mTOR, cGAS-STING, and p53/pRb disruption. These interactions may promote cytokine production, oxidative stress, DNA damage, epithelial-mesenchymal transition, extracellular matrix remodeling, immune evasion, and resistance to therapy. The gut-prostate axis further links intestinal dysbiosis and microbial metabolites with systemic IGF-1 signaling and castration resistance. Conclusions: Microbial genomic consortia in the prostate and gut may shape inflammatory, metabolic, and immune networks that influence PCa initiation and progression. However, most available data remain correlative and are limited by low-biomass sampling, contamination risk, and heterogeneous study designs. Future research should prioritize rigorous contamination control, longitudinal and prostate-specific mechanistic studies, and integrated multi-omic approaches to clarify causality and identify actionable microbial targets for prevention, diagnosis, and therapy.},
}
@article {pmid42073604,
year = {2026},
author = {Chakrabarti, T and Lee, M},
title = {Advances in Multi-Modal Biomarkers for Immunotherapy Response in Non-Small Cell Lung Cancer: ctDNA, Microbiome, and Radiomics.},
journal = {Cancers},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/cancers18081281},
pmid = {42073604},
issn = {2072-6694},
abstract = {Lung cancer remains the leading cause of cancer-related mortality worldwide, and although immunotherapy has transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC), durable benefit is limited to a subset of patients. PD-L1 immunohistochemistry and tumor mutational burden, while clinically utilized, demonstrate imperfect predictive capacity, underscoring the need for more robust biomarkers. This review highlights emerging multimodal biomarkers-including circulating tumor DNA (ctDNA), the gut microbiome, and artificial intelligence (AI)-driven radiomics-as promising tools to enhance the prediction of immunotherapy response. Longitudinal ctDNA monitoring offers a minimally invasive method to assess tumor burden dynamics, detect early molecular response, distinguish pseudo-progression from true progression, and stratify risk, with ctDNA clearance correlating with improved survival outcomes. The gut microbiome has also been associated with ICI efficacy, as specific bacterial taxa and composite scoring systems correlate with treatment response, though methodological heterogeneity limits clinical translation. Radiomic analyses leveraging CT and PET imaging extract quantitative tumor features that, when integrated with clinical and molecular data, demonstrate improved predictive performance compared to single-modality approaches. Despite promising advances, challenges including assay standardization, external validation, data harmonization, interpretability of AI models, and infrastructure requirements remain barriers to widespread adoption. Multimodal integration of genomic, microbiome, and imaging biomarkers represents a critical step toward precision immuno-oncology, with prospective validation needed to translate these approaches into improved outcomes for patients with advanced NSCLC.},
}
@article {pmid42073615,
year = {2026},
author = {Singh, B and Marotta, F and Mal, G and Sharma, R and Gopinath, D and Jairath, G and Rialch, A},
title = {Microbiome and Diet Interplay: An Emerging Frontier in PDAC Diagnosis and Prevention.},
journal = {Cancers},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/cancers18081292},
pmid = {42073615},
issn = {2072-6694},
abstract = {Pancreatic ductal adenocarcinoma (PDAC), which remains undetected till advanced stages of progression, is becoming a more common and aggressive PC with high mortality rates. Trending unhealthy dietary habits, sedentary life, obesity, diabetes, high body mass index (BMI), and perturbed gut microbiota, also known as dysbiosis, increase the PDAC incidences. There is an urgent need to delve into reliable and cost-effective biomarkers and strategies to diagnose and prevent the disease. Microbial remedies and dietary phytonutrients that restore gut microbial balance may be the prospective preventive measures. This article intends to recommend the hypothesis that PDAC is incepted and characterized by microbial signatures and can be managed by integrating evidenced-based complimentary approaches entailing diet, nutraceuticals, microbial interventions and life style modifications with standard therapies. The futuristic longitudinal and mechanistic studies to unravel host-microbiota and the host-microbiome interactions will allow deeper aetiologic and mechanistic insights into PDAC to evolve therapies and recommendations for better pancreatic health.},
}
@article {pmid42073632,
year = {2026},
author = {Liang, B and Liu, X and Zhang, T and Xing, D},
title = {Sex as a Contextual Modifier in Colorectal Cancer: Integrating Tumor Sidedness, Molecular Subtype, Immune Ecology, and Early-Onset Disease.},
journal = {Cancers},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/cancers18081309},
pmid = {42073632},
issn = {2072-6694},
support = {ZR2023QC117//Natural Science Foundation of Shandong Province, China/ ; },
abstract = {Colorectal cancer (CRC) shows consistent sex-related differences in incidence, anatomic distribution, molecular subtype, immune context, and clinical outcome. However, these differences are often discussed through broad parallel themes such as hormones, genetics, or the microbiome, rather than through the biological settings in which sex meaningfully modifies tumor behavior. This review argues that sex is most informative in CRC when treated as a contextual modifier whose relevance emerges only after integrating tumor sidedness, mismatch repair status, oncogenic background, immune ecology, and age at onset. The clearest signals arise from interaction-based contexts, particularly when sex is interpreted together with tumor sidedness and dMMR/MSI-H or BRAF-linked disease states. Current evidence indicates that women are enriched for proximal or right-sided, microsatellite instability-high, mismatch repair-deficient, CpG island methylator phenotype-high, and BRAF-associated CRC, whereas men more often present with distal disease and a higher overall burden. Mechanistic studies further show that sex-related differences extend beyond hormone exposure to include KRAS-STAT4-KDM5D signaling, site-specific immune-checkpoint programs, metabolic phenotypes, epigenetic biomarker variation, and microbiota-hormone crosstalk. These effects are most evident in defined clinical niches, particularly right-sided CRC, mismatch repair-deficient disease, BRAF-mutated metastatic CRC, and early-onset CRC. A sex-aware, subtype-aware, and location-aware framework therefore offers a more clinically useful interpretation of CRC heterogeneity than descriptive male-versus-female comparisons alone.},
}
@article {pmid42073998,
year = {2026},
author = {Basher, AA and Rejili, M and Ahmed, AA and Essa, MOA and Ibrahim, NA and Basher, NS and Husien, HM and Saleh, AA and Abdulrahman, MY and Jan, RU and Adam, SY and Cai, D},
title = {Epigenetic Alterations in Microbiome-Host Interactions in Inflammatory and Autoimmune Diseases.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083354},
pmid = {42073998},
issn = {1422-0067},
support = {[grant number IMSIU-DDRSP 2602].//This work was supported and funded by the Deanship of Scientific Research at Imam Mohammad lbn Saud Islamic University (IMSIU)./ ; },
mesh = {Humans ; *Epigenesis, Genetic ; *Autoimmune Diseases/genetics/microbiology/immunology ; *Inflammation/genetics/microbiology ; *Gastrointestinal Microbiome ; Animals ; DNA Methylation ; Dysbiosis/genetics/microbiology ; *Microbiota ; },
abstract = {Inflammatory and autoimmune diseases are now understood to be significantly influenced by the intricate interactions between the microbiome and host physiology. This review investigates the function of epigenetic dysregulation in microbiome-host interaction and its consequences for health and disease. Epigenetic modifications, including DNA methylation, histone modifications, and non-coding RNA-associated regulation, are key mechanisms that control gene expression without altering the underlying DNA sequence. Microbial metabolites and community composition alterations can cause disruptions in these epigenetic processes, resulting in dysregulated immune responses and the initiation of chronic inflammatory conditions. In particular, the diversity of gut microbiota alters host epigenetic patterns, affecting T cell differentiation, inflammatory modulation, and tissue homeostasis. Aberrant epigenetic modifications contribute to the pathogenesis of autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) by promoting inflammation and autoimmunity. Similarly, gut microbiota dysbiosis has been implicated in the development and progression of inflammatory bowel disease (IBD). Identifying the reciprocal interaction between epigenetic alterations and microbiome dynamics provides unique insights into therapeutic options targeted at restoring microbial homeostasis to prevent disease progress. Consequently, understanding the intricacies of epigenetic dysregulation in microbiome-host interactions represents a significant sector in biomedical research and highlights the promise for precision medicine approaches in treating inflammatory and autoimmune diseases. The potential for microbiome-based therapies to affect host epigenetic landscapes requires additional research, paving the way for innovative therapeutic paradigms targeted at improving host resilience and restoring immunological balance. The purpose of this review is to synthesize current knowledge on how epigenetic dysregulation and microbiome-host interactions drive inflammatory and autoimmune diseases and to highlight emerging therapeutic opportunities.},
}
@article {pmid42074015,
year = {2026},
author = {Papacocea, RI and Iliuță, FP and Papacocea, IR},
title = {Gut Microbiome Dysregulation Across Schizophrenia Spectrum Disorders: Bacteria-, Fungi- and Virome-Level Alterations with Molecular and Immunological Implications.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083372},
pmid = {42074015},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Schizophrenia/microbiology/immunology ; *Virome ; *Bacteria ; Dysbiosis/microbiology ; *Fungi ; Animals ; },
abstract = {Schizophrenia spectrum disorders (SSD) are severe psychiatric conditions characterized by disturbances in cognition, emotion, and behavior, with increasing evidence suggesting an involvement of the gut microbiome in their pathophysiology. This PRISMA-informed structured review synthesizes 114 studies using a taxa-centered framework that maps microbial changes across SSD stages and phenotypes and serves as a structural basis for identifying cross-study patterns. Across heterogeneous cohorts, convergent alterations include depletion of short-chain fatty acid (SCFA)-producing taxa (including Faecalibacterium, Roseburia, and Coprococcus) and enrichment of potentially pro-inflammatory and fermentative taxa (such as Proteobacteria, Enterobacteriaceae, Streptococcus, Collinsella, and Desulfovibrio). These taxonomic patterns suggest potential functional alterations, including reduced SCFA availability. Reduced abundance of butyrate-producing taxa has been associated with impaired intestinal barrier function and increased microbial translocation (e.g., lipopolysaccharide), which may contribute to the activation of immune pathways, including Toll-like receptor 4 signaling and elevated inflammatory markers such as IL-6 and TNF-α. Additional alterations reported across studies include changes in lactate metabolism, bile acid profiles, aromatic amino acid metabolism, and the tryptophan-kynurenine pathway. These pathways may interact with neurobiological processes relevant to SSD, including glutamate-GABA balance, NMDA receptor function, microglial activation, and synaptic regulation, although much of the current evidence remains associative. Multi-kingdom studies and fecal microbiota transplantation models provide further support for the functional relevance of these observations, though causal relationships remain to be fully established. Overall, SSD-associated dysbiosis appears to reflect ecosystem-level metabolic alterations rather than isolated taxonomic abnormalities, supporting a Microbiota-Gut-Immune-Glia conceptual framework and highlighting the gut ecosystem as a potential therapeutic target.},
}
@article {pmid42074058,
year = {2026},
author = {Monsó, E and Casadevall, C and Quero, S and Pascual-Guàrdia, S and Enríquez-Rodríguez, CJ and Millares, L and Montón, C and Faner, R and Capilla, S and Seijo, LM and Castro-Acosta, A and Alvarez-Martínez, C and Sibila, O and Peces-Barba, G and Cosio, BG and Agustí, A and Gea, J},
title = {Bronchial and Systemic Relationships of Haemophilus in Chronic Obstructive Pulmonary Disease.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083416},
pmid = {42074058},
issn = {1422-0067},
support = {PI15/00167, PI15/02042, PI18/00934, SAF 2014-54371//Fondo de Investigaci&#xf3;n Sanitaria, Instituto de Salud Carlos III; FEDER Ministerio de Econom&#xed;a y Competitividad; Fundaci&#xf3; Pla Armengol; Centro de Investigaci&#xf3;n Biom&#xe9;dica en Red Area de Enfermedades Respiratorias (CIBERES) - CIBERES is an initiative of the/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology ; Male ; Female ; *Haemophilus/genetics/isolation &amp; purification ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Bronchi/microbiology ; Sputum/microbiology ; Microbiota ; Biomarkers/blood ; },
abstract = {The aim of the study was to assess the microbial composition of bronchial secretions in chronic obstructive pulmonary disease (COPD), focusing on the impact of the exacerbation patterns on the common components of the respiratory flora and their relationship with inflammatory proteins. A total of 72 clinically stable COPD patients provided sputum and blood samples for 16S rRNA gene amplification and peripheral biomarkers. Beta-diversity analyses of the bronchial microbiome showed significant differences between infrequent and frequent (≥2) exacerbators (p = 0.001). Haemophilus was underrepresented in frequent exacerbators (relative abundance [RA] 0.07 [0.003-0.31] vs. 0.24 [0.06-2.36], p = 0.02) while the presence of Pseudomonas was increased (7.70 [0.66-11.68] vs. 1.11 [0.37-2.88], p = 0.01). Eight common taxa, Prevotella, Moryella, Atopobium, Megasphaera, Parvimonas, Veillonella, Bulleidia and Selenomonas, showed significant decreases in their RAs when exacerbations required hospitalization. RAs of Haemophilus and eight common taxa were positively correlated (p < 0.01). Among them, Porphyromonas, Leptotrichia and Selenomonas showed a negative correlation with blood interleukin-8 (IL-8) (p < 0.01) and an equivalent correlation was found for Haemophilus parainfluenzae. Frequent exacerbations cause a decrease in the RA of Haemophilus and have a more extensive impact when hospitalization is required. The RAs of common bronchial bacteria were closely related and some of them were inversely associated with blood IL-8 levels.},
}
@article {pmid42074073,
year = {2026},
author = {Guix, FX},
title = {Metatranscriptomic Reanalysis of Alzheimer's Brains Identifies Low-Biomass Microbial Signals Including Enrichment of Acinetobacter radioresistens.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083430},
pmid = {42074073},
issn = {1422-0067},
support = {2025-URL-Proj-007//Universitat Ramon Llull/ ; },
mesh = {*Alzheimer Disease/microbiology/genetics/metabolism/pathology ; Humans ; *Acinetobacter/genetics/isolation &amp; purification ; Aged ; *Transcriptome ; Female ; Male ; *Brain/metabolism/microbiology ; Biomass ; Aged, 80 and over ; Microbiota ; Gene Expression Profiling ; },
abstract = {Alzheimer's disease (AD) is characterized by progressive cognitive decline and the accumulation of amyloid-β (Aβ) plaques and tau neurofibrillary tangles. Beyond genetic and proteostatic mechanisms, infection- and dysbiosis-based models of AD have gained renewed attention, including the antimicrobial protection hypothesis, in which Aβ may participate in innate immune defense. Here, we reanalyzed ribosomal depleted (Ribo-Zero) RNA-seq data from dorsolateral prefrontal cortex (DLPFC) samples from the Mount Sinai Brain Bank cohort (GSE53697) to screen for non-human transcripts. Reads underwent quality control and adapter trimming, taxonomic classification with Kraken2, abundance re-estimation with Bracken, and differential abundance testing with edgeR. Across 17 samples (9 advanced AD and 8 controls), we detected low-biomass microbial signals, with Acinetobacter radioresistens showing enrichment in the AD group (FDR = 0.018). Several additional taxa showed suggestive group differences but did not remain significant after multiple testing correction, including Lactobacillus iners (FDR = 0.051). We also performed an exploratory in silico analysis of an A. radioresistens biofilm-associated protein homolog, identifying predicted amyloidogenic motifs and surface-exposed regions that may be relevant to cross-seeding hypotheses, although no mechanistic inference can be drawn without experimental validation. Given the technical challenges of inferring microbial signals from post-mortem brain RNA-seq data, including contamination risk, low microbial biomass, and overwhelming host background, these findings should be interpreted as hypothesis-generating and warrant orthogonal validation in larger, microbiome-aware cohorts.},
}
@article {pmid42074113,
year = {2026},
author = {Adisornprasert, Y and Kumwan, B and Meachasompop, P and Rajitdumrong, C and Chaemlek, P and Srisapoome, P and Buncharoen, W and Paankhao, N and Umputhorn, N and Choppradit, C and Sangmek, P and Hatachote, S and Chokmangmeepisarn, P and Sriphairoj, K and Uchuwittayakul, A},
title = {Isolation, Identification, Virulence and Pathogenic Features of Lactococcus garvieae from Cage-Cultured Tilapia (Oreochromis niloticus) in Thailand.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083469},
pmid = {42074113},
issn = {1422-0067},
support = {PRP6807030620//he Agricultural Research Development Agency (Public Organization), ARDA/ ; },
mesh = {Animals ; *Lactococcus/pathogenicity/isolation &amp; purification/genetics ; Thailand/epidemiology ; *Fish Diseases/microbiology/epidemiology ; Virulence ; *Cichlids/microbiology ; *Gram-Positive Bacterial Infections/veterinary/microbiology ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; Phylogeny ; },
abstract = {Lactococcosis caused by Lactococcus garvieae is an emerging threat to warmwater aquaculture, yet evidence integrating field outbreaks with robust molecular confirmation and controlled virulence testing remains limited for Thailand's cage-cultured tilapia. From May to October 2025, acute mortality events were investigated in cage-cultured Nile tilapia (Oreochromis niloticus) in a reservoir in Ubon Ratchathani Province, Thailand. Suspected outbreaks were defined by abrupt daily mortality exceeding 5% accompanied by septicemia-like clinical signs. Water quality during sampling covered the following ranges: temperature 28.6-31.9 °C, pH 6.5-7.0, salinity 0.02-0.03 ppt, electrical conductivity 0.036-0.046 mS/cm, TDS 22.20-26.50 mg/L, total alkalinity 17.0-34.0 mg/L as CaCO3, total hardness 12.0-60.0 mg/L as CaCO3, dissolved oxygen 6.5-7.0 mg/L, and NH3 were below the limit of detection. Full-length 16S rRNA tissue profiling revealed strong tissue partitioning: blood microbiomes were consistently dominated by Lactococcus and L. garvieae at the species level, whereas gills showed higher richness and mixed communities with multiple opportunistic taxa. Culture isolation was more reliable from blood than gills, yielding 16 Gram-positive, catalase-negative isolates (AAHM-LG2501-AAHM-LG2516) that clustered within the L. garvieae clade in near full-length 16S rRNA phylogenetic analysis and were separated from closely related Lactococcus lineages. A representative blood isolate (AAHM-LG2501) showed dose-dependent virulence in controlled challenges, with an LD50 of ~1.05 × 10[5] CFU/fish by intraperitoneal injection and an LC50 of ~1.20 × 10[6] CFU/mL by immersion. Histopathology supported systemic dissemination, with injection producing more consistent multi-organ lesions than immersion, particularly in head kidney, liver, and spleen, while gills exhibited route-associated epithelial and vascular alterations. Together, these findings confirm L. garvieae as a major etiological agent of septicemic outbreaks in cage-cultured tilapia in Thailand and support a practical surveillance framework prioritizing blood sampling, molecular confirmation, and risk-based monitoring to guide biosecurity and vaccine-oriented prevention.},
}
@article {pmid42074145,
year = {2026},
author = {Staun-Ram, E and Volkowich, A and Glass-Marmor, L and Miller, A},
title = {Immunotherapy-Mediated Modulation of the Gut Microbiota in Multiple Sclerosis: The Effects of High-Efficacy (Cladribine) and Moderate-Efficacy (Interferon Beta-1a) Treatments.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083500},
pmid = {42074145},
issn = {1422-0067},
support = {na//Merck Serono Ltd., an affiliate of Merck KGaA./ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Multiple Sclerosis/drug therapy/microbiology/immunology/therapy ; Male ; Female ; *Interferon beta-1a/therapeutic use/pharmacology ; Adult ; *Immunotherapy/methods ; Middle Aged ; Longitudinal Studies ; Fatty Acids, Volatile/metabolism ; Treatment Outcome ; },
abstract = {Interactions between the gut microbiota, immune system, and brain seem to be involved in the pathogenesis and disease activity of multiple sclerosis (MS). Some MS disease-modifying therapies (DMTs) have been shown to alter the microbiota, but whether this is related to their specific mode of action or indirectly related to their immune-modulatory effect is unknown. In this longitudinal study, we characterized the effects of two DMTs on the microbiota under similar conditions and populations: the injectable, moderate-efficacy DMT interferon beta-1a (INFβ-1a) and the oral, high-efficacy DMT cladribine tablets (CladT). Taxonomic differences were identified following 6 months of therapy for each DMT, and both were associated with the elevation of short-chain fatty acid (SCFA) producers from the Lachnospiraceae, Lactobacillaceae, and Ruminococcaceae families (Firmicutes), while members of Bacteroidetes and Proteobacteria were reduced. Moreover, a higher abundance of Alphaproteobacteria and Betaproteobacteria at baseline was associated with disease activity within 1-2 years of follow-up, while a higher abundance of Lachnospiraceae, Ruminococcaceae, Bifidobacteriaceae, and Streptococcaceae microbes, among others, was associated with no evidence of disease activity (NEDA). Our results provide supporting evidence that alteration of the microbiota by DMTs is part of their beneficial effect, and while some modifications seem to be DMT-specific, MS-DMTs in general promote SCFA-producing microbes, which positively correlate with a favorable clinical outcome. Future therapeutic strategies for PwMS may benefit from microbiome modulation, contingent upon additional mechanistic and interventional studies.},
}
@article {pmid42074155,
year = {2026},
author = {Kurhaluk, N and Mazur, Z and Kołodziejska, R and Tkaczenko, H},
title = {Gut Microbiota, Diet and Lipid Metabolism in Adolescents with NAFLD and Their Role in Preventive Strategies.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083511},
pmid = {42074155},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Non-alcoholic Fatty Liver Disease/metabolism/prevention &amp; control/microbiology/etiology ; *Lipid Metabolism ; Adolescent ; Dysbiosis ; *Diet ; Animals ; Liver/metabolism ; },
abstract = {Adolescence is a metabolically vulnerable period, during which rapid physiological maturation coincides with the dynamic remodelling of the gut microbiome. This narrative review summarises evidence from 2015 to 2025 to clarify how disturbances to the gut-liver axis driven by dysbiosis contribute to the development and progression of non-alcoholic fatty liver disease (NAFLD) in young people. Based on a systematic search of the databases PubMed, Scopus and Web of Science, we outline the basis of bidirectional communication between the gut and liver and emphasise how microbial imbalance alters the handling of lipids in the liver by enhancing de novo lipogenesis, impairing fatty acid oxidation and disrupting AMPK signalling and mitochondrial function. Consistent findings from clinical and experimental studies show that adolescents with NAFLD exhibit reduced microbial diversity, the enrichment of ethanol- and LPS-producing taxa, and altered short-chain fatty acid profiles. Each of these is associated with hepatic inflammation and metabolic reprogramming. Microbial molecules, including LPS, secondary bile acids and branched-chain amino acid metabolites, activate TLR4-NF-κB pathways, promote Kupffer cell activation and intensify oxidative stress. These mechanisms intersect with factors specific to adolescence, such as increased adiposity, hormonal shifts and diet-induced metabolic strain. Dietary patterns emerge as key modulators of these processes. Westernised diets promote dysbiosis and endotoxemia, whereas Mediterranean, fibre-rich and plant-based diets enhance SCFA production, strengthen epithelial integrity and modulate adiponectin-dependent hepatic metabolism. Micronutrient-sensitive epigenetic regulation, particularly that involving folate, choline and polyphenols, also plays a role in shaping lipid homeostasis and inflammatory tone. We also highlight emerging evidence that the activation of cytoprotective pathways, especially Nrf2, is dependent on lifestyle factors and links antioxidant-rich functional foods and physical activity to improved mitochondrial resilience and microbiome stability. We evaluate therapies targeting the microbiome, including probiotics, prebiotics, synbiotics and postbiotics, which reduce endotoxemia, restore microbial balance and complement dietary strategies. Thus, these findings emphasise the importance of age-specific, mechanistically informed interventions that integrate diet quality, microbial ecology, and the molecular pathways that govern metabolic health in adolescents with NAFLD.},
}
@article {pmid42074229,
year = {2026},
author = {Baltacıoğlu, A and Acar, O and Sönmez, C and Sağlıcan, Y and Argun, &#xd6;B and Kural, AR and Yıldırım, A and İnce, &#xdc; and Serdar, MA and Özpınar, A},
title = {Serum Trimethylamine-N-Oxide and Its Precursors as a Diagnostic Biomarker Panel for Non-Muscle-Invasive Bladder Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083591},
pmid = {42074229},
issn = {1422-0067},
mesh = {Humans ; *Methylamines/blood ; Male ; *Urinary Bladder Neoplasms/blood/diagnosis/pathology ; *Biomarkers, Tumor/blood ; Middle Aged ; Aged ; ROC Curve ; Case-Control Studies ; Choline/blood ; Carnitine/blood ; Betaine/blood ; Non-Muscle Invasive Bladder Neoplasms ; },
abstract = {Non-muscle-invasive bladder cancer (NMIBC) is characterized by high recurrence rates and necessitates lifelong cystoscopic surveillance, underscoring the need for minimally invasive biomarkers to improve early detection and risk stratification. Therefore, this study aimed to investigate the role of trimethylamine-N-oxide (TMAO) and its precursors as diagnostic biomarkers for NMIBC. A total of 50 male patients with NMIBC (25 pTa and 25 pT1) were included in this study. Additionally, 52 age-matched healthy individuals were included as controls. Serum TMAO and its dietary precursors were quantified using liquid chromatography-tandem mass spectrometry. Group differences were analyzed using nonparametric tests, associations were assessed using Spearman's correlation, and diagnostic performance was evaluated using receiver operating characteristic (ROC) analysis. Multivariate logistic regression was performed to identify independent predictors, and a composite risk score was generated. Serum TMAO, carnitine, and choline levels were significantly higher in patients with NMIBC than in controls (p ≤ 0.0001), whereas betaine showed a nonsignificant trend toward higher levels (p ≥ 0.05). The pathological stage (pTa vs. pT1) showed the strongest correlation with TMAO levels. The ROC analysis revealed that TMAO had the highest individual diagnostic accuracy (area under the curve [AUC] = 0.875, 95% confidence interval [CI] 0.812-0.939), whereas carnitine and choline provided complementary diagnostic performance. In multivariate models, TMAO, carnitine, and choline remained independent predictors of NMIBC (p ≤ 0.0001). A composite risk score integrating all four metabolites demonstrated excellent discriminatory capacity (AUC = 0.958, 95% CI 0.926-0.991). The TMAO metabolic axis can be used as a minimally invasive biomarker panel for NMIBC. Further large, prospective, multicenter studies integrating metabolomic and microbiome profiling are needed to validate the findings.},
}
@article {pmid42074240,
year = {2026},
author = {Thye, AY and Lim, HX and Kumari, Y and Tan, LT and Letchumanan, V and Pusparajah, P and Chan, KG and Lee, LH and Law, JW},
title = {A Review of Probiotic Interventions for Necrotizing Enterocolitis and Sepsis in Preterm Infants.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083602},
pmid = {42074240},
issn = {1422-0067},
mesh = {Humans ; *Probiotics/therapeutic use ; *Enterocolitis, Necrotizing/microbiology/therapy/prevention &amp; control ; Infant, Premature ; *Sepsis/microbiology/therapy ; Infant, Newborn ; Gastrointestinal Microbiome ; Bifidobacterium ; },
abstract = {Necrotizing enterocolitis (NEC) and sepsis/late-onset sepsis (LOS) are significant contributors to preterm infant morbidity and mortality, with prematurity and low birth weight representing major risk factors for these interconnected conditions. Although the pathogenesis of NEC and LOS is not fully understood, there is a clear association with an immature intestinal mucosal barrier, which may enable bacterial invasion and translocation, resulting in an inflammatory cascade. Increasing recognition of the gut microbiome as a marker for health and disease has driven interest in probiotics, particularly Bifidobacterium spp. and Lactobacillus spp., as potential adjunctive agents for the prevention and management of NEC and LOS in preterm infants, which is the area of focus of this review. The focus of this paper was to analyze clinical studies using different probiotic strains, and compare single-strain versus multi-strain probiotic formulations. Several studies support that probiotic supplementation in preterm infants has the potential to decrease NEC incidence and, to a lesser extent, sepsis/LOS. Nonetheless, inconsistent results due to strain differences and clinical heterogeneity limit the widespread adoption of this mode of therapy, as do safety concerns in this vulnerable population. Further high-quality standardized studies are necessary to establish consistent guidelines for probiotic use in preterm infants.},
}
@article {pmid42074307,
year = {2026},
author = {Hwang, JH and Choi, YK},
title = {Mechanistic Insights into Multiherb Formulations for Antibiotic-Associated Diarrhea: A Systematic Review of Preclinical Studies on Microbiome-Host Interactions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083663},
pmid = {42074307},
issn = {1422-0067},
support = {NRF-2022R1A2C1013518//National Research Foundation of Korea/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Diarrhea/chemically induced/drug therapy/microbiology ; *Anti-Bacterial Agents/adverse effects ; Animals ; Humans ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; },
abstract = {Antibiotic-associated diarrhea (AAD) is primarily driven by disruption of the gut microbiota accompanied by intestinal mucosal injury. Although multiherb formulations are widely used in East Asian medicine, their collective ecological effects and integrated microbiome-host mechanisms have not been systematically synthesized. This systematic review included 17 preclinical studies that investigated multiherbal formulations in AAD models. Given the substantial heterogeneity in the formulation composition, experimental design, and analytical platforms, a descriptive synthesis was performed. The included formulations were categorized into four clusters based on their shared herbal composition: Qiwei Baizhu San (QWBZP), Lizhong Tang (LZT), Gegen Qinlian Tang (GQT), and other supportive multiherbal formulations. The cluster-based synthesis revealed distinct convergent therapeutic strategies. The QWBZP and LZT clusters primarily supported the restoration of host metabolic and digestive functions, whereas the GQT cluster exhibited potent pathogen control effects with the suppression of opportunistic taxa. Across all clusters, a convergent microbiome-host response emerged, characterized by enrichment of commensal bacteria (e.g., Lactobacillus), upregulation of tight junction proteins (e.g., ZO-1, occludin), and attenuation of pro-inflammatory mediators (e.g., TNF-α, myeloperoxidase). Multiherb formulations in AAD models not only act as microbial modulators but also function as host-directed modulators that stabilize the intestinal homeostatic niche. Botanical interventions may facilitate endogenous microbiome recovery by reinforcing mucosal integrity and reducing environmental resistance. This ecological framework provides a rationale for future translational studies evaluating integrated herbal-probiotic strategies and precise microbiome management for patients with AAD, while further clinical validation is warranted.},
}
@article {pmid42074337,
year = {2026},
author = {Liu, X and Chen, Y and Zhou, X and Xiao, Y and Yuan, X and Su, N and Chen, C and Yan, Q and Chen, X},
title = {Bacillus subtilis and Trichoderma harzianum Reshape Rhizosphere Microbiome and Reprogram Root Transcriptome to Promote Mungbean Growth Under Continuous-Cropping Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083699},
pmid = {42074337},
issn = {1422-0067},
support = {2025YFE0121200//National Key R&amp;D Program of China/ ; CARS-08//China Agriculture Research System of MOF and MARA-Food Legumes/ ; JBGS[2021]004//Jiangsu Seed Industry Revitalization Project/ ; },
mesh = {*Bacillus subtilis/physiology ; *Rhizosphere ; *Vigna/growth &amp; development/microbiology/genetics ; *Plant Roots/microbiology/genetics/growth &amp; development ; *Transcriptome ; *Microbiota ; Soil Microbiology ; Metagenomics ; *Hypocreales/physiology ; Gene Expression Profiling ; },
abstract = {Mungbean (Vigna radiata) is an important cash crop, yet the production is significantly compromised by continuous cropping. Beneficial microbial inoculation offers a promising strategy to alleviate the stresses through rhizosphere modulation and host physiological reprogramming. This study evaluated the efficacy of two biological control agents, Bacillus subtilis (B. subtilis) and Trichoderma harzianum (T. harzianum), in promoting mungbean growth under continuous-cropping conditions. Both individual applications of B. subtilis and T. harzianum significantly improved plant biomass, root system architecture, and yield. Combined metagenomic and transcriptomic analyses were conducted to unravel the underlying mechanisms. According to metagenomic analysis, both B. subtilis and T. harzianum were responsible for significant changes in beta diversity without significantly affecting the alpha diversity of the rhizosphere microbial community. T. harzianum recruited Chitinophagaceae unclassified, Abditibacterium, Hydrogenophilaceae unclassified, Methylophilaceae unclassified, and Chimaeribacter, while Bs recruited Candidatus Saccharibacteria unclassified. Transcriptomic analysis indicated that T. harzianum induced more extensive transcriptional reprogramming than B. subtilis. The enrichment analysis revealed both shared and distinct responses triggered by the two treatments. These findings suggest that B. subtilis and T. harzianum alleviate continuous-cropping stress through distinct yet complementary mechanisms involving rhizosphere microbiome modulation and mungbean transcriptional reprogramming. This study provides a sustainable strategy for legume cultivation.},
}
@article {pmid42074799,
year = {2026},
author = {Jimenez de Nunzio, S and Pilo, J and Bruna Del Cojo, M and Arias-Macias, CM and Manso de Gustin, B and Nunes, F and Lago Pacheco, E and Esteban Escobar, C and Tercero-Mora, F and Portal-Nuñez, S and Adell Perez, A and Macias Gonzalez, M},
title = {Clinical Profile, Risk Factors, and Microbial Dysbiosis in Periodontitis: Findings from an Adult Cohort and Microbiome-Based Predictive Models.},
journal = {Journal of clinical medicine},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/jcm15082994},
pmid = {42074799},
issn = {2077-0383},
abstract = {Background/Objective: Periodontitis is a chronic inflammatory disease influenced by clinical, behavioral, and microbial determinants. However, the contribution of these factors to disease remains a topic of debate, particularly in untreated adult populations. This study aims to characterize the clinical, epidemiological, and microbial features associated with periodontitis in an adult cohort and to compare the discriminatory performance of microbiome-based predictive models with conventional clinical-behavioral models. Methods: A cross-sectional study was conducted in 943 adults. Periodontal status was determined by experienced clinicians according to the 2017 World Workshop on the Classification of Periodontal and Peri-implant Diseases and Conditions. Clinical variables, behavioral factors (smoking, bruxism, diet), intraoral conditions (caries and malocclusion), and systemic comorbidities were recorded. The oral microbiome was analyzed using targeted PCR for selected periodontal bacteria. Predictive models were constructed using logistic regression and least absolute shrinkage and selection operator (LASSO) variable selection. Results: Periodontitis was diagnosed in 47.2% of participants. Age, smoking, and bruxism were significantly associated with periodontitis. Malocclusion was the only significant intraoral predictor (OR = 2.00). Individuals with periodontitis exhibited increased levels of periodontopathogens, including P. gingivalis, T. forsythia, and E. corrodens, along with reduced levels of S. mutans. Microbiome-based models demonstrated superior discriminatory performance (AUC = 0.76, LASSO). E. corrodens and C. sputigena were independently associated with greater probing depth (p < 0.001). Conclusions: Microbiome-based predictive models, particularly at the species level, showed better discriminatory performance than conventional clinical-behavioral models. These findings support the potential utility of salivary microbial signatures as adjunctive, non-invasive biomarkers of periodontal inflammatory status.},
}
@article {pmid42074869,
year = {2026},
author = {Carnazzo, SM and Fanos, V},
title = {The Microbiota-Gut-Brain Axis Across the Lifespan: From Neurodevelopment to Neurodegeneration.},
journal = {Journal of clinical medicine},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/jcm15083065},
pmid = {42074869},
issn = {2077-0383},
abstract = {The microbiota-gut-brain axis (MGBA) is a complex bidirectional communication network integrating neural, endocrine, immune, and metabolic pathways linking intestinal microbiota to central nervous system function. Increasing evidence indicates that microbiota-derived signals are critical regulators of neurodevelopment and may contribute to vulnerability to neurodegenerative disorders across the lifespan. In this narrative review, we synthesize experimental and clinical evidence to define the key biological mechanisms underlying microbiota-brain interactions. Converging data indicate that immune activation, barrier dysfunction, and microbial metabolites, particularly short-chain fatty acids and tryptophan-derived compounds, represent central mediators linking gut dysbiosis to neuroinflammatory and neurodegenerative processes. Early-life microbial perturbations, driven by factors such as antibiotic exposure, diet, and psychosocial stress, appear to induce long-term immunometabolic programming that may increase susceptibility to neurological disorders later in life. Clinical studies consistently associate dysbiosis with neurodevelopmental conditions and major neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease; however, causal relationships remain incompletely defined due to heterogeneity and the predominance of observational data. Overall, the available evidence supports a lifespan model in which microbiota-driven immune and metabolic dysregulation contributes to both early neurodevelopmental trajectories and late-life neurodegeneration. While microbiome-based biomarkers and therapeutic strategies show promise, their clinical translation requires validation in longitudinal and interventional studies.},
}
@article {pmid42074887,
year = {2026},
author = {Bodó, D and Szabó, BV and Kiss, T and Csupor, D and Tóth, B},
title = {Prenatal and Early-Life Exposure to Microbiome-Modulating Medications and the Risk of Childhood Food Allergy: A Systematic Review and Meta-Analysis.},
journal = {Journal of clinical medicine},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/jcm15083086},
pmid = {42074887},
issn = {2077-0383},
support = {J&#xe1;nos Bolyai Research Scholarship//Hungarian Academy of Sciences/ ; },
abstract = {Background/Objectives: Several recent human studies have associated the use of certain medicines, such as antibiotics and antacids, with allergic conditions, potentially through microbiome disruption. In contrast, probiotics which may prevent dysbiosis, could have protective effects. Our meta-analysis aimed to evaluate the impact of these drugs (consumed during pregnancy or early life) on the risk of childhood food allergy, based on the available literature. Methods: Literature searches were conducted in the EMBASE, PubMed, Cochrane, and Web of Science databases using predefined PICO criteria. Overall, our meta-analysis included 25 studies involving 1,662,861 mothers and 5,164,280 children. Results: Using the random-effects model, we found that prenatal and early life antibiotic use (up to 2 years of age) was associated with higher odds of food allergy in childhood (OR: 1.34; 95% CI [1.10, 1.63], OR: 1.53; 95% CI [1.18, 1.98], respectively). Proton pump inhibitors were also associated with a risk of food allergies (OR: 2.65; 95% CI [1.22-5.77]), whereas the impact of H2-receptor antagonists was non-significant (OR: 2.07; 95% CI [0.96-4.45]). Probiotic use during the first two years of life was not associated with decreased risk for food allergy in children (OR: 1.25; 95% CI [0.46, 3.38]). Conclusions: These findings suggest an association between microbiome-disrupting medications during pregnancy and early childhood and an increased risk of childhood food allergy, especially those with a family history of food allergy. However, due to the predominantly observational design of the included studies, causality cannot be established. These results highlight the need for cautious and judicious use of such medications in these populations.},
}
@article {pmid42074989,
year = {2026},
author = {Di Renzo, T and Reale, A and Nazzaro, S and Iovanna, D and Evangelista, D and Gautam, V and Guida, B and Carrano, R and Cataldi, M},
title = {Impact of Probiotics, Prebiotics and Synbiotics Supplementation in Chronic Kidney Disease: A Comprehensive Review of Clinical Trials.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081176},
pmid = {42074989},
issn = {2072-6643},
support = {PNRR-MAD-2022-12376812//Ministry of Health/ ; },
mesh = {Humans ; *Probiotics/administration &amp; dosage/therapeutic use ; *Synbiotics/administration &amp; dosage ; *Prebiotics/administration &amp; dosage ; *Renal Insufficiency, Chronic/therapy/microbiology ; Gastrointestinal Microbiome ; *Dietary Supplements ; Dysbiosis ; Clinical Trials as Topic ; },
abstract = {Chronic kidney disease (CKD) is a progressive condition associated with metabolic disturbances, systemic inflammation, and the accumulation of gut-derived uremic toxins. Increasing evidence highlights the role of gut microbiota dysbiosis in the progression of CKD through the gut-kidney axis. Consequently, microbiome-targeted nutritional strategies, including probiotics, prebiotics, and synbiotics, have emerged as promising complementary approaches to modulate intestinal microbial composition and metabolic functions. This review summarizes and critically evaluates the current clinical evidence regarding the use of these interventions in CKD patients. Clinical studies indicate that supplementation with probiotics, prebiotics, and synbiotic formulations may promote beneficial shifts in the composition of the gut microbiota, enhance saccharolytic fermentation, and increase the production of short-chain fatty acids (SCFAs). These changes have been associated with reduced circulating levels of gut-derived uremic toxins such as indoxyl sulfate and p-cresyl sulfate, as well as with the attenuation of systemic inflammation and oxidative stress. However, available trials remain heterogeneous in terms of study design, probiotic strains, prebiotic substrates, dosing regimens, and patient populations, and are frequently limited by small sample sizes and short intervention durations. As a result, evidence for improvements in renal function and long-term clinical outcomes remains inconclusive. While synbiotics may offer theoretical advantages by combining microbial supplementation with targeted substrates that support microbial growth and metabolic activity, current evidence does not consistently demonstrate superior clinical efficacy. Overall, these interventions often improve surrogate biomarkers, but their effects on renal function and hard clinical outcomes remain uncertain. Larger, longer-duration multicenter randomized controlled trials with standardized formulations are needed to establish their clinical utility and to better elucidate microbiota-host interactions in CKD. Advancing this field may support the development of personalized microbiome-based therapeutic strategies aimed at modulating the gut-kidney axis and ultimately improving clinical outcomes in CKD patients.},
}
@article {pmid42075006,
year = {2026},
author = {Zhang, X and Chen, F and Luo, Y and Li, D and Ji, J and Ma, L and Ma, C and Hu, X},
title = {Young Human-Derived Microbiota Ameliorates Cognitive Decline and Reproductive Senescence in Aged Mice.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081193},
pmid = {42075006},
issn = {2072-6643},
support = {2023YFF1104005//National key research and development program/ ; },
mesh = {Animals ; Mice ; Humans ; Male ; Bifidobacterium/growth &amp; development ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology/therapy ; *Cellular Senescence/physiology ; Mice, Inbred C57BL ; Reproduction/physiology ; Dysbiosis/microbiology/therapy ; *Aging/physiology/psychology ; },
abstract = {Background/Objectives: Age-related gut microbiota dysbiosis leads to systemic oxidative stress, chronic inflammation, and multi-organ functional decline. However, there is limited evidence supporting microbiota-based therapies for aging. This study aimed to examine the effect of gut microbiota from young donors, particularly those with increasing Bifidobacteria levels through dietary intervention, on age-related declines in fertility, cognition, and reproduction. Methods: We conducted experiments using gut microbiota from young human donors, with or without pre-conditioning with barley leaves (BL), to transplant into aged male mice. Hippocampal metabolome and behavioral assessments were used to identify differences in recognitive regulation during aging. Moreover, testis tissue, semen quality, and offspring studies were determined to investigate the beneficial effects on fertility and underlying mechanism. Conclusions: This preliminary dietary treatment promotes the growth of Bifidobacterium in aged recipient mice. Aged male mice received young fecal microbiota transplants (yFMTs), BL-conditioned yFMTs (BLyFMTs), and a combined treatment of BLyFMT plus recipient BL supplementation. The combined approach significantly increased intestinal Bifidobacterium levels and effectively restored hippocampal metabolomic profiles and cognitive behavior. Additionally, yFMT-based treatments mitigated structural damage to the seminiferous tubules and prevented the germ cell depletion. Consistently, those interventions improved sperm quality and mechanistically enhanced hypothalamic-pituitary-gonadal (HPG) axis activity in aged recipients. These findings highlight Bifidobacterium as a key factor in microbiome-driven rejuvenation, enhancing the effectiveness of yFMTs in addressing aging-related declines.},
}
@article {pmid42075007,
year = {2026},
author = {Deng, Z and Wang, Y and Shuai, J and Chen, M and Yang, S and Liu, D and Ye, X and Chen, S and Pan, H},
title = {Bifidobacterium animalis ssp. lactis 420 and Cordyceps militaris Synergistically Modulate the Gut Microbiota by Increasing Mucin 2 Production.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081195},
pmid = {42075007},
issn = {2072-6643},
support = {2025C01099//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; 2022YFF1100204//National Key R&amp;D Program of China/ ; 2024A23//Jiashan Science and Technology Funds/ ; },
mesh = {*Gastrointestinal Microbiome ; *Cordyceps/physiology ; Animals ; *Mucin-2/metabolism/biosynthesis ; *Probiotics/pharmacology ; Diet, High-Fat/adverse effects ; Mice ; Mice, Inbred C57BL ; Male ; *Bifidobacterium animalis/physiology ; *Obesity/prevention &amp; control/microbiology/etiology ; Akkermansia ; Colon/metabolism/microbiology ; Goblet Cells/metabolism ; Verrucomicrobia/growth &amp; development ; },
abstract = {BACKGROUND: Probiotics and medicine food homology are known to offer gentle approaches to prevent obesity, although it is difficult with such approaches to satisfy consumers' requirements to lose weight quickly. The probiotic strain Bifidobacterium animalis ssp. lactis 420 (B420) and Cordyceps militaris synergistically prevented obesity and related disorders in high-fat diet (HFD)-fed mice.<br><br>METHODS: The synergistic effects correlated with improved gut integrity, diminished systemic inflammation, and enhanced glucose homeostasis. Gut microbiota analysis revealed that the bloom of the commensal Akkermansia muciniphila contributed to the synergistic effects by inducing a profound shift in HFD-induced gut microbiota disorder.<br><br>RESULTS: The bloom of A. muciniphila was significantly correlated with a boost in mucin 2 within the colon, achieved through increased goblet cell quantity and elevated mucin 2 expression. To reveal the collaborating pathway, we found that Cordyceps militaris did not promote the propagation of B420 in vitro or in vivo. Moreover, heat-killed B420 could not enhance the preventive efficacy of Cordyceps militaris against obesity caused by the HFD.<br><br>CONCLUSIONS: The metabolites of live B420 and Cordyceps militaris-derived metabolites in the gut microbiota collaboratively promoted the production of mucin 2. Thus, our results reveal a mechanism by which a combination of probiotics and medicine food homology enhance their therapeutic effects against obesity.},
}
@article {pmid42075020,
year = {2026},
author = {Sybilski, AJ and Balas, W},
title = {Nutrition at the Frontier of Allergy-From Oral Challenges to the Microbiome.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081207},
pmid = {42075020},
issn = {2072-6643},
mesh = {Humans ; *Food Hypersensitivity/immunology/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Food allergy and related allergic conditions represent a growing public health challenge [...].},
}
@article {pmid42075029,
year = {2026},
author = {Asayesh, M and Nazarzadeh, A and Jamshidi, S and Keramat, S and Ryszkiel, I and Stanek, A},
title = {Modulation of Gut Microbiota Through Dietary Fibers to Enhance Regulatory T Cell-Based Immunotherapy in GVHD Following Hematopoietic Stem Cell Transplantation.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081216},
pmid = {42075029},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Graft vs Host Disease/therapy/immunology/microbiology/prevention &amp; control ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Dietary Fiber/administration &amp; dosage ; *T-Lymphocytes, Regulatory/immunology ; *Immunotherapy/methods ; Prebiotics ; Dysbiosis ; Fecal Microbiota Transplantation ; Probiotics ; },
abstract = {Graft-versus-host disease (GVHD) is one of the principal complications seen in the recipients of allogenic hematopoietic stem cell transplantation (allo-HSCT), and persists as a leading cause of post-transplant morbidity and mortality. Increasing evidence highlights the crucial influence of the gut microbiome (GM) on transplant outcomes. Microbial dysbiosis, characterized by reduced bacterial diversity and pathogenic overgrowth, is strongly associated with higher rates of complications and mortality. Patients with lower microbial diversity exhibit poorer overall survival (OS) and an increased incidence of acute GVHD (aGVHD). Conversely, restoration of beneficial commensal communities has been shown to enhance immune homeostasis, mitigate GVHD severity, and decrease infection risk. Emerging therapeutic strategies now focus on modulating the intestinal microbiome through dietary interventions, probiotics, prebiotics, and fecal microbiota transplantation (FMT). It has been demonstrated that bacterial metabolites, such as short-chain fatty acids (SCFAs) from the diet, especially a diet rich in fibers, reduce the occurrence/severity of GVHD by inducing regulatory T cells (Tregs), which release anti-inflammatory cytokines and regulate the host immune system. Hence, the implementation of dietary fibers (DFs) could increase beneficial commensals, Treg induction, and improve outcomes such as GVHD and OS in recipients of allo-HCT. Hereupon, this review addresses how a fiber-rich diet modulates GM composition, reinforces epithelial barrier integrity, and improves the efficacy of Treg-based immunotherapy by stabilizing their regulatory phenotype and increasing their functional persistence, ultimately leading to a reduction in GI complications associated with GVHD. Unlike prior reviews that primarily cover the microbiome-GVHD axis or Treg therapies in isolation, this review emphasizes fermentable dietary fibers as a mechanistically grounded, clinically actionable strategy to support Treg stability and persistence via microbiota-derived metabolites. We integrate mechanistic evidence with emerging clinical feasibility data and ongoing trials of prebiotic supplementation in allogeneic HSCT.},
}
@article {pmid42075038,
year = {2026},
author = {Makwana, N and Arpe, L and Ivanova, A and Evans-Howells, H and Trigg, C and Van de Bor, B and Walsh, J and Weaver, A and Wood, R and Venter, C and Vandenplas, Y and Meyer, R},
title = {The Role of Hydrolysed Rice Formula in the Dietary Management of Infants with Cow's Milk Allergy: A UK Healthcare Perspective.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081225},
pmid = {42075038},
issn = {2072-6643},
mesh = {Humans ; *Milk Hypersensitivity/diet therapy ; Infant ; *Infant Formula/chemistry ; *Oryza/chemistry ; United Kingdom ; Animals ; Breast Feeding ; Protein Hydrolysates ; Female ; Infant, Newborn ; },
abstract = {Cow's milk allergy (CMA) remains one of the most common food allergies in infancy, requiring the avoidance of cow's milk and its derivatives. Breast milk is the best source of nutrition for infants. For those infants with CMA whose mothers are unable to breastfeed or choose not to, extensively hydrolysed formulas (eHFs) are widely recommended as first-line milk substitutes, whereas hydrolysed rice formulas (HRFs) are increasingly recognised as a viable alternative. This concept paper provides a healthcare professional (HCP) perspective on HRF, drawing on expert consensus from two meetings convened in 2025. Discussions noted the long history of safe and effective HRF use in Europe, its nutritional adequacy, and the evolving international guidelines supporting HRF as an alternative first-line option. A key meeting outcome was the development of a practical decision tree to help UK clinicians decide when HRF should be the preferred choice. Key considerations for its use in non-breastfed infants include the following: parental/caregiver stress related to persistent symptoms; ongoing symptoms despite multiple interventions; cultural and lifestyle choices; religious dietary requirements; and specialists' recommendations. Secondary considerations highlighted by HCPs include the following: proven reactions whilst infants are breast-milk-fed together with parental request for formula; faltering growth; multiple symptoms; taste acceptance (older infants); and parental preference based on experience. The role of functional components, such as prebiotics and human milk oligosaccharides (HMOs), was noted in regard to the emerging evidence of benefits to the microbiome and immune development. The experts emphasised the importance of engaging HCPs across all levels of CMA care and addressing challenges in translating current guidance into treatment practice. It was concluded that, overall, HRF represents a nutritionally complete, plant-based alternative that has been shown to be well tolerated (taste, symptoms) in clinical studies. It can be used to broaden therapeutic options for infants with CMA in the UK who are not exclusively fed breast milk.},
}
@article {pmid42075043,
year = {2026},
author = {Feng, J and Huang, Y and Lai, S and Zhao, T and Xie, Y and Zhu, X and Liu, L and Tang, D and Yan, A},
title = {The Gut-Adipose-Tumor Axis in Obesity-Related Cancer.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081230},
pmid = {42075043},
issn = {2072-6643},
support = {81900775//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Obesity/complications ; *Gastrointestinal Microbiome/physiology ; *Adipose Tissue/metabolism ; Tumor Microenvironment ; *Neoplasms/etiology ; Animals ; Dysbiosis ; Carcinogenesis ; Inflammation ; },
abstract = {The global obesity epidemic has emerged as a major driver of cancer incidence and mortality, with accumulating evidence highlighting the gut-adipose-tumor axis as a critical mediator of obesity-related carcinogenesis. The gut-adipose-tumor axis is a tripartite communication network, wherein the intestinal microbiome, adipose tissue, and tumor microenvironment engage in dynamic bidirectional crosstalk that alters cancer susceptibility and progression. This review synthesizes current understanding of the epidemiology, pathophysiology, therapeutic implications, and future directions of this axis. Obesity-induced gut dysbiosis leads to systemic dissemination of pro-inflammatory microbial products and metabolites. These gut-derived signals profoundly influence adipose tissue homeostasis, exacerbating chronic low-grade inflammation, promoting macrophage infiltration and polarization, and disrupting adipokine secretion patterns. Dysfunctional adipose tissue generates cancer-promoting mediators and metabolic perturbations. The convergence of gut-derived and adipose-derived signals creates a systemic pro-carcinogenic environment that reshapes the tumor microenvironment through multiple mechanisms. Understanding the gut-adipose-tumor axis as an integrated biological system offers opportunities for cancer prevention and treatment. This is of significant importance for exploring the mechanisms of obesity-related carcinogenesis and developing new therapeutic approaches for obesity-related cancers.},
}
@article {pmid42075044,
year = {2026},
author = {Smółka, L and Strugała, M and Blady, K and Kursa, K and Pomianowski, B and Stanek, A},
title = {Venous Thromboembolism and Gut Dysbiosis: Mechanistic Links Between Endotoxemia, Microbial Metabolites, and Thromboinflammation.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081231},
pmid = {42075044},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/complications/microbiology ; *Venous Thromboembolism/microbiology/etiology ; *Endotoxemia/microbiology/complications ; *Thromboinflammation/microbiology ; Animals ; },
abstract = {Background: Venous thromboembolism (VTE), including deep vein thrombosis and pulmonary embolism, is increasingly recognized as a thromboinflammatory disorder involving coagulation, innate immunity, endothelial dysfunction, and vascular homeostasis. Emerging evidence suggests that gut microbiome-related inflammatory and metabolic signals may influence pathways potentially relevant to VTE through intestinal barrier dysfunction, microbial translocation, and microbiome-derived metabolites. This review critically examines the direct and indirect evidence relating gut dysbiosis to mechanisms potentially relevant to venous thrombogenesis. Methods: A structured literature search of PubMed, Scopus, and Web of Science was conducted from database inception to February 2026. Observational, translational, experimental, preclinical, and selected genetic studies were narratively synthesized across heterogeneous evidence types. Results: Available evidence suggests that intestinal barrier dysfunction and microbial translocation may increase systemic exposure to lipopolysaccharide and other microbial products, potentially contributing to inflammatory signaling and procoagulant responses. Proposed downstream effects include tissue factor (TF) activation, platelet reactivity, neutrophil extracellular traps (NETs) formation, complement signaling, endothelial perturbation, and impaired balance of anticoagulant and fibrinolytic pathways. Microbiome-derived metabolites, including trimethylamine N-oxide (TMAO), phenylacetylglutamine (PAGln), bile acids, and short-chain fatty acids (SCFAs), have been linked, mainly in experimental or non-VTE settings, to thrombosis-related biology. However, most evidence remains indirect, associative, or experimental, whereas direct human VTE-specific evidence is limited and heterogeneous. Conclusions: The gut microbiome-VTE axis is biologically plausible and supported mainly by mechanistic and indirect evidence, but current data are insufficient to support strong causal conclusions. Further longitudinal, well-phenotyped, mechanistically informed studies are needed to determine whether microbiome-related pathways have measurable clinical relevance in human VTE.},
}
@article {pmid42075050,
year = {2026},
author = {Rodenes-Gavidia, A and Mas-Capdevilla, A and Florit, A and Enrique López, M and González-Hedström, D and Lamelas, A and Martorell, P and Chenoll, E and Illescas-Armijo, V and Martínez-Blanch, J and Antolín, A and Alcaide-Hidalgo, JM and Mariné-Casadó, R and Rojas, A and Rago, L},
title = {Bifidobacterium animalis subsp. lactis CECT 8145 BPL1[®] Laxative Effects in Loperamide-Induced Constipated SD Rats.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081237},
pmid = {42075050},
issn = {2072-6643},
mesh = {Animals ; *Constipation/chemically induced/therapy/microbiology/drug therapy ; Loperamide ; *Probiotics/pharmacology/administration &amp; dosage ; Gastrointestinal Microbiome/drug effects ; *Laxatives/pharmacology ; *Bifidobacterium animalis ; Rats, Sprague-Dawley ; Rats ; Male ; Gastrointestinal Transit/drug effects ; Feces/microbiology ; Disease Models, Animal ; },
abstract = {Background: Constipation is a common gastrointestinal (GI) state for which probiotics have shown promise as a relief. This study examined the laxative effects of the strain Bifidobacterium animalis subsp. lactis CECT 8145 (BPL1[®]) in a loperamide-induced rat model of constipation. Methods: Fifty-nine rats were divided into control and loperamide-induced constipation groups. Animals received a 3-day intervention with either placebo or probiotic BPL1[®] at two doses: 1.5 × 10[8] CFU (colony-forming units) (low) and 3 × 10[9] CFU (high). The study assessed several parameters to determine the probiotic's effect, including: stool and gut characteristics, gastrointestinal transit time (GTT), gene expression and gut microbiome composition. Results: While loperamide significantly decreased stool number, weight and humidity, BPL1[®] supplementation effectively restored these parameters, being more pronounced at a high dose. Microbiome analysis showed that BPL1[®] at a low dose reduced the abundance of Muribaculaceae and Muribaculum gordoncarteri, associated with constipation. In addition, Muribaculaceae abundance was negatively correlated with stool humidity. Functional microbiome profiling indicated that BPL1[®] suppressed pathways related to mucin degradation, vancomycin resistance and isoleucine biosynthesis while promoting L-lactate and pyridoxal-P (vitamin B6) biosynthesis, which may support gut motility and barrier integrity. Conclusions:Bifidobacterium animalis subsp. lactis BPL1[®] exhibits potential as a functional probiotic for relieving constipation through improving stool excretion and consistency, inducing taxonomic changes and beneficial functional modulation of the intestinal microbiome. These findings justify further investigation into the mechanisms of BPL1[®] as a probiotic for constipation management.},
}
@article {pmid42075070,
year = {2026},
author = {Beresescu, FG and Ion, RM and Monea, A and Ormenisan, A and Bereczki-Temistocle, DL and Beresescu, L and Bors, A},
title = {Age-Related Differences in Oral Microbiota Among Obese Patients with Periodontitis: A Systematic Review.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081256},
pmid = {42075070},
issn = {2072-6643},
support = {Research Grant Number 511/2/17.01.2022.//George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, Romania, Research Grant Number 511/2/17.01.2022./ ; },
mesh = {Humans ; *Obesity/microbiology/complications ; *Periodontitis/microbiology/complications ; *Microbiota ; Age Factors ; *Mouth/microbiology ; Adult ; Dysbiosis/microbiology ; Middle Aged ; *Aging ; Aged ; Female ; Male ; },
abstract = {Background: Obesity and periodontitis are linked through inflammatory and metabolic pathways, and the oral microbiota may mediate this interaction. Age-related changes in immunity, salivary function, and cumulative exposure may modify obesity-associated periodontal dysbiosis. Objective: We sought to synthesize the potential for age-related differences in the oral microbiota of adult obese patients with periodontitis and assess the strength of current literature in supporting age-specific interpretations. Methods: A systematic search of PubMed/MEDLINE, Scopus, and Embase identified 1088 records. After screening and full-text assessment, 50 studies that met the criteria for focused qualitative synthesis remained. Within that review corpus, 10 representative adult human studies provided the most direct evidence linking obesity or overweight, periodontal phenotype, oral microbiota, and age-relevant interpretation. Risk of bias was appraised with the Newcastle-Ottawa Scale. Results: Direct head-to-head microbiome comparisons between younger and older obese adults with periodontitis are rare. Direct evidence links obesity to greater periodontal inflammatory burden, enrichment of classical periopathogens and bridging taxa, and shifts in community structure. Contextual aging studies have suggested that older adults may more often harbor lower-diversity, persistence-oriented communities enriched in stress-tolerant, proteolytic, or opportunistic taxa, whereas younger obese adults more often show inflammation-amplifying consortia enriched in classical periopathogens and bridging taxa. However, these patterns remain largely hypothesis-generating because the evidence base is heterogeneous and predominantly cross-sectional. Conclusions: Age likely modifies the obesity-periodontitis-microbiota axis, but direct comparative evidence on adults remains limited. The current literature supports cautious age-aware interpretation within a systematic review framework rather than definitive age-specific microbial signatures or treatment algorithms.},
}
@article {pmid42075071,
year = {2026},
author = {Michel, A and Pourié, G and Kökten, T},
title = {Consequences of Western and Mediterranean Diets' Nutrients on the Microbiota-Gut-Brain Axis.},
journal = {Nutrients},
volume = {18},
number = {8},
pages = {},
doi = {10.3390/nu18081258},
pmid = {42075071},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diet, Mediterranean/adverse effects ; *Brain/physiology ; *Diet, Western/adverse effects ; *Brain-Gut Axis/physiology ; Dysbiosis ; *Nutrients ; *Gastrointestinal Tract/microbiology ; Neurodegenerative Diseases ; },
abstract = {Background: The prevalence of neurodegenerative diseases like Alzheimer's and mental disorders like depression or anxiety appears higher in patients with gastrointestinal tract diseases like inflammatory bowel disease (IBD). Conversely, depressed patients have higher rates of gastrointestinal disorders. These observations suggest bidirectional communication between the brain and the gastrointestinal tract, the so-called "gut-brain axis". Moreover, an altered microbiota, called "dysbiosis", has been reported in these diseases, highlighting the network between gut microbes and their host. The emergence of the microbiota as a key regulator of the gut-brain dialog has led to the establishment of the concept of the "microbiota-gut-brain axis". Objectives: In this narrative review, we outline the main interaction channels between the gastrointestinal tract and the brain. Then, we summarize current knowledge of two major diets (i.e., Western and Mediterranean diets) and the principal dietary components that modulate the microbiota-gut-brain axis to discuss the mechanisms putatively involved in intestinal, psychiatric, and neurological disorders. Conclusions: Diet is a major factor influencing the gut microbiota, and consequently, also putatively systemic mechanisms through the microbiota-gut-brain axis. Indeed, the composition of the diet is crucial for health and disease. Despite the main role of diet, the physiological, cellular, or molecular mechanisms involved in the complex communication between the microbiome, gut, and brain are still poorly understood.},
}
@article {pmid42075139,
year = {2026},
author = {Hu, Z and Zhang, Z and Huang, X and Yu, Y and Deng, Y and Song, P and Liu, Y and Zhang, L and Yang, X},
title = {Effects of Differentiation Plasmodiophora brassicae Physiological Races on the Rhizosphere Microbial Community Structure of Oilseed Rape.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040742},
pmid = {42075139},
issn = {2076-2607},
support = {2024YFD1400801//National Key Research and Development Program of China/ ; 2025ZNSFSC1117//Sichuan Science and Technology Program/ ; 1+9KJGG006//"1+9" Key Scientific and Technological Project of Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-3//Sichuan Innovation Team of National Modern Agricultural Industry Technology System/ ; },
abstract = {Clubroot caused by Plasmodiophora brassicae is a devastating soil-borne disease of oilseed rape, and physiological race differentiation of the pathogen greatly hinders disease control. The differential regulatory mechanisms of different P. brassicae races on the rhizosphere microecology remain unclear. This study aimed to reveal the race-specific effects of P. brassicae on the rhizosphere microenvironment, microbial community and nitrogen cycling of oilseed rape. A pot inoculation experiment was conducted with two typical races from Sichuan Province (race 4 CZ and race 2 KD), combined with soil physicochemical determination, high-throughput sequencing and functional prediction. The results showed that CZ exhibited a higher infection rate but a lower disease index than KD. Both races significantly decreased soil pH and reshaped soil nutrient profiles. Notably, CZ treatment caused a more pronounced pH decrease and was characterized by NH4[+]-N accumulation, whereas KD treatment was dominated by NO3[-]-N enrichment. Bacterial alpha diversity was increased by both races, following the order KD > CZ > CK. In contrast, fungal alpha diversity was decreased by both races, showing the pattern CK > KD > CZ. Distinct rhizosphere microbial community structures were formed under different race infections, and both races reduced the abundance of nitrogen-fixing bacteria and related functional genes. These findings indicate that distinct P. brassicae races shape race-specific rhizosphere microenvironments by differentially regulating soil acidification, nutrient availability and nitrogen-cycling functional microorganisms, thereby driving divergent pathogenic outcomes. This study is the first to reveal differential regulation of the rhizosphere microecology by distinct physiological races of P. brassicae, offering new insights for region-specific management of clubroot disease.},
}
@article {pmid42075142,
year = {2026},
author = {He, R and Zhou, K and Ni, J and Chen, Z and Yao, C and Fu, M and Lü, H and Yao, W},
title = {Cascade Dams and Seasonality Jointly Structure Gut Microbiome Biogeography in Saurogobio punctatus.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040745},
pmid = {42075142},
issn = {2076-2607},
support = {No 2022YFC3204201//National Key Research and Development Program of China/ ; },
abstract = {Cascade dams fragment river habitats, but how seasonal hydrology modulates the biogeography and assembly of fish gut microbiota remains unclear. We surveyed gut bacterial communities of the omnivorous fish Saurogobio punctatus across 10 reaches separated by cascade dams in the Qijiang River during the wet (summer) and dry (winter) seasons using 16S rRNA gene amplicon sequencing. Sampling was synchronized among reaches to minimize temporal variability. Winter exhibited stronger differentiation among reaches and a steeper distance-decay pattern, and reach-scale environmental heterogeneity (especially dissolved inorganic nitrogen) was more stable under weak hydrodynamics. Null model analyses showed that stochastic processes dominated in summer, with dispersal-related processes and drift being prominent under high connectivity, whereas deterministic assembly increased in winter and was mainly associated with homogeneous selection. Compositionality-aware differential abundance analysis (ANCOM-BC2) identified 409 genera with a significant seasonal differential abundance after adjusting for reach (FDR q < 0.05). Random forest classification, used as a complementary prediction-oriented feature-ranking analysis, indicated higher reach discriminability in winter, with Nitrospirota ranking among the top features. PLS-PM indicated that α-diversity had the strongest direct association with β-diversity in the specified model, whereas spatial and environmental effects were linked to β-diversity mainly through indirect, α-diversity-mediated pathways. Biologically, α-diversity may reflect an integrative summary of the within-gut taxon pool shaped by host filtering and environmentally derived inputs (e.g., diet- and habitat-associated sources), which can influence the magnitude of between-reach compositional turnover. Together, these results show that seasonal hydrological regimes tune spatial turnover and assembly of fish gut microbiota in cascade-regulated rivers.},
}
@article {pmid42075145,
year = {2026},
author = {Niraula, K and Costa, ML and Wolff, L and Cabral, H and McQuade, M and de Carvalho, LAL and Silva, D and Sousa, A and Vilchez, JI},
title = {Nature Already Did the Screening: Drought-Driven Rhizosphere Recruitment Enables Inoculant Discovery in Tomato and Reveals a Candidate Novel Paracoccus Species.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040747},
pmid = {42075145},
issn = {2076-2607},
support = {UID/04551/2025, DOI: 10.54499/UID/04551/2025//FCT - Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia, I.P., through Green-it Bioresources for Sustaina-bility R&amp;D Unit/ ; UID/PRR/04551/2025, DOI: 10.54499/UID/PRR/04551/2025//FCT - Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia, I.P., through Green-it Bioresources for Sustaina-bility R&amp;D Unit/ ; LA/P/0087/2020, DOI: 10.54499/LA/P/0087/2020//LS4FUTURE Associated Laboratory/ ; },
abstract = {Drought is a major constraint on crop productivity, and microbial inoculants are increasingly explored to mitigate plant water stress. However, most inoculant discovery pipelines rely on trait-based screening performed outside the ecological context in which beneficial plant-microbe interactions naturally arise. In natural soils, drought-exposed plants can reshape the rhizosphere environment by altering carbon allocation and root exudation, thereby selectively recruiting microorganisms compatible with water-limited conditions and effectively performing an ecological pre-selection. Here, we captured this process during early seedling establishment and leveraged drought-driven rhizosphere recruitment as a nature-guided strategy to nominate bacterial inoculant candidates. Tomato seedlings were grown in natural agricultural soil microcosms under well-watered and drought-stressed regimes, and cultivable bacteria were comparatively isolated from rhizosphere and bulk soil fractions. Recruitment-prioritized isolates were subsequently characterized through biochemical assays and genome-informed analyses to provide functional and taxonomic context and were evaluated in early inoculation assays under water stress. Drought-recruited isolates displayed distinct plant-associated responses, and genome-scale taxonomy indicated that one drought-associated isolate represents a genomically distinct lineage within the genus Paracoccus. Together, these findings highlight drought-driven rhizosphere recruitment as an ecologically grounded framework for identifying stress-compatible bacterial candidates and uncovering previously undescribed rhizosphere diversity.},
}
@article {pmid42075146,
year = {2026},
author = {García, G and Campos, MDC and Soto, J and Diaz, A and Buchaca, E and Martínez, D and Bernal, M and Escobar, V and Rodríguez, L and Valdés, E and Nuez, M and Domínguez, N and Sichel, L and Cano, RJ},
title = {Effects of the Synbiotic Formulation EDC-HHA01 on Glucose Regulation in Adults with Type 2 Diabetes and Prediabetes: A Randomized, Placebo-Controlled Study.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040749},
pmid = {42075146},
issn = {2076-2607},
support = {N/A//Chauvell, LLC/ ; },
abstract = {Microbiome-targeted interventions have shown promise for metabolic health, yet clinical evidence remains inconsistent, particularly across stages of metabolic disease. This study evaluated the metabolic effects, safety, and tolerability of EDC-HHA01, a microbiome-informed, non-pharmacologic intervention, in adults with prediabetes (PD) or Type 2 Diabetes (T2DM). In a randomized, double-blind, placebo-controlled clinical trial, participants received EDC-HHA01 or placebo for six months. The study was adequately powered (≥80%) for the primary endpoint. Outcomes included changes in glycated hemoglobin (HbA1c), indices of insulin resistance, markers of metabolic endotoxemia, safety-related laboratory parameters, and exploratory patient-reported measures. Analyses were stratified by metabolic status and background metformin use. In participants with PD, EDC-HHA01 supplementation was associated with a statistically and clinically meaningful reduction in HbA1c compared with placebo, supported by concordant improvements in fasting insulin, insulin resistance indices, and reductions in endotoxemia markers. In participants with T2DM, changes were directionally similar but attenuated and did not reach statistical significance. The intervention was well tolerated, with no serious adverse events, high adherence, and no clinically relevant adverse changes in renal or lipid parameters. Exploratory patient-reported outcomes indicated favorable acceptability but were not interpreted as efficacy endpoints. EDC-HHA01 was associated with biologically coherent, stage-dependent metabolic effects, most evident in PD. These findings support further investigation of microbiome-informed strategies as metabolic support in early-stage dysregulation.},
}
@article {pmid42075158,
year = {2026},
author = {Ma, J and Zhang, M and Liu, Q and Wang, X},
title = {Mechanical Damage Modulates Bacterial and Fungal Succession on the Surface of Hypsizygus marmoreus During Refrigerated Storage.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040762},
pmid = {42075158},
issn = {2076-2607},
support = {[grant number 20261042300840X]//Student Research Development Program (SRDP) of Ocean University of China/ ; },
abstract = {Despite the importance of surface microbiota in postharvest quality, the effects of mechanical damage on microbial succession in Hypsizygus marmoreus during refrigerated storage remain insufficiently understood. In this study, 16S rRNA gene and ITS amplicon sequencing were used to characterize the bacterial and fungal communities on intact and mechanically damaged H. marmoreus during 15 days of storage at 4 °C. Storage time, rather than mechanical damage, was the main driver of whole-community variation, although mechanical damage accelerated visible spoilage assessed qualitatively. Bacterial communities showed pronounced temporal turnover, shifting from early Firmicutes-rich assemblages to late-stage Proteobacteria-dominated communities, especially Pseudomonas. In contrast, fungal communities remained largely dominated by Ascomycota throughout storage, although mechanically damaged mushrooms showed a greater late-stage occurrence of opportunistic yeasts such as Candida. Predicted functional and phenotypic analyses further suggested late-stage increases in Gram-negative, aerobic, biofilm-forming, stress-tolerant, and potentially pathogenic bacterial traits. Because these traits were inferred from 16S rRNA gene-based prediction rather than measured directly, they should be interpreted cautiously. Overall, the results suggest that maintaining the physical integrity of H. marmoreus during postharvest handling may help preserve quality and delay the emergence of spoilage-associated microbial traits during refrigerated storage.},
}
@article {pmid42075160,
year = {2026},
author = {Matera, M and Biagioli, V and Leo, S and Drago, L},
title = {Probiotics and Antibiotics: From Empirical Practice to a Biological Rationale for Targeted Choice During Antibiotic Therapy.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040763},
pmid = {42075160},
issn = {2076-2607},
abstract = {Antibiotic therapy represents one of the strongest ecological perturbations of the human gut microbiota, inducing rapid and often prolonged alterations in community structure, metabolic activity, and functional resilience. While the use of probiotics to mitigate antibiotic-associated dysbiosis is widely adopted in clinical practice, probiotic selection is still largely empirical and insufficiently grounded in biological compatibility with specific antibiotic pressures. In this conceptual review, antibiotics are reframed not merely as antimicrobial agents, but as ecological forces that shape microbial survival, quiescence, and recolonization dynamics. We propose a biologically informed framework that distinguishes genetic antibiotic resistance from functional or ecological insensitivity, highlighting how microbial traits, such as the absence or inaccessibility of the antibiotic target, metabolic state, sporulation, and cellular architecture, influence the persistence of probiotics during antibiotic exposure. By integrating the mechanisms of action of antibiotics with key physiological and structural features of probiotic microorganisms, we develop a conceptual framework aimed at rationalizing the compatibility of probiotics and antibiotics. This framework does not imply clinical efficacy but provides an interpretative tool to guide hypothesis generation, experimental validation, and the design of future targeted probiotic strategies. A more ecologically grounded approach to probiotic selection may ultimately improve microbiota support during antibiotic therapy and advance personalized microbiome modulation.},
}
@article {pmid42075183,
year = {2026},
author = {van Essen, RRT and Kaur, J and Li, T and Sawbridge, TI},
title = {Isolation of N-Fixing Bacteria from Warm-Season Pasture Grasses and the Evaluation of Nitrogen Effects on the Bacterial Communities Present in Cenchrus clandestinus.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040786},
pmid = {42075183},
issn = {2076-2607},
support = {DB F.2//DairyBio 21-26, Future Forages Program/ ; },
abstract = {Nitrogen is essential for plant growth. Reliance on synthetic nitrogen fertilisers, however, is costly and contributes to soil degradation. Utilising nitrogen-fixing bacteria as biofertilisers may offer a sustainable alternative, reducing fertiliser costs and environmental impact. In this study, we attempted to isolate nitrogen-fixing bacteria from 14 seed batches of warm-season pasture grasses and successfully isolated bacteria from three of these batches. Whole genome sequencing confirmed the presence of the nif operon within all three isolates. Two seed batches of Cenchrus clandestinus (Hochst. ex Chiov.) Morrone from which nif-containing bacteria were isolated, along with two 'nif'-negative C. clandestinus seed batches, were used in nitrogen-limiting growth assays. This was done to evaluate the effect of the presence of seed-associated nitrogen-fixing bacteria within a seed batch on nitrogen-limited plant growth and the associated plant microbiome composition, using 16S amplicon sequencing of root and shoot samples. Initial plant growth assays revealed significantly reduced root length between plants grown from seed batches harbouring nitrogen-fixing bacteria and those without, under limiting nitrogen availability, but no resulting shoot biomass reduction was observed. The plant microbiomes of these nif-positive seed batches were also statistically similar to each other, compared to the nif-negative seed batch plants. Plant microbiomes of all four C. clandestinus seed batches were significantly different from their original seed microbiomes, showing shifts in community composition. This study demonstrates the presence of potential nitrogen-fixing bacteria associated with warm-season pasture grass seeds at low abundance and reveals differences in plant-associated bacterial community composition between seed batches harbouring and lacking these bacteria.},
}
@article {pmid42075197,
year = {2026},
author = {Alikhan, H and White, B and Sterrett, JD and Farag, M and Lowry, CA and Dawud, LM and Judge, T and Perez, L and DeSipio, J and Phadtare, S},
title = {A Gut Signature of Microbiome, Bile Acid, and Quorum-Sensing Profiles Is Associated with Helicobacter pylori Infection and Disease Progression.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040801},
pmid = {42075197},
issn = {2076-2607},
support = {NA//Camden Health Research Initiative grant/ ; },
abstract = {Recent evidence suggests that Helicobacter pylori can act outside stomach by influencing the gut microbiome. We hypothesize that interactions between H. pylori and the gut microbiome, and the resulting changes in the gut chemicals (bile acids and bacterial signaling molecules involved in quorum sensing, e.g., autoinducer-2/AI-2), influence pathogen survival, antibiotic response, and disease progression. Our gut microbiome, bile acid, and AI-2 analyses showed that H. pylori patients had decreased alpha diversity (p = 0.05), increased AI-2 concentration (p = 0.019), decreased taurine-conjugated bile acids, and increased unconjugated bile acids. A co-occurring module of Prevotella, Holdemanella, and Subdoligranulum, was higher in patients (p = 0.04) and relative abundance of Allisonella was positively associated with levels of unconjugated bile acids, chenodeoxycholic acid, and cholic acid (p = 0.05 and 0.02, respectively). Our study is the first to characterize the gut microbiome-metabolome signature (bile acids and AI-2) in H. pylori patients. Abundance of certain bacteria that deconjugate bile acids along with increased AI-2 possibly gives selective advantage for H. pylori growth, further reducing microbial diversity. Taurine-conjugated bile acids inhibit H. pylori growth. We propose a model describing interplay of these factors in H. pylori disease progression, suggesting therapeutic targets worth exploring with rising antibiotic resistance.},
}
@article {pmid42075205,
year = {2026},
author = {Xin, Y and Chen, L and Ijaz, M and Chen, R and Manzoor, N and Alrafaie, A and Wang, X and Luo, J and Li, B and Shou, L},
title = {Symbiotic Bacterial Diversity, Functional Profiling and Antibiotic Susceptibility of the Red Imported Fire Ant.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040808},
pmid = {42075205},
issn = {2076-2607},
support = {2024-02-08-00-12-F00045//Shanghai Agricultural Science and Technology Innovation Project/ ; PSAU/2026/R/1447//Prince Sattam bin Abdulaziz University/ ; },
abstract = {The red imported fire ant (RIFA), Solenopsis invicta, is a globally invasive pest that causes substantial ecological, agricultural, and public health challenges. Conventional control strategies primarily depend on chemical insecticides, which present environmental risks and limited long-term efficacy. In this study, we comprehensively investigated the bacterial microbiota of S. invicta and compared it with a sympatric non-target ant species (Pheidole nodus) to explore the ecological significance and biocontrol potential of symbiotic bacteria. High-throughput 16S rRNA sequencing revealed that the symbiotic bacterial community of S. invicta exhibited markedly higher richness and diversity. A total of 1651 amplified sequence variants (ASVs) were identified, of which 1089 ASVs are unique to the RIFAs, and 460 are unique to non-target ants. Linear discriminant analysis effect size (LEfSe) highlighted 33 biomarker taxa (score > 6.5), with strong enrichment of Stenotrophomonas, Serratia, Pseudomonas, Luteibacter, Bradyrhizobium, Brucella, Smaragdicoccus, Gordonia, and Aeromonas. Functional predictions and enzymatic assays in vitro demonstrated that dominant cultivable genera, particularly Stenotrophomonas (SI-7, SI-17), Serratia (SI-1, SI-3, SI-6, SI-18), and Pseudomonas (SI-2, SI-8, SI-9, SI-11, SI-19), exhibit substantial proteolytic and lipolytic activity, suggesting key roles in nutrient metabolism and host ecological adaptability. Antibiotic susceptibility profiling further revealed that florfenicol shows broad-spectrum inhibitory activity against these dominant symbionts. These findings indicate that disrupting dominant symbiotic bacteria may impair host physiology and thus serve as a targeted control strategy. Overall, the study elucidates the diversity, functional potential, and biocontrol applicability of the S. invicta microbiome, providing a foundation for developing sustainable, microbiome-based pest management approaches.},
}
@article {pmid42075207,
year = {2026},
author = {Ozkul, C and Duman, E and Kocak, E and Karakan, YT and Cindoruk, C and Gurkan, OE and Cindoruk, M and Karakan, T},
title = {Oral-Gut Microbiome Axis in Crohn's Disease: A Potential Role of Ectopic Colonization.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040810},
pmid = {42075207},
issn = {2076-2607},
abstract = {Recently, an oral-gut communication axis has been proposed. Herein, we review clinical studies reporting differences in oral microbial communities in inflammatory bowel diseases (IBDs), with a focus on Crohn's Disease (CD), as well as evidence from experimental models. While available studies support evidence for the direct transmission of oral-derived bacteria to gut, further work is needed to clarify whether such transmission results in stable colonization of intestinal niches and the establishment of a persistent host-microbe state that influences host physiology. To date, evidence from clinical and murine studies suggests three routes of the oral-gut axis, which in turn directly or indirectly exacerbate intestinal inflammation and contribute to IBD pathogenesis: (i) direct invasion of pathobionts through swallowing, (ii) migration of the oral pathogen activated pro-inflammatory immune cells, (iii) systemic inflammation triggered by oral pathogens such as Porphyromonas gingivalis. Although the role of oral microbiome in systemic diseases is becoming more apparent, sophisticated clinical and experimental studies are needed to elucidate the direct and indirect oral-gut communication mechanisms, including the contribution of oral microbial metabolites. Future directions may include evaluating the diagnostic and therapeutic potential of the oral microbiome and metabolome.},
}
@article {pmid42075212,
year = {2026},
author = {John, OP and Afolabi, KO and Ngene, AC and Tanimowo, WO and Adewoyin, MA and Osho, MB and Reuben, RC},
title = {Enterococcus Species: Multifaceted Probiotic Potential and Safety Considerations.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040815},
pmid = {42075212},
issn = {2076-2607},
abstract = {Enterococcus spp. are common but not predominant commensal bacteria that inhabit the gastrointestinal tracts of humans and animals and are widely distributed in various environmental matrices and diverse food sources. Multiple strains of beneficial enterococci are increasingly utilized as protective cultures, alternatives to antibiotics, and probiotics for controlling pathogens, mitigating disease, modulating the microbiome, and supporting overall host health. They also support food fermentation and safety, enhance sensory properties, and produce bioactive compounds such as bacteriocins with strong pathogen-inhibitory activity and multifarious health benefits. Despite their advantages in health and agrifood systems, their association with healthcare-associated infections and the spread of antimicrobial resistance raises concerns about their safety. These risks underscore the need for stringent safety evaluations before their use as probiotics, alternatives to antibiotics, or protective cultures. Here, we provide a comprehensive atlas of the multifaceted probiotic and antimicrobial potential, as well as safety considerations of beneficial enterococci. This would provide a valuable resource for future research, regulatory assessments, and applications in the agrifood system and healthcare.},
}
@article {pmid42075219,
year = {2026},
author = {Masood, M and Ozog, D and Ma, T and Ceresnie, M and Pourang, A and Johnson, CC and Qiu, X and Levin, A and Veenstra, J},
title = {Skin Microbiome Patterns Associated with Basal Cell Carcinoma: A Case Series.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040822},
pmid = {42075219},
issn = {2076-2607},
abstract = {Basal cell carcinoma (BCC) is the most common malignancy worldwide, yet the role of the skin microbiome in BCC remains poorly defined. In this cross-sectional observational case series, we compared the cutaneous microbiome of BCC lesions with matched perilesional and control skin using whole-genome shotgun sequencing in an intra-patient, multi-site sampling design. BCC samples demonstrated reduced microbial richness and significant shifts in community composition compared with matched control skin. Specifically, BCC lesions exhibited significantly lower Chao1 diversity (β = -484.6, 95% CI: -772.1 to -197.2, p = 0.003). Differences in overall microbial composition were confirmed by PERMANOVA analysis based on Bray-Curtis and Jaccard distance metrics (R[2] = 12.6% and 9.7%, respectively; both p = 0.01). At the species level, Cutibacterium acnes was significantly reduced in BCC samples compared with controls (β = -0.31, 95% CI: -0.45 to -0.16, p = 0.0004), corresponding to an approximately 27% lower geometric mean relative abundance. Functional profiling suggested shifts in microbial metabolic potential, with pathways related to redox balance and lipid-associated processes differentially represented in BCC samples relative to controls. Together, these findings demonstrate that BCC lesions are associated with localized alterations in microbial diversity, community composition, and inferred functional potential. These results support the presence of a tumor-associated microbiome signature in BCC; however, further studies in larger and more diverse cohorts are needed to determine whether these changes contribute to tumor development or reflect adaptation to the tumor microenvironment.},
}
@article {pmid42075229,
year = {2026},
author = {Lai, R and Wang, Z and Liu, P and Tong, J and Ahmed, Z and Cui, R and Gu, Y and Luo, G},
title = {Environmental Altitude and Host Genetics Shape Divergent Microbiota and a Conserved Resistome in Porcine Intestinal Niches.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040832},
pmid = {42075229},
issn = {2076-2607},
support = {Grant No. RQD2025005//Southwest Minzu University Research Startup Funds/ ; 32472888//National Natural Science Foundation of China/ ; XZ202501ZY0147//Science and Technology Projects of Xizang Autonomous Region/ ; 2024YFHZ0373//Sichuan Science and Technology Program/ ; sccxtd-2026-08//Program for Pig Industry Technology System Innovation Team of Sichuan Province/ ; 2024MS150//he Sichuan Provincial Administration of Traditional Chinese Medicine Science and Technology Research Special Project/ ; },
abstract = {Environmental stressors and host genetics influence gut microbiota and antimicrobial resistance, but their combined effects across intestinal niches remain poorly unexplored. We conducted a metagenomic analysis of 60 jejunal and cecal samples from 30 native Chinese pigs across three altitudes (500 m, 1400 m, and 3850 m). The aim was to disentangle the interactive impacts of altitude, breed, and intestinal site on microbiome structure and antibiotic resistome dynamics. The cecal microbiota was taxonomically conserved and strongly associated with breed. Conversely, while jejunal communities exhibited structural variations among the sampled cohorts, differences in alpha diversity (Shannon index, p < 0.01) appeared to be primarily associated with breed differences rather than an independent altitudinal effect. High-altitude Tibetan pigs showed an enrichment of Bifidobacterium and Pseudomonas, which may be linked to hypoxia adaptation. Despite a shared core resistome (88 ARG types), the cecum harbored significantly higher ARG abundance than the jejunum within-breed comparisons of Tibetan pigs across altitudes; this revealed stable ARG profiles (p > 0.05) suggesting that, although some descriptive differences were observed, the independent effect of altitude weakens when the genetic effect is taken into account. Furthermore, carbohydrate-active enzymes (e.g., CBM13, GH33) correlated positively with ARG abundance. In conclusion, the jejunum appears to act as an environmentally responsive niche, while the cecum exhibits a higher ARG abundance that is closely associated with the host breed.},
}
@article {pmid42075232,
year = {2026},
author = {Toma, R and Hu, L and Shen, N and Patridge, E and Wohlman, R and Banavar, G and Vuyisich, M},
title = {The Human Gut Microbiome Activity Is Resilient and Stable for up to Six Months: A Large Stool Metatranscriptomic Study.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040835},
pmid = {42075232},
issn = {2076-2607},
abstract = {The human microbiome influences health and disease through diverse biochemical and functional outputs (e.g., enzymes, structural proteins, metabolites, and other cellular components) that affect nearly every aspect of human physiology. Metatranscriptomics (MT), an unbiased RNA sequencing approach, is a high-throughput and high-content method that quantifies both gut microbial taxonomy and active biochemical functions. Because microbial community composition and gene expression are dynamic, understanding temporal variation in the gut metatranscriptome across multiple time scales is essential. Here, we report the temporal dynamics of gut microbiome species and functions using a large cohort (n = 6157) with a clinically validated stool MT test. We quantified microbiome stability from hours to years and assessed taxonomic and functional resilience to major luminal perturbations, such as colonoscopy bowel preparation. Longitudinal analyses of samples collected within the same day, and across days, weeks, months, and years, revealed consistently high stability in both composition and gene expression within a single day and, importantly, across an approximate six-month period. Among individuals reporting stable diets and no antibiotic exposure, taxonomic and functional profiles remained stable for up to three years. Following colonoscopy preparation, our preliminary study of the microbiome demonstrated strong resilience, returning to its pre-procedure state within one week. Overall, these findings demonstrate that the gut microbiome is generally stable over a six-month time frame, with longer-term changes occurring gradually. These findings support the robustness of stool-based MT profiling for species-level and pathway-resolved functional analysis in longitudinal research and health applications.},
}
@article {pmid42075233,
year = {2026},
author = {Mousa, WK and AlShami, R and Ghemrawi, R},
title = {Shared Microbial Blueprints Underlying Symbiotic Plasticity in Desert Plant Endophytes.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040836},
pmid = {42075233},
issn = {2076-2607},
support = {SWARD-F23-020.//Sandooq Al Watan/ ; },
abstract = {The desert ecosystem harbors a resilient microbial community that sustains plant life under extreme stress. Understanding the endophytic microbiota of desert flora provides key insights into how these microorganisms enable plant survival and maintain ecological balance in arid landscapes. To date, the endophytic bacterial communities of dominant desert plants in the Arabian Peninsula have not been comprehensively characterized. Here, we investigated the endophytic microbiota of five co-adapted desert species, namely, Schweinfurthia papilionacea, Sesuvium verrucosum, Ochtocloa compressa, Helianthemum nummularium, and Convolvulus arvensis. These plants coexist in hyper-arid habitats and exhibit exceptional tolerance to drought, salinity, and nutrient scarcity. We hypothesized that, despite their phylogenetic divergence, these plants host functionally convergent microbial communities shaped by desert selection pressures. Using 16S rRNA gene amplicon sequencing, we obtained 3.4 million high-quality reads from 25 samples. Clustering at 97% similarity revealed 35 phyla and 17 dominant genera, highlighting notable microbial richness and ecological complexity. Alpha-diversity indices showed comparable species richness across hosts, while beta-diversity indicated community differentiation driven by environmental filtering. The dominant phyla included Pseudomonadota, Actinomycetota, Cyanobacteriota, and Bacillota, reflecting microbial adaptation to extreme desert conditions. Functional pathway prediction revealed enrichment of genes associated with DNA repair and protein turnover, suggesting metabolic flexibility and enhanced survival under stress. Overall, this study provides a comparative metagenomic insight into the endophytic bacterial communities of five desert plant species, uncovering a consistent pattern of functional convergence across diverse hosts. The findings suggest the presence of shared functional traits among the endophytic microbiota examined here, offering preliminary evidence for microbial contributions to plant resilience in arid environments.},
}
@article {pmid42075234,
year = {2026},
author = {Pan, W and Gao, L and Xu, Y and Guo, H and Abdulla, A and Abdurim, A and Liu, X and Gao, X and Wu, H},
title = {Comparative Effects of Exogenous Organic Amendments on Rhizosphere Microbial Communities and Soil Properties in Continuous Cropping Watermelon.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040837},
pmid = {42075234},
issn = {2076-2607},
support = {xjnkywdzc-2025003-12-04//Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; XJARS-06-06//Earmarked Fund for Xinjiang Agriculture Research System/ ; },
abstract = {Continuous cropping obstacles in watermelon are closely linked to rhizosphere microbial imbalance, posing a major threat to the sustainability of the industry in Xinjiang. Exogenous additives are widely used to regulate soil health, yet comprehensive comparisons of their mechanisms and effects remain limited. In this study, a field experiment was conducted under continuous watermelon cropping conditions in Xinjiang to evaluate the impact of eight treatments, including chemical fertilizer (NPK) alone and its combination with organic fertilizer (NPKM), glucose (NPKG), oxalic acid (NPKOA), amino acids (NPKGA), citric acid (NPKCA), and acetic acid (NPKAA), with unfertilized soil as the control (CK). Treatment effects were assessed through soil physicochemical analysis, fruit quality evaluation, and high-throughput sequencing (16S rRNA and ITS). Among all treatments, NPKM showed the greatest improvement in soil fertility, increasing soil organic matter by 13.91%, total nitrogen by 23.08%, and single fruit weight by 35.75% compared to CK. NPKGA also enhanced fruit weight (+33.06% vs. CK) and increased catalase activity, while oxalic acid exhibited the strongest activation of alkaline phosphatase. Microbiome analysis revealed that NPKM and NPKAA significantly reshaped both bacterial and fungal community structures. NPKM enriched beneficial taxa such as unclassified Chitinophagaceae and Lophotrichus, whereas NPKCA enriched the biocontrol bacterium Pseudomonas chlororaphis. Soil organic matter and total nitrogen were identified as key environmental drivers, showing significant positive correlations with core bacterial genera (Dokdonella) and negative correlations with the pathogenic fungus Alternaria. Collectively, this study elucidates the distinct mechanisms of various additives by linking treatment-specific microbial shifts to key soil factors and crop performance, providing a theoretical and technical framework for mitigating watermelon continuous cropping obstacles through rhizosphere environmental regulation.},
}
@article {pmid42075236,
year = {2026},
author = {Wang, Z and Ma, C and Huang, H and Ke, S and Lv, J and Hu, J and Wang, S and Bao, Z},
title = {Holo-2bRAD: A Hologenomic Method for High-Resolution Analysis of Coral Microbiomes During Bleaching.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040840},
pmid = {42075236},
issn = {2076-2607},
support = {2025B1111180001//Guangdong S&amp;T Program/ ; 2025A04J3824//GCI Science &amp; Technology (China)/ ; SOLZSKY2025013//Department of Science and Technology of Hainan Province/ ; },
abstract = {Coral reefs are biodiversity hotspots increasingly threatened by climate-induced bleaching, yet profiling the coral holobiont-the host and its associated microbiota-remains technically challenging due to high host-DNA contamination (often >95%) and the lack of comprehensive reference databases. Here, we present holo-2bRAD, a type IIB restriction site-associated DNA sequencing approach. This method, strategically integrated with a meticulously curated hologenome database (comprising 404,946 microbial genomes and 56 coral-derived metagenome-assembled genomes), effectively overcomes overwhelming host contamination (~99%). We demonstrate its exceptional species specificity (99.92%) in profiling Galaxea fascicularis (Linnaeus, 1767; Order Scleractinia, Family Euphylliidae) holobionts across bleaching severities, thereby validating its technical feasibility. Leveraging this high-resolution tool, our hologenome analysis revealed significant restructuring of coral-associated microbiota during bleaching, where microbial shifts (e.g., depletion of beneficial Thermoanaerobacterium thermosaccharolyticum and enrichment of stress-responsive bacteria) correlated more strongly with bleaching phenotypes than host genetic variation. By providing cost-effective, multi-domain hologenome profiling at unprecedented resolution, holo-2bRAD offers a practical tool for investigating holobiont dynamics and developing microbiome-informed coral conservation strategies.},
}
@article {pmid42075280,
year = {2026},
author = {Cannon, M and Stevenson, BS},
title = {In Vitro Inhibition of Pathogens by Polyols: Optical Density-Based Screening and Implications for the Oral-Systemic Axis.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040884},
pmid = {42075280},
issn = {2076-2607},
support = {unrestricted//Swanson Fund/ ; },
abstract = {Polyols are widely used as non-cariogenic sweeteners in foods and oral care products, yet their comparative activity against diverse oral microbes and their potential relevance to the oral-systemic axis remain incompletely defined. Here, we performed an in vitro, optical density (OD)-based screening of four polyols-allulose, D-mannose, erythritol, and xylitol-against Streptococcus mutans, Streptococcus anginosus, Candida albicans, and Fusobacterium nucleatum. Cultures were grown with polyols at 1-20% (w/v), and OD600 was recorded at organism-specific endpoints (~24 h). Allulose, erythritol, and xylitol produced strong, concentration-dependent suppression of streptococcal growth at ≥5-10%, whereas C. albicans showed minimal changes across the tested range. F. nucleatum was highly sensitive to allulose, D-mannose, and xylitol at ≥5% (reducing OD to ≤13% of the untreated control), while low concentrations of D-mannose and erythritol increased OD beyond that of the control, suggesting species-specific utilization or stress responses. One-way ANOVA with Tukey's HSD post hoc testing supported significant between-polyol differences for most concentrations in Streptococcus spp. and F. nucleatum. Collectively, these results identify polyol- and taxon-specific growth phenotypes that can inform the formulation of swallow-safe oral hygiene products and motivate follow-up work in polymicrobial biofilm models and clinical studies targeting oral inflammation and downstream systemic risk.},
}
@article {pmid42075295,
year = {2026},
author = {Liu, Y and Sun, X and Lai, J and Wei, S and Sheng, Y and Zhang, Y and Zhang, Q and Ye, P and Huang, L and Zeng, H},
title = {Research Progress on Rhizosphere Microbiota for Controlling Soil-Borne Diseases: Mechanisms, Applications, and Challenges.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040900},
pmid = {42075295},
issn = {2076-2607},
support = {2025ZNSFSC0203//Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; },
abstract = {Soil-borne diseases pose a severe threat to global agricultural production and food security. Traditional chemical control methods face significant challenges, including environmental pressure, pathogen resistance, and food safety concerns. The rhizosphere microbial community, often termed the plant's 'second genome', plays a pivotal role in maintaining plant health and defending against pathogen invasion. Recent advances in multi-omics technologies, synthetic microbial communities (SynComs) construction, and rhizosphere metabolomics have significantly advanced our understanding of the mechanisms by which rhizosphere microbiomes suppress soil-borne diseases. This review systematically summarizes the following: 1. key drivers of rhizosphere microbial community assembly, particularly plant "cry for help" signaling; 2. core beneficial microbial taxa and their disease-suppressive mechanisms; 3. the critical role of microbial interaction networks; 4. microbiome-based management strategies and their application progress; and 5. current challenges and future research directions. Compared with previous reviews that separately discussed rhizosphere microbiota, disease-suppressive soils, synthetic microbial communities (SynComs), or prebiotics, this review uniquely integrates multiple levels of regulation, from plant genetic determinants ('M genes') and root exudate-mediated 'crying for help' to microbiome engineering (SynComs and prebiotics) and cross-kingdom interactions (bacteria-fungi-protists-phages). A central conceptual axis of 'M genes → microbiome engineering → breeding' is proposed, bridging plant genetics, microbial ecology, and crop improvement for durable disease suppression. Ultimately, this work aims to provide a theoretical foundation for developing efficient and sustainable green control technologies against soil-borne diseases.},
}
@article {pmid42075308,
year = {2026},
author = {Jian, Y and Xiong, K and Zou, J and Du, X and Liu, S and Yue, Y and Gao, J and Guo, W and Wang, Q},
title = {Ammonia Exposure Elevated 5-HT Expression, Reprogrammed Transcriptome and Microbiota Community in Yellow Catfish (Pelteobagrus fulvidraco) Gill During Early Ontogeny.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040912},
pmid = {42075308},
issn = {2076-2607},
support = {2022YFD2400900//National Key Research and Development Program/ ; },
abstract = {The accumulated ammonia within the recirculating aquaculture systems threaten fish health, while little is known about the influences during early fish ontogeny. Using larval and juvenile yellow catfish (Pelteobagrus fulvidraco) as a model, a comprehensive experiment exposing fish to varying total ammonia nitrogen concentrations (0, 10, 20 mg/L for larvae; 0, 25, 125 mg/L for juveniles) was conducted to evaluate the effects on gill transcriptome and microbiota along with the serotonergic regulation. First, the serotonin (5-HT) signal, which controls oxygen chemoreception and ventilation, was mainly detected in the surface of the body of the larvae, and then shifted to gill filaments of juveniles, showing a transition from cutaneous to branchial respiration. Both larval and juvenile yellow catfish exhibited reduced survival, damaged gill structure, and elevated 5-HT expression after ammonia exposure, as well as upregulated tph1b, slc6a4b, scgn and lama5 expression with the increased ammonia concentration, indicating the effects on respiratory function via serotonergic regulation. Further transcriptome analysis was conducted in juveniles to identify the differentially expressed genes (DEGs) and thus, to illustrate more detailed responses after ammonia exposure; KEGG enrichment analysis of DEGs indicated the coping strategy shifted from metabolic buffering to metabolic elimination via glutamine synthesis with the increased ammonia level. The qRT-PCR experiment also identified the increased expression of genes involved in the urea cycle-such as ass1, asl and glula-with the increased ammonia level. Considering the potential contributary role of microbiome to gill health, 16S sequencing was conducted on the gill in the control and the 125 mg/L ammonia-exposed group. Ammonia exposure at 125 mg/L induced significant variation in Simpson index and a marked decline in β diversity. Notably, the abundance of opportunistic pathogens such as Pseudomonadota increased, while the abundance of Deinococcota and Deinococcus-which were renowned for exceptional stress resistance capacity-decreased after ammonia exposure. Thus ammonia exposure disrupts the transcriptomic and microecological balance within gill mucosa, which may elevate the risk of pathogenic infection. Overall, our study provided the first evidence of serotonergic regulation on early fish respiration during ammonia exposure, and also offered new theoretical insights into the involvement of microorganisms in ammonia toxicity.},
}
@article {pmid42075311,
year = {2026},
author = {Cruells, A and Eguren, C and Robainas Barcia, A and Martínez, H and Sharaf, M and Ruiz, C and Sánchez-Baos, A and Carrón, N and Bou, L and Pérez, M and De Lucas, R and Guerra-Tapia, A},
title = {Shotgun Metagenomic Characterization of Acne Microbiota Before and After Treatment with a Topical Biotechnological Phytocomplex: Understanding Skin Dysbiosis.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040915},
pmid = {42075311},
issn = {2076-2607},
abstract = {This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, metagenome assembly, functional annotation, and phage identification. Results showed that after treatment, microbial diversity increased, reflecting a more balanced microbial composition. Cutibacterium acnes levels were reduced, particularly virulent IA1/IA2 phylotypes, whereas non-pathogenic or unclassified strains increased. Opportunistic pathogens such as Klebsiella pneumoniae were no longer detected, and beneficial genera including Psychrobacter and Dermabacter were enriched. Functional analysis showed reduced virulence- and biofilm-related pathways, alongside enhanced tryptophan metabolism, SCFA production, lipid synthesis, and riboflavin and folate biosynthesis. Fungal populations, dominated by Malassezia, became more evenly distributed, with notable post-treatment reductions in M. arunalokei, Exophiala spinifera, and Wickerhamomyces anomalus. Phage populations mirrored bacterial changes, with enrichment of Cutibacterium-associated phages post-treatment. These findings demonstrate that the phytocomplex promotes functional rebalancing of the skin microbiota by reducing pathogenic features while maintaining ecosystem stability. The inhibition of quorum sensing, potentially mediated by N-acyl-homoserine lactone acetylation, emerged from metabolic pathway annotation as a hypothetic key mechanism impairing bacterial communication and virulence associated with acne vulgaris.},
}
@article {pmid42075321,
year = {2026},
author = {Wang, W and Wang, Z and Zhang, P and Zhang, J},
title = {Environmental Regulation of Gut Microbial Networks Links to Growth Variation in Schizopygopsis younghusbandi Across Contrasting Aquaculture Systems.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040925},
pmid = {42075321},
issn = {2076-2607},
support = {XZ202501JD0019; XZ202402ZD0005; XZ202401ZY0059//Science and Technology Program of Tibet Autonomous Region/ ; XZ202501JD0019//the Base and Talent Program Projects of Science and Technology Program of Tibet Autonomous Region/ ; 42371170//National Natural Science Foundation of China/ ; //the Agricultural and Animal Husbandry Science and Technology Innovation Project/ ; },
abstract = {Schizopygopsis younghusbandi is an endemic and economically important fish in the Qinghai-Xizang Plateau, but its aquaculture is limited by harsh environmental conditions and incomplete understanding of host-microbiome-environment interactions. This study applied metagenomic sequencing to examine how different culture environments affect growth, water microbial communities, and gut microbiome network stability. Three-year-old juveniles (initial body weight 50.57 ± 1.88 g) were reared for 90 days in five systems: conventional pond (P), wetland (WL), concrete tank (G), river (R), and recirculating aquaculture system (RC). No significant differences in initial body weight or length were observed among groups (p > 0.05). Fish in the RC system achieved the highest final body weight, weight gain rate, and specific growth rate (p < 0.05), while survival rates were highest in the river and RC groups and lowest in ponds (p < 0.05). Microbial diversity and community composition differed significantly among culture modes, with bacterial and protozoan communities showing the strongest environmental responsiveness. Co-occurrence network analyses revealed that RC and G systems exhibited higher network complexity, density, and proportion of positive correlations, reflecting enhanced microbial interaction and ecological stability, whereas the WL system showed reduced network connectivity. Correlation analysis indicated that bacterial abundance was positively associated with total nitrogen, total phosphorus, and dissolved oxygen (p < 0.05), highlighting environmental regulation of microbial assemblages. Overall, the aquaculture environment shapes gut microbial networks, which closely relate to growth performance. Recirculating aquaculture systems can mitigate growth limitations in plateau fish by stabilizing the environment and reinforcing gut microbial communities, providing a sustainable strategy for high-altitude aquaculture development.},
}
@article {pmid42075340,
year = {2026},
author = {Cheng, L and Shen, Q and Wang, Y},
title = {Root-Zone Nitrogen Fertilization Increases Oilseed Rape Yield: Reprogramming Rhizosphere N-Cycling and Strengthening Soil-Plant Coupling.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081137},
pmid = {42075340},
issn = {2223-7747},
support = {2024J0487//Scientific Research Fund Project of the Education Department of Yunnan Province/ ; 202304BQ040005//Project of Science and Technology Department of Yunnan Province/ ; },
abstract = {Root-zone nitrogen fertilization (RZF) can increase crop N uptake and yield, yet the underlying rhizosphere N-cycling functional mechanisms remain insufficiently resolved. In a field experiment with winter oilseed rape (Brassica napus L.), RZF was compared with conventional fertilization (CF) under the same N input rates, alongside a zero-N control (N0). Compared with CF, RZF significantly increased seed yield (by 0.44 t ha[-1]) and aboveground N uptake (by 20.45 kg ha[-1]), while simultaneously enriching rhizosphere mineral N pools (NH4[+]-N and NO3[-]-N by 54.50% and 56.02%, respectively). Shotgun metagenomics revealed that RZF reprogrammed rhizosphere N-cycling functional potential, characterized by enhanced nitrogen fixation, reduced nitrification and denitrification, and a tendency toward increased assimilatory nitrate reduction. These module-level shifts were supported by concordant changes in key functional genes, indicating greater genetic potential for N retention and assimilation (nifD, glnA, gltB, nasA, napB, nrfA) and reduced potential for nitrification- and denitrification-driven N losses (amoB/C, narI, nirK, norB). Taxonomic composition analysis showed enrichment of Bradyrhizobium and suppression of key nitrifier taxa (Nitrosospira and a Nitrososphaeraceae-affiliated taxon) under RZF. Rhizosphere pH exhibited the strongest Mantel correlation with multiple N-cycling modules, and rhizosphere available N (AN; sum of NH4[+]-N and NO3[-]-N) was positively associated with plant N traits and yield. Structural equation modeling supported a pathway in which a functional balance index (retention/assimilation vs. loss/oxidation) increased AN (0.22), and AN strongly promoted yield (0.90). Collectively, these results elucidate a rhizosphere-centered mechanism whereby localized N placement strengthens soil-plant N coupling and enhances crop productivity through reprogramming microbial N-cycling functional potentials, positioning rhizosphere N processes as a key mechanistic bridge for microbiome-informed optimization of root-zone fertilization.},
}
@article {pmid42061662,
year = {2026},
author = {Mahooti, M and Safaei, F and Abdolalipour, E and Ahmadbeigi, G and Shokouhi, H and Fallah, T and Zare, D},
title = {Short-chain fatty acid-producing probiotics: an effective approach for modulating gut dysbiosis and mitigating inflammatory responses.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108520},
doi = {10.1016/j.micpath.2026.108520},
pmid = {42061662},
issn = {1096-1208},
abstract = {Alterations in the intestinal microbiome participate with inflammatory responses and associate with pathological outcomes, along with changing the production of myriad metabolites such as short-chain fatty acids. A growing body of evidences have indicated that different dietary components, like polyphenols, may also increase short-chain fatty acids production by gut microbiota, playing a preventative role against various diseases, such as type 2 diabetes (T2D), obesity, cardiovascular diseases (CVD), and even mitigate inflammation attributed to disorders like those observed in COVID-19 and even cancer. Some infectious illnesses alter the microbiome, resulting in a decrease in the production of fermentative products, such as short-chain fatty acids. Managing the microbiome with probiotics to compensate the changes caused by these diseases leads to improvements in the microbiome and a reduction in inflammation. This reduction may even have positive effects in managing cancer. In this review, we compile cutting-edge discoveries on probiotic-derived SCFAs, highlighting their mechanisms associated with their prophylactic and therapeutic potential and their impact across infectious and non-infectious diseases, particularly in mitigating inflammation. Therefore, this review seeks to facilitate the development, evaluation, and clinical implementation of SCFAs-based interventions in future studies, particularly in preventive and therapeutic clinical settings.},
}
@article {pmid42061740,
year = {2026},
author = {Li, Y and Zhang, L and Paster, BJ and Xiao, J},
title = {Microbial alteration after intensive fluoride varnish treatment in children with early childhood caries: An exploratory study.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106720},
doi = {10.1016/j.jdent.2026.106720},
pmid = {42061740},
issn = {1879-176X},
abstract = {OBJECTIVE: In this study, we aimed to evaluate the effect of an intensive fluoride varnish (FV) regimen on oral microbial communities in children with early childhood caries (ECC).<br><br>METHODS: Twenty-six children, aged 2 to 5 years, diagnosed with early-stage ECC, were included. They were treated with 5% NaF varnish three times over 2 weeks. Pooled supragingival plaque samples (n&#x202f;=&#x202f;70) were collected and used for extracting total bacterial DNA. The microbial composition was analyzed using the Human Oral Microbe Identification Next-Generation Sequencing (HOMINGS) method.<br><br>RESULTS: Analysis of 6,172,618 high-quality 16S rRNA amplicons revealed significant changes in the relative abundance of oral microbiome taxa at the phylum level immediately after FV treatment (p&#x202f;=&#x202f;0.021). Although the relative abundance of several known cariogenic species decreased, none of the shifts were statistically significant at the 1-week visit or persisted at the 2-week visit. At the genus level, children with higher mutans streptococci levels showed higher relative abundance of Bacteroidetes, Firmicutes, and Spirochaetes (p&#x202f;=&#x202f;0.001, p&#x202f;=&#x202f;0.023, and p&#x202f;=&#x202f;0.001), respectively. At the species level, FV treatment significantly increased the relative abundance of Corynebacterium durum (p&#x202f;=&#x202f;0.009) and Neisseria sicca (p&#x202f;=&#x202f;0.031) but did not significantly disrupt commensals within the microbial community.<br><br>CONCLUSIONS: Intensive FV application alone does not significantly alter the core oral microbiome of children with untreated ECC. The treatment may temporarily reduce the cariogenic microbial burden immediately after treatment. However, the long-term effects of FV on the oral microbiome still remain uncertain.},
}
@article {pmid42061771,
year = {2026},
author = {Wang, K and Jin, K and Fei, Q and Li, T and Wang, S and Yu, X and Wu, W and Ye, L},
title = {Mucosal-Associated Invariant T (MAIT) cells in the Tumor Microenvironment: Opportunities and Challenges.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105340},
doi = {10.1016/j.critrevonc.2026.105340},
pmid = {42061771},
issn = {1879-0461},
abstract = {Mucosal associated constant T (MAIT) cells are a unique subset of innate T lymphocytes that play a critical role in the host's defense against bacterial and viral pathogens. However, its function in the tumor microenvironment (TME) remains controversial. This review systematically explores the dual role of MAIT cells in tumor immunity by integrating existing literature evidence, and proposes a three-level causal hierarchy that determines the functional fate of MAIT cells. In order to solve the prognostic paradox across cancer types, we introduced the barrier and systemic tumor classification criteria. Based on the above mechanisms, we explored clinical translation pathways such as MR1 targeted intervention, iPSC derived reMAIT cells, and CAR-MAIT engineering. Future research should utilize spatial omics and dynamic tracking techniques to achieve a shift from descriptive observations to precise predictive healthcare driven by biomarkers.},
}
@article {pmid42061776,
year = {2026},
author = {Li, SQ and Wang, JN and Zhao, SN and Feng, G and Sun, YD},
title = {Microbiota-Targeted Nanoplatforms for Colorectal Cancer Immunotherapy.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108219},
doi = {10.1016/j.phrs.2026.108219},
pmid = {42061776},
issn = {1096-1186},
abstract = {Colorectal cancer (CRC) remains a major global health burden, and immunotherapy efficacy is often restricted by an immunosuppressive tumor microenvironment (TME). Emerging evidence highlights the pivotal role of the gut microbiota in shaping tumor progression and therapeutic responses. This review first summarizes the bidirectional crosstalk between gut microbiota and the CRC immune microenvironment, detailing how specific microbial species and metabolites regulate key immune cells (MDSCs, Tregs, TAMs, DCs, CD8[+] T cells, and CD4[+] T cells) through pathways such as NF-κB, RIG-I lactylation, AhR, and cGAS-STING. Based on these insights, we then examine microbiota-targeted nanoplatforms (lipid/protein-based, polymer-based, and inorganic systems) that enable precise modulation of microbial composition and function. These nanoplatforms synergize with immune checkpoint inhibitors, cancer vaccines, CAR-T cells, and oncolytic viruses by reshaping the microbiota and reprogramming the TME. Despite promising preclinical outcomes, challenges remain, including microbiome heterogeneity, biosafety concerns, slow clinical translation, and pharmacokinetic hurdles. Overall, microbiota-targeted nanoplatforms represent a novel and integrative strategy to improve CRC immunotherapy.},
}
@article {pmid42061905,
year = {2026},
author = {Kaste, JAM and Matthews, ML},
title = {Predictive multispecies constraint-based metabolic modeling: case studies and best practices.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {42061905},
issn = {1477-4054},
mesh = {Humans ; *Models, Biological ; Animals ; *Metabolic Networks and Pathways ; Mice ; Computational Biology/methods ; Microbiota ; },
abstract = {The last decade has seen a proliferation of studies and techniques for the modeling and analysis of metabolic interactions between distinct species, including microbes, plants, mice, and humans. Many studies in this area are explanatory, but a subset present predictive models aimed at either achieving specific biotechnological aims or furthering our understanding of the biological systems in question. Recent work suggests that the analysis frameworks and models that have been developed in the area of microbiome research are unreliable for accurately characterizing species-to-species interactions. In light of this development, the development of this subfield of metabolic modeling and its latest stumbling block are put into historical context. Several case studies of validated and predictive multispecies constraint-based metabolic models are then discussed. From these case studies, general principles are extracted that readers and practitioners in this area may find useful for evaluating and carrying out future multispecies metabolic modeling.},
}
@article {pmid42062245,
year = {2026},
author = {Korten, NM and Blischke, L and Thelen, AC and Schulze Eckel, A and van Egmond, M and Verspohl, V and Neumann, M and Kneisel, L and Tran, M and Beyer, C and Herpertz-Dahlmann, B and Keller, L and Bang, C and Andreani, NA and Seitz, J and Trinh, S and Voelz, C},
title = {From gut to brain: effects of fecal microbiota transplants from humans to rats on hippocampal gene regulation - a study on anorexia nervosa.},
journal = {Translational psychiatry},
volume = {16},
number = {1},
pages = {},
pmid = {42062245},
issn = {2158-3188},
mesh = {*Fecal Microbiota Transplantation ; *Hippocampus/metabolism ; *Anorexia Nervosa/therapy/microbiology/genetics/metabolism ; Animals ; Female ; Humans ; *Gastrointestinal Microbiome ; Rats, Wistar ; Rats ; Brain-Derived Neurotrophic Factor/metabolism ; Adult ; Adolescent ; Anti-Bacterial Agents/pharmacology ; Young Adult ; Disease Models, Animal ; Gene Expression Regulation ; },
abstract = {Fecal microbiota transplantation (FMT) has emerged as a novel approach for understanding anorexia nervosa (AN), a complex eating disorder characterized by severe underweight, fear of weight gain and distorted body image. Patients with AN show alterations in the gut microbiome, brain structure, and inflammatory processes, indicating the importance of the microbiome‒gut‒brain axis in AN pathology. This study aimed to investigate whether FMT from patients with AN into antibiotic-treated rats could transfer a phenotype associated with the disease inducing AN-like symptoms and hippocampal alterations. Female Wistar rats received antibiotics followed by FMT from healthy controls, patients with AN, or water. Gut microbiota effects were assessed through 16S rRNA gene sequencing, alongside post-mortem analyses of glial cells, neurogenesis markers, and inflammatory markers. The results revealed dysregulated microbial diversity after antibiotic treatment, which was partially restored after FMT. Successful transfer of human bacterial species was observed, but AN-like symptoms and changes in glial/neuronal counts were not detected. Notably, a decrease in hippocampal Bdnf expression was detected in the antibiotic control group, which was reversed by healthy control stool transplantation but not in the AN-transplanted group. Similar patterns were observed for neuroinflammation and Mki67, a marker of cell neogenesis. These findings suggest potential links between microbial changes, neuroinflammation and neuroplasticity in the hippocampus with the potential to correct deficits with FMT. Future studies should extend these findings by exploring the combination of FMT and starvation phases to better understand the roles of specific microbial populations in neuroinflammatory processes and, ultimately, clinical outcomes in AN.},
}
@article {pmid42062403,
year = {2026},
author = {Radwan, HM and El Menofy, NG and Tharwat, EK and Mysara, M and Radwan, SMR},
title = {Metagenomic profiling of microbial communities and the resistome within Egyptian hospital wastewater and tap water.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42062403},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; Egypt ; *Metagenomics/methods ; Hospitals ; *Drinking Water/microbiology ; Humans ; *Microbiota/genetics ; Water Microbiology ; *Metagenome ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a worldwide health concern that compromises the successful treatment of a growing array of infectious diseases, particularly in low- and middle-income countries. AMR is exaggerated by the spread of antimicrobial resistance genes (ARGs) across humans, animals, and environmental reservoirs like water and soil. Hospital wastewater (HWW) is the main source of antimicrobial resistance in the environment. The current study used high throughput metagenomic nanopore sequencing to investigate the microbial abundance and ARGs associated with both HWW and tap water in five different hospitals in Cairo, Egypt. The bacterial community composition of the HWW microbiome identified 25 taxonomic families. The most abundant genera in HWW were Acinetobacter (6%) and Propioniciclav (5%) out of 101 unique genera while, the most abundant in tap water were Enterococcus (53%), Escherichia (15%), and Francisella (14%) out of 89 unique genera. Alpha diversity analysis revealed significantly greater microbial diversity in the HWW samples than in the tap water samples (P value > 0.05), moreover beta diversity analysis revealed a significant difference in the microbial community composition between the tap water and HWW samples (P value > 0.05) using Chao metric for richness estimation and Shannon metric for richness and evenness estimation. Total ARG analysis revealed absence of ARGs in tap water using the three databases, while comparable levels of ARGs were detected in HWW across the five hospitals. In total, 45, 28, and 28 ARG subtypes were identified in the HWW samples using ResFinder, CARD, and the NCBI AMRFinderPlus databases, respectively. The most abundant AMR mechanisms among the five hospitals were linked to the inhibition of protein synthesis. Using the ResFinder database, streptogramin resistance genes were most prevalent in Hospitals 1 and 5 (15% and 40%, respectively); using CARD, aminoglycoside, lincosamide, and macrolide resistance genes were most predominant (relative abundances 35-60%). Using NCBI AMRFinderPlus, streptomycin, tetracycline, and macrolide resistance genes were most prevalent (relative abundances 30.1-60%). Detection of plasmid replicons in HWW identified 39 different plasmid-associated replication genes via the PlasmidFinder database. The Col440l-1, colRNAI-1 and Col440ll-1 plasmid replicons were the most detected across the five hospitals with relative abundances of 16.6%, 10.9% and 9.6%, respectively. This study revealed different microbial communities among HWW and tap water in addition to the widespread occurrence of ARGs and AMR encoding plasmid replicons in the HWW in the five different hospitals in Cairo, Egypt indicating a significant risk associated with HWW, necessitating the implementation of preventative measures to avert their environmental diffusion. To our knowledge, this is one of the first Egyptian studies to apply Oxford Nanopore long-read metagenomic sequencing for simultaneous profiling of microbial communities and the resistome in HWW and tap water, using three ARG databases across five hospitals in two seasons.},
}
@article {pmid42062458,
year = {2026},
author = {Tikhonova, P and Mekonnen, Z and Belanger, KD and Ay, A and Davenport, ER and Taye, B},
title = {Microbiome responses to anthelmintic treatment depend on pre-treatment helminth infection status in young Ethiopian children.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01625-3},
pmid = {42062458},
issn = {2730-664X},
abstract = {BACKGROUND: Mass deworming programs using anthelmintic drugs are a common public health strategy for controlling soil-transmitted helminth (STH) infections in high-risk, low-income countries. However, whether routine deworming induces long-term changes in gut microbiome composition remains unclear. We used longitudinal data to examine how anthelmintics alter the gut microbiome profiles of Ethiopian children.<br><br>METHODS: Fecal samples were collected from school-aged children enrolled in a mass deworming program in Jimma, Ethiopia, before and after receiving a 400&#x2009;mg dose of albendazole. Baseline samples were collected from 132 participants between April and May 2020, prior to treatment. Follow-up samples were obtained one year later from 67 children who remained in the study.<br><br>RESULTS: We observed a significant change in gut microbiome diversity metrics one year following treatment, characterized by fewer observed taxa and increased community evenness (Shannon and Simpson indices, p&#x2009;<&#x2009;0.01), indicating substantial perturbation of microbial community structure. Furthermore, we identified six significantly enriched genera post-treatment (FDR-adjusted p&#x2009;<&#x2009;0.05) among participants who were helminth-negative at the baseline, including Blautia, Senegalimassilia, Coprococcus 1, Marvinbryantia, Clostridium sensu stricto 1, and Lachnospiraceae ND3007 group. In contrast, individuals who had at least one egg count of Ascaris lumbricoides, Trichuris trichiura, or hookworm before treatment exhibited enrichment in five taxa (Senegalimassilia, Lachnospiraceae ND3007 group, Lachnospiraceae FCS020 group, Collinsella, and Intestinimonas).<br><br>CONCLUSIONS: Our findings suggest that baseline helminth infection status influences the microbiome changes induced by anthelmintic treatment. Further controlled animal studies are needed to clarify how anthelmintic treatment affects taxon shifts in gut microbiota.},
}
@article {pmid42062487,
year = {2026},
author = {Sharma, D and Voigt, RM and Hall, DA and Cantu-Jungles, TM and Shaikh, M and Engen, PA and Jones, J and Li, S and Hamaker, BR and Forsyth, CB and Bishehsari, F and de Menezes, EGM and Norris, PJ and Goetz, CG and Keshavarzian, A},
title = {Prebiotic intervention changes host and microbe proteomes in plasma extracellular vesicles of Parkinson's disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50859-7},
pmid = {42062487},
issn = {2045-2322},
support = {1U01DK140923-01/NH/NIH HHS/United States ; },
abstract = {We hypothesize that intestinal microbiome dysbiosis may contribute to Parkinson's disease (PD) pathogenesis. Our prior proof-of-concept clinical trial demonstrated that a precision prebiotic intervention improved microbiota dysbiosis and alleviated gastrointestinal and motor symptoms in PD patients. Building on this, we analyzed plasma extracellular vesicles (EVs) from participants to explore EVs as a dynamic PD biomarker and to assess the systemic effects of a microbiota-directed intervention. Using mass spectrometry-based proteomics of EVs from PD and healthy control (HC) participants, we identified distinct human and bacterial proteins in plasma-derived EV. Crucially, this offers a holistic systemic readout of the microbiota-gut-brain axis by quantifying both host and microbial components. We found that EV proteomic profiles differed between PD and HC samples as well as between unmedicated/mild and medicated/moderate PD participants. Furthermore, the microbiota-directed prebiotic intervention induced an acutely modifiable PD signature, shifting host and microbial EV proteomic profiles toward the HC profile. Using a combined 16-feature host-microbe signature, we built a multiple linear regression model that accurately distinguishes PD status from HC (R[2] = 0.88) and successfully stratified disease severity (R[2] = 0.72). Based on these findings, we suggest that: (1) a precision prebiotic mixture can modulate PD-associated proteomic signatures and (2) plasma EV proteomics may be a platform to capture these biological responses and to explore potential diagnostic and staging biomarkers in the context of microbiome-targeted interventions.},
}
@article {pmid42062488,
year = {2026},
author = {Feng, J and Zhou, S and Huang, J and Wen, X and Zhou, G and Zhang, G and Shi, Q and Xie, X},
title = {A comparative analysis of skin bacteria in healthy individuals through traditional cultivation and high-throughput sequencing techniques.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51175-w},
pmid = {42062488},
issn = {2045-2322},
support = {2023A1515012057//Natural Science Foundation of Guangdong Province/ ; 2021GDASYL-20210103008//GDAS' Project of Science and Technology Development/ ; },
abstract = {The human skin microbiota is intricately linked to the microenvironmental niche of its habitat. Different skin sites may harbor distinct bacterial community structures due to their unique microenvironments. To elucidate the site-specific distribution patterns of skin bacterial communities, this study employed an integrated approach combining traditional microbial cultivation methods with 16S rRNA gene high-throughput sequencing to analyze 105 skin swab samples collected from the forehead, volar forearm, and scalp of 35 healthy individuals. A total of 675 bacterial strains encompassing 41 species and 18 genera were isolated by traditional culture-based methods. Staphylococcus and Cutibacterium were the dominant genera in different skin sites, with S. capitis, S. epidermidis, S. hominis, and C. acnes identified as the predominant species. High-throughput sequencing analyses revealed that the forehead and forearm harbored similar microbiota profiles, while the scalp displayed a more distinct bacterial community characterized by reduced alpha diversity and elevated relative abundances of Cutibacterium, Staphylococcus, and Lawsonella genera. The findings from both traditional cultivation methods and high-throughput sequencing suggested that the human skin bacterial community exhibits strong site-specificity. In contrast to the significant variations observed across different skin sites, gender and age exerted minimal effects on microbiota composition. These results suggest that microenvironmental factors play a more substantial role than age- and gender-related factors in shaping the diversity and community structure of the human skin microbiota.},
}
@article {pmid42062589,
year = {2026},
author = {Wang, Y and Isasi, CR and Stuebe, AM and Louis-Jacques, AF and Hu, J and Hu, G and Daviglus, ML and Boerwinkle, E and Burk, RD and Kaplan, RC and Qi, Q and Peters, BA},
title = {Gestational diabetes and risk of type 2 diabetes: exploring the role of the gut microbiome in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).},
journal = {Diabetologia},
volume = {},
number = {},
pages = {},
pmid = {42062589},
issn = {1432-0428},
support = {11-23-PDF-60//American Diabetes Association/ ; R01DK132011/DK/NIDDK NIH HHS/United States ; K01HL160146; R01HL148094; R01HL140976/HL/NHLBI NIH HHS/United States ; R01MD011389/HL/NHLBI NIH HHS/United States ; U54GM104940/GM/NIGMS NIH HHS/United States ; },
abstract = {AIMS/HYPOTHESIS: Women with a history of gestational diabetes mellitus (GDM) have an elevated risk of type 2 diabetes in their later life, yet the underlying mechanisms of this remain unclear. We aimed to investigate the long-term impact of GDM on gut microbiota and related metabolites and to explore whether such alterations may contribute to type 2 diabetes risk.<br><br>METHODS: Among parous women from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), we identified microbial species associated with a history of GDM (visit 2, 2014-2017, n=1525), and serum metabolites associated with both a history of GDM (visit 1, 2008-2011, n=2968) and GDM-related microbiota (visit 2, n=391). We further examined prospective associations of the GDM-related microbiome (visit 2, n=925) with incident type 2 diabetes over 6 years of follow-up, and of microbial-related metabolites (visit 1, n=2341) with incident type 2 diabetes over 12 years.<br><br>RESULTS: Among 1525 US Hispanic/Latino parous women (median age: 58 years), seven species differed between women with and without a history of GDM, including higher abundances of four species (e.g. Parabacteroides merdae CAG:48, a proinflammatory taxon) and lower abundances of three species (e.g. Dialister sp. CAG:588, a short-chain fatty acid producer). Fifteen metabolites were associated with both a history of GDM and the GDM-related microbiome in a consistent direction, nine of which (e.g. saturated sphingomyelins and unsaturated fatty acids) were associated with glycaemic traits and incident type 2 diabetes. Using these microbial-related metabolites as proxy measures, proxy analysis suggested a positive relationship between the GDM-related microbiome and type 2 diabetes (r=0.55, p=0.036). A metabolite score derived from the nine microbial-related metabolites mediated an estimated 20% (95% CI 9%, 42%) of the association between a history of GDM and type 2 diabetes.<br><br>CONCLUSIONS/INTERPRETATION: A history of GDM is associated with an unfavourable gut microbiota and related metabolites in US Hispanic/Latino women, suggesting a potential role of the gut microbiota in GDM-related type 2 diabetes.},
}
@article {pmid42062603,
year = {2026},
author = {Xu, T and Yang, Y and Zhu, R and Lin, W and Li, J and Zheng, Y and Zhang, P and Zhang, G and Zhao, G and Jiao, N},
title = {DeepSeMS: revealing the hidden biosynthetic potential of the global ocean microbiome with a large language model.},
journal = {Nature computational science},
volume = {},
number = {},
pages = {},
pmid = {42062603},
issn = {2662-8457},
support = {32470098//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170542//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92451303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbial-derived secondary metabolites (SMs) hold great therapeutic potential but are predominantly discovered from cultured species, representing only a fraction of microbial biodiversity. Advances in metagenomics have unveiled reservoirs of biosynthetic gene clusters (BGCs), but translating genomic sequences into precise chemical structures remains challenging owing to the structural complexity of cryptic BGCs and the context-dependent substrate tolerance and cross-reactivity of modular biosynthetic domains. Here we present DeepSeMS, a transformer-based large language model that accurately predicts secondary metabolite chemical structures from BGC sequences. By encoding biosynthetic genes as functional domains and leveraging a feature-aligned data augmentation, DeepSeMS outperformed existing methods and successfully generated chemically valid predictions for 96.38% of cryptic BGCs. Applying DeepSeMS to a global ocean metagenome, we characterized over 60,000 secondary metabolites, revealing chemical diversity, ecological specificity and considerable biomedical potential, especially as antibiotics. This study underscores the capability of deep learning-driven approaches in revealing hidden biosynthetic potential of Earth's largest, yet largely unexplored, microbial ecosystem.},
}
@article {pmid42062664,
year = {2026},
author = {Kieliszek, M},
title = {Selenium: From Redox Signaling to Interactions with the Gut Microbiome.},
journal = {Biological trace element research},
volume = {},
number = {},
pages = {},
pmid = {42062664},
issn = {1559-0720},
abstract = {Selenium is an element that plays a crucial role in the proper functioning of the body. It is a component of selenoproteins, which exhibit strong antioxidant properties. This allows it to neutralize reactive oxygen species and protect cells from oxidative stress. It also plays a crucial role in supporting the proper functioning of the immune system. In this context, particular importance is attributed to its influence on the Th1/Th2 immune response and the activity of T lymphocytes and NK cells. There is a mutual relationship between selenium and the intestinal microbiota. Microorganisms in the gastrointestinal tract participate in the accumulation, transformation, and differentiation of selenium's chemical forms. These processes influence selenium's bioavailability and its activity in the host organism. The development of metagenomic methods has enabled the identification of specific selenium-dependent metabolic pathways within the microbiome. This represents an important research direction in the development of this field of biotechnology. In turn, appropriate selenium levels and selenoprotein activity influence the composition of the intestinal microbiota and the metabolite profile it produces. It is worth emphasizing that in the context of the development of microbiome engineering, there are also emerging concepts of designing probiotics capable of controlled selenium biotransformation. The beneficial properties of selenium for organisms depend on its appropriate chemical form and dose. It is worth noting that selenium deficiency can impair the antioxidant system, leading to a redox imbalance. Such processes can weaken the integrity of the intestinal barrier, leading to the development of various gastrointestinal diseases. Therefore, the interaction with intestinal microflora is such a crucial element of selenium's action. Microorganisms inhabiting the digestive tract participate in the processes of accumulation and transformation of various chemical forms of this element. These biochemical properties of microorganisms are crucial for the bioavailability of selenium in the human body. Therefore, the appropriate form of selenium is crucial for the proper functioning of the intestinal barrier. This article discusses the importance of selenium in redox processes and in the function of the gut microbiota. It highlights the potential role of this element in the prevention and treatment of gastrointestinal diseases. Future research should focus on further understanding these interactions and developing targeted approaches that utilize selenium-dependent pathways to restore intestinal homeostasis.},
}
@article {pmid42062837,
year = {2026},
author = {Ntemiri, A and Kyriacou, A and Kakagianni, M},
title = {The Dairy Ruminant Gut Microbiome: Profile, Responsiveness to Seasonality and Impact on Milk Quality.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70317},
pmid = {42062837},
issn = {1462-2920},
support = {//HEAL-Link/ ; },
mesh = {Animals ; Seasons ; *Gastrointestinal Microbiome ; *Milk/standards/microbiology ; Goats/microbiology ; Cattle ; *Ruminants/microbiology ; Sheep/microbiology ; Rumen/microbiology ; Dairying ; },
abstract = {The gut microbiome (GM) and particularly the rumen microbiome (RM) affect the ruminant health and they are associated with milk quality and safety. The bovine RM has been extensively studied due to the importance of cattle in Agriculture. Studies of the gastrointestinal microbiome (GITM) of other livestock ruminants like goats, lag behind, comparatively. Sheep and goat rearing sustains livelihoods in unprivileged areas, globally. Dominant ruminant GM shaping factors are host and diet. Exposure to seasonal stimuli (e.g., diet) is associated with livestock GITM shifts. These seasonal microbial changes correlate with milk production and milk microbiota (MM) variation, with mechanistic links to remain unclear. The seasonality impact could be intensified during extensive rearing. Goats are frequently described as resilient livestock due to behavioural and dietary adaptability. If the goat GM responsiveness to seasonal stimuli plays a functional role in the livestock resilience and milk quality remains unresolved. Goats are discussed here as a comparatively underexplored system for investigating microbiome-mediated adaptation to variable environments. Here, we overviewed the current knowledge on the ruminant GM with emphasis to goats, and how seasonality may affect its configuration, and explored evidence linking seasonal GM variation to MM, milk quality and safety.},
}
@article {pmid42063001,
year = {2026},
author = {Zheng, X and Wu, W and Zhang, Y and Zhang, J and Ma, F},
title = {Impact of intra-tumoral microbiome on the efficacy of neoadjuvant immunochemotherapy in patients with locally advanced oral squamous cell carcinoma.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42063001},
issn = {1479-5876},
support = {Y-MSDPU2022-0547//Beijing Xisike Clinical Oncology Research Foundation/ ; PKUSS-2023CRF1012//the Clinical Research Foundation of Peking University School and Hospital of Stomatology/ ; CICAMS-MOCP2022015//the Cultivation project of Medical Oncology Key Foundation of Cancer Hospital Chinese Academy of Medical Sciences/ ; 2022YFC2504200//the National Key Research and Development Program of China/ ; CICAMS-MOY&amp;M-202401//the Medical Oncology Innovation Team of Cancer Hospital Chinese Academy of Medical Sciences ,Y&amp;M Cultivation project of Cancer Hospital Chinese Academy of Medical Sciences/ ; },
mesh = {Humans ; *Neoadjuvant Therapy ; *Mouth Neoplasms/microbiology/therapy/drug therapy/pathology ; *Microbiota ; Female ; Male ; *Carcinoma, Squamous Cell/microbiology/therapy/pathology/drug therapy ; *Immunotherapy ; Middle Aged ; Treatment Outcome ; Aged ; Adult ; },
abstract = {OBJECTIVE: The predictive value of intratumoral microbiota for the efficacy of neoadjuvant immunochemotherapy, as well as the changes in microbiota before and after treatment, has remained largely unexplored.<br><br>METHODS: We employed 2bRAD sequencing for Microbiome (2bRAD-M) to analyze 42 specimens from patients with locally advanced&#xa0;oral squamous cell carcinoma (OSCC), focusing on trends in intratumoral microbiota changes before and after neoadjuvant immunochemotherapy, and predicting responses to the treatment.<br><br>RESULTS: (1) There was no significant difference between the MPR_before group and nMPR_before group in terms of &#x3b1; diversity and &#x3b2; diversity at baseline, but Ralstonia_sp.000620465, Methylobacterium_rhodesianum, Methylobacterium_jeotgali, RH_AL1_sp.901457705, Rothia_sp.002418375, and Rothia_mucilaginosa_A, which were enriched in immune-related signaling pathways, were significantly more abundant in the nMPR_before group&#xa0;and could&#xa0;predict the efficacy of neoadjuvant immunotherapy&#xa0;(AUC=0.74)&#xa0;. (2) Importantly, both the &#x3b1; and &#x3b2; diversity of intratumoral microbiota significantly decreased after neoadjuvant immunochemotherapy, regardless of whether we compared the&#xa0;MPR_before group with MPR_after group or the&#xa0;nMPR_before group with nMPR_after group. (3) The abundance of Deinococcus_geothermalis was significantly higher in the nMPR_after group, while Burkholderia_vietnamiensis was enriched in the MPR_after group. These differential microbial populations between the nMPR_after group and MPR_after group were enriched in metabolism-related pathways such as carbon fixation in photosynthetic organisms, taurine and hypotaurine metabolism, and genetic information processing pathways, including homologous recombination and DNA replication.<br><br>CONCLUSION: Neoadjuvant immunochemotherapy markedly alters intratumoral microbiota diversity. Baseline and post-treatment microbiota differences between MPR and nMPR groups implicate specific signaling pathways that may influence treatment efficacy in locally advanced OSCC.},
}
@article {pmid42063103,
year = {2026},
author = {Aleman, J and Vernetti, L and Schurdak, ME and DeBiasio, R and LaRocca, G and Yechoor, VK and Taylor, DL and Stern, AM and Miedel, MT},
title = {Recapitulation of clinical and molecular hallmarks of lipid-induced hepatic insulin resistance in a zonated, vascularized human liver acinus microphysiological system during metabolic dysfunction-associated steatotic liver disease (MASLD) progression.},
journal = {BMC biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12896-026-01158-6},
pmid = {42063103},
issn = {1472-6750},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) impacts ca. 30% of the global population and is very heterogeneous, making it a challenge to develop therapeutics. The heterogeneity arises from genetics, co-morbidities, the microbiome, and lifestyle. To help address this challenge, we have refined the human vascularized liver acinus microphysiological system (vLAMPS), which provides an all-human platform for drug development, satisfying recently updated federal requirements for the use of New Approach Methodologies (NAMs). By introducing clinically relevant media perturbations and employing several diverse and reproducible in situ and systemic measurements, we show that the vLAMPS can recapitulate key structural and functional aspects of normal physiology, acinus zonation, and all stages of MASLD progression including stellate cell activation and fibrosis. Importantly, in this study we also demonstrate that several hallmarks of lipid-induced hepatic insulin resistance paralleled MASLD progression. These included reduction of insulin receptor substrate 2 (IRS2) protein, compromised insulin receptor mediated insulin clearance, enhanced pericentral lipid accumulation, increased Very-low-density lipoprotein (VLDL) secretion, and enhanced hepatic glucose output mediated by increased periportal nuclear translocation of Forkhead box protein O1 (FOXO1). These results suggest that the mechanisms underlying MASLD progression in vLAMPS are clinically relevant and support the tenable hypothesis that the hepatic insulin resistant state plays both a causal and consequential role in a vicious cycle driving disease progression.},
}
@article {pmid42063119,
year = {2026},
author = {Famakinde, DO and Lonergan, C and Wells, D and Gobert, GN and McVeigh, P},
title = {Dietary variations drive divergent phenotypic, transcriptomic, and metatranscriptomic profiles in Biomphalaria glabrata, a schistosomiasis vector snail.},
journal = {Parasites &amp; vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07403-3},
pmid = {42063119},
issn = {1756-3305},
abstract = {BACKGROUND: The freshwater snail Biomphalaria glabrata is an important natural vector for the human parasitic trematode Schistosoma mansoni, which causes schistosomiasis. In the laboratory, B. glabrata are routinely maintained on simple lettuce diets. We aimed to explore and compare the impact of alternative diets on snail performance, global gene expression, and microbiome.<br><br>METHODS: Snails were raised in groups on fresh lettuce (FL), fish food (FF), and artificial snail gel (SG) diets for 8 weeks, while measuring dietary impacts on growth, survival, and fecundity. RNA sequencing (RNA-Seq) was performed to correlate dietary phenotypes with changes in the snail transcriptome and associated microbial metatranscriptome.<br><br>RESULTS: Fish food (FF) and SG diets markedly enhanced snail&#xa0;growth, survival, and fecundity, with FF generating the highest fecundity rate. RNA-Seq identified 21,887 expressed genes in the snail's transcriptome. Of these, diet significantly modulated 6501 genes (padj&#x2009;<&#x2009;0.01), representing 13.0% of the predicted genes in the B. glabrata genome. Fish food (FF) and SG diets drove upregulation of genes associated with antimicrobial immunity, growth, and reproduction, while elevated expression of genes linked to xenobiotic metabolism and oxidative stress was observed in FL-fed snails. Metatranscriptomic analysis identified 104 microbial classes, with a total of 23 classes significantly enriched in FF and SG snails, including short-chain fatty acid (SCFA)-producing and nutrient-cycling bacteria. A significant correlation (r&#x2009;=&#x2009;0.63, P&#x2009;=&#x2009;0.001) linked differentially expressed genes to enriched microbial transcripts, highlighting the impact of diet on key snail health and performance metrics.<br><br>CONCLUSIONS: This work is the first nutritranscriptomic analysis of laboratory-bred B. glabrata. We describe key insights into the diet-phenotype-transcriptome-microbiome axis, which will inform dietary precision and optimisation for laboratory culture of B. glabrata. These data also highlight fundamental aspects of snail biology that could be exploited for molecular snail control approaches.},
}
@article {pmid42063124,
year = {2026},
author = {He, Y and Meng, J and Luo, W and Yu, M and Zhang, N and Chen, C and Yu, L},
title = {The kynurenine pathway storm in epilepsy: mechanisms and therapeutic implications.},
journal = {Acta epileptologica},
volume = {8},
number = {1},
pages = {},
pmid = {42063124},
issn = {2524-4434},
support = {2023YFS0080//The Key R&amp;D Projects of Science and Technology Department of Sichuan Province/ ; KY2022SJ0035//The Health Care Promotion Institute/ ; },
abstract = {The kynurenine pathway (KP) is the main route for tryptophan (TRP) degradation and plays a crucial role in neuroinflammation, oxidative stress and neurotransmission, which holds significant clinical significance. The dysregulation of this pathway is closely related to neurological disorders such as epilepsy, and its metabolic products can promote the occurrence of epileptic seizures and comorbid depression. This review aims to clarify the complex mechanisms of the KP in the occurrence and development of epilepsy and to explore its potential as a therapeutic target for epilepsy and comorbid depression. This is a narrative review and synthesis of the current literature. We reviewed animal experiments and clinical studies, elaborating in detail on how metabolites of the KP and their key enzymes function in the context of epilepsy by regulating neuroinflammation, oxidative stress, glutamatergic signaling, and the gut-brain axis. We also explored the interaction between antiseizure medications (ASMs) and the KP, and evaluated the potential value of targeting key enzymes (such as indoleamine 2,3-dioxygenase, IDO) as a new therapeutic strategy for epilepsy. This review particularly focuses on the promoting effect of KP imbalance on comorbid depression, clarifying how IDO-mediated TRP metabolism changes constitute a common mechanism basis, jointly leading to the occurrence of epilepsy and depression-like behaviors. The occurrence and development of epilepsy are closely related to the imbalance of the KP, specifically manifested as a decrease in kynurenic acid (KYNA) level and an increase in quinolinic acid (QA) level. The IDO-mediated shift of TRP metabolism towards the KP is established as a critical mechanism underlying depression comorbidity in epilepsy. Therapeutic modulation of this pathway, through targeting key enzymes like IDO and restoring the KYNA/QA balance, presents a viable strategy for improving the cerebral microenvironment. This approach holds promise for enhancing seizure control, counteracting drug resistance, and concurrently alleviating comorbid depressive symptoms.},
}
@article {pmid42063193,
year = {2026},
author = {Martín-Vivaldi, M and Martínez-García, &#xc1; and Peralta-Sánchez, JM and Schaub, M and Arlettaz, R and Martín-Platero, AM and Martínez-Renau, E and Barón, MD and Ruiz-Rodríguez, M and López-Hernández, E and Martínez-Bueno, M and Valdivia, E and Soler, JJ},
title = {The uropygial gland of the European hoopoe as a symbiotic organ.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42063193},
issn = {2524-4671},
abstract = {BACKGROUND: Animals rely on symbiotic bacteria living within/on their tissues for multiple functions, while simultaneously needing to protect themselves via immune functions or other defenses from potentially pathogenic microorganisms that could invade those tissues. As a result, interactions with complex assemblages of bacteria have driven the evolution of host strategies to control established symbioses. One such strategy involves the development of organs specialized in maintaining associations with beneficial members of the microbial community — so-called symbiotic organs. These organs are characterized by compartmentalizing spaces where favorable conditions for the beneficial bacteria are promoted, while preventing colonization of other tissues. Although several model systems of symbiotic organs have been studied in animals, none have been recognized in non-aquatic vertebrates except for the intestinal crypts of mammals. Here, we propose that bird´s uropygial glands may be specialized symbiotic organs.<br><br>RESULTS: We tested this hypothesis using the uropygial gland of the hoopoe (Upupa epops) as a model, which hosts a complex bacterial community that includes antimicrobial-producing symbionts. First, we examined whether the uropygial gland supports a specific symbiotic community, by comparing the microbiome composition of the uropygial secretions and eggshell surfaces in two European hoopoe populations. Additionally, using histological staining and fluorescence in situ hybridization, we looked for structural specializations for compartmentalization and bacterial targeting in the glands of nesting hoopoes in comparison to non-breeding individuals lacking the symbiosis. Results show that, in comparison with bacterial communities of the eggshells, those of the uropygial gland were more conserved between both populations. Moreover, uropygial glands of nesting hoopoes were strictly compartmentalized by a special tissue, properties that are absent in the non-breeding individuals lacking the symbiosis. Finally, bacteria were organized within the organ, suggesting the existence of special physical niches to promote specialized mutualistic symbionts.<br><br>CONCLUSIONS: All evidence supports that the hoopoe uropygial gland is a specialized symbiotic organ for bacterial cultivation, paving the way for new insights into vertebrates&#x2019; exocrine glands&#x2019; role in microbial symbiosis.<br><br>CLINICAL TRIAL NUMBER: Not applicable.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00543-y.},
}
@article {pmid42063196,
year = {2026},
author = {Liu, Z and Meng, C and Shen, J and Wang, H and Guo, J and Zhao, J and Mu, C and Zhu, W},
title = {Dietary regulation on gut resistome linked with microbial amino acid metabolism in pigs.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42063196},
issn = {2524-4671},
support = {National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; },
abstract = {UNLABELLED: Dietary protein plays a crucial role in shaping the gut microbiome and modulating intestinal amino acid metabolism. Gut microbiome is recognized as a reservoir for carrying antimicrobial resistance genes. However, the relationship between amino acids metabolism and antibiotic resistome remains poorly understood. Here, a pig model was used to study this relationship by comparing the impact of dietary casein hydrolysate diet with those of an intact casein diet. Metabolomics analysis revealed that casein hydrolysate supplementation primarily altered amino acid metabolism, characterized by significantly reduced levels of several amino acids, including tyrosine and glutamine, accompanied by increased levels of amino acid–derived metabolites. Metagenomics analyses indicated that these metabolic shifts were closely associated with microbial changes in the gut, particularly the genera Escherichia and Bifidobacterium. Consistently, microbial genes related to amino acid transport and metabolism exhibited higher abundances. Notably, the abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were significantly enriched in response to casein hydrolysate supplementation. Integrated metabolome–resistome correlation analyses revealed significant associations between multiple amino acids, including tyrosine and glutamine, and distinct ARG subtypes, indicating a tight coupling between amino acid metabolism and antibiotic resistance potential. Metagenomics binning and assembly further resolved the taxonomic origins of these functional traits. Specifically, in Escherichia fergusonii and Bifidobacterium thermophilum, genes related to amino acid metabolism, ARGs, and MGEs were co-localized on the same contigs with close genomic proximity. Together, these findings highlight a strong link between microbial amino acid metabolism and the resistome, suggesting that dietary casein hydrolysate reshapes both microbial metabolic functions and antibiotic resistance potential within the intestinal ecosystem.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00542-z.},
}
@article {pmid42063218,
year = {2026},
author = {Liu, WH and Xiao, CL and Luo, ZY and Zhu, YJ and Li, WR and Ren, H and Guo, Z and Luo, JQ},
title = {Host genetic variants in the lactose metabolism pathway associated with bifidobacterium abundance have prognostic value for immunotherapy efficacy.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70472},
pmid = {42063218},
issn = {1476-5381},
support = {CPA-Z05-ZC-2024002//Chinese Pharmaceutical Association Hospital Pharmacy Department/ ; 82404778//National Natural Science Foundation of China/ ; 82474016//National Natural Science Foundation of China/ ; 2026JJ80910//Scientific Foundation of Hunan/ ; 2025JGB077//Degree &amp; Postgraduate Education Reform Project of Central South University/ ; },
abstract = {BACKGROUND AND PURPOSE: The potential predictive and therapeutic value of Bifidobacterium in immune checkpoint inhibitor (ICI) treatment has been widely studied. However, the value of its genetic determinants on the prognosis of ICI treatment remains unclear.<br><br>EXPERIMENTAL APPROACH: We examined the associations between 11 single nucleotide polymorphisms (SNPs) located at host genes associated with Bifidobacterium abundance and the outcomes of ICI treatment in 370 eligible Chinese cancer patients.<br><br>KEY RESULTS: LCT/MCM6 SNPs, rs3739020, rs3739022, rs56263017 and rs55809728, were strongly associated with overall survival (OS), and the LCT haplotype analysis showed that genetically predicted lactose poor metabolisers exhibited significantly poorer OS (P-value&#x2009;=&#x2009;0.002, adjusted HR&#x2009;=&#x2009;0.45, 95%CI&#x2009;=&#x2009;0.27-0.74). In polygenic SNP analysis, the genetically inferred high galactose level carriers exhibited significantly prolonged OS (P-value&#x2009;=&#x2009;0.007, adjusted HR&#x2009;=&#x2009;0.32, 95%CI&#x2009;=&#x2009;0.14-0.73) and progression-free survival (PFS, P-value&#x2009;=&#x2009;0.001, adjusted HR&#x2009;=&#x2009;0.45, 95%CI&#x2009;=&#x2009;0.29-0.71). All four SNPs and the lactose metabolic phenotype were not associated with the occurrence of overall immune-related adverse events (irAEs). Two-sample mendelian randomisation analysis showed genetically predicted Bifidobacterium abundance correlated with lactose metabolism pathway abundance (P value&#x2009;=&#x2009;0.012, Beta coefficient&#x2009;=&#x2009;0.549).<br><br>CONCLUSIONS AND IMPLICATIONS: Lactose metabolism pathway SNPs, which are linked to Bifidobacterium abundance in prior studies, have prognostic value for immunotherapy efficacy in Chinese cancer patients, and the genetically predicted lactose extensive and intermediate metabolisers exhibited better immunotherapy efficacy. These findings remain exploratory and require further validation with direct microbiome and metabolite measurements.},
}
@article {pmid42063308,
year = {2026},
author = {Darawshy, F and Segal, LN},
title = {Localized Microbial-Immunometabolic Interactions and Early Lung Cancer.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {19},
number = {5},
pages = {269-271},
doi = {10.1158/1940-6207.CAPR-26-0031},
pmid = {42063308},
issn = {1940-6215},
mesh = {Humans ; *Lung Neoplasms/immunology/microbiology/pathology/metabolism ; *Microbiota/immunology ; *Carcinoma, Non-Small-Cell Lung/immunology/microbiology/pathology/metabolism ; Lung/microbiology/immunology ; Animals ; },
abstract = {The composition of lower airway microbiome has been linked to the development and progression of non-small cell lung cancer (NSCLC). Recent research has transitioned from viewing the lung microbiome as a bystander to a central player in carcinogenesis. Enrichment of oral commensals, specifically Veillonella, Prevotella, and Streptococcus, in the lower airways is associated with upregulated oncogenic pathways and increased inflammatory immune tone. A new integrative multiomic analysis by Weinberg and colleagues involving patients with early-stage NSCLC further supports these associations. By comparing bronchoalveolar lavage fluid from tumor-affected lobes against unaffected lobes within the same patient, researchers identified a localized microbial-immunometabolic niche. Key findings include an enrichment of the Veillonella-Streptococcus-Prevotella taxa and the metabolic byproduct stearic acid (SA) in tumor-affected sites. Ex vivo, SA stimulates macrophages into a "polyfunctional" state, secreting pro-inflammatory cytokines like MIP-1β and RANTES. This secretome could induce neoplastic transformation in lung epithelial cells, facilitating anchorage-independent growth. These insights shift paradigms toward metabolically driven innate immune reprogramming induced by the lung microbiome as an early event in tumor development, offering new strategies for diagnosis, therapy monitoring, and preventive interventions. See related article by Weinberg et al., p. 229 .},
}
@article {pmid42063421,
year = {2026},
author = {Banchi, P and Mila, H and Selma-Royo, M and Tal, S and Péron, F and Gaillard, V},
title = {The perinatal microbiota in dogs and cats: a narrative review from human research to veterinary practice.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1817504},
pmid = {42063421},
issn = {2297-1769},
abstract = {Early-life microbial colonization is increasingly recognized as a key determinant of host development and health. While the perinatal microbiota has been extensively studied in humans, comparable knowledge in dogs and cats remains limited. The present review synthesizes current evidence on the perinatal microbiota in dogs and cats, placing it in the context of advances from human microbiome research while emphasizing biological and management factors relevant to veterinary medicine. The prenatal period represents a window of exposure to the maternal microbiota, which is a key contributor to fetal development, while the occurrence of viable microbial colonization of the fetus in healthy pregnancies is not supported by evidence neither in humans nor in companion animals. After reviewing the features of the maternal gut and vaginal microbiota, particular attention is given to the birth process as a major ecological transition, with delivery mode and birth environment shaping early microbial exposure in species-specific ways. The postnatal period is characterized by rapid microbial succession driven by physiological maturation, early nutrition, and environmental factors. We examine the role of colostrum and milk in shaping neonatal gut microbiota assembly, integrating evidence from human studies with emerging data in dogs. We also discuss how maternal care and other environmental exposures contribute to early microbiota development. Finally, we evaluate microbiota-oriented interventions in veterinary settings, including maternal probiotic supplementation, and discuss their potential benefits and limitations based on available evidence. Throughout the review, we discuss current clinical approaches to the perinatal microbiota in companion animals and identify major research gaps. We conclude by emphasizing the need for well-designed longitudinal and ideally multicentric studies integrating maternal, neonatal, and environmental microbiota data and aimed at developing evidence-based microbiome-informed strategies in veterinary practice.},
}
@article {pmid42063498,
year = {2026},
author = {Xiang, L and Wang, X and Wen, M and Wang, X and Zhang, Y and Tian, W and Liu, M and Zhang, W},
title = {Metagenomic insights into the rhizosphere microbiome dysbiosis associated with tobacco bacterial wilt.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809980},
pmid = {42063498},
issn = {1664-302X},
abstract = {Tobacco bacterial wilt, caused by Ralstonia solanacearum, threatens global tobacco production. While the rhizosphere microbiome defends against soil-borne pathogens, mechanisms underlying how bacterial wilt reshapes microbial community structure, function, and ecological interactions remain poorly understood. Here, we employed metagenomic sequencing to investigate taxonomic and functional alterations in the rhizosphere microbiome of symptomatic (S) and asymptomatic (A) tobacco plants across two locations (Fenggang and Bozhou), establishing four groups: FA, FS, BA, and BS. Quality control of sequencing data showed no technical bias between groups (p > 0.05). Contrary to the paradigm that pathogen invasion reduced microbial diversity, alpha diversity analysis revealed higher species richness (Sobs) in symptomatic soils, whereas community evenness (Shannon and Simpson indices) remained unchanged, suggesting selective reshuffling rather than microbiome collapse. Beta-diversity analysis revealed significant compositional shifts associated with disease status (PERMANOVA, R [2] = 0.713, p = 0.001), with symptomatic communities displaying greater heterogeneity. Taxonomic profiling revealed consistent enrichment of the pathogen R. solanacearum and opportunistic bacteria (including Stenotrophomonas and Pseudomonas) in symptomatic rhizospheres, concomitant with depletion of putative beneficial taxa (Candidatus_Solibacter, Luteitalea, and Metarhizium). Functional annotation indicated a metabolic shift from homeostatic maintenance to stress adaptation and pathogenicity. Symptomatic soils exhibited significant enrichment of virulence factors, including motility and secretion system genes, microbial defense mechanism genes (COG), and antibiotic resistance genes (CARD). Additionally, increased abundance of carbohydrate-active enzymes (CAZy)-particularly glycoside hydrolases-suggested intensive nutrient acquisition from decaying tissues. Co-occurrence network analysis revealed that asymptomatic communities formed denser, competition-driven networks characterized by a higher proportion of negative correlations. Disease destabilized these networks by reducing connectivity and, crucially, rewired interactions of R. solanacearum from negative to positive associations with taxa such as Sphingobium, thereby reflecting erosion of competitive constraints and pathogen incorporation into cooperative networks. Our findings revealed that bacterial wilt drove multi-layered dysbiosis, encompassing pathogen-driven taxonomic selection, functional shifts toward stress adaptation and intensified competition, and collapse of stable antagonistic networks associated with plant health. This study provided mechanistic insights into microbiome-mediated disease progression and identified specific microbial taxa and network properties as candidate targets for ecological disease management and early diagnostic indicators.},
}
@article {pmid42063501,
year = {2026},
author = {Yang, H and Yan, L and Feng, H and Qi, F and Kong, F and Yu, Q and Zhu, W and Liang, C and Zhang, J and Zhang, Z},
title = {Multi-omics landscape of lung mycobiome dysbiosis: Candida albicans drives the invasive progression of lung adenocarcinoma.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1811749},
pmid = {42063501},
issn = {1664-302X},
abstract = {The transition from minimally invasive adenocarcinoma (MIA) to invasive adenocarcinoma (IAC) marks a decisive turning point in lung cancer progression. While the bacterial microbiome is a recognized component of the tumor microenvironment, the specific contribution of the lung mycobiome to this invasive shift remains largely obscure. Using an integrated multi-omics approach, this study maps the fungal ecosystem dynamics across the MIA-to-IAC spectrum. Notably, invasive tissues exhibited a significant elevation in fungal diversity, a finding that stands in sharp contrast to the traditional view of disease-associated microbial loss. We identified Candida albicans as the pivotal biomarker distinguishing invasive from indolent lesions. Crucially, functional integration reveals that this fungal enrichment is not merely an association but appears to actively orchestrate a pro-tumorigenic shift in the host's immune and metabolic landscape. These findings uncover a novel fungal-driven mechanism of tumor invasiveness, suggesting that the lung mycobiome serves as both a hidden driver of progression and a valuable target for early therapeutic intervention.},
}
@article {pmid42063504,
year = {2026},
author = {Yu, B and Zhao, WW and Tao, L and Li, K},
title = {The microbiota-gut-brain axis perspective: mechanisms and intervention strategies for the comorbidity of chronic constipation and depression.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1800520},
pmid = {42063504},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic constipation and depression are highly prevalent worldwide. These two conditions frequently co-occur in clinical practice. Accumulating evidence indicates that gut microbiota dysbiosis mediates this comorbidity through the microbiota-gut-brain axis (MGBA).<br><br>METHODS: This narrative review systematically summarizes current research on MGBA bidirectional communication mechanisms, gut microbiota alterations in comorbid patients, and microbiota-targeted intervention strategies.<br><br>RESULTS: The MGBA facilitates bidirectional communication through four major pathways: neural pathways via the vagus nerve, immune pathways via cytokines, endocrine pathways via the HPA axis, and metabolic pathways via short-chain fatty acids and neurotransmitter precursors. Gut dysbiosis is associated with comorbidity and may contribute to its pathogenesis through multiple mechanisms. First, neurotransmitter metabolism becomes dysregulated, particularly in the serotonin and GABA systems. Second, chronic low-grade inflammation develops with elevated pro-inflammatory cytokines. Third, intestinal barrier dysfunction occurs, leading to increased permeability and bacterial translocation. Fourth, HPA axis hyperactivity emerges. Fifth, production of microbial metabolites is altered, including short-chain fatty acids and tryptophan metabolites. Comorbid patients exhibit characteristic microbiota signatures. These include reduced abundance of butyrate-producing bacteria such as Faecalibacterium, Roseburia, and Coprococcus. Microbial diversity decreases significantly. Pro-inflammatory taxa become enriched. Several evidence-based interventions show promise. These include psychobiotics, fecal microbiota transplantation, and dietary modifications such as Mediterranean diet and high-fiber intake. Exercise and integrative approaches including traditional Chinese medicine also demonstrate beneficial effects.<br><br>CONCLUSION: The gut microbiota represents a critical hub connecting gastrointestinal and mental health. Microbiota-targeted therapies offer promising strategies for managing chronic constipation-depression comorbidity. Future research should establish causal relationships and develop reliable microbial biomarkers. Precision medicine approaches based on individual microbiome profiles are needed to optimize therapeutic outcomes.},
}
@article {pmid42063710,
year = {2026},
author = {Lu, H and Hu, X and Chen, Y and He, J},
title = {Colorectal cancer in ulcerative colitis: unraveling mechanisms and advancing surveillance and chemoprevention.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1793470},
pmid = {42063710},
issn = {2234-943X},
abstract = {Patients with ulcerative colitis (UC) have an increased risk of developing colorectal cancer through inflammation-driven carcinogenesis distinct from sporadic disease. Although the relative risk remains elevated, contemporary population-based studies indicate a substantial decline in absolute incidence, likely reflecting improved disease control, biologic therapies and structured surveillance colonoscopy. This review synthesizes current evidence on the epidemiology and determinants of colitis-associated colorectal cancer (CAC), highlighting key risk modifiers such as disease extent and duration, persistent inflammation, family history, and primary sclerosing cholangitis. We further summarize advances in understanding the molecular and immunologic mechanisms underlying CAC, including genomic instability, immune dysregulation, oxidative stress, microbiome alterations, and tumor microenvironment remodeling. Emerging molecular and histologic biomarkers that may enhance risk stratification and guide precision surveillance are discussed. In addition, contemporary surveillance approaches and evolving chemoprevention strategies are critically evaluated. Collectively, this review outlines current challenges and future directions for individualized CRC prevention in patients with UC.},
}
@article {pmid42063761,
year = {2026},
author = {Chen, YJ and Yang, BW and Gu, ZC and Han, J},
title = {Interplay between circadian rhythms, gut microbiota, and MASLD: from mechanistic foundations to therapeutic opportunities.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1767462},
pmid = {42063761},
issn = {2296-858X},
abstract = {Metabolic dysfunction-associated fatty liver disease (MASLD), previously known as non-alcoholic fatty liver disease (NAFLD), has become the most common chronic liver disease worldwide. Although excessive lipid accumulation, insulin resistance, and chronic low-grade inflammation are recognized as the main pathophysiological drivers, an increasing body of research indicates that the relationship between circadian rhythms, gut microbiota, and liver metabolism is far more complex than previously imagined, forming a systemic regulatory network. Disruption of circadian rhythms can affect the temporal coordination of metabolic pathways in the liver and other surrounding tissues. At the same time, the gut microbiota itself also exhibits circadian rhythm variations. The dysregulation of these rhythms, leading to microbial imbalance, intestinal permeability defects, and imbalances in microbial metabolites, can exacerbate lipid deposition and inflammatory responses in the liver. Research shows that important microorganisms can produce short-chain fatty acids, regulate bile acid balance, and enhance intestinal barrier function, creating a synergistic effect with the host's circadian rhythms. Conversely, during circadian disruption, the proliferation of harmful symbionts can exacerbate the entry of lipopolysaccharides into the bloodstream, oxidative stress, and the development of steatohepatitis. This relationship among the three establishes the ' circadian rhythm-gut microbiota-liver axis' as a new model for understanding the mechanisms underlying MASLD and for developing temporal therapies and microbiome interventions. This review systematically explores how circadian rhythms regulate the relationship between the gut microbial ecology and liver metabolism, focusing on the microbial species closely related to the interaction between circadian rhythms and MASLD. It also introduces emerging therapeutic strategies, including time-restricted feeding, circadian probiotics, postbiotics supplementation, and circadian rhythm drugs. These findings collectively suggest that targeting the temporal dimension of the interactions between the host and microbiota holds clinical potential for the prevention and treatment of MASLD.},
}
@article {pmid42063777,
year = {2026},
author = {Zhu, M and Sun, C and Zhang, Y and Na, Y and Wang, Y and Zhao, Q and Gu, Y},
title = {Blepharitis driven by microbiome dysbiosis and Demodex infestation: possible pathogenic mechanisms.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1801375},
pmid = {42063777},
issn = {2296-858X},
abstract = {Blepharitis is a chronic inflammation of the eyelid margin that is mediated by the immune system. It is one of the common ocular surface diseases and often leads to serious sequelae that threaten vision, such as dry eye syndrome due to insufficient tear secretion, corneal neovascularization, and stubborn chalazion. Elucidating its precise etiology is therefore imperative. Emerging high-throughput sequencing and metagenomic analyses have unveiled a quantitative and qualitative disruption of the periocular microbiome (dysbiosis), characterized by the expansion of specific bacterial species such as Staphylococcus aureus, coupled with episodic blooms of Demodex. These perturbations are no longer considered epiphenomena. In this review, we reveal the possible mechanisms of the role of blepharitis and microbiota dysbiosis.},
}
@article {pmid42063820,
year = {2026},
author = {Aguilar Ramos, MA and Gutkin, S and David, M and Shabat, D and Balskus, EP},
title = {Chemiluminescent Probes Allow for the Rapid Identification of Colibactin-Producing Bacteria.},
journal = {JACS Au},
volume = {6},
number = {4},
pages = {2377-2386},
pmid = {42063820},
issn = {2691-3704},
abstract = {The pks (or clb) gene cluster, which produces the genotoxic natural product colibactin, is encoded by human gut Enterobacteriaceae, including many commensal strains of E. coli. Colibactin cross-links DNA and is implicated in colorectal cancer development, highlighting the importance of identifying colibactin-producing gut bacteria within biological samples. In this study, we develop phenoxy-dioxetane chemiluminescent probes that selectively react with a critical colibactin biosynthetic enzyme, the serine peptidase ClbP. We show that these chemiluminescent probes have superior sensitivity, speed, and detection capabilities compared with previously reported fluorescent ClbP probes. Furthermore, we employ these chemiluminescent probes to detect pks [+] E. coli directly in complex stool suspensions. These probes will enable multiple applications requiring the detection of colibactin-producing bacteria, including the identification of ClbP inhibitors and the screening of clinical samples.},
}
@article {pmid42063908,
year = {2026},
author = {Kateete, DP and Lubega, C and Nasinghe, E and Mbabazi, M and Galiwango, R and Jjingo, D},
title = {Gut microbial profiles of COVID-19 patients in Uganda.},
journal = {African health sciences},
volume = {26},
number = {1},
pages = {1-15},
pmid = {42063908},
issn = {1729-0503},
mesh = {Humans ; *COVID-19/microbiology/epidemiology ; Uganda/epidemiology ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; Middle Aged ; SARS-CoV-2 ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Bacteria/isolation &amp; purification/genetics ; },
abstract = {BACKGROUND: The role of the microbiome in COVID-19 outcomes remains an area of exploration. We comprehensively explored the gut microbiome of Ugandan COVID-19 patients and inferred potential implications.<br><br>METHODS: Stool and demographic data were collected from 100 COVID-19 confirmed cases at the covid isolation and treatment centers in Kampala during the first and second waves of the pandemic in Uganda (2020 and 2021, respectively). 16S rRNA sequencing was performed on the DNA extracted from stool, followed by bioinformatics analysis. Machine-learning techniques were used to determine microbes that were associated with disease severity.<br><br>RESULTS: We observed differences in microbial composition between COVID-19 patients and healthy controls. Pathogenic bacteria such as Klebsiella oxytoca, Salmonella enterica and Serratia marcescens had an increased presence in COVID-19 disease states, especially severe cases. Additionally, there was an increase in opportunistic pathogens like Enterococcus species, along with a decrease in beneficial microbes, such as Alphaproteobacteria, when comparing mild and severe cases. Machine-learning identified age and microbes like Ruminococcaceae, Bacilli, Enterobacteriales, porphyromonadaceae and Prevotella copri as predictive of severity.<br><br>CONCLUSION: The microbiome likely plays a role in the dynamics of SARS-CoV-2 infection in Ugandan patients. The shift in abundance of specific microbes can moderately predict severity of COVID-19 in this population.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid42063947,
year = {2026},
author = {Chatthanathon, P and Wongsawaeng, D and Chetwittayachan, T and Cheibchalard, T and Leelahavanichkul, A and Kowitdamrong, E and Sayasathid, J and Somboonna, N},
title = {Air Bacterial Microbiomes in Hospitals: Case Studies from a Metropolis and a Small City of Thailand.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0068},
pmid = {42063947},
issn = {2001-0370},
abstract = {Experimental objective: Hospital air can act as a reservoir of opportunistic and antimicrobial-resistant microorganisms, which may contribute to hospital-acquired infections. However, the composition of airborne bacterial communities and the factors shaping them within hospital environments remain insufficiently characterized. This study investigated airborne bacterial microbiomes across hospital areas and sampling approaches and compared hospitals located in a metropolis versus a smaller city in Thailand. Methods: Air samples were collected from various hospital zones using active air-pump sampling and passive air-grille or high-efficiency particulate air-filter swab approaches at King Chulalongkorn Memorial Hospital in Bangkok and Naresuan University Hospital in Phitsanulok. Microbiota were analyzed using 16S ribosomal RNA gene sequencing, followed by bioinformatic analyses. Results: Bacterial community compositions and alpha-diversity varied significantly along sampling method, hospital area, and geographic location. Passive air-grille swabs captured higher microbial biomass and diversity, consistent with accumulated microbiome deposition over time. Areas with open and semiopen ventilation (e.g., restaurant and outpatient departments) exhibited higher bacterial diversity than filtered areas (e.g., operating rooms). The metropolitan hospital showed higher abundances of Cutibacterium, Acinetobacter, Curtobacterium, and members of Comamonadaceae, whereas the hospital in the smaller city displayed greater overall diversity. High-efficiency particulate air-filter samples showed reduced diversity but enriched in spore-forming taxa. Predicted functional profiles also differed between sampling approaches and hospital locations, including pathways that might be related with human diseases. Conclusion: Hospital air microbiomes were heterogeneous and influenced by environmental conditions and sampling strategy. These findings provide insights for factor correlations and may inform improved air-quality management strategies.},
}
@article {pmid42064071,
year = {2026},
author = {Wang, Q and Zhang, F and Xin, Y and Yang, R and Tang, Z and Wu, Z and Ming, J},
title = {The human microbiome reshapes the breast cancer immune-metabolic-hormonal microenvironment.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1774211},
pmid = {42064071},
issn = {1664-3224},
mesh = {Humans ; *Breast Neoplasms/metabolism/immunology/microbiology/therapy/etiology/pathology ; *Tumor Microenvironment/immunology ; Female ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Animals ; Estrogens/metabolism ; },
abstract = {Beyond established risk factors such as genetics and hormones, the human microbiome has emerged as a pivotal player in breast cancer pathogenesis. This review delineates the technological evolution in breast microbiome research, spanning traditional culture methods to high-throughput sequencing and cutting-edge spatial omics. We elucidate the role of the gut-breast axis in modulating breast cancer development through its influence on estrogen metabolism, immune responses, and microbial metabolites. Furthermore, we analyze the distinctive compositional features of the intratumoral microbiota and their dual, context-dependent roles in promoting invasion, inducing immunosuppression, and driving metabolic reprogramming within the tumor microenvironment. Novel microbiome-based therapeutic strategies, including targeted microbiota depletion, engineered microbial therapeutics, and dietary interventions, are summarized. Finally, we discuss the translational potential of microbiome research in refining breast cancer risk prediction, evaluating treatment responses, and advancing personalized prevention and treatment strategies, ultimately contributing to improved patient outcomes.},
}
@article {pmid42064150,
year = {2026},
author = {Yu, X and Fan, L and Fan, S and Li, H},
title = {AI digital-twin ecosystem translating gut-microbiome-neuroimmune signals into precision sleep-mood interventions.},
journal = {Frontiers in psychiatry},
volume = {17},
number = {},
pages = {1703605},
pmid = {42064150},
issn = {1664-0640},
abstract = {We present a novel AI-powered "gut-brain-sleep" digital-twin nursing ecosystem (G-B-S DT-N) that translates microbiome and neuroimmune signals into precision interventions for sleep and mood disorders. The ecosystem integrates four key layers: Microbiome Dynamics, Neuro-immune Interface, Sleep-Cognition-Emotion Circuits, and Person-Nurse-Environment Triad. These layers leverage multi-omics data, EEG sleep microstructure, real-time sensors, and EMR feeds to create a dynamic, patient-specific architecture. Uncertainty-aware explainable AI (XAI) modules ensure privacy and interpretability, enabling causal inference through advanced machine learning techniques. Adaptive care pathways, including precision pre-/post-biotic delivery and circadian light prescriptions, are optimized via nurse-in-the-loop reinforcement learning. The digital twin is operationalized through a five-step closed-loop workflow in hospital and community settings. Quantum-accelerated simulations and a proposed RCT (D-TWIN-RCT) will assess efficacy compared to standard care. Social, legal, and ethical frameworks protect data sovereignty and autonomy. This ecosystem offers a scalable solution for managing complex comorbidities, positioning nursing as a key driver of microbiome-precision medicine.},
}
@article {pmid42064151,
year = {2026},
author = {Osredkar, J and Finderle, P and Godnov, U and Jekovec-Vrhovšek, M and Vidova, V and Elliott, JP and Fabjan, T and Avguštin, G and Osredkar, D and Kumer, K},
title = {Faecal inflammatory protein markers in children with autism spectrum disorder are comparable to their healthy siblings.},
journal = {Frontiers in psychiatry},
volume = {17},
number = {},
pages = {1792801},
pmid = {42064151},
issn = {1664-0640},
abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a complex neurodevelopmental condition often accompanied by gastrointestinal (GI) symptoms. Inflammatory proteins in stool have been proposed as potential biomarkers, but evidence remains inconsistent. We compared fecal levels of α1-antitrypsin (A1AT), immunoglobulin A (IgA), and calprotectin (Cal) in 57 children with ASD and 57 biological siblings without ASD. Sibling designs are now preferred to disentangle ASD-specific biology from shared environmental and microbiome factors. Participants were carefully screened to exclude recent antibiotic use, digestive problems, gastrointestinal infections, and abnormal dietary patterns, thereby controlling for major factors known to influence gut inflammatory markers.<br><br>METHODS: Stool samples were thawed, freeze-dried, and proteins extracted using ammonium bicarbonate buffer with sodium deoxycholate. After BCA quantification, samples were reduced, alkylated, spiked with stable isotope-labelled peptides, and digested with trypsin. Peptides were purified and analyzed by UHPLC-MS/MS (Agilent 6495A) in dynamic SRM mode. Quantification used internal standards and normalization to total protein. Ratios of IgA1/IgA2 and S100A8/S100A9 were calculated. ASD severity was evaluated using the Childhood Autism Rating Scale (CARS).<br><br>RESULTS: Children with ASD showed trends toward higher IgA and calprotectin and lower &#x3b1;1-antitrypsin compared with siblings, but differences were not statistically significant. Subgroup analysis suggested different distribution patterns in moderate versus severe ASD, including higher IgA in the moderate group and altered S100A8/S100A9 ratio in the severe group. These subgroup findings were exploratory, derived from critically underpowered post-hoc analyses (severe subgroup: n = 11 pairs, ~18% power for medium effects), and should be considered hypothesis-generating only, pending validation in adequately powered pre-registered studies.<br><br>CONCLUSIONS: The results are consistent with recent meta-analyses reporting no consistent evidence of gut inflammation in ASD. Larger, sex-matched studies with full assay validation are needed to clarify the role of stool proteins in ASD.},
}
@article {pmid42064210,
year = {2026},
author = {Ding, X and Wang, J and Wang, Y and Xu, H and Liu, Y},
title = {Therapeutic modulation of the gut microbiota by traditional Chinese medicine in the management of cholestatic liver injury.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1807162},
pmid = {42064210},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Medicine, Chinese Traditional/methods ; Dysbiosis/drug therapy ; *Cholestasis/drug therapy/microbiology ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Animals ; Bile Acids and Salts/metabolism ; Liver/pathology/drug effects ; *Liver Diseases ; },
abstract = {Cholestatic liver injury (CLI) is a complex pathology characterized by impaired bile excretion and a lack of effective curative therapies. Emerging evidence indicates that the gut microbiota plays a critical role in the pathogenesis of CLI via the gut-liver axis. Specifically, gut dysbiosis disrupts bile acid homeostasis, triggers immune-mediated inflammation, exacerbates oxidative stress, and dysregulates multiple signaling pathways, thereby accelerating hepatic damage. Traditional Chinese Medicine (TCM) offers a distinct therapeutic advantage through its multi-component, multi-target mechanisms. Many studies have shown that TCM herbal extracts and some formulas can attenuate CLI by restructuring the gut microbiome. These interventions work by promoting beneficial bacterial proliferation, restoring intestinal barrier integrity, modulating bile acid receptors, and suppressing inflammation and fibrosis. This review synthesizes current mechanisms linking gut dysbiosis to CLI and evaluates recent advances in TCM-based strategies that target the gut microbiota, offering theoretical insights for novel clinical interventions.},
}
@article {pmid41851245,
year = {2026},
author = {Azmi, SZK and Kurnia, D and Nurpalah, R and Virgianti, DP and Padilah, R and Nafisah Ruswadi, LF and Subroto, T},
title = {Characterization of anticariogenic mycosymbiotic fungi associated with the medicinal plant Piper crocatum.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41851245},
issn = {2045-2322},
abstract = {UNLABELLED: The escalating antibiotic resistance in oral pathogens, particularly Streptococcus mutans, necessitates the discovery of alternative bioactive scaffolds. While Piper crocatum (red betel) is an ethnobotanically significant plant, its symbiotic mycobiota remains a negligible niche compared to heavily mined species like P. nigrum or P. betle. This study explored the diversity of fungal syimbiont from P. crocatum as potential anticariogenic agents. Fungal samples were isolated from leaves collected across 13 locations in Tasikmalaya, Indonesia. Purification for each fungi was conducted using the hyphal tip transfer technique, yielding 66 axenic isolates. Phenetic characterization was employed as a dereplication strategy to select ten representative based on 33 morphotypes for screening. Similarity analysis was conducted using the Jaccard coefficient via the UPGMA, then visualized in RStudio using the ape and ggtree packages to generate a phenetic dendrogram. One representative isolate from each major cluster was selected for bioactivity screening, with priority given to isolates producing visible extracellular exudates. Results indicated a positive correlation between colony pigmentation and bioactivity, with isolate t5-059 exhibiting the strongest inhibition against S. mutans (21.5 mm). Molecular identification via ITS rDNA resolved the bioactive strains as Colletotrichum truncatum (t5-059), Colletotrichum cliviae (t-9052), Torula canangae (t10-062), and Aspergillus clavatonanicus (t1-007). The recurrence of these specific taxa across geographically heterogeneous sites supports the hypothesis of host filtering, where P. crocatum selects for a core microbiome. These findings highlight P. crocatum as a reservoir of unique fungal associates capable of producing potent metabolites for oral health applications.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41703-z.},
}
@article {pmid41872736,
year = {2026},
author = {Deng, Y and Kang, Q and Yang, B and Wang, Y and Zhou, Y and Yu, P and Tong, Z and Dong, J and Huang, X and Wu, W and Wu, J and Zhu, Y and He, X and Guo, L},
title = {Divergent pathogenic strategies of Fusarium species in Panax notoginseng and biocontrol by a Bacillus-Serratia consortium.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41872736},
issn = {1471-2229},
support = {CARS-21//China Agriculture Research System of MOF and MARA/ ; 202102AE090042, 202204BI090003, 202205 AF150018, and 2021JH002//Major Science and Technology Project of Yunnan and Kunming/ ; YNQR-QNRC-2020-073//Yunnan Xingdian Talent Support Program; Young Talent Program of High-level Talent Plan in Yunnan Province/ ; 202301 BD070001-138//Yunnan Agricultural Joint Special Project - Key Projects/ ; },
abstract = {UNLABELLED: Fusarium-induced root rot severely constrains Panax notoginseng cultivation, yet the differential pathogenicity and ecological interactions among coexisting Fusarium species remain poorly understood. By isolating three pathogenic isolates—Fusarium oxysporum LP1 and F. solani LP2/LP3—we uncovered a distinct ecological trade-off: F. oxysporum exhibits higher niche occupancy, whereas F. solani demonstrates markedly greater virulence. To manage this disease, we engineered the Bacillus subtilis-Serratia marcescens synthetic microbial consortium (BS) comprising antagonistic strains XY-6 and XB-7. BS application significantly enhanced disease suppression (56%) compared with single-strain treatments (21%–25%). Mechanistic evaluations revealed a synergistic triple-mode of action: (i) direct pathogen inhibition via cell-free filtrates (38% reduction); (ii) activation of host systemic resistance, evidenced by substantially increased peroxidase (133%) and superoxide dismutase (173%) activities; and (iii) beneficial restructuring of the rhizosphere fungal community, characterized by Mortierellomycota enrichment, elevated α-diversity, and fortified microbial interaction networks. Collectively, this study illuminates the ecological trade-off between virulence and niche fitness among Fusarium species, and provides a robust, sustainable microbiome-engineering strategy for mitigating soil-borne diseases in medicinal crops.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08617-4.},
}
@article {pmid42061404,
year = {2026},
author = {Su, Q and Chen, S and Lau, LH and Lui, RN and Wang, Y and Xu, Z and Cheung, CP and Ching, JYL and Shen, X and Peng, Y and Tun, HM and Ianiro, G and Rubin, D and Chang, EB and Chan, FKL and Ng, SC},
title = {Artificial intelligence-driven donor-recipient gut microbiome matching for optimized fecal microbiota transplantation.},
journal = {Cell reports},
volume = {},
number = {},
pages = {117301},
doi = {10.1016/j.celrep.2026.117301},
pmid = {42061404},
issn = {2211-1247},
abstract = {Fecal microbiota transplantation (FMT) has emerged as a promising therapy for gastrointestinal diseases, yet its clinical efficacy remains individually variable. Here, we analyze multi-kingdom and functional profiles in pre- and post-FMT metagenomes from 515 FMTs across 30 cohorts and 12 diseases, in which 94 metagenomes from 44 FMTs are newly collected. We reveal a robust association between clinical efficacy and post-FMT microbiome convergence of recipients toward donors, across diseases. To predict post-FMT microbial convergence, we develop MOZAIC (Microbiome Matching Optimization via Artificial Intelligence), a framework that integrates multi-dimensional donor-recipient microbiota features. MOZAIC achieves an average area under the curve (AUC) of 0.88 and accuracy/recall >0.80 in forecasting microbiome convergence, with 78.7% accuracy in predicting clinical outcomes, and retrospectively simulates a 1.44-fold improvement (from 49.4% to 71.0%) in clinical response rates over baseline. This study establishes microbiome convergence as a key mediator of FMT and provides a scalable tool for precision matching in microbiota-based therapies.},
}
@article {pmid42061466,
year = {2026},
author = {McEvoy, CT and Idrose, NS and Dharmage, SC and Bui, DS and Simpson, SJ and Patchen, B and Marshall, NE and Kelly, RS and Lynch, SV and McDonald, CM and Sood, BG and Pratt, C and Vitalis, D and Lu, Q and Carroll, KN and Duijts, L and Forno, E and Venter, C and Prakash, YS and Miller, AN and DeMeo, DL and Subbarao, P and Britt, RD and Sengupta, S and McGrath-Morrow, SA and Litonjua, AA},
title = {Maternal and Perinatal Nutritional Programming of Lung Health and Disease in Childhood and Early Adulthood: Research Gaps and Opportunities; NHLBI/NIH Workshop Report.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.03.029},
pmid = {42061466},
issn = {1097-6825},
abstract = {The National Heart, Lung, and Blood Institute (NHLBI)-sponsored workshop, Maternal and Perinatal Nutritional Programming of Lung Health and Disease in Childhood and Early Adulthood: Research Gaps and Opportunities, was convened (October 24-25, 2024) to explore how nutrition before, during, and after pregnancy influences lung development and respiratory health across the lifespan. The workshop focused on identifying critical knowledge gaps, mechanistic pathways, and intervention opportunities. Presentations spanned maternal dietary patterns, specific nutrient supplementation, gestational weight gain, and the role of maternal obesity in offspring wheeze and asthma. The role of early postnatal nutrition, particularly human milk for preterm infants at risk for bronchopulmonary dysplasia (BPD) was emphasized. Emerging areas included circadian rhythms and the maternal and infant microbiome, metabolome, and epigenome in mediating nutrition-related respiratory outcomes. Research needs included randomized trials of dietary interventions, mechanistic studies to elucidate biological pathways, and implementation strategies to integrate nutritional interventions into practice. Vulnerable populations were emphasized, including preterm infants and families experiencing food insecurity. Participants emphasized the need for a coordinated research agenda to inform future interventions that could improve outcomes across generations.},
}
@article {pmid41993453,
year = {2026},
author = {Liber, JA and Coelho, MA and He, SY},
title = {Aimea gen. nov. defines a novel plant-associated yeast genus in Microbotryomycetes with three novel species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41993453},
issn = {2692-8205},
abstract = {Plant tissues and surfaces are among the largest microbial habitats on Earth, and commensal yeasts are common members of these communities, where they can contribute to plant-microbe interactions including the biological control of plant diseases. Here, we describe a novel genus, Aimea, of unpigmented, plant-associated basidiomycete yeasts, in the class Microbotryomycetes, and name three new species (A. erigeronia, A. cardamina, and A. sorghi) represented by four isolates from leaves and roots of multiple hosts. We characterize these taxa through analyses of metabolic requirements, tolerance to differences in osmolarity, pH, and temperature, and enzymatic activities. In parallel, we generate near-chromosome-scale hybrid genomes annotated with transcriptome data. We employ whole-genome and multilocus phylogenetic approaches to infer the placement of these species within a monophyletic clade. We use comparative genomics to examine how the gene content of these yeasts differs from that of other members of the Microbotryomycetes, including an apparent proliferation of retrotransposons. We further demonstrate the genetic transformability of these taxa using Agrobacterium tumefaciens-mediated transformation. The description of these new species, together with high-quality genome resources and a genetic transformation protocol, establishes a foundation for experimental studies of these novel plant-associated yeasts and their interactions with hosts and other microbes.},
}
@article {pmid42053842,
year = {2026},
author = {Sysak, A and Górska, S},
title = {Extracellular Vesicles in Allergy: From Cellular Communication to Clinical Implications.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {69},
number = {1},
pages = {},
pmid = {42053842},
issn = {1559-0267},
support = {2021/43/I/NZ7/00693//National Science Centre of Poland/ ; },
abstract = {Extracellular vesicles (EVs) are lipid bilayer-enclosed particles released by both eukaryotic and prokaryotic cells and represent an evolutionarily conserved system of intercellular communication. By transporting bioactive cargo, including proteins, lipids, microRNAs, EVs enable the transfer of molecular signals between cells, thereby regulating immune homeostasis and inflammatory responses. In allergic diseases, EVs have emerged as key mediators linking epithelial barriers, immune cells, and the microbiome. EVs derived from epithelial, immune, and microbiota-associated cells may contribute to the initiation, amplification, and persistence of allergic inflammation by modulating barrier integrity, immune cell polarization, and cytokine signaling pathways. Disease-specific alterations in EV cargo reflect underlying pathogenic mechanisms, positioning EVs as promising non-invasive biomarkers for disease diagnosis, stratification, and monitoring. In parallel, accumulating experimental evidence highlights the therapeutic potential of EVs as cell-free immunomodulatory agents capable of suppressing allergic inflammation and promoting immune tolerance. This review synthesizes current knowledge on extracellular vesicles across three major allergic diseases: asthma, atopic dermatitis, and food allergy, integrating mechanistic insights with diagnostic and therapeutic advances. By incorporating highly recent literature and covering a broad spectrum of EV sources and engineered vesicle-based strategies, the review provides a comprehensive overview of how EV-mediated cellular communication translates into clinically relevant applications in allergy.},
}
@article {pmid42054893,
year = {2026},
author = {Nkoh, JN and Wu, Z and Shang, C and Zhang, Q and Wang, J and Ntie-Kang, F and Hussain, MA},
title = {Differential long-term tolerance to copper and salt stress by Bruguiera gymnorhiza and Kandelia obovata is driven by species-specific metabolic modulation and rhizobacterial recruitment.},
journal = {Plant physiology and biochemistry : PPB},
volume = {234},
number = {},
pages = {111310},
doi = {10.1016/j.plaphy.2026.111310},
pmid = {42054893},
issn = {1873-2690},
abstract = {The resilience of the plant phytobiome to environmental stress hinges on multitrophic interactions. This study reveals how Bruguiera gymnorhiza L. savigny and Kandelia obovata Sheue &amp; al achieve differential tolerance to copper (Cu) toxicity and salt stress through distinct rhizobacterial recruitment and root metabolic modulation strategies. Using multiomics and chemical approaches, we analyzed rhizobacterial community dynamics, root/rhizosphere metabolic profiles, root/leaf antioxidant enzyme activities, and rhizosphere physicochemical properties. The results revealed that metabolic modulation was the primary stress response mechanism, especially in the less tolerant B. gymnorhiza. Based on the number of differentially abundant metabolites, lipids and lipid-like molecules dominated stress response in both the roots and rhizospheres, except in the roots of K. obovata, where phenylpropanoids and polyketides dominated. The marked differences observed in eicosanoid metabolism between the roots and rhizospheres highlight how species-specific adjustments determine stress tolerance levels. These distinct metabolic strategies influenced species-specific rhizobacterial recruitment, optimizing nutrient uptake and growth. Specifically, K. obovata exhibited more effective enrichment of stress-tolerant rhizobacteria (e.g., Bacteroidota, Firmicutes, and Proteobacteria), which was correlated with improved tolerance under all stresses and improved growth under Cu and Cu-salt stress. In contrast, B. gymnorhiza relies on the synergistic effect of Cu-salt stress to recruit beneficial consortia (Proteobacteria) for 11.5% growth promotion. Thus, tolerance to Cu/salt stress relies on species-specific microbiome-metabolite cross-talk, with the inherent adaptability of K. obovata outperforming the stress-dependent responses of B. gymnorhiza. These findings underscore microbiome-assisted restoration following species-specific management strategies.},
}
@article {pmid42054907,
year = {2026},
author = {Yang, Q and He, S and Xiang, B and Chen, Y},
title = {Hexavalent chromium exposure disrupts gut microbial structure and metabolic function in broiler chickens.},
journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)},
volume = {95},
number = {},
pages = {127874},
doi = {10.1016/j.jtemb.2026.127874},
pmid = {42054907},
issn = {1878-3252},
abstract = {Hexavalent chromium (Cr(VI)) is a pervasive environmental contaminant with well-documented toxicity, yet its impact on the gut microbiome remains poorly understood. This study investigated the effects of chronic dietary Cr(VI) exposure (37 mg/kg feed for 40 days) on the gut microbiota of broiler chickens using 16S rDNA sequencing and bioinformatic analysis. While alpha diversity remained unchanged, significant shifts in beta diversity indicated substantial structural reorganization of microbial communities. Taxonomic analysis revealed a decrease in Firmicutes and an increase in Proteobacteria and Cyanobacteria at the phylum level, along with genus-level alterations including enrichment of Romboutsia and depletion of Enterococcus. Functional prediction via PICRUSt2 further indicated disruptions in key metabolic pathways, particularly the phosphotransferase system (PTS), galactose metabolism, and propanoate metabolism. These findings elucidate a novel mechanism through which chromium exposure may induce toxicity, via disruption of gut microbial structure and function, and underscore the importance of the gut microbiome in mediating chemical toxicity, providing new insights for assessing ecological and health risks of heavy metal exposure.},
}
@article {pmid42054964,
year = {2026},
author = {Autuori, M and Neyrinck, AM and Lengelé, L and Olivera, EV and Rombaux, M and Rodriguez, J and Cani, PD and Walter, J and Bindels, LB and Delzenne, NM},
title = {Breath volatilome analysis reveals new gut microbiome-related metabolites that discriminate high versus low dietary fibre intake.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106662},
doi = {10.1016/j.clnu.2026.106662},
pmid = {42054964},
issn = {1532-1983},
abstract = {BACKGROUND &amp; AIMS: Gut bacteria produce a wide variety of metabolites that are playing important roles in human health. Dietary fibres (DF) are beneficial nutrients that have been shown to modulate key intestinal functions when fermented by gut bacteria. Since most bacteria-derived metabolites are volatile, their presence in exhaled breath allows to propose new non-invasive methods to study DF-microbiome interactions in humans. We aimed to identify potential novel biomarkers of gut microbiota activity released in exhaled breath following the consumption of DF at breakfast, upon untargeted analysis in healthy volunteers.<br><br>METHODS: 14 volunteers (7 women/7 men, 21 &#xb1; 2 years old) participated to two test days at a one-month interval, where they received either a low-(2.6 g) or high-(16.1 g) fibre breakfast. Before each test days, stools were collected to evaluate the microbiota composition using Illumina sequencing (V5-V6 region of 16S rRNA gene). Throughout the test days, breath samples were analysed using selected-ion flow-tube mass spectrometry (SIFT-MS). A sparse partial least squares-discriminant analysis (sPLS-DA) identified 30 signals that best discriminated between test days, corresponding to 173 candidate breath compounds.<br><br>RESULTS: The gut microbiota of the volunteers remained stable one month apart. The composition of exhaled breath shifted starting from 5 h after the high-fibre breakfast ingestion. Ninety compounds were identified as potential metabolites of gut microbes, with 81 showing increased concentrations after the high-fibre breakfast. These included acrylic acid (positively correlated with Faecalibacterium/Ruminococcaceae/Bacillota and negatively correlated with Bifidobacterium/Bifidobacteriaceae/Actinomycetota). The high-fibre breakfast also led to increases in limonene, ethylbenzene/xylene, p-cymene, and methionol that were positively correlated with the genus Faecalibacterium. Moreover, positive correlations were observed between cyclooctane/ethylcyclohexane, methanol and the phylum Bacillota. Dimethyl disulfide was strongly negatively correlated with the genus Bacteroides and its family Bacteroidaceae.<br><br>CONCLUSION: This study shows that DF consumption at breakfast stimulates the production of exhaled bacteria-derived metabolites reflecting profound changes in the metabolic activity of the gut microbiota. We also identified new potential biomarkers of DF intake, that are not directly linked to DF fermentation. Specific bacteria known to play a role in gut barrier, immunity and host metabolism were associated with those new metabolites.},
}
@article {pmid42055251,
year = {2026},
author = {van Dijk, LLA and Rijsbergen, LC and Havelaar, AC and Hartog, YD and Koutstaal, RW and Groen, K and de Vries, RD and de Swart, RL},
title = {Innate airway responses shape permissiveness to human respiratory syncytial virus.},
journal = {Virus research},
volume = {},
number = {},
pages = {199734},
doi = {10.1016/j.virusres.2026.199734},
pmid = {42055251},
issn = {1872-7492},
abstract = {The interaction between human respiratory syncytial virus (HRSV) and the innate immune system has been demonstrated both in vitro and in vivo. Disruption of interferon (IFN) signaling pathways increases susceptibility and permissiveness to HRSV infection, whereas pretreatment of cells with IFN confers (partial) resistance. This suggests that HRSV disease severity is likely influenced by a pre-existing antiviral state of the respiratory epithelium, driven by baseline or primed expression of type I and type III IFNs. Here, we investigated whether prior exposure to respiratory bacteria or viruses alters in vitro susceptibility and permissiveness to HRSV infection by shaping an antiviral state using both immortalized cell lines and airway organoid models. In A549 cells, pre-exposure to S. aureus had the most significant impact by reducing HRSV infection and inducing robust interferon responses. However, this effect was not reproduced in airway organoids. Conversely, sequential virus infection experiments in airway organoids revealed that prior infection with human parainfluenza virus type 3 (HPIV‑3) reduced the spread of subsequent HRSV infection. In addition to interferon signaling this proved to be associated with epithelial damage mediated by HPIV-3 infection. Collectively, these findings show that HRSV susceptibility and permissiveness are influenced by the up- or downregulation of specific anti- and pro-viral factors induced by prior bacterial or viral exposure, together with the maintenance or disruption of epithelial integrity. Understanding these interactions could be crucial when identifying specific risk groups for severe HRSV-associated disease and the development of targeted HRSV interventions.},
}
@article {pmid42055298,
year = {2026},
author = {Choi, J and Shin, N and Jin, D and Xu, E and Kwon, Y and Park, S and Lee, U and Lee, J and Oh, YK},
title = {Intestinal microenvironment-modulating nanomedicines for inflammatory bowel disease.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114953},
doi = {10.1016/j.jconrel.2026.114953},
pmid = {42055298},
issn = {1873-4995},
abstract = {Inflammatory bowel diseases present a highly restrictive intestinal microenvironment for drug delivery, in which epithelial injury, chronic inflammation, and microbial dysbiosis collectively impair transport, retention, and therapeutic efficacy. Excessive reactive oxygen species (ROS), mucus barrier disruption, altered luminal acidity, hydrogen sulfide accumulation, and abnormal enzymatic activity destabilize therapeutic cargos and limit access to inflamed tissues. These pathological features have motivated the development of nanocarriers designed either to directly modulate biochemical abnormalities, such as ROS scavenging and H2S removal, or to respond to disease-associated biochemical cues including ROS, luminal pH, enzymatic activity, and mucus abnormalities. In parallel, modulation of the immunological microenvironment has been pursued through nanomedicine platforms engineered to regulate inflammatory signaling, enhance mucosal targeting, protect therapeutic payloads from premature degradation, and prolong local residence. Complementary microbiome-oriented delivery strategies, including engineered probiotics, nanoparticles that release postbiotic factors, and carriers coated with microbial membranes, leverage host microbe interactions to achieve localized and sustained therapeutic effects. Despite substantial progress, effective delivery remains constrained by patient specific variability, spatial heterogeneity of inflammatory conditions, and limited durability of mucosal retention. Integrating biochemical responsiveness, immune modulation, and microbiome informed targeting represents a promising direction for advancing precision nanomedicine in inflammatory bowel diseases.},
}
@article {pmid42055311,
year = {2026},
author = {Cao, Z and Lin, Y and Li, W and He, L and Wang, H and Sun, L and Wang, X and Chen, L and Li, E},
title = {Physiological and metabolic responses of juvenile Chinese mitten crab (Eriocheir sinensis) to dietary hydrolyzed anchovy-cottonseed protein and amino acid supplementation.},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology},
volume = {285},
number = {},
pages = {111238},
doi = {10.1016/j.cbpb.2026.111238},
pmid = {42055311},
issn = {1879-1107},
abstract = {This study investigated the physiological and metabolic responses of juvenile Chinese mitten crab (Eriocheir sinensis) to dietary inclusion of coenzymatically hydrolyzed anchovy-cottonseed protein (HACP) with or without arginine and methionine supplementation. A 56-day feeding trial was conducted. Juvenile crabs were fed a control diet containing 15% fishmeal and experimental diets in which fishmeal was partially replaced by HACP at graded levels (5%, 10%, and 15%). Increasing dietary HACP levels significantly affected growth performance, feed intake, digestive enzyme activities, hepatopancreatic condition, and intestinal microbial composition. The 5% HACP inclusion maintained growth performance and protein utilization comparable to the control, whereas higher inclusion levels reduced feed intake and digestive enzyme activity, suggesting potential alterations in digestive enzyme activity and metabolic status. Arginine and methionine supplementation partially alleviated these effects by enhancing trypsin and lipase activities, reducing hepatopancreatic stress indicators, and improving antioxidant status, suggesting potential improvements in nutrient utilization and metabolic responses. Microbiota and metabolomic analyses further revealed coordinated shifts in intestinal microbial composition and metabolic pathways associated with amino acid, lipid, and energy metabolism. Overall, these findings indicate that dietary HACP influences physiological function through integrated effects on digestion, metabolism, and microbiome-metabolome interactions, and highlight the role of amino acid balance in mediating metabolic response under altered dietary protein composition.},
}
@article {pmid42055337,
year = {2026},
author = {Nitin, N and Daneshgar, P and Kniffen, D and Vicaretti, SD and Whitmore, B and Kipchumba, L and Quin, C and Gibson, DL and Bergstrom, KSB and Zandberg, WF},
title = {Longitudinal analysis of human milk oligosaccharides (HMOs) and Mucin-2-glycans in infants reveals enrichment of sulfated and glucuronic acid-bearing HMOs.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {113099},
doi = {10.1016/j.jbc.2026.113099},
pmid = {42055337},
issn = {1083-351X},
abstract = {In infants, the acquisition of an adult-like gastrointestinal (GI) microbiome begins at birth, fully developing by toddlerhood. This colonization is influenced by the diet which, in breast-fed infants, contains high concentrations of soluble human milk oligosaccharides (HMOs), prebiotics bearing structural-resemblance to the glycans that decorate Mucin-2 (MUC2). MUC2 is the first line of defense between the microbiota and the underlying mucosal tissues; it also provides a nutrient-rich habitat for GI commensal microbes. The research described herein builds on two earlier findings: the ability to sample MUC2 adhering to the surface of stool samples and the discovery of a class of sulfated HMOs within human milk. Studies have shown that de-sulfation of MUC2-borne glycans is a key for their metabolism by GI microbes in vitro and, if sulfated glycans are otherwise metabolically-resistant, two hypotheses follow. First, in contrast with major prebiotic HMOs, sulfated HMOs will be enriched in the infant GI tract; second, high abundances of glyco-epitopes like sulfation in HMOs will deflect the microbiome's metabolic activity away from MUC2 leading to detectible changes in the host glycome. We show that both HMOs and MUC2 could be non-invasively sampled from the same infant stool samples. Capillary electrophoresis analyses of paired milk/stool samples demonstrated significant enrichment of sulfate-containing HMOs in stool. High-resolution mass spectrometry (HRMS) was used to detect numerous sulfated HMOs, including a new class concurrently containing glucuronic acid (GlcA) residues. Infant MUC2-derived glycans were also analyzed by HRMS; this is the first reported semi-quantitative longitudinal study and provides a benchmark for future research.},
}
@article {pmid42055352,
year = {2026},
author = {Abdessamad, H and Abdallah, D and Attieh, R and Eid, S and Nahal, J and Jamal, O and Fakih, A and Zahran, K and Khalil, A and Helmy, S and Ibrahim, A and Moghnieh, R},
title = {Revisiting Fluoroquinolone Prophylaxis in Hematological Malignancies and Hematopoietic Cell Transplantation: A Decade of Evidence and Gaps in Understanding the Impact of Gut Colonization with Fluoroquinolone-Resistant Enterobacterales.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107824},
doi = {10.1016/j.ijantimicag.2026.107824},
pmid = {42055352},
issn = {1872-7913},
abstract = {Rising antimicrobial resistance necessitates reevaluation of fluoroquinolone (FQ) prophylaxis (FQP) in patients with hematologic malignancies undergoing intensive chemotherapy or hematopoietic cell transplantation (HCT). This narrative review synthesizes recent evidence on the clinical efficacy of FQP and the modifying effect of gut colonization with fluoroquinolone-resistant Enterobacterales (FQRE). FQP consistently reduced febrile neutropenia and bloodstream infections, particularly in autologous HCT and selected chemotherapy cohorts. However, its benefit was context-dependent, with diminished or absent effects in allogeneic HCT and in settings with higher background FQ resistance (≥30%). Breakthrough infections during prophylaxis were predominantly caused by FQ-resistant organisms, reflecting strong selective pressure. Baseline colonization with FQRE further increased the risk of bloodstream infection and reduced the likelihood of benefit from prophylaxis. Mortality was not significantly affected across populations. Microbiome data suggest that FQP exerts a selective effect on Gram-negative gut colonization rather than causing broad disruption of microbial diversity. Overall, the effectiveness of FQP is strongly influenced by resistance epidemiology and colonization status. These findings support a shift toward more individualized, resistance-informed prophylaxis strategies within antimicrobial stewardship frameworks.},
}
@article {pmid42055363,
year = {2026},
author = {Zhang, K and Qiu, MT and Shao, YH and Liu, J and Tu, ZC},
title = {High-tryptophan diet mitigates parvalbumin-induced allergic responses via gut microbiome remodeling and immune modulation.},
journal = {International journal of biological macromolecules},
volume = {364},
number = {},
pages = {152245},
doi = {10.1016/j.ijbiomac.2026.152245},
pmid = {42055363},
issn = {1879-0003},
abstract = {Parvalbumin-induced food allergy model in BALB/c mice were established to investigate the intervention effect of high- tryptophan (Trp) diet on allergic responses. Trp suppressed histamine and IL-6 release from the sensitized KU812 cells, effectively mitigated parvalbumin-induced cellular sensitization. High-Trp diet alleviated allergic symptoms, reduced the organ index of the spleen and serum specific IgE, IgG, IgG1 and IgG2a levels, alongside suppressed Th2-type immune responses in mice. Meanwhile, Trp not only influenced the relative abundance of allergy-related gut microbiome, such as Faecalibaculum, Romboutsia, Lachnoclostridium unclassified_f__Lachnospiracea and norank_f__Ruminococcaceae, but also increased the production of short-chain fatty acids. Meanwhile, Trp enhanced the expression of intestinal tight junction proteins, repaired the impaired intestinal barrier in allergic mice, and also induced the phosphorylation of STAT3 and enhanced the expression of Reg3γ, then may activated the AhR/IL-22 signal pathway in murine intestinal epithelial cells. These findings demonstrated that high-Trp diet mitigated parvalbumin-induced allergic responses were responsible for gut microbiome remodeling and immune modulation.},
}
@article {pmid42056070,
year = {2026},
author = {López, I and Pineda, C and Camargo, A and Arenas, C and Torrano, A and Glorieux, G and Aguilera-Tejero, E},
title = {Supplementation with Enterococcus lactis (SF68) and its association with biochemical parameters and inflammatory biomarkers related to renal impairment in dogs with chronic kidney disease.},
journal = {The veterinary quarterly},
volume = {46},
number = {1},
pages = {2665483},
pmid = {42056070},
issn = {1875-5941},
mesh = {Animals ; Dogs ; *Probiotics/administration &amp; dosage/therapeutic use ; *Renal Insufficiency, Chronic/veterinary/therapy/blood ; Biomarkers/blood ; *Dog Diseases/blood/therapy ; Male ; Female ; Gastrointestinal Microbiome ; *Enterococcus ; Dietary Supplements ; Animal Feed/analysis ; Inflammation/veterinary ; Arginine/analogs &amp; derivatives/blood ; Diet/veterinary ; },
abstract = {To investigate the influence of probiotic supplementation on parameters of renal function, dogs with chronic kidney disease (CKD) received a commercial probiotic formulation containing Enterococcus lactis SF68 (n = 8) or placebo (n = 8) for 60 days. Gut microbiome was investigated by comparing with healthy dogs (n = 10). Blood biochemistry, urinalysis, inflammatory and oxidative markers, uremic toxins and blood pressure were monitored. Higher presence of Lachnospiraceae family, Blautia bacterial species and Ruminococcus gnavus group was observed in dogs with CKD when compared with healthy dogs. Adding the probiotic to the diet decreased the abundance of Ruminococcus gnavus. Probiotic treatment resulted in a significant reduction in plasma concentrations of symmetric dimethylarginine (SDMA), from 1.50 ± 0.18 to 1.35 ± 0.16 µmol/l (p = 0.008), and indoxyl sulfate (IxS), from 19.1 ± 6.8 to 12.8 ± 4.8 µmol/l (p = 0.04). Cytokine inflammatory markers did not show significant changes. An increase in urine protein-to-creatine ratio, 1.5 ± 0.6 vs 1.2 ± 0.5, and in systolic blood pressure, 163 ± 11 vs 144 ± 6 mmHg (p = 0.033), was observed in the placebo group but not in dogs receiving probiotic. In conclusion, feeding Enterococcus lactis SF68 to dogs with CKD results in changes in intestinal microbiota that are associated with a decrease in plasma concentrations of IxS and SDMA and a reduction in proteinuria and systolic blood pressure.},
}
@article {pmid42056166,
year = {2026},
author = {Wang, M and Liu, X and Liu, S and Xin, W and Liu, H and Zhao, Z and Wei, J and Lu, X and Liu, P and Chen, Q and Yang, S},
title = {Characteristics of the rhizosphere microbial communities of different mulberry varieties in saline soil.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48685-y},
pmid = {42056166},
issn = {2045-2322},
support = {2022C02065//the Project of Major Social and Public Welfare in Zhejiang Province/ ; NY202401//Coastal Characteristic Plant Innovation and Utilization Project/ ; },
abstract = {Mulberry is a common crop with different varieties of resistance. Understanding the differences in rhizosphere soil microbial community characteristics among different salt-tolerant mulberry varieties in saline soils is important for the rational development and utilization of coastal saline soils. Using high-throughput sequencing, we compared the rhizosphere microbiota of salt-tolerant variety Guoxuan3 (GX3) and the salt-sensitive variety A18 in coastal saline soils, with bare soil as a control. Bare, unplanted soil (CK) collected from the same field was used as a baseline control to distinguish plant-driven effects from background soil microbial structure. The results revealed that 1236 bacterial OTUs and 396 fungal OTUs were identified from the mulberry rhizosphere samples. The dominant bacteria in the mulberry rhizosphere were Proteobacteria and Actinobacteria, while the dominant fungi were Ascomycota and Basidiomycota. Significant differences in microbial composition were observed between varieties. The salt-tolerant GX3 specifically enriched Rozellomycota and key genera, including Nocardioides, Aspergillus, and Fusicolla in its rhizosphere. Mulberry varieties shape distinct rhizosphere microbiomes. Salt-tolerant GX3 recruits beneficial bacteria like Nocardioides, Georgenia, Azoarcus through organic acids, enhancing nutrient cycling and stress resistance. Salt-sensitive A18 inhibits beneficial fungi such as Calcarisporiella, accumulates phenolics, and enriches nitrifying Nitrospira, indicating nitrogen cycle inefficiency under salinity. Plant salt tolerance links to rhizosphere microbiome shaping, highlighting the need to consider both bacterial and fungal communities for coastal saline soil phytoremediation, aiding marginal ecosystem utilization.},
}
@article {pmid42056339,
year = {2026},
author = {Thenappan, DP and Joshi, V},
title = {Host genotype Impacts the Assembly and Functional Potential of Bacterial Communities in the Spinach Phyllosphere Within Commercial Organic Farming Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02762-x},
pmid = {42056339},
issn = {1432-184X},
support = {2022-51300-37886//USDA-NIFA-OREI/ ; 9647-1//USDA- NIFA- HATCH/ ; },
}
@article {pmid42056655,
year = {2026},
author = {Wu, K and Hu, HW and Gupta, D and Li, Y and He, ZY and Wang, F and He, JZ},
title = {Core Microbial Taxa Strengthen Root Microbial Network Stability Under Drought Stress.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70307},
pmid = {42056655},
issn = {1462-2920},
support = {IH200100023//Australian Research Council/ ; 4-H808GTH//Department of Agriculture, Fisheries and Forestry, Australian Government/ ; },
mesh = {*Plant Roots/microbiology ; *Droughts ; *Soil Microbiology ; *Microbiota ; *Triticum/microbiology/growth &amp; development ; Rhizosphere ; Stress, Physiological ; *Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Drought stress is intensifying globally, but its effects on plant-associated microbiome diversity and stability remain poorly understood. We grew wheat under drought stress and sampled bulk soils, rhizosphere soils and roots across three growth stages to quantify microbial diversity, co-occurrence network stability and the contributions of core taxa to network stability. Drought affected microbial diversity depending on microbial kingdoms, plant niches and growth stages. We further found that drought stress reduced the complexity and stability of microbial networks in the rhizosphere soils while enhancing those in the roots, mainly through shifts in the abundances of core taxa (i.e., taxa that are widely distributed across samples, specific to drought stress and highly connected in the network). Three types of analyses (shared operational taxonomic units, network keystone nodes and taxa with high specificity and occupancy values) were employed to identify the core taxa enriched in the roots under drought stress, including Glycomyces and Thermoactinomycetaceae, which were typical drought-tolerant taxa that are important for maintaining root microbial network stability. Environment stress usually disrupts microbial community stability, but we found drought stress enriched core taxa, enhancing drought-tolerant crop root microbiomes stability. Our findings provide a blueprint for enhancing crop stress tolerance via microbiome manipulation.},
}
@article {pmid42056687,
year = {2026},
author = {Wedell, E and Shen, C and Warnow, T},
title = {Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2981},
number = {},
pages = {37-52},
pmid = {42056687},
issn = {1940-6029},
mesh = {*Phylogeny ; *Software ; *Metagenomics/methods ; Algorithms ; Likelihood Functions ; *Computational Biology/methods ; },
abstract = {Phylogenetic placement is the problem of adding sequences to an existing phylogenetic tree. While many techniques have been developed for this problem, methods based on optimizing maximum likelihood, such as pplacer and EPA-ng, have been shown to provide the highest accuracy. Unfortunately, these methods are limited to at most moderately large placement trees due to their design. SCAMPP and Batch-SCAMPP are two methods that have been developed to improve the scalability of both pplacer and EPA-ng to very large trees, while maintaining high accuracy. Here, we describe these methods and show how to use them in two applications: metagenomics, including taxon identification and abundance profiling, and incrementally growing large trees. SCAMPP and Batch-SCAMPP are available in open-source form on GitHub and PyPI.},
}
@article {pmid42056825,
year = {2026},
author = {Rafieian-Naeini, HR and Keshavareddy, VPR and Katha, HR and Gyawali, I and Lee, DJ and Kim, Y and Kim, WK},
title = {Effect of dietary wheat on the progression of Histomonas meleagridis infection in turkey poults.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106970},
doi = {10.1016/j.psj.2026.106970},
pmid = {42056825},
issn = {1525-3171},
abstract = {Blackhead disease (Histomoniasis), caused by Histomonas meleagridis (HM), remains a major constraint to turkey production, and dietary factors that may influence disease progression are poorly defined. This study evaluated whether moderate wheat inclusion alters HM outcomes in turkey poults. A total of 432 one-day-old male turkey poults (Nicholas) were allocated to a 2 × 3 factorial arrangement with HM challenge (HM+ or HM-) and dietary wheat inclusion (0, 15, or 30%), yielding 6 treatments with 6 replicates (12 birds/replicate) for a 22-d experimental period. Diets were formulated to be isocaloric and isonitrogenous. Growth performance (BW, feed intake, BWG, FCR, and mortality) was assessed during d 0-12, d 13-16, and d 17-22. Additional parameters included infection rate and lesion severity (ceca and liver), clinical presentation, ileal digesta viscosity, intestinal histomorphology, jejunal cytokine/tight junction mRNA abundance, bone formation by calcein labeling, bone mineral density/content by DEXA, and cecal microbiota. Wheat × HM interactions were not detected for growth performance, mortality, lesion distributions, infection rate, clinical scores, or jejunal gene expression (P > 0.05). Wheat inclusion improved early performance prior to challenge. Poults fed 15% or 30% wheat had greater BW at d 12 and 16, with increased BWG and improved FCR during the pre-challenge/early infection periods (P < 0.05), whereas BW at d 22 was not influenced by wheat. In contrast, HM challenge markedly reduced BW, feed intake, and BWG, worsened FCR during d 17-22, and increased mortality (P ≤ 0.001). Dietary wheat did not mitigate HM-induced cecal and liver lesions, infection rate, or clinical presentation. HM challenge profoundly disrupted cecal microbiota, reducing alpha diversity and shifting community structure, characterized by expansion of Enterobacteriaceae and reduction of Lachnospiraceae. In conclusion, 15% wheat inclusion supported improved early growth and bone apposition under non-challenged conditions, but HM challenge overwhelmingly dictated disease severity and associated physiological and microbiome outcomes regardless of wheat level.},
}
@article {pmid42056921,
year = {2026},
author = {Li, B and Zhang, Y and Li, Z and Chen, Z and Guo, Z and Wu, W and Tan, L and Dong, L and Zhang, X and Lyu, X and Hu, M and Long, Q},
title = {A novel serum metabolite classifier for identifying Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) integrating metabolomics and machine learning.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-026-04842-1},
pmid = {42056921},
issn = {1471-230X},
support = {No.82302586//the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) presents a growing global health burden, while reliable non-invasive biomarkers for identifying affected individuals remain limited. This study aimed to characterize serum metabolomic signatures associated with steatosis and fibrosis and to develop a clinically applicable metabolite-based classifier.<br><br>METHODS: Untargeted serum metabolomics was performed in a FibroScan-characterized discovery cohort (n&#x2009;=&#x2009;35) to identify candidate metabolic features associated with hepatic steatosis and fibrosis burden. To provide biological context for the observed metabolic alterations, 16&#xa0;S rDNA sequencing was subsequently conducted in paired fecal samples from a subset of participants (n&#x2009;=&#x2009;27). Differential metabolites were then subjected to LASSO regression for feature selection and used to construct a random forest diagnostic model in a validation cohort comprising healthy controls (n&#x2009;=&#x2009;19) and ultrasound-confirmed MASLD patients (n&#x2009;=&#x2009;52).<br><br>RESULTS: Metabolomic profiling revealed distinct metabolic patterns across different degrees of steatosis and fibrosis. A total of 55 and 46 metabolites were identified as differentially abundant in relation to steatosis and fibrosis burden, respectively. Microbiome analysis indicated alterations in gut microbial composition, and integrative correlation analysis suggested several potential microbe-metabolite associations, including two metabolite-genus pairs showing relatively strong correlations. LASSO regression selected a panel of ten metabolites as the most informative diagnostic features. Using these metabolites as input variables, a random forest classifier was constructed and achieved an area under the receiver operating characteristic curve (AUROC) of 0.87. Incorporation of four clinical variables (BMI, ALT, triglycerides, and HDL cholesterol) further improved model performance, yielding an AUROC of 0.94.<br><br>CONCLUSION: This study characterizes systemic metabolic alterations associated with MASLD and presents a non-invasive diagnostic model integrating serum metabolites with clinical indicators. Together, these findings highlight the potential utility of metabolomics-assisted approaches for identifying MASLD and for improving biological understanding of disease-associated metabolic changes.},
}
@article {pmid42057114,
year = {2026},
author = {Zhou, CY and Qi, YF and Li, HJ and Zhang, C and Lin, BX and Lin, JT and Wu, YL and Zheng, MM and Zhong, WZ},
title = {Current and future immunotherapies for NSCLC.},
journal = {Journal of hematology &amp; oncology},
volume = {19},
number = {1},
pages = {},
pmid = {42057114},
issn = {1756-8722},
support = {2024ZD0529400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 82573732//National Natural Science Foundation of China/ ; 82241235//National Natural Science Foundation of China Major Joint Project on Key Scientific Issues of Lung Cancer/ ; KA0120231004//National High-Level Talents Special Support Program/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology/genetics/pathology ; *Lung Neoplasms/therapy/immunology/pathology/genetics ; *Immunotherapy/methods/trends ; Immune Checkpoint Inhibitors/therapeutic use ; Biomarkers, Tumor ; },
abstract = {Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related mortality worldwide. Immune checkpoint inhibitors targeting the PD-1/PD-L1 and CTLA-4 axes have fundamentally transformed its treatment landscape. This narrative review traces the evolution of NSCLC immunotherapy, from advanced-stage monotherapy and chemoimmunotherapy to its critical expansion into early-stage disease, highlighting the paradigm shift brought by neoadjuvant, adjuvant, and perioperative strategies. We examine essential clinical challenges, including optimal treatment duration, management of brain metastases, immune-related adverse events, and mechanisms of primary and acquired resistance, with a focus on genomic alterations like KRAS co-mutations with STK11 and KEAP1. Furthermore, we critically evaluate the evolving biomarker landscape, moving beyond PD-L1 to encompass circulating tumour DNA, microbiome composition, and multiparametric approaches like T-cell receptor clonality. Finally, we provide an in-depth exploration of next-generation strategies, including bispecific antibodies, novel checkpoint targets, mRNA vaccines, antibody-drug conjugates, and advanced cellular therapies. While significant progress has been made, refining biomarker-driven selection and optimizing combination sequencing remain paramount. This thorough synthesis highlights promising future directions to overcome these hurdles and improve long-term survival in NSCLC.},
}
@article {pmid42057125,
year = {2026},
author = {Tan, SSL and Garg, V and Dhiman, A and Bansal, N and Conway, P},
title = {Inflammaging and the role of micronutrients as immunomodulators: a pathway to healthy aging.},
journal = {Immunity &amp; ageing : I &amp; A},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12979-026-00569-5},
pmid = {42057125},
issn = {1742-4933},
abstract = {BACKGROUND: Healthy aging is increasingly challenged by inflammaging, a chronic, low‑grade inflammatory state primarily exacerbated by gut microbiota dysbiosis and declining immune function. Persistent digestive and systemic inflammation, along with immunosenescence, contributes to multiple age‑related diseases. Micronutrients regulate key components of immune system and support the composition and function of the gut microbiota, underscoring their emerging role as modulators of inflammaging.<br><br>MAIN BODY: This narrative review synthesizes current evidence insights on how micronutrients regulate cellular and molecular drivers of inflammaging, with emphasis on immune function and gut microbiota imbalance. Adequate intakes of vitamins A, B&#x2011;complex, C, D, E, and K, together with trace elements (zinc, selenium, magnesium, iron, and copper), supports both innate and adaptive immune response, genomic and epigenetic stability, mitochondrial efficiency, telomere integrity, and immune regulation. Importantly, micronutrients influence gut microbial composition and inflammatory signaling pathways, thereby mitigating dysbiosis-driven digestive inflammation, a major contributor to systemic inflammaging. The review also delineates the bidirectional micronutrient-microbiome relationship, whereby microbial composition shapes nutrient bioavailability, while micronutrients influence microbial diversity, short&#x2011;chain fatty acid production, and inflammatory signaling.<br><br>CONCLUSION: Micronutrient sufficiency may help reduce digestive inflammation, restore microbial balance, and modulate immune pathways implicated in inflammaging. However, translating these benefits requires robust assessment of micronutrient status and gut microbiota. Developing standardized evaluation and microbiota&#x2011;informed nutrition strategies may enable more precise targeted interventions to support healthy aging.},
}
@article {pmid42057164,
year = {2026},
author = {Cabello, AM and Salles, S and Domínguez-Huerta, G and Capo, E and Camarena-Gómez, MT and García-Gómez, C and Sánchez, A and Mangot, JF and Cerezo, I and Bautista, R and Pérez, P and García, R and Ruiz, JM and Mercado, JM and Ferrera, I},
title = {Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00893-9},
pmid = {42057164},
issn = {2524-6372},
abstract = {BACKGROUND: Coastal ecosystems face increasing threats from eutrophication, driven by excess nutrient inputs that lead to ecosystem-disruptive algal blooms (EDABs). The Mar Menor coastal lagoon, located in the south-eastern Iberian Peninsula, has experienced severe ecological disruption since 2015, beginning with a Synechococcus‑dominated cyanobacterial bloom and followed by major shifts in eukaryotic phytoplankton composition. However, the mechanisms that affect phytoplankton dynamics in this coastal environment remain unknown. Here, we investigate the spatiotemporal dynamics of prokaryotic communities in the lagoon after the initial Synechococcus bloom using three years of 16S rRNA gene sequencing data and evaluate how environmental factors shape these patterns. In addition, we examine the fine‑scale diversity and dynamics of Synechococcus variants through metagenomics (petB gene) and use genome‑resolved analyses to identify functional traits associated with their succession in the lagoon. Finally, to investigate the role of biotic interactions in regulating cyanobacterial growth, we examine the temporal dynamics of cyanophages.<br><br>RESULTS: Microbial communities in the waters of the Mar Menor responded rapidly and consistently to short&#x2011;term environmental fluctuations and showed a weak seasonal signal in alpha and beta diversity. Prokaryotic assemblages associated with two deoxygenation events following extreme weather conditions (intense rainfall in autumn 2019 and unusually high temperatures in summer 2021) illustrated how episodic disturbances can drive substantial shifts in microbial composition; notably, Synechococcus became particularly prevalent after the intense rainfall event. Fine&#x2011;scale analyses of 16S rRNA and petB gene variants revealed that a restricted set of Synechococcus lineages dominated throughout the study period. Comparative genomic analyses of these cyanobacterial populations highlighted distinct functional repertoires, including genes involved in osmoprotectant biosynthesis, diverse toxin-antitoxin systems, herbicide resistance, and multiple viral defense mechanisms, present only in specific variants. Finally, temporal analyses of viral assemblages indicated that cyanophages played a key role in modulating Synechococcus population dynamics.<br><br>CONCLUSIONS: The temporal dynamics of prokaryotic communities in the Mar Menor indicate that the lagoon remains in an altered, non&#x2011;equilibrium state, likely sustained by recurrent anthropogenic and climatic pressures. The contrasting microbial responses observed during two different deoxygenation events underscore the ecosystem's complexity. This study highlights the importance of incorporating microbial community analyses into long&#x2011;term monitoring of threatened coastal systems, and the power of comparative genomics for identifying functional traits that enable cyanobacterial proliferation in disturbed ecosystems.},
}
@article {pmid42057198,
year = {2026},
author = {Dikareva, E and van Best, N and Bervoets, L and West, CE and Rossel, C and Driessen, C and Mommers, M and Penders, J},
title = {The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01660-8},
pmid = {42057198},
issn = {1756-994X},
support = {09150162410022/ZONMW_/ZonMw/Netherlands ; 2021-01637//Vetenskapsr&#xe5;det/ ; 967569//V&#xe4;sterbotten L&#xe4;ns Landsting/ ; 529051010//The Netherlands Organization for Health Research and Development (ZonMw) through the European Union Joint Programming Initiative-A Healthy Diet for a Healthy Life/ ; },
abstract = {BACKGROUND: The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.<br><br>METHODS: Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.<br><br>RESULTS: Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value&#x2009;=&#x2009;0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.<br><br>CONCLUSIONS: This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.},
}
@article {pmid42057229,
year = {2026},
author = {Wu, Y and Chen, K and Hu, T and Luo, Y and Zhang, Y and Yang, G and Wang, J and Zhu, Y},
title = {Lactobacillus johnsonii-derived extracellular vesicles modulate gut microbiota metabolites and macrophage-related immune responses against Salmonella Typhimurium infection.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-026-01750-w},
pmid = {42057229},
issn = {1297-9716},
support = {2023YFC3404301//National Key Research and Development Program of China/ ; },
abstract = {Salmonella Typhimurium is a significant pathogen causing diarrhea in weaned piglets, capable of triggering systemic inflammation and severe intestinal damage. As bioactive components of gut microbiota, extracellular vesicles (EVs) derived from Lactobacillus johnsonii (Lj-EVs) are likely to penetrate the intestinal mucus layer and reach host cells, potentially mediating host-microbiome interactions. Here, we found that Lj-EVs improved the intestinal barrier and attenuated intestinal injury in mice infected with S. Typhimurium. Multi-omics analysis showed that Lj-EVs intervention enriched mucin-utilizing Akkermansia. Moreover, Lj-EVs were associated with metabolic alterations, characterized by enhanced oxidative phosphorylation during homeostasis and suppression of HIF-1α-mediated glycolysis during infection. Proteomic profiling showed that Lj-EVs enriched functional proteins related to oxidative phosphorylation, indicating their potential immunomodulatory role. Notably, Lj-EVs modulated macrophage-mediated immune responses, contributing to limiting bacterial dissemination and alleviating intestinal inflammation. In conclusion, our study demonstrates that Lj-EVs alleviate Salmonella infection by reducing bacterial burden and confer metabolic and immunomodulatory benefits. These findings provide new evidence for future investigation of the protective roles of probiotic vesicles.},
}
@article {pmid42057366,
year = {2026},
author = {Murakami, K},
title = {Comprehensive management of immune-related adverse events: predictive strategies, mechanistic insights, and therapeutic approaches.},
journal = {Immunological medicine},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/25785826.2026.2664951},
pmid = {42057366},
issn = {2578-5826},
abstract = {Immune checkpoint inhibitors (ICIs) have been game changer in cancer therapy but can trigger diverse immune-related adverse events (irAEs) that impact multiple organs. This review offers a unified perspective on irAE risk assessment, underlying mechanisms, and therapeutic strategies aimed at maintaining anticancer efficacy while safeguarding patient well-being. We explore predictive tools-including baseline profiles of several cytokines, HLA genotype, and markers such as interleukin-6-for identifying high-risk individuals. Key drivers of irAEs were dysregulated T- and B-cell responses, antigenic cross-reactivity, and gut microbiome imbalances. Management follows a graduated approach: initial glucocorticoid intervention, followed by biologics (anti-TNF agents, IL-6 receptor blockers) or small-molecule inhibitors (JAK inhibitors) in refractory cases. Real-world data support cautious ICI use in pre-existing autoimmune disorders under stringent monitoring. We also discuss the emerging notion of "inverse irAEs," where immunosuppression may predispose to secondary malignancies, underscoring the importance of long-term surveillance. Finally, we highlight the urgent need for expansive, multicenter studies to refine irAE management to enhance therapeutic outcomes.},
}
@article {pmid42057740,
year = {2026},
author = {Wang, JL and Huang, SY and Chen, ZT and Zhou, Y and Kuzyakov, Y and Chen, JH and Ma, XM},
title = {Functional Resistance of Microbiome to Differently Charged Nanoplastics in Rhizosphere Hotspots Soil.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17636},
pmid = {42057740},
issn = {1520-5118},
abstract = {Nanoplastics (NPs) pose greater soil ecological risks than microplastics due to their surface charge-dependent uptake, transport, and accumulation in plants. However, how differently charged NPs affect maize growth and microbial functional resistance in rhizosphere hotspots remains unclear. Here, we investigated the effect of positively (PS-NH2) and negatively (PS-SO3H) charged NPs on maize growth, enzyme activities and gene abundance, microbial resistance, and functional properties in acidic soil using soil zymography, 16S rRNA sequencing, and metagenomics. PS-NH2 showed stronger inhibitory effects on maize growth than PS-SO3H, mainly through reducing microbial diversity and weakening N and P cycling-related enzyme activities and resistance. Conversely, PS-SO3H maintained higher microbial resistance. Functional hotspots microbial species (particularly in Actinobacteria) alleviated NPs toxicity by accelerating N and P cycling to meet the demand for nutrients limiting maize growth. This study provides a mechanistic basis for assessing soil NPs risk with implications for agricultural sustainability and food safety.},
}
@article {pmid42057783,
year = {2026},
author = {Harshvardhan, and Kaur, M and Grover, V and Pinnaka, AK and Korpole, S},
title = {Metagenomic insights into oral microbiota dynamics in diabetic and non-diabetic periodontal disease: a pilot study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1799124},
pmid = {42057783},
issn = {1664-302X},
abstract = {INTRODUCTION: Subgingival microbial dysbiosis is one of the key reasons behind periodontitis, a chronic inflammatory disease, which is further get severe in the presence of type 2 diabetes mellitus (T2D). Although changes in taxonomic composition have been well established, the functional interactions and metagenomic profiles across different stages of the disease remain unclear.<br><br>METHODS: A shotgun metagenomic analysis was performed on subgingival dental plaque samples from 16 individuals, divided into healthy, staged periodontitis, and diabetic periodontitis groups. Group-wise DNA pooling was done for maximum DNA yield. Further, Alpha/beta diversity, taxonomic profiling, pathogen-probiotic ratios, and metabolic pathway abundance were analyzed and studied.<br><br>RESULTS: The healthy group showed the highest alpha diversity, especially in the core biosynthetic pathways. On the other hand, the earlier stages of periodontitis showed a unique community structure and the lowest alpha diversity. Early periodontitis also showed the highest abundance of commensals like Actinomyces and Bifidobacterium, along with increased UMP/guanosine and L-arginine biosynthesis pathways. The advanced periodontitis group had an increase of red complex bacteria and loss of probiotics. An increase of the degradative pathways, such as L-histidine degradation, had also been observed in this stage. The diabetic periodontitis group had a distinct microbial profile that included Capnocytophaga and a considerable metabolic shift toward lipid metabolism and glycolysis, with higher overall microbial diversity than the other periodontitis groups.<br><br>CONCLUSION: The results clearly show that the subgingival microbial and functional patterns are different across the stages of the disease and metabolic status, which can be developed for underscoring the importance of targeting early metabolic shifts to prevent dysbiosis.},
}
@article {pmid42057790,
year = {2026},
author = {Zhu, B and Fu, C and Fan, D and Wang, Y and Sheng, P and Feng, J and Wang, X},
title = {The impact of antibiotic exposure on obesity and metabolic phenotypes via the gut microbiota.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1782016},
pmid = {42057790},
issn = {1664-302X},
abstract = {Antibiotics are among the most commonly used anti-infective agents in modern medicine. However, their long-term effects on the gut microbiome have attracted increasing attention. Epidemiological studies and animal experiments in recent years suggest that antibiotic exposure can disrupt the structure and function of the gut microbiota, thereby affecting host energy metabolism, fat deposition, and immune homeostasis. Such disruptions may contribute to the development of obesity and related metabolic phenotypes. Different classes of antibiotics exert markedly distinct effects on the gut microbiota. Broad-spectrum antibiotics such as macrolides, lincosamides, and fluoroquinolones often induce more pronounced and prolonged microbial alterations, whereas the effects of certain β-lactam antibiotics appear relatively transient. Antibiotic-induced gut dysbiosis can influence host metabolism through multiple mechanisms, including reduced short-chain fatty acid production, disrupted bile acid metabolism, impaired intestinal barrier function, and chronic low-grade inflammation. These alterations may promote fat accumulation, insulin resistance, and disruption of immune homeostasis. Early-life antibiotic exposure occurs during a critical developmental window for gut microbiota maturation and may exert more profound effects on long-term metabolic health. Recent advances in multi-omics technologies have further illuminated the complex interaction network among antibiotics, the microbiome, and host metabolism. Microecological intervention strategies, such as probiotics and synbiotics, show potential for improving metabolic abnormalities associated with antibiotic-induced dysbiosis. However, their efficacy is strain-specific, and the overall effect size remains limited. This review summarizes current research progress on how antibiotic exposure influences obesity and metabolic phenotypes through the gut microbiota, outlines the underlying mechanisms, and discusses potential applications of microbiological intervention strategies. It also provides insights into antibiotic-related metabolic risks and future precision intervention approaches.},
}
@article {pmid42057793,
year = {2026},
author = {Bautista, J and López-Cortés, A},
title = {The hallmarks of host-microbiome decoupling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1801100},
pmid = {42057793},
issn = {1664-302X},
abstract = {The human host and its resident microbiome maintain continuous interactions that influence immune regulation, metabolism, neuroendocrine signaling, epithelial barrier function, and circadian organization. Although multi-omics approaches have improved mechanistic understanding of host-microbiome interactions, dominant translational models remain largely based on compositional descriptions and often do not capture persistence, systemic propagation, or temporal instability in microbiome-associated disease. Host-microbiome decoupling is defined here as a progressive reduction in functional coordination between host regulatory systems and microbial ecological behavior. The concept refers to conditions in which microbial signals, activities, or rhythmic patterns no longer remain aligned with host physiological regulation. A hallmarks-based framework is proposed to examine biological domains in which coordination between host regulation and microbial ecology deteriorates. Core hallmarks include breakdown of signaling fidelity, microbiome-driven immune miscalibration, barrier compartment failure, endocrine-microbiome uncoupling, ecological destabilization, and temporal desynchronization between host circadian programs and microbial oscillations. Additional dimensions include pathological microbial metabolite dominance with epigenetic embedding, endocrine and neuro-microbiome regulatory uncoupling, ecological destabilization of microbiome functional capacity, and temporal desynchronization between host circadian programs and microbial oscillations. Across inflammatory, metabolic, neurodegenerative, and neoplastic conditions, microbial activity may operate outside normal ecological constraints, influencing immune regulation, metabolic signaling, neuroimmune communication, and tumor-associated processes. Within this framework, resilience, signaling proportionality, host responses appropriately scaled to microbial input, and temporal coordination represent central properties of host-microbiome compatibility.},
}
@article {pmid42058119,
year = {2026},
author = {Qu, HL and Li, JN and Gao, Y and Zhang, XB and Yang, SD},
title = {From association to intervention: Semantic trajectories and knowledge frontiers in epilepsy-gut microbiota research revealed by bibliometrics and NLP.},
journal = {IBRO neuroscience reports},
volume = {20},
number = {},
pages = {609-624},
pmid = {42058119},
issn = {2667-2421},
abstract = {BACKGROUND: Research on the epilepsy-gut microbiota axis is accelerating, yet its conceptual evolution and translational signals remain difficult to track across disciplines. Here, we propose a semantic-bibliometric fusion framework that combines network-based science mapping with phrase- and topic-level natural language processing (NLP) to resolve both structural and linguistic dynamics in the field.<br><br>METHODS: Publications indexed in the Web of Science Core Collection from January 1997 to November 17, 2025 were retrieved and analyzed using CiteSpace, VOSviewer, Pajek, and Scimago Graphica, complemented by an NLP pipeline for topic modeling and temporal phrase tracking. In total, 516 records were included.<br><br>RESULTS: Annual output rose sharply after 2021 and peaked in 2024, with China and the United States leading contributions. Beyond conventional hotspots, semantic analyzes revealed a field-wide shift from early infection/safety-oriented discourse to mechanism- and intervention-driven themes dominated by the microbiota-gut-brain axis.<br><br>CONCLUSION: The most prominent and expanding intervention clusters involved the ketogenic diet, short-chain fatty acids, probiotics, and fecal microbiota transplantation, while "Mendelian randomization" emerged as a nascent frontier signaling movement from correlation to causal inference. By integrating knowledge-network topology with discourse dynamics, this study delivers an up-to-date, multi-resolution map of epilepsy-microbiome research and highlights actionable directions for future work, including causal validation, multi-omics stratification, and trial-ready microbiome-informed interventions.},
}
@article {pmid42058141,
year = {2026},
author = {Ferraz, M and Santos, J and Vieira da Silva, M},
title = {A systematic review of indoor air quality in schools settings: Focus on microbiome and their relation to particulate matter and chemical pollutants.},
journal = {Public health in practice (Oxford, England)},
volume = {11},
number = {},
pages = {100790},
pmid = {42058141},
issn = {2666-5352},
abstract = {OBJECTIVES: Indoor air quality (IAQ) in schools is a growing concern due to its impact on children's health. Continuous exposure to indoor air pollutants, such as particulate matter (PM), carbon dioxide (CO2), and microorganisms, such as bacteria and fungi, can affect school performance, increase absenteeism, and trigger respiratory problems. This systematic review aimed to analyze the potential correlation between the presence of microorganisms and PM and chemical pollutants in school indoor environments.<br><br>STUDY DESIGN: A systematic literature review was conducted using the methodology PRISMA and 25 articles were selected.<br><br>METHODS: The current systematic review follow the steps: definition of research objectives; selection of the science databases; definition of keywords; establishment of the inclusion and exclusion criteria, evaluation process and evaluation and management of selected studies.<br><br>RESULTS: The findings highlight the significant presence of airborne microorganisms, including bacteria and fungi, often associated with PM and chemical pollutants such as CO2 and volatile organic compounds (VOCs). Positive correlations between CO2 and bacteria were observed in ten studies and were statistically significant in six of them. Both positive and negative correlations between fungi and CO2 were reported. Fungal genera such as Aspergillus spp. And Cladosporium spp. Were associated with particulate matter (PM). In general, the concentrations of bacteria and fungi were often correlated with PM levels, with larger particles (PM10) favoring the adhesion and transport of microorganisms, while smaller particles (PM2.5) remain suspended in the air for longer periods, increasing exposure.<br><br>CONCLUSIONS: Despite the methodological variations among the various studies, the results reinforce the need to create effective interventions to reduce pollutant concentrations to minimize health risks for occupants.},
}
@article {pmid42058331,
year = {2026},
author = {Gupta, S and Anushree, and Doke, G and Misra, D and Shukla, AK and Honey, B},
title = {Shared Pathophysiology and Early Detection Biomarkers in Endometriosis and Polycystic Ovary Syndrome (PCOS): Opportunities for AI-Enabled Screening.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e106013},
pmid = {42058331},
issn = {2168-8184},
abstract = {Endometriosis and polycystic ovary syndrome (PCOS) are common, multifactorial gynecological disorders shaped by endocrine imbalance, immune dysfunction, metabolic disruption, genetic susceptibility, and environmental exposures. Despite their major contribution to infertility and long-term cardiometabolic morbidity, early detection remains poor because symptoms are nonspecific, phenotypes are heterogeneous, and diagnosis is still dominated by single-modality and symptom-driven pathways. This review addresses this gap by synthesizing 2015-2025 evidence on shared and disease-specific biological mechanisms and evaluating how artificial intelligence (AI) can improve scalable screening and risk stratification. A narrative and integrative methodology was applied using peer-reviewed studies retrieved from PubMed, Scopus, Web of Science, and Google Scholar, emphasizing diagnostic rigor and external validity. Key findings identify convergent pathways involving chronic low-grade inflammation, adipokine dysregulation, oxidative stress, microbiome-mediated estrogen signaling, ferroptosis-linked iron imbalance, mitochondrial dysfunction, and epigenetic regulation through microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Promising early-detection signals include age-stratified anti-Müllerian hormone (AMH) thresholds, circulating cell-free deoxyribonucleic acid (cfDNA) methylation markers, and reproductive tract microbial signatures. AI-based models, including transformer architectures and multimodal machine learning, show strong potential to integrate clinical, hormonal, imaging, omics, and digital symptom phenotyping into reproducible early screening frameworks. Clinical translation requires standardized diagnostic definitions, longitudinal multi-ethnic cohorts, explainable algorithms, and prospective validation. AI-enabled precision screening offers a practical pathway to shorten diagnostic delay and improve reproductive outcomes.},
}
@article {pmid42058649,
year = {2026},
author = {Kwarteng, A and Amedorme, D and Addy, HPK and Amewu, EKA and Osei-Poku, P and Larbi, A},
title = {Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {6677609},
pmid = {42058649},
issn = {1687-918X},
abstract = {Brukina, a traditional fermented beverage smoothie made from milk and millet, is popular in Ghana and other West African countries due to its tasty flavor, high nutritional content, and affordability. Despite its widespread consumption, the nature of its production through artisanal fermentation processes presents concerns regarding microbial consistency, nutritional optimization, and food safety. This literature review explores the potential of metagenomic approaches to uncover microbial diversity, functional capacity, and safety profiles of Brukina. By integrating insights from amplicon-targeted and shotgun whole-genome sequencing studies on fermented foods, we highlight how next-generation sequencing technologies can characterize lactic acid bacteria, yeast, and other microorganisms that drive fermentation. Additionally, we discuss how metagenomics can identify functional genes influencing carbohydrate metabolism, flavor and aroma generation, and production of antimicrobial resistance compounds. Thus, metagenomics provides a powerful framework for assessing public health risks and nutritional benefits. Bioinformatic tools have also been highlighted, and their relevant application in analyzing sequenced data to achieve taxonomic classification, identification of biochemical pathways, and functional profiling of microbial ecology of fermented foods. This review outlines key research gaps and recommends future directions, including starter culture development, standardization of Brukina production, multi-omics integration in metagenomics, and microbiome-informed food safety standards. Metagenomic profiling of Brukina holds promise for improving product quality, consumer safety, and scientific understanding of traditional fermented foods. By tackling the challenges raised, metagenomic techniques can be extremely helpful in maximizing Brukina fermentation, guaranteeing food safety, and maintaining the customs that give this product its distinctive character.},
}
@article {pmid42058850,
year = {2026},
author = {Yang, M and Wan, M and Yang, L},
title = {Ecological strategies determine continuous cropping susceptibility in Panax and Achyranthes.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1791596},
pmid = {42058850},
issn = {1664-462X},
abstract = {INTRODUCTION: Medicinal plants frequently suffer from severe continuous cropping problems, yet it remains unclear whether divergent ecological strategies underlie species-specific susceptibility to this problem.<br><br>METHODS: In this study, we investigated rhizosphere assembly patterns in three continuous cropping-sensitive Panax species (P. ginseng, P. quinquefolius, P. notoginseng) and the resilient species Achyranthes bidentata by analyzing paired cultivated and uncultivated soil samples from four major production regions in China. We measured soil physicochemical properties and enzyme activities and characterized bacterial (16S) and fungal (ITS) communities via amplicon sequencing. Plant-specific effects were quantified using Log2 fold change relative to uncultivated controls.<br><br>RESULTS: The Panax species aggressively remodeled their rhizosphere, inducing significant acidification and ammonium accumulation (Log2 FC up to 1.64 in P. notoginseng) while suppressing nitrification enzymes, and assembled fungal-dominated microbiomes enriched with pathogenic Nectriaceae, including Ilyonectria (LDA = 4.2) and Neocosmospora (LDA = 5.3). Their co-occurrence networks showed reduced stability, with negative correlations as low as 3.2%, and functional prediction indicated activated terpenoid metabolism (+74.8%). In contrast, A. bidentata maintained a neutral pH while specifically increasing available phosphorus (Log2 FC = +1.74) and nitrate nitrogen (Log2 FC = +0.74), and it enriched beneficial Actinobacteria by 15-85% and Hypocreales fungi. Its networks retained structural stability, with negative correlations of 12.7-18.6%. Plant species explained 60.5% of bacterial and 46.2% of fungal community variation, overwhelmingly exceeding the effect of soil compartment.<br><br>CONCLUSION: We conclude that Panax employs a resource-acquisitive strategy that assembles unstable, pathogen-prone microbiomes, whereas A. bidentata adopts a resource-conservative strategy that fosters resilient communities. This ecological framework offers a predictive basis for developing tailored microbiome management in medicinal plant cultivation.},
}
@article {pmid42058859,
year = {2026},
author = {Zhang, Q and Gu, M and Li, G and Jing, H and Qi, M and Li, H and Li, M and Ding, L and Li, Z and Wei, P and Ji, X and Zhu, T and Zhao, H},
title = {Synergistic effects of biochar and microbial inoculants on rice productivity and soil fertility are mediated by a nitrogen-dependent microbial pathway.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1804182},
pmid = {42058859},
issn = {1664-462X},
abstract = {Excessive nitrogen (N) fertilizer application threatens soil health and sustainable rice production. We hypothesized that the combined application of biochar and microbial inoculants (B+M) could maintain rice yield under reduced N input through microbiome-mediated mechanisms, and that this effect may depend on an N threshold. To test this hypothesis, pot and field experiments were conducted using the rice cultivar Nanjing 9108 with four treatments: conventional N (CK), and three B+M treatments with 20% N reduction (N80), 40% N reduction (N60), and 0% N reduction (N100). The results indicated that compared to CK, the N100 and N80 treatments increased rice yield by 10.4-11.7% and 4.1-4.9%, and improved Nitrogen Partial Factor Productivity (NPFP) by 7.8-11.7% and 28.6-30.0%, respectively. In contrast, the N60 reduced yield by 3.9-4.6%. In pot experiments, 16S rRNA gene sequencing revealed that N100 and N80 enriched bacterial phyla (e.g., Proteobacteria, Actinobacteria, Chloroflexi, and Bacteroidota) and enhanced microbial functional genes linked to metabolism, genetic information processing, cellular processes, and environmental information processing, thereby increasing soil nutrient availability. Structural equation modeling demonstrated that the soil bacterial community was the fundamental driver of yield enhancement (model fit: χ[2]/df = 1.13, RMSEA = 0.042, CFI = 0.961). However, under 40% N reduction, the abundance of key phyla declined and microbial functional potential weakened, leading to reduced soil nutrient availability and yield. These findings reveal an N dependent microbial-mediated pathway governing the synergistic effects of biochar and microbial inoculants, identifying 20% N reduction with B+M as an optimal strategy for sustainable rice intensification.},
}
@article {pmid42058946,
year = {2026},
author = {Asadi, N and Yaslianifard, S and Hasheminejad, M and Qorbani, M and Mohammadzadeh, M},
title = {Population‑Specific Diversity of Dominant Vaginal Lactobacillus Species in Healthy Iranian Women and Those with Vaginitis: A Molecular Case‑Control Study.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {586988},
pmid = {42058946},
issn = {1179-1411},
abstract = {BACKGROUND: Lactobacillus species play a key role in maintaining vaginal microbial homeostasis and protecting against genital infections. Disruption of this microbial balance can increase susceptibility to vaginitis. Population-specific variations in the composition of vaginal Lactobacillus communities may influence disease risk and therapeutic responses. This study aimed to evaluate the distribution of major vaginal Lactobacillus species in healthy Iranian women and those with vaginitis using species-specific molecular assays.<br><br>METHODS: In this case-control study, 100 women with clinically confirmed vaginitis and 100&#xa0;healthy controls were enrolled. Vaginal swabs were examined by Gram staining, followed by DNA extraction and PCR amplification using universal and species-specific 16S rRNA primers targeting L. iners, L. crispatus, L. acidophilus, L. gasseri, and L. jensenii. Associations between bacterial species and clinical status were evaluated using Odds Ratio (OR), Relative Risk (RR), Phi coefficient (&#x3a6;), and Chi-square tests.<br><br>RESULTS: Lactobacillus spp. were detected in 97% of healthy women compared with 53% of symptomatic participants. L. jensenii and L. acidophilus were significantly more prevalent in healthy individuals, demonstrating strong protective associations with vaginal health. In contrast, L. iners was more frequently detected in women with vaginitis, consistent with its proposed role as a transitional species associated with microbiome instability. Although L. crispatus is often reported as protective in other populations, it did not show a statistically significant protective association in this study population.<br><br>CONCLUSION: Our findings highlight the protective association of dominant Lactobacillus species, particularly L. jensenii and L. acidophilus, in maintaining vaginal microbial balance. The higher prevalence of L. iners among symptomatic women further supports its association with disturbed vaginal microbiota. These results suggest the presence of population-specific microbial patterns and underscore the importance of considering regional microbiome characteristics when developing diagnostic approaches and probiotic-based interventions.},
}
@article {pmid42059388,
year = {2026},
author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA},
title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0360225},
doi = {10.1128/spectrum.03602-25},
pmid = {42059388},
issn = {2165-0497},
abstract = {The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology. Self-collected vaginal swabs and questionnaires on dietary, menstrual, and health information were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Medication regimen, along with disease activity and severity, was captured for the RA cohort. Vaginal swabs were subjected to long-read 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, C-reactive protein, and anti-citrullinated protein antibodies (ACPAs). Vaginal microbial richness and Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal interleukin (IL)-18 and epidermeal growth factor (EGF) levels were increased in the RA group; IL-18 correlated with multiple microbial features, whereas EGF levels were not associated with bacterial composition or other host factors. When faceted by diet and menopausal status, several immune markers were increased in the RA vaginal environment. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines. We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, and disease activity and severity. This work opens a new avenue in the multidisciplinary approach to RA patient care.IMPORTANCERheumatoid arthritis (RA) is a debilitating autoimmune disease that disproportionately impacts women. Although it is widely recognized that microbial factors can trigger or aggravate RA symptoms and alter disease progression, it is unknown whether RA impacts the microbiota and immune responses within the vaginal tract. In this study, we compare the vaginal microbial communities and immune (cytokine) profiles in women with RA and healthy controls. Within RA patients, we also evaluate how these factors relate to clinical RA symptoms, RA biomarkers, and RA-related medications. Overall, we found that RA was associated with increased microbial diversity and multiple inflammatory markers, some of which were also associated with RA biomarkers and disease activity. These findings suggest that the vaginal tract may be an additional tissue impacted by RA disease, and further research is needed to understand mechanisms and potential for therapeutic intervention.},
}
@article {pmid42059393,
year = {2026},
author = {Zhang, T and Yu, Y and Zhang, C and Zhang, M and Yuan, S and Wang, Y and Dai, K and Zhang, L and Su, Y and Zhang, M},
title = {Multi-omics analysis reveals the alterations in the tumor microbiome and metabolome associated with cervical cancer lymph node metastasis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0224725},
doi = {10.1128/spectrum.02247-25},
pmid = {42059393},
issn = {2165-0497},
abstract = {UNLABELLED: Lymph node metastasis (LNM) is the primary mode of cervical cancer (CC) metastasis and is associated with a poorer prognosis. A comprehensive understanding of the underlying mechanisms driving LNM is critical to improving CC patient outcomes. Previous studies have demonstrated that alterations in the intratumor microbiome contribute to tumor progression, with metabolic regulation as a key mechanism. This study aims to investigate the role of intratumor microbiota and tumor metabolism in CC LNM. The microbiome analysis revealed significant differences in the diversity and composition of the intratumor microbiome between CC with and without LNM. Caulobacter and Porphyromonas were the most prominent genus markers for CC with LNM and CC without LNM, respectively. Alterations in tumor metabolism were also observed through global untargeted metabolomics and high-resolution spatial metabolomics, with pathways such as breast cancer, prolactin signaling, histidine metabolism, ovarian steroidogenesis, cysteine and methionine metabolism, and estrogen signaling being significantly altered in CC with LNM. Correlation analysis identified a strong association between specific intratumor microbes (especially Porphyromonas and Virgibacillus) and tumor metabolism. Additionally, our findings suggest a potential trend of phospholipid upregulation in tumor tissues during CC LNM. In summary, our findings underscore the critical role of intratumor microbiota and tumor metabolism in CC LNM, providing valuable insights for developing novel diagnostic markers and therapeutic strategies to address this challenging aspect of cervical cancer.<br><br>IMPORTANCE: This study comprehensively characterized the intratumor microbiota and tumor metabolism associated with lymph node metastasis (LNM) of cervical cancer (CC) by performing 16S ribosomal RNA sequencing, global untargeted metabolomics, and high-resolution spatial metabolomics on surgical CC specimens. Our findings revealed distinct compositions and diversities of intratumor microbiota between CC with and without LNM. Each group exhibited specific bacterial genera that could potentially serve as diagnostic tools for CC LNM, and Caulobacter and Porphyromonas were the most prominent biomarkers for CC with and without LNM, respectively. The significantly different distribution trend of metabolites was also observed between CC with and without LNM. Correlation analysis identified a strong association between specific intratumor microbes (especially Porphyromonas and Virgibacillus) and tumor metabolism. This study not only provides valuable insights for developing novel diagnostic markers and therapeutic strategies for CC LNM but also contributes to a deeper understanding of the underlying molecular mechanisms of it.},
}
@article {pmid42059394,
year = {2026},
author = {Murphy, MM and Pinnell, LJ and Doster, E and Wolfe, CA and Baker, LA and Machado, VS and Morley, PS},
title = {Early-life development of the microbiome and resistome in antibiotic-naïve dairy calves.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0251025},
doi = {10.1128/spectrum.02510-25},
pmid = {42059394},
issn = {2165-0497},
abstract = {This study aimed to characterize early-life changes in the fecal microbiome and resistome of calves. Fecal samples were collected from 49 Holstein heifers born and raised at a large organic dairy in Texas without antimicrobial drug exposures. Samples were collected from five age groups: early pre-weaning at 2-3 days old (Pre 1), late pre-weaning at 5 weeks old (Pre 2), prior to weaning at 12-13 weeks old (Pre 3), post-weaning in group hutches at 12-13 weeks old (Post 1), and later post-weaning at 13-14 weeks old (Post 2). Fecal samples were analyzed using 16S rRNA gene sequencing to characterize microbial communities and target-enriched shotgun sequencing to characterize antimicrobial resistance genes in the resistome. Richness of microbial communities increased as calves aged through the Pre 1, 2, and 3 samplings, before plateauing in the Post 1 and 2 groups. Diversity also increased in the Pre 1 and 2 groups, remaining similar thereafter. In contrast, resistome richness and diversity decreased during early life and then stabilized at around 5 weeks of age (Pre 2). Changes in microbial community structures were dramatic during the first 12 weeks, largely due to a significant decrease in the relative abundance (RA) of Pseudomonadota (Proteobacteria) and an increase in the RA of Bacillota (Firmicutes) and Bacteroidota. The resistome changed with an increased RA of tetracycline resistance genes, while drug and biocide resistance genes decreased. The apparent stabilization of microbial community features after 12 weeks of age may reflect a period when gut microbiome structure begins to establish greater stability.IMPORTANCEEarly-life development of the gut microbiome can have lasting effects on animal health, immune maturation, and productivity. Using 16S rRNA gene sequencing together with target-enriched metagenomic sequencing, we provide an in-depth characterization of the fecal microbiome and resistome of antibiotic-naïve dairy calves during early life. We demonstrate that microbiome diversity increased with age while resistome diversity decreased, revealing distinct temporal trajectories and suggesting ecological succession as a potential driver of resistance gene dynamics independent of antimicrobial drug exposure. Major resistome features appeared to stabilize earlier than overall microbiome structure, highlighting critical windows in early development when resistance gene composition may be most dynamic. These findings establish an important baseline for interpreting microbiome-resistome interactions and for evaluating how management practices and antimicrobial exposures may influence calf health and antimicrobial resistance ecology in dairy production systems.},
}
@article {pmid42059464,
year = {2026},
author = {Yu, K and Wang, N and Huang, X and Qiu, Y and He, X and Zhu, X and Zhou, X and Yu, P and Wei, G and Pi, Y and Ni, T},
title = {Environmental Enrofloxacin Exposure as a Modifiable Driver of Mitochondria-Mediated Intestinal Aging and Barrier Dysfunction.},
journal = {Aging cell},
volume = {25},
number = {5},
pages = {e70526},
pmid = {42059464},
issn = {1474-9726},
support = {2023YFC3603300//National Key Research and Development Program of China/ ; 2023SHZDZX02//Shanghai Municipal Science and Technology Major Project/ ; },
mesh = {*Enrofloxacin/adverse effects ; *Mitochondria/drug effects/metabolism ; Animals ; Humans ; *Aging/drug effects ; Gastrointestinal Microbiome/drug effects ; *Intestinal Mucosa/drug effects/metabolism ; *Anti-Bacterial Agents/adverse effects ; Zebrafish ; *Intestines/drug effects/pathology ; Female ; *Environmental Exposure/adverse effects ; Middle Aged ; Male ; Aged ; },
abstract = {Environmental antibiotic pollution is an underexplored contributor to gut aging and chronic intestinal diseases. We provide evidence that chronic exposure to enrofloxacin (ENR), a commonly detected veterinary antibiotic, accelerates gut aging and disease progression through a mitochondria-centered mechanism. In a population-based cross-sectional analysis, recent antibiotic use was associated with increased biological age and a higher risk of diarrhea in middle-aged and older adults, supporting a link between antibiotic exposure and impaired gut health and aging processes. Using zebrafish and intestinal epithelial cell models, we demonstrate that low-dose ENR exposure impairs intestinal function, characterized by increased permeability, reduced mucus secretion, tight junction disruption, and chronic inflammation. Multi-omics profiling revealed that ENR induced gut microbial dysbiosis, reduced metabolic diversity, and intestinal hypoxia. Mitochondrial dysfunction, particularly impaired oxidative phosphorylation, was identified as the key driver of epithelial damage. Remarkably, treatment with pyrroloquinoline quinone, a mitochondrial-targeted antioxidant, reversed ENR-induced mitochondrial injury, restored intestinal integrity, reduced inflammation, and partially normalized the microbiome. Stratified analyses in the human cohort showed that higher gut microbiota-related diet quality and antioxidant capacity mitigated antibiotic-associated aging and diarrhea risk. These findings highlight mitochondrial protection and microbiota optimization as promising therapeutic strategies.},
}
@article {pmid42059507,
year = {2026},
author = {Osei-Karikari, K and Jones, K and Erickson, A and Myles, IA},
title = {Emerging microbiome-based therapies for atopic eczema: clinical insights and future development.},
journal = {Expert opinion on emerging drugs},
volume = {},
number = {},
pages = {},
doi = {10.1080/14728214.2026.2667256},
pmid = {42059507},
issn = {1744-7623},
abstract = {INTRODUCTION: Despite growing evidence that environmental factors and microbiome dysbiosis constitute the majority of disease pathogenesis, most current therapies target inflammation, barrier dysfunction, and/or S. aureus overgrowth. However, given the emerging understanding of microbiome-mediated and environmentally driven disease mechanisms, expanding therapeutic strategies to include dysbiosis and upstream environmental contributors represents a promising direction for future research.<br><br>AREAS COVERED: This manuscript will review the strengths and limitations of the standard treatments for AD, including emollients, topical corticosteroids, calcineurin inhibitors, and systemic immunomodulators. The focus however will be on the emerging microbiome-based therapies, specifically products containing live microorganisms (biotherapeutics). The potential for, and challenges against, biotherapeutics to grow within the market of AD treatment will be discussed.<br><br>EXPERT OPINION: Immune suppressive approaches will remain limited to symptomatic control. These treatments will also be limited by tradeoffs inherent to the balance between symptom control and side effects of immune suppression. To successfully aide patients, topical biotherapeutics will need to overcome pharmaceutical-centric paradigms, academic dogma, and regulatory inertia. Limitations in current therapies, patient need, along with the potential to offer prevention against AD development, will likely propel biotherapeutics forward.},
}
@article {pmid42059556,
year = {2026},
author = {Dunham, SJB and Willkeen, GA and Darby, B and Corley, JM and Hahn, A and Klapper, I and Bean, HD and Caverly, LJ and Thornton, CS and Martin, C and Quinn, RA and Widder, S and Bailey, BA and Wagner, BD and Garg, N and Planet, PJ and Hunter, RC and LiPuma, JJ and Rohwer, F and Whiteson, KL},
title = {The Guild Model of CF Airway Microbial Ecology.},
journal = {mBio},
volume = {},
number = {},
pages = {e0366825},
doi = {10.1128/mbio.03668-25},
pmid = {42059556},
issn = {2150-7511},
abstract = {Ecological guilds are groups of organisms that utilize the same class of resources and occupy similar niches, regardless of their taxonomic identities. Here we propose the Guild Model for Cystic Fibrosis Airway Microbial Ecology, which considers the ecological function and wider role of each microbe in the ecosystem. This model consists of four functional guilds: (i) "Brewers" metabolize host-derived substrates (e.g., mucins) and produce fermentation products; (ii) "Drunkards" exploit the metabolic niche built by Brewers, consuming fermentation products and secreting exopolysaccharides to build biofilms; (iii) "Putrifiers" produce toxic compounds causing inflammation and tissue necrosis; and (iv) "Nihilists" are specialist pathogens characterized by intracellular or lytic life cycles and cytotoxin production. By focusing on microbial function and the broader community context, this model offers a refined framework for interpreting cystic fibrosis airway ecology. Although developed for CF, the Guild Model is adaptable to other diseases influenced by microbial ecology.},
}
@article {pmid42059571,
year = {2026},
author = {Čepić, A and Rausch, P and Geese, T and Dempfle, A and Grassl, GA and Baines, JF},
title = {Host genetics shapes the recovery of the gut microbiome after antibiotic treatment: the role of the blood group related B4galnt2 gene.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0164025},
doi = {10.1128/msystems.01640-25},
pmid = {42059571},
issn = {2379-5077},
abstract = {UNLABELLED: The intestinal microbiota is integral to host health, metabolism, and colonization resistance. Antibiotics can disrupt microbial homeostasis, leading to dysbiosis and altered colonization resistance. While antibiotic-induced microbiota disruption is well-documented, less is known about how host genetics shapes post-antibiotic recovery. Here, we investigate the impact of B4galnt2, a blood-group-related glycosyltransferase gene, on microbiota recovery following antibiotic treatment. Using a longitudinal, multi-omic approach-including 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-we compare the microbiota dynamics of B4galnt2[+/-] and B4galnt2[-/-] mice after treatment with streptomycin, kanamycin, and vancomycin. Our findings reveal that B4galnt2[-/-] mice exhibit faster recovery of microbial diversity and composition following streptomycin treatment compared to their B4galnt2[+/-] counterparts. This accelerated recovery is associated with higher relative abundance of taxa such as Blautia, Dorea, and other Lachnospiraceae, and increased expression of motility-related genes, and differential regulation of antibiotic resistance genes (ARGs), including the aminoglycoside nucleotidyltransferase genes aadA and aadE. Genotype-dependent differences in recovery were most pronounced following streptomycin and were not consistently observed with kanamycin or vancomycin, indicating an antibiotic-by-genotype interaction shaped by the B4galnt2-associated microbiota. These results underscore the role of host genetics in shaping microbiota response and recovery following antibiotic exposure. By demonstrating the interplay between glycosylation-mediated microbiota composition, antibiotic response, and microbial recovery, our study may provide insights into the potential for personalized approaches to mitigate dysbiosis-related health outcomes.<br><br>IMPORTANCE: Antibiotic treatments disrupt the gut microbiome, often leading to long-term alterations that potentially affect host health. While much is known about how antibiotics cause microbial dysbiosis, little is understood about the factors that could influence the speed of microbial community recovery, such as host genetic differences. Using a mouse model, this study reveals that genetic variation at the blood group-related B4galnt2 gene significantly alters recovery after streptomycin treatment. Mice lacking intestinal B4galnt2 expression recover faster, with distinct changes in microbial composition, activity, and antibiotic resistance gene expression. These findings highlight how a single host gene can shape microbiota dynamics following antibiotic-induced disruption. The work emphasizes the importance of considering host genetic factors when predicting microbiome responses to antibiotics and suggests potential for genotype-guided strategies to reduce the adverse effects of microbiome-targeted therapies.},
}
@article {pmid42059606,
year = {2026},
author = {Yin, K and Ma, S and Yang, J and Feng, M and Zuo, Y and Wang, F},
title = {Gut microbiota composition and tumor immune features in meningioma patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0248525},
doi = {10.1128/spectrum.02485-25},
pmid = {42059606},
issn = {2165-0497},
abstract = {UNLABELLED: Meningiomas are prevalent intracranial tumors with poorly understood extraneural drivers. While the gut-brain axis influences neuro-oncogenesis, meningioma-specific gut microbiome alterations and their clinical implications remain uncharacterized. This study integrated 16S rRNA sequencing of fecal samples from 15 treatment-naïve WHO grade I meningioma patients (MPs) and 15 healthy controls (HCs) with immunohistochemical profiling of tumor immune infiltrates (MPO[+] neutrophils, CD68[+] macrophages, CD3[+] T cells). Compared with HCs, MPs exhibited significantly reduced alpha diversity (Shannon index, P = 0.026) and distinct beta diversity (permutational multivariate analysis of variance, P < 0.0009). Taxonomic analysis revealed enrichment of Proteobacteria (28.82% vs. 2.46%, P = 0.001), specifically Escherichia_Shigella at the genus level (25.95% vs. 1.61%, P = 0.008), along with depletion of Bacteroidaceae and Ruminococcaceae. LEfSe identified Escherichia_Shigella as the top meningioma-enriched biomarker. In diagnostic modeling, Escherichia_Shigella achieved an area under the receiver operating characteristic curve of 95.11% (95% CI: 86.91%-100%) for WHO grade I meningioma detection. Critically, Escherichia_Shigella abundance positively correlated with intratumoral MPO[+], CD68[+], and CD3[+] cell densities (all P < 0.05), whereas Ruminococcaceae showed inverse correlations. The 16S rRNA sequencing data are publicly available in the GSA database under accession number CRA027974. This study provides the first evidence of gut dysbiosis in grade I meningioma, characterized by Escherichia_Shigella dominance and depletion of immunomodulatory commensals. This signature correlates with increased immune infiltration and holds promise as a novel biomarker.<br><br>IMPORTANCE: Detailed exploration of host-microbe interactions can be worthwhile. Gut dysbiosis has been implicated in neuroinflammation, blood-brain barrier disruption, and oncogenesis in multiple cancer types, including gliomas. However, the gut microbiota composition and metabolic characteristics in patients with meningioma have not been previously reported. To address these critical knowledge gaps, we conducted a case-control study integrating 16S rRNA sequencing, clinical phenotyping, and immunohistochemical profiling. Our study revealed significant alterations in the gut microbiota of MPs, characterized by reduced alpha diversity, enrichment of Proteobacteria, and depletion of beneficial taxa, including Bacteroidaceae and Ruminococcaceae. Critically, we identified Escherichia_Shigella as a potential diagnostic biomarker and demonstrated strong correlations between elevated Escherichia_Shigella/Enterobacteriaceae abundance and increased intratumoral infiltration of MPO&#x207a; neutrophils, CD68&#x207a; macrophages, and CD3&#x207a; T cells. These findings are the first evidence that gut microbiome dysbiosis is closely associated with meningioma inflammation.},
}
@article {pmid42059625,
year = {2026},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0362625},
doi = {10.1128/spectrum.03626-25},
pmid = {42059625},
issn = {2165-0497},
abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.<br><br>IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.},
}
@article {pmid42059647,
year = {2026},
author = {Ma, X and Jiang, Z and Yang, T and Zhang, H and Lu, W and Liu, K and Fan, X and Yang, G and Wu, S},
title = {Integrated multi-omics analysis reveals gut dysbiosis and altered energy metabolism in Chinese ALS patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0060926},
doi = {10.1128/spectrum.00609-26},
pmid = {42059647},
issn = {2165-0497},
abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder with a complex etiology. Emerging evidence implicates gut microbiota dysbiosis in ALS pathology via the gut-brain axis, yet the specific integrative profile of the gut microbiome, virome, and metabolome, particularly in Chinese patients, remains incompletely characterized. Although global diversity indices showed no significant differences, taxonomic analysis revealed distinct compositional shifts. The ALS microbiome was characterized by a significant depletion of beneficial anti-inflammatory genera, specifically Akkermansia and Faecalibacterium, and an expansion of opportunistic pathogens such as Escherichia and oral-associated taxa (e.g., Streptococcus). We also observed a specific alteration in the gut virome, with viral genera including Puppervirus and Donellivirus enriched in ALS patients. Functionally, the ALS microbiome exhibited a marked upregulation of pathways involved in L-ascorbate (vitamin C) degradation and fatty acid biosynthesis, suggesting a microbial contribution to systemic oxidative stress. Metabolomic analysis corroborated these findings, identifying 271 differentially expressed metabolites. ALS patients showed elevated levels of inflammatory lipids (e.g., LysoPC) and metabolic intermediates of the tricarboxylic acid (TCA) cycle, alongside a downregulation of antioxidants. Integrative analysis highlighted profound dysregulation in porphyrin metabolism, oxidative phosphorylation, and energy homeostasis. Our findings demonstrate that ALS is associated with a specific dysbiotic gut ecosystem characterized by the loss of protective commensals, unique viral signatures, and functional metabolic reprogramming that exacerbates host oxidative stress and energy deficits. These results provide new insights into gut-brain interactions and highlight microbial antioxidant depletion as a potential therapeutic target.IMPORTANCEAmyotrophic lateral sclerosis (ALS) is a devastating disease with no cure. While gut bacteria are known to influence brain health, we still do not understand exactly how they contribute to ALS progression. In this study, we used advanced DNA sequencing and chemical analysis to deeply examine the gut ecosystem of ALS patients. Beyond just cataloging which bacteria are present, we discovered what they are doing: the ALS microbiome actively breaks down vitamin C (a critical antioxidant) and disrupts energy metabolism. We also found a loss of protective bacteria that maintain the gut barrier. These findings are significant because they suggest that the gut microbiome in ALS patients may be actively fueling the disease by depleting the body's antioxidant reserves. This points to a new potential treatment strategy: targeting these specific bacterial functions or replenishing specific metabolites to protect motor neurons.},
}
@article {pmid42059891,
year = {2026},
author = {Pang, H and Peng, B and Yan, X and Wang, J and Lu, Y and Yuan, X and Zhang, Y and Zhang, L and Huang, J and Zhang, Y and Yang, R and Ma, X and Wang, X and Fan, C and Zhang, L and Song, W and Cheng, Y and Liang, S and Wang, Y and Zheng, W and Li, G},
title = {Pregnancy-induced hypertension are preceded by prenatal perturbations of the gut microbiome and metabolome.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-026-06221-1},
pmid = {42059891},
issn = {1420-9071},
support = {2024ZD0532100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; No. Lingjunrencai-02-02//High-level construction project of public health technical personnel in Beijing Municipal Health System/ ; },
}
@article {pmid42060056,
year = {2026},
author = {Böhm, D and Guchelaar, HJ and Smidt, ML and Deenen, MJ},
title = {Microbiome-Modulating Strategies in Anticancer Therapy: A Review of Current Evidence and Recommendations for Further Treatment Improvement.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42060056},
issn = {1867-1314},
}
@article {pmid42060063,
year = {2026},
author = {Lee, SY and Cho, KS},
title = {Burkholderia sp. ZF6-mediated mitigation of Cd and Zn stress in contaminated soil: effects on Chinese cabbage growth and rhizosphere microbial communities.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42060063},
issn = {1614-7499},
support = {2022R1A2C2006615//National Research Foundation of Korea/ ; },
abstract = {This study investigated the effects of Burkholderia sp. ZF6, a plant growth-promoting bacterium with heavy metal resistance genes (cadA and zntA), on the growth of Chinese cabbage (Brassica rapa subsp. pekinensis) and cadmium (Cd)/zinc (Zn) removal in contaminated soils. ZF6 inoculation significantly increased root biomass (over twofold) and enhanced soil Cd and Zn removal efficiencies by approximately 2-4 times (19.9% for Cd and 11.5% for Zn). The abundance of cadA and zntA genes increased by 1.2-2.7 times, suggesting an enrichment of heavy metal-resistant microbial populations. Microbial community analysis showed that ZF6 inoculation reshaped the rhizosphere microbiome, increasing the relative abundance of genera such as Klebsiella, Agrobacterium, Burkholderia, Sphingomonas, and Pseudomonas. Notably, the abundance of Burkholderia, corresponding to ZF6, exhibited an increasing trend over time. Network analysis further indicated that microbial interactions became more complex in ZF6-treated soils (1.7-4.5-fold higher connectivity). Correlation analysis revealed that zntA abundance was associated with selected functional genes (e.g., K04565 and K01534) and inversely related to soil Cd concentration, suggesting a potential link between microbial functional potential and metal dynamics. Overall, ZF6 inoculation facilitated the restructuring of soil microbial communities to favor heavy metal-resistant bacteria. These findings highlight the potential of ZF6 as a scalable microbial-assisted phytoremediation strategy, although further validation under field conditions is required.},
}
@article {pmid42060722,
year = {2026},
author = {Rodriguez Hernandez, CJ and Cruz-Cruz, A and Shrestha, CL and Terekhova, M and Chen, P and Perpich, J and Potempa, B and Carey, K and Rohlfing, M and Peeples, ME and Grayson, MH and Potempa, J and Artyomov, M and Lamont, RJ and Bagaitkar, J},
title = {Gingipain proteases from the bacterium Porphyromonas gingivalis confer protection against airway viral infection.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {18},
pages = {e2503100123},
doi = {10.1073/pnas.2503100123},
pmid = {42060722},
issn = {1091-6490},
support = {DE031756//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDR)/ ; },
mesh = {*Porphyromonas gingivalis/enzymology ; Animals ; Mice ; Humans ; Gingipain Cysteine Endopeptidases ; *Respiratory Syncytial Virus Infections/immunology/prevention &amp; control/virology ; *Cysteine Endopeptidases/metabolism ; *Adhesins, Bacterial/metabolism ; Sendai virus/immunology ; Interferons/metabolism ; Respiratory Syncytial Viruses/immunology ; Mice, Inbred C57BL ; *Respiratory Tract Infections/virology/immunology ; },
abstract = {Physical interactions with bacterial colonizers at mucosal barrier surfaces can have beneficial or detrimental effects on viral infectivity and transmission. The oropharyngeal mucosal surface is a major portal of entry for many pathogenic respiratory viruses, such as respiratory syncytial virus (RSV), and also harbors a rich and diverse microbiome. Whether oropharyngeal bacteria directly or indirectly influence host susceptibility to respiratory viruses remains unknown. Here, we show that Porphyromonas gingivalis, an oral pathobiont, potently and uniquely suppresses airway epithelial antiviral immunity by degrading interferons (IFNs) and transcriptionally repressing multiple IFN-stimulated genes (ISGs), which are essential for providing resistance to viral infection. Despite inducing a state of IFN hyporesponsiveness, we found that P. gingivalis counterintuitively protected against severe infection by RSV and the closely related murine-specific Sendai virus (SeV) in two independent models: human airway bronchial epithelial transwell cultures and airway infection in mice. This protection was conferred by the activity of P. gingivalis cysteine proteases (gingipains) that cleaved envelope glycoproteins on RSV and SeV, thereby impairing their infectious capacity. Thus, our data show a nuanced role for P. gingivalis in modulating host susceptibility to viral infection. While P. gingivalis can significantly inhibit host IFN responses, its proteases preemptively reduce viral infectious capacity, protecting the host from severe damage associated with respiratory infections.},
}
@article {pmid42060821,
year = {2026},
author = {Yeasmin, F and Babu, MR and Saha, P and Biswas, S and Guha, A and Islam, T and Gupta, DR and Rahman, MM},
title = {Draft genome sequence of Bacillus cereus HS120, a probiotic candidate isolated from the gut of hilsa (Tenualosa ilisha).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0015126},
doi = {10.1128/mra.00151-26},
pmid = {42060821},
issn = {2576-098X},
abstract = {Bacillus cereus HS120 was isolated from the stomach of a healthy hilsa (Tenualosa ilisha) in Nabogonga River, Bangladesh. Here, we present a 5,673,590-bp draft genome with 35.23 % GC content, which encodes numerous biosynthetic gene clusters for secondary metabolites and lacks detectable virulence factors, supporting its potential as an aquaculture probiotic.},
}
@article {pmid42060842,
year = {2026},
author = {Arroyo-Mendoza, M and Lorenzi, H and Phillips, GJ and Hinton, DM},
title = {Escherichia coli pathobionts and Crohn's disease: varied genetic paths leading to similar phenotypes.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0001626},
doi = {10.1128/jb.00016-26},
pmid = {42060842},
issn = {1098-5530},
abstract = {Crohn's disease (CD), an inflammatory bowel disease that arises from an immune attack on the gastrointestinal tract, affects roughly 1.6 million Americans. The etiology of CD and the other major irritable bowel disease, ulcerative colitis, is not known, but host genetics and immunology, the gut microbiome, and environmental factors are all thought to be involved. In addition, adherent-invasive Escherichia coli (AIEC) strains, which are able to adhere to and invade epithelial cells and macrophages, are frequently found to be associated with CD. Besides their adherence and invasion properties, key features that distinguish AIEC from commensal E. coli include increased biofilm formation, increased antibiotic resistance, and survival/replication within macrophages. However, these pathobionts lack genetic features typical of frank pathogens. Thus, the potential role AIEC plays in CD pathogenesis is not clear. The E. coli pathobiont LF82, isolated from the ileum of a patient with CD, has been a well-studied, prototypic AIEC. Dozens of single-nucleotide polymorphisms (SNPs) distinguish LF82 and other AIEC from commensal E. coli, suggesting that some of these genetic features might account for particular LF82 phenotypes. In this review, we summarize changes in the CD gut, the association of AIEC with CD, genes and SNPs associated with AIEC, and recent work connecting a specific SNP within a bacterial RNA polymerase gene to the expression of genes associated with the LF82 lifestyle.},
}
@article {pmid42061010,
year = {2026},
author = {Garrigós, M and Jiménez-Peñuela, J and Saavedra, I and Veiga, J and García-López, MJ and Garrido, M and Ruiz-López, MJ and Figuerola, J and Moreno-Indias, I and Martínez-de la Puente, J},
title = {Corrigendum to 'Interactions between urbanization, malaria infection and avian cloacal microbiome' [Environ. Res. 297 (2026) 124073].},
journal = {Environmental research},
volume = {301},
number = {},
pages = {124397},
doi = {10.1016/j.envres.2026.124397},
pmid = {42061010},
issn = {1096-0953},
}
@article {pmid42061087,
year = {2026},
author = {Cavaleri, MP and Ardondi, L and Vitali, I and Sileo, L and Ferroni, L and Cappucci, IP and Rigon, L and Burgio, F and Franceschini, D and Degasperi, M and Pezzotti, G and Rubini, G and Rubini, A and Lovatti, L and Pinton, P and Zavan, B},
title = {Apple derived extracellular vesicles as positive modulators of glial inflammation and gut-brain axis signaling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {156},
number = {},
pages = {158232},
doi = {10.1016/j.phymed.2026.158232},
pmid = {42061087},
issn = {1618-095X},
abstract = {Plant-derived extracellular vesicles (PDEVs) are emerging as bioactive dietary particles with the capacity to modulate mammalian physiology. Here, we characterize the structure and functional properties of apple-derived extracellular vesicles (ADEVs) and evaluate their relevance to neuroimmune and gut-brain communication. ADEVs exhibit canonical PDEV features and elicit rapid IP3-dependent Calcium (Ca[2+]) signaling in fibroblasts while preserving blood-brain barrier integrity. Neural assays reveal marked cell-type specificity: ADEVs are efficiently internalized by glial cells and activate glial Ca[2+] signaling yet display minimal neuronal uptake and no detectable Ca[2+] response in differentiated SH-SY5Y neurons. Consistent with this selectivity, ADEVs attenuate TNF-α-induced cytokine secretion in activated glia but remain inert in resting neural cells. Although capable of encapsulating L-DOPA efficiently, ADEVs fail to deliver functional neuroprotection against rotenone toxicity, indicating limited neuronal compatibility for dopaminergic cargo. In parallel, using advanced in vitro colon simulation platforms, ADEVs modulate the colonic microbiome in a dose-dependent manner, promoting carbohydrate fermentation and short-chain fatty acid production while reducing proteolytic metabolism under physiologically relevant conditions, with sustained, region-specific effects during prolonged exposure. In vivo, ADEV administration in dogs with chronic intestinal inflammation is associated with altered circulating serotonin levels, suggesting engagement of gut-brain neurochemical pathways with potential implications for mood regulation. Collectively, these findings identify ADEVs as biocompatible, glia-responsive plant vesicles with potential neuromodulatory activity, while delineating intrinsic constraints in their use as neuronal drug-delivery systems.},
}
@article {pmid42061103,
year = {2026},
author = {Aliniay-Sharafshadehi, S and Sheykhhasan, M and Sharifi, K and Ansari-Mohseni, A and Yousefi, MH and Afkhami, H and Mehdipour, A and Aghaali, M},
title = {Dental Pulp Stem Cells for the Management of Plaque Biofilm-Associated Infections : A Review.},
journal = {International dental journal},
volume = {76},
number = {4},
pages = {109559},
doi = {10.1016/j.identj.2026.109559},
pmid = {42061103},
issn = {1875-595X},
abstract = {This structured narrative review synthesises current evidence (2000-2025) on the antimicrobial, immunomodulatory, and regenerative properties of dental pulp stem cells (DPSCs) in the context of plaque-induced gingivitis and oral biofilm infections. We systematically reviewed peer-reviewed literature from PubMed, Scopus, and Web of Science via keywords related to DPSCs, oral biofilms, antimicrobial peptides (eg, β-defensins, LL-37), and immunomodulation. Unlike conventional antimicrobial therapies that solely target pathogen eradication, DPSCs offer a dual-function strategy: (1) direct microbial control through the secretion of antimicrobial peptides that disrupt Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans and (2) resolution of inflammation via macrophage M2 polarisation, suppression of IL-1β/TNF-α (Interleukin-1β and Tumor Necrosis Factor-α), and microbiome rebalancing. Additionally, DPSCs support periodontal tissue regeneration through trophic signalling and differentiation into periodontal lineage cells. Critically, no clinical trials to date have evaluated DPSCs for the management of gingivitis. This review highlights DPSCs as promising, antibiotic-sparing therapeutic candidate and outlines key knowledge gaps for future translational research.},
}
@article {pmid42061108,
year = {2026},
author = {van Kalkeren, CAJ and van Deuren, T and Huang, W and Park, SQ and Blaak, EE and Adam, TC},
title = {Neurocognition and food cue-related brain reactivity after fiber supplementation within a high-protein, plant-based diet in individuals with overweight and prediabetes: A randomized-controlled trial (the DISTAL-study).},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106668},
doi = {10.1016/j.clnu.2026.106668},
pmid = {42061108},
issn = {1532-1983},
abstract = {BACKGROUND: The increasing prevalence of obesity and related diseases, such as type 2 diabetes mellitus (T2DM) and neurocognitive dysfunction, warrants sustainable and effective strategies for treatment and prevention. A healthy diet, containing dietary fibers that are fermented by the gut microbiome, produces short-chain fatty acids, among other metabolites, known to alleviate insulin resistance. SCFA also may protect against neurocognitive decline and increase satiety through food-reward-related pathways of the gut-brain axis, thereby contributing to sustainable dietary habits and counteracting obesity and -related diseases. We therefore studied the effects of dietary fibers in the context of a high-protein, partially plant-based diet on neurocognitive functioning and food-reward related brain activity.<br><br>METHODS: This 12-week RCT compared a potato fiber and sugar beet pectin supplement to an isocaloric placebo (maltodextrin), both within a high-protein (&#xb1;45% plant-based) diet. We investigated the effects on food-reward-related brain activity using functional magnetic resonance imaging (fMRI) with visual food stimuli, comprising high-calorie, low-calorie, and non-food items. Neurocognitive performance was tested with the Cambridge Neurocognitive Test Automated Battery (CANTAB). Furthermore, satiety hormones, stress, and general well-being were assessed, and associations with cardiometabolic markers were explored.<br><br>RESULTS: Overall, there was a trend towards an increased amygdala BOLD response over time in the fiber group compared to placebo, independent of visual stimuli conditions. The change in amygdala activity was positively associated with increased colonic permeability in both groups. After the intervention, both groups showed improvements in psychomotor speed, visual memory, and learning abilities, and reported less subjective hunger after 12 weeks on a high-protein, partially plant-based diet. General well-being, stress, and satiety hormone concentrations remained unchanged.<br><br>CONCLUSION: Twelve weeks of fiber supplementation did not change brain activity induced by visual food cues in reward-related brain regions. However, the high-protein, partially plant-based diet seemed to provide neurocognitive benefits, improving psychomotor speed and memory, and decrease perceived hunger.},
}
@article {pmid42061238,
year = {2026},
author = {Rahman, FA and Granados, EAF and Adhikari, Y and Naeem, M and Rochell, S and Bourassa, D and Poudel, S},
title = {Longitudinal analysis of broiler cecal microbiome: unraveling the species level dynamics across age and sex.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106911},
doi = {10.1016/j.psj.2026.106911},
pmid = {42061238},
issn = {1525-3171},
abstract = {This study investigated the longitudinal dynamics of the cecal microbiome in male and female broiler chickens from hatch (d 0) to market age (d 42) using full-length 16S rRNA gene sequencing via Oxford Nanopore Technology. Microbial composition, diversity, and differential abundance were assessed across four time points (d 0, 14, 28, and 42). Alpha diversity analyses showed no significant differences between male and female within the same age group. The longitudinal comparisons revealed significantly lower diversity on d 0 compared to later timepoints in both male and female. Beta diversity analyses using Bray-Curtis and Jaccard metrics demonstrated distinct microbial community clustering at d 0 and a major compositional shift by d 14. PERMANOVA confirmed age as a significant factor influencing microbial composition. However, both sex and age influenced the dominant bacterial species. On d 0, Enterococcus faecalis was the most abundant in both males (58.57%) and females (61.35%). Whereas on d 42, Romboutsia ilealis (14.12%) became the predominant species in female and Negativibacillus massiliensis (9.7%) in males. In addition to the variation in the dominant species, differential abundance analysis revealed that bacterial species such as Clostridium celatum, C. disporicum, C. jeddahitimonense, and C. saudiense, had significantly higher abundance at d 0 compared to later time points in both males and females. Whereas bacterial species such as Bittarella massiliensis, Turicibacter bilis,and Turicibacter sanguinis had significantly higher abundance at d 28 and 42. Furthermore, core microbiome analysis showed microbial richness plateaued at approximately 330-350 species from d 14 onward. Our results indicate that early microbial communities are more sex-specific and they gradually converge over time probably due to extrinsic environmental factors.},
}
@article {pmid42061249,
year = {2026},
author = {Biasato, I and Hassan, T and Buzzanca, D and Bagatella, S and Schiavone, A and Capucchio, MT and Gasco, L and Kenéz, &#xc1; and Ferrocino, I},
title = {Gut health in broiler chickens fed a mixture of Hermetia illucens and Tenebrio molitor meals: does it have a key role in shaping bird performance?.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106966},
doi = {10.1016/j.psj.2026.106966},
pmid = {42061249},
issn = {1525-3171},
abstract = {Insect meals are promising sustainable protein sources for poultry, but comprehensive insights into their effects on gut health and growth performance are lacking. This study is the first to elucidate relationships between gut health parameters and performance in broilers fed Hermetia illucens (HI) and Tenebrio molitor (TM) meals at 5% or 10% inclusion levels, singly or in a 1:1 combination. A 37-day trial used 420 male Ross 308 chicks randomly allocated to seven treatments: control (C), HI5 (5% HI), HI10 (10% HI), TM5 (5% TM), TM10 (10% TM), MIX5 (5% MIX), and MIX10 (10% MIX). By integrating intestinal histomorphometry, mucin histochemistry, multi-organ histopathology, and multi-omics cecal microbiome characterization, we identified key structural, microbial, and metabolic biomarkers associated with performance variations (false discovery rate [FDR]<0.05 and P < 0.05 for microbiome and histomorphology, respectively). High-performing groups (MIX5, TM5) showed microbiomes enriched in short-chain fatty acid-producing bacteria (Veillonellaceae, Butyricicoccus, Limosilactobacillus crispatus), positively correlated with ADG and ADFI (FDR<0.05) and negatively correlated with FCR (FDR<0.05). Favorable metabolomic profiles (increased dopamine, tyramine, malic and orotic acids; reduced 3-deoxyglucosone, hexanoylcarnitine [FDR<0.05]) and preserved balance between neutral (positively correlated with BW and ADFI [P < 0.05]) and acidic mucins (positively correlated with BW, ADFI and ADG, and negatively correlated with FCR [P < 0.05]) were also observed. Low-performing groups (MIX10, HI10) displayed microbiomes dominated by Ruminococcaceae, Alistipes, and l-Eubacterium (negatively correlated with FCR and associated with purine metabolism alterations [FDR<0.05]), alongside worsened morphology (tendency for reduced villus height in MIX10 [P = 0.07], positively and negatively correlated with ADG and FCR, respectively [P < 0.05], and thinner mucosal/muscular layers [P < 0.05]) and decreased neutral mucins (P < 0.05). TM10 maintained unaffected growth performance via beneficial taxa (Limosilactobacillus crispatus, Tyzzerella), and reduced Campylobacter jejuni and antimicrobial resistance genes (FDR<0.05). Jejunal inflammation, negatively correlated with ADG (P < 0.05), was not influenced by dietary treatments (P > 0.05). In conclusion, specific taxa (Butyricicoccus, Veillonellaceae, Limosilactobacillus crispatus), metabolites (dopamine, tyramine, malic and orotic acids), and mucosal features (villus height, mucin composition) were identified as biomarkers of optimal performance in insect-fed broilers.},
}
@article {pmid42061266,
year = {2026},
author = {Li, T and Wang, P and Zhi, Z and Li, Q and Guo, T and Zhou, J and Zhang, H and Zhang, J and Zhang, J},
title = {Modulation of cecal microbiota and metabolite profiles by Zanthoxylum bungeanum seeds enhances antioxidant capacity and meat quality in Pekin ducks.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {107010},
doi = {10.1016/j.psj.2026.107010},
pmid = {42061266},
issn = {1525-3171},
abstract = {Zanthoxylum bungeanum seeds (ZBS) are a bioactive-rich byproduct with potential as antibiotic alternatives, yet their systemic effects on waterfowl remain unclear. This study investigated the effects of dietary ZBS supplementation on growth performance, physiological status, meat quality, and the microbiome-metabolome profile in Pekin ducks. A total of 240 ducks (14-day-old) were assigned to four treatments containing 0% (CG), 1.5% (LG), 3.0% (MG), or 4.5% (HG) ZBS for 21 days. Trend analysis revealed a significant quadratic dose-response for growth performance (P< 0.05), identifying 1.5% as the optimal inclusion level for maximizing body weight. Physiologically, ZBS supplementation enhanced antioxidant capacity and liver function by linearly upregulating serum SOD, CAT, and GSH-Px activities while significantly reducing MDA, ALT, AST, and triglyceride levels (P< 0.05). Regarding meat quality, ZBS linearly increased breast meat redness (a*) and facilitated the linear deposition of glutamic acid and alpha-linolenic acid, mirroring the ZBS nutrient profile (P < 0.05). Consequently, this deposition optimized key nutritional indices, characterized by a linear reduction in the n-6/n-3 polyunsaturated fatty acid ratio (P< 0.01) and an improved BCAA/AAA ratio. Mechanistically, 16S rRNA sequencing indicated a beneficial filtering effect where ZBS reduced alpha diversity by suppressing inflammation-associated genera (Desulfovibrio, Fusobacterium) while enriching beneficial fermenters (Faecalibacterium, Barnesiella). Metabolomics further identified upregulated antioxidant and immunomodulatory metabolites, such as orsellinic acid and purine analogs, which correlated with improved host health. Collectively, ZBS functions as an ecological modulator that promotes liver health and meat nutritional value in a linear manner, while optimizing growth performance quadratically, with 1.5% identified as the optimal dosage.},
}
@article {pmid42061335,
year = {2026},
author = {Zhu, T and Hussain, M and Shi, C and Ruan, Y and Gao, X and Zhu, J and Wu, G},
title = {Transgenerational sublethal effects of emamectin benzoate and indoxacarb on Telenomus remus: Integrative insights from host-associated microbiome and transcriptome analyses.},
journal = {Ecotoxicology and environmental safety},
volume = {317},
number = {},
pages = {120193},
doi = {10.1016/j.ecoenv.2026.120193},
pmid = {42061335},
issn = {1090-2414},
abstract = {The extensive application of synthetic insecticides like emamectin benzoate (EB) and indoxacarb (IN), threatens ecologically beneficial parasitoids such as Telenomus remus. This study evaluated the transgenerational impacts of continuous exposure (over seven generations) to EB and IN on T. remus by integrating toxicity assays, life-history analysis, microbiome profiling, and transcriptomics. Acute risk assessment indicated EB posed a moderate risk (Risk Quotient, RQ > 50), while IN showed low acute risk (RQ < 50). After multigenerational selection, T. remus developed only minor tolerance (ratios of 1.47 for EB and 1.46 for IN) but incurred significant fitness costs; prolonged development (EB: 10.33 days vs. control: 9.00 days), reduced parasitism (EB: 82.07%; IN: 85.00% vs. control: 90.29%), and shortened female longevity. Host-associated microbiome analysis revealed disrupted community homeostasis, with a notable decline in dominant Wolbachia abundance (from 33.20% in controls). Transcriptomics identified limited differentially expressed genes (53 for EB, 52 for IN), suggesting physiological adaptation, with key changes enriched in detoxification (e.g., cytochrome P450s, UGTs) and immune pathways. Integrated correlation analyses (Mantel tests) linked microbial dysbiosis to altered host gene expression and reduced fitness. These findings highlight that even insecticides with low acute toxicity (like IN) or those inducing only minor tolerance shifts can cause severe transgenerational impairments. Correlations between microbiome alterations and transcriptomic changes suggest potential interactive mechanisms that warrant further validation. Field application rates and ecological risk assessments should be re-evaluated to account for these chronic sublethal effects to conserve T. remus in sustainable agro-ecosystems.},
}
@article {pmid41863002,
year = {2026},
author = {Wang, Y and Ling, W and Ouyang, L and Zhang, S and Zhou, H and Luo, T and Liu, S and Tang, J and Zhou, Z and Tang, L and Wang, Z and Wei, F and Huang, G},
title = {A lagging recovery: the delayed restoration of gut microbial diversity in Rhinolophus sinicus post-hibernation.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41863002},
issn = {2524-4671},
support = {32192420//National Natural Science Foundation of China/ ; 32322015//National Natural Science Foundation of China/ ; 20233ACB209001//Natural Science Foundation of Jiangxi Province/ ; 2023SSY02081//Jiangxi Provincial Key Laboratory of Conservation Biology/ ; },
abstract = {BACKGROUND: Hibernation enables animals to survive extreme environments, yet gut microbiome dynamics across the full hibernation cycle remain poorly understood, particularly in chiropterans with unique physiological traits. This study aimed to precisely characterize seasonal microbial succession in wild Rhinolophus sinicus using 16S rRNA gene sequencing across 6 physiological stages, with a focus on taxonomic and functional shifts linked to hibernation-associated fasting and post-hibernation activity.<br><br>RESULTS: Alpha diversity followed a pronounced V-shaped trajectory, declining during hibernation and recovering only gradually&#x2014;remaining suppressed in the early active stage and rebounding markedly by mid&#x2013;late active stages. Beta diversity revealed a clear separation between hibernation and active phases, with physiological stage explaining 34.9% of community variation. At the phylum level, Pseudomonadota was the dominant taxon during hibernation, while Bacillota became the most abundant phylum in the active period. At the genus level, Yokenella was the core genus in the hibernation stage, and Lactococcus was the dominant genus in the active period. Functional predictions showed enrichment of lipid and amino acid metabolism during hibernation, supporting energy maintenance under fasting, while active-phase microbiota were oriented toward carbohydrate metabolism, matching increased energy demands.<br><br>CONCLUSIONS: Our findings demonstrate that hibernation drives directional restructuring of the gut microbiota in R. sinicus, offering new insights into microecological strategies underlying bat survival under extreme conditions.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00552-x.},
}
@article {pmid41864867,
year = {2026},
author = {Ma, W and Bai, B and Liu, M and Sheng, P and Bao, J and Song, C and Liu, J and Ma, H and Du, S and Ge, G and Jia, Y and Wang, Z},
title = {Synergistic effects of cellulase and lactic acid bacteria(Pediococcus pentosaceus and Levilactobacillus brevis) on alfalfa silage fermentation and microbial dynamics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41864867},
issn = {1471-2180},
support = {(2025YFHH0210)//Research and Demonstration of High-Quality Forage Supply and Efficient Breeding Technology System for Dairy Cows/ ; },
abstract = {UNLABELLED: This study evaluated the effects of Lactic acid bacteria and cellulase, individually and in combination, on fermentation quality and microbial community dynamics of alfalfa silage. Six treatments were tested, including control, cellulase alone and two lactic acid bacteria species (Pediococcus pentosaceus, Levilactobacillus brevis) applied individually or in combination with cellulase. The results showed that Levilactobacillus brevis in combination with cellulase, producing higher lactic acid concentrations, lower pH (< 4.2) to the other treatments. The microbiome analysis revealed that Lactiplantibacillus was dominant, while undesirable bacterium Achromobacter was suppressed. Functional prediction of microbial communities analysis indicated a higher predicted abundance of sequences associated with pyruvate metabolism, glycolysis/gluconeogenesis and starch and sucrose metabolism pathways. These findings provide insights into optimizing alfalfa silage quality through synergistic use of cellulase and lactic acid bacteria silage inoculants with high metabolic stability.<br><br>GRAPHICAL ABSTRACT: [Image: see text]},
}
@article {pmid42010622,
year = {2026},
author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M},
title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42010622},
issn = {1756-994X},
support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; },
abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood.<br><br>METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages.<br><br>RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution.<br><br>CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-026-01646-6.},
}
@article {pmid42049742,
year = {2026},
author = {Guarino-Vignon, P and Louis, E and Pham, HP and Orianne, G and Tkacz, E and Brot, L and Mazzetti, E and Sedda, D and Ruffié, P and Rolhion, N and D'Haens, G and Hadida, B and Langella, P and Sokol, H},
title = {Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn's Disease: a first in human trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72375-y},
pmid = {42049742},
issn = {2041-1723},
abstract = {A marked decrease in Faecalibacterium prausnitzii is a hallmark of Crohn's disease (CD)-associated dysbiosis and predicts disease relapse. Here, we present the development and first-in-human evaluation of F. prausnitzii strain EXL01 for CD treatment. The EXL01-strain demonstrates anti-inflammatory effects in four models of colitis in rodents. A first-in-human, open-label, single-arm study of oral EXL01 was conducted in eight adult participants with mild to moderate CD, following corticosteroids-induced clinical response or remission. The primary endpoint was safety, and secondary endpoints included clinical, endoscopic, histological, molecular, and microbiome assessments. Exploratory endpoints included mucosa transcriptome and cytokine levels. EXL01 is well-tolerated with no treatment-related adverse events. Six participants completed the study; two discontinued treatment due to disease flare. While gut microbiota composition remains largely stable, transcriptomic analyses reveal distinct changes in ileal gene expression following EXL01 treatment, notably modulation of immune-related genes and upregulation of energy metabolism pathways. Compared to participants who remained in remission, those who flared show higher baseline systemic inflammation markers and innate immunity gene expression. These findings demonstrate that oral administration of EXL01 is feasible and well tolerated and establishes proof-of-concept for F. prausnitzii as a first-in-class live biotherapeutic for CD. ClinicalTrials.gov registration: NCT05542355.},
}
@article {pmid42050189,
year = {2026},
author = {Mesnage, R and Ferguson, S and Nechalioti, PM and Cercelaru, L and Hbous, MA and Docea, AO and Tsatsakis, A and Kouretas, D and Antoniou, MN},
title = {Impact of glyphosate and its mixture with 2,4-D and dicamba on gut biochemical function, intestinal barrier integrity and microbiome composition in adult rats with prenatal commencement of exposure.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
pmid = {42050189},
issn = {1432-0738},
support = {26/53/2/31.05.2022//Universitatea de Medicin&#x103; &#x15f;i Farmacie din Craiova/ ; },
}
@article {pmid42050215,
year = {2026},
author = {Seneff, S and Boros, LG},
title = {The essential role of hydrogen gas recycling by gut microbes in reducing deuterium load in host mitochondria: is trimethylamine oxide a deuterium sensor?.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {3},
pages = {},
pmid = {42050215},
issn = {1573-3890},
mesh = {*Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Deuterium/metabolism ; *Mitochondria/metabolism ; *Hydrogen/metabolism ; Mice ; },
abstract = {BACKGROUND: The human gut microbiome plays many essential roles, but an often-overlooked role is to maintain an abundant supply of deuterium depleted (deupleted) nutrients to fuel the host mitochondria. Excess deuterium (heavy hydrogen) damages mitochondrial ATP synthase nanomotors, leading to a decrease in matrix water production with increased reactive oxygen species (ROS) and inefficient ATP production. A microbial metabolite, trimethylamine N-oxide (TMAO) is a powerful signaling molecule whose plasma levels are high in association with many chronic diseases, including diabetes, fatty liver disease, and atherosclerosis, as well as cancer and dementia. Thus, TMAO is an important gut-host signaling molecule that serves as a marker for an imbalanced microbiome that is unable to fully metabolize trimethylamine (TMA), an important step in maintaining a deupleted nutrient supply.<br><br>AIM OF REVIEW: In this paper, we present a hypothesis that TMAO is a marker for deuterium overload in the methylation pathway, in addition to its role as an indicator of a disrupted gut microbiome. The original study that brought attention to TMAO involved feeding mice synthetic choline with fully deuterated methyl groups. Fully deuterated TMAO was subsequently detected in the plasma. By contrast, a diet rich in eggs, a natural source of choline (a precursor to TMAO), does not raise TMAO levels. Many of the pathologies that are linked to elevated TMAO can also be viewed as strategies to promote the supply of deupleted water to the mitochondria, systemically.<br><br>KEY SCIENTIFIC CONCEPTS: The mantra that "food is medicine" is well supported by the powerful role that gut dysbiosis plays in influencing human health and disease.},
}
@article {pmid42050221,
year = {2026},
author = {Izah, SC and Ogwu, MC and Alum, EU},
title = {Innovative approaches to mitigating persistent toxic substances and their impacts on soil health and human well-being.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {42050221},
issn = {1573-2959},
mesh = {*Soil Pollutants/analysis ; Humans ; *Environmental Monitoring/methods ; *Soil/chemistry ; *Environmental Restoration and Remediation/methods ; Agriculture ; *Hazardous Substances/analysis ; Environmental Pollution/prevention &amp; control/statistics &amp; numerical data ; },
abstract = {Persistent toxic substances (PTS), including heavy metals, persistent organic pollutants (POPs), and persistent, mobile, and toxic/very persistent and very mobile (PMT/vPvM) substances present an increasing menace to soil health, alimentary systems, atmospheric cleanliness as well as human health. Despite the large amount of literature on each of the individual groups of contaminants, there is still no unified model that connects the dynamics of the soil-atmosphere environment, bioaccumulation in the food chain, new detection techniques, and policy measures. This review presents an interdisciplinary synthesis of dynamics in the PTS in the agricultural environment, explicitly incorporating (i) historic contaminants and emerging PMT/vPvM chemicals, (ii) soil-crop-livestock-human transfer pathways, and (iii) the state-of-the-art remediation and monitoring technologies into a single management framework. We critically evaluated conventional remediation methods alongside next-generation methods, such as engineered consortia of microorganisms, synergistic phytotransformation of plants and microbes, biochar-assisted immobilization, nanosensor-based detection, IoT-based soil sensing, precision agriculture, machine-learning-driven risk prediction, and blockchain-based traceability. Contrary to the previous reviews, which only take into account the remediation, detection, and policy separately, this study presents a systems-based approach, which integrates technological innovation, sustainable agronomic practices, and multilayered governance tools (such as the Stockholm Convention, REACH, and national soil action plans). We highlight the fact that the combination of smart agricultural technology and regenerative land management will help reduce the accumulation of PTS and maintain productivity, especially in resource-scarcity settings. The review outlines the research gaps, including contaminant-microbiome interactions, longitudinal deterioration of ecosystem services, and socioeconomic barriers to technology adoption. We propose a transdisciplinary roadmap that aligns environmental toxicology, soil science, public health, and policy innovation to mitigate PTS and safeguard food security. This integrative approach provides a strategic framework for advancing sustainable management of persistent toxic substances in agricultural systems.},
}
@article {pmid42050297,
year = {2026},
author = {Park, SH and Park, SB and Kang, J and Shin, S and Kim, GY and Bong, Y and Gu, M and Lee, YS and Bin, G and Seo, W},
title = {Multiomics characterization of an alcohol-induced hepatocellular carcinoma mouse model.},
journal = {Lab animal},
volume = {},
number = {},
pages = {},
pmid = {42050297},
issn = {1548-4475},
support = {2018R1A5A2025286//National Research Foundation of Korea (NRF)/ ; 2021R1A6C101A442//National Research Foundation of Korea (NRF)/ ; 2021R1C1C1009445//National Research Foundation of Korea (NRF)/ ; RS-2024-00404418//National Research Foundation of Korea (NRF)/ ; RS-2024-00439963//National Research Foundation of Korea (NRF)/ ; NIAAA, BG//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {Hepatocellular carcinoma (HCC) is a major global health problem, ranking as the sixth most frequently diagnosed cancer and the third leading cause of cancer-related mortality worldwide. Although the incidence of viral infection-mediated HCC has decreased in recent years, the incidence of alcohol- and metabolic dysfunction-associated HCC has increased, driven by changes in lifestyle and diet. Excessive alcohol consumption contributes to advanced liver diseases, including liver fibrosis, cirrhosis and HCC. Despite the clinical relevance of alcohol-associated HCC, there are no suitable animal models that adequately reflect the pathophysiological features of alcohol-associated HCC in humans. Here, to address this limitation, we established a mouse model of alcohol-associated HCC through the combined administration of N-diethylnitrosamine and carbon tetrachloride (CCl4), followed by administration of an alcohol-containing Lieber-DeCarli diet. The results indicated that chronic alcohol exposure in the presence of N-diethylnitrosamine and CCl4 substantially accelerated HCC development, which was characterized by increased oxidative stress, inflammation and severe fibrosis. Furthermore, we found that chronic ethanol consumption disrupted hepatic immunity, characterized by natural killer/natural killer T cell depletion, increased PD1[+]CD8[+] cells, reduced cytotoxicity and elevated inflammation. We also observed marked alterations in the gut microbiome following chronic alcohol administration. These immunological and microbiome alterations fostered an immunosuppressive microenvironment that accelerated HCC progression. Our newly developed mouse model induced liver tumorigenesis within a relatively short timeframe and recapitulated the clinical and pathological features of alcohol-associated HCC. The model therefore represents a valuable tool for studying the mechanisms underlying alcohol-associated HCC and related chronic liver diseases.},
}
@article {pmid42050317,
year = {2026},
author = {Lima, ALA and Costa, SS and do Socorro Dos Reis, R and de Souza, DC and Baião, GC and Moreira, RG and Rogez, HLG and das Graças, DA and Viana, RB and Marques, JM},
title = {Age Influences the Bacterial Composition of Samples From Buffaloes in the Marajó Archipelago, Pará, Brazilian Amazon.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70330},
pmid = {42050317},
issn = {1758-2229},
support = {88887.633228/2021-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animals ; *Buffaloes/microbiology ; Brazil ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Feces/microbiology ; *Milk/microbiology ; *Microbiota ; Cattle ; Female ; Age Factors ; Soil Microbiology ; },
abstract = {Buffalo milk stands out for its nutritional qualities and is mainly produced in Brazil in the Amazon region, particularly in the Marajó Archipelago, State of Pará. In this context, the milk microbiome is an intriguing and underexplored research topic. This study tested the hypothesis that the buffalo milk microbiome could share taxa with faeces, pasture soil and calf spittle. A possible correlation between generations was also explored. Samples of milk, faeces, spittle and pasture soil were analysed using a 16S rRNA metabarcoding approach, revealing significant phylogenetic and ecological differences among matrices. Beta-diversity analysis showed clustering between milk samples from heifers and cows, as well as proximity between soil and buffalo samples (milk and faeces). Relative abundance analysis identified shared taxa between buffaloes and their calves, though no clustering was observed between generations. A total of 15 bacterial families were found across all matrices, with Staphylococcaceae, Planococcaceae and Enterobacteriaceae being the most prominent. The milk microbiota was similar among animals of different ages. The grouping pattern varied depending on the animal and matrix, but not on the maternal relationship. Despite compositional differences, the shared taxa reinforce the idea of interaction among the studied microbial communities.},
}
@article {pmid42050358,
year = {2026},
author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y},
title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70567},
pmid = {42050358},
issn = {1365-3040},
support = {2024CXPT072//Key R&amp;D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; },
abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.},
}
@article {pmid42050578,
year = {2026},
author = {Srisanoi, K and Curado, TFF and Leles, C and Egli, A and Rooney, AM and Srinivasan, M},
title = {From culture-based to 16S sequencing approaches: oral microbiota changes in aging, frailty, and oral hypofunction - a systematic review.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08387-3},
pmid = {42050578},
issn = {1472-6831},
}
@article {pmid42050719,
year = {2026},
author = {Yang, D and Yang, L and Yang, J and Wang, G},
title = {Beyond the known: prospective research directions for the gut-brain axis in obesity and type 1 diabetes mellitus.},
journal = {Diabetology &amp; metabolic syndrome},
volume = {18},
number = {1},
pages = {},
pmid = {42050719},
issn = {1758-5996},
abstract = {BACKGROUND: This letter engages with the seminal review by Argyrakopoulou et al. Obesity and the Gut-Brain Axis in Type 1 Diabetes Mellitus: Terra Incognita? Curr Obes Rep, https://doi.org/10.1007/s13679-025-00654-8IF:11.0Q1B1 . on the putative role of the gut-brain axis in the rising prevalence of obesity within type 1 diabetes mellitus (T1DM).<br><br>OBJECTIVE: We aim to commend the authors while proposing key future research avenues to advance the field from correlation to causation and therapeutic application. We also seek to integrate recent high-impact evidence to contextualize our perspectives.<br><br>MAIN POINTS: First, we emphasize the need for deep mechanistic studies using gnotobiotic models and targeted metabolomics to delineate the causal role of specific microbial metabolites, informed by recent concepts of host genetic regulation of the gut-liver axis (e.g., via p53/PI3K/AKT/Wnt signaling) and microbiota composition in metabolic disease pathophysiology (1, 2). Second, we highlight the imperative for longitudinal cohort studies to determine the temporal relationship between gut dysbiosis, autoimmunity, and subsequent metabolic complications. Finally, we discuss the promising intersection of microbiome science with emerging therapeutics, including next-generation probiotics and GLP-1 receptor agonists, whose efficacy may be partly mediated through the gut-brain axis.<br><br>CONCLUSION: By addressing these priorities and integrating recent knowledge, the scientific community can translate this compelling paradigm into tangible clinical benefits for patients with T1DM.},
}
@article {pmid42050755,
year = {2026},
author = {Russnak, V and Koll, R and Keuter, S and Sanders, T and Dähnke, K},
title = {The Elbe Estuary Microbiome Shifts With Salinity and Discharge and Depends on Fresh Organic Matter and Nutrient Availability.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70349},
pmid = {42050755},
issn = {1758-2229},
support = {03F0864C//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 407270017/RTG2530//Deutsche Forschungsgemeinschaft/ ; 496691966/FA 1568//Deutsche Forschungsgemeinschaft/ ; MOSES//Helmholtz Association/ ; 101000518//European Commission/ ; },
mesh = {*Estuaries ; *Salinity ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Seasons ; RNA, Ribosomal, 16S/genetics ; Germany ; Nutrients/analysis ; *Seawater/microbiology/chemistry ; Biodiversity ; Nitrogen/analysis ; },
abstract = {The Elbe Estuary (Germany) stretches 142 km from the weir in Geesthacht to the North Sea. It is classified as mesotidal, partially mixed and heavily impacted by anthropogenic activities and modifications. Despite well-documented changes in ecosystem status, little is known about the microbial community in its surface water. In this study, we used 16S rDNA sequencing to characterise bacterial communities in surface water of the Elbe Estuary. Samples were collected across three seasons (winter, spring, and summer) in 2021 and 2022, to assess the relationship between environmental factors and bacterial community structure. Our analyses revealed that bacterial community diversity and composition varied seasonally and along the estuary stretch and were closely linked to physicochemical properties. Alpha diversity was highest in winter and in oligohaline samples. Distance-based redundancy analysis showed that salinity, discharge, temperature, inorganic nitrogen (NO2), and silicate are key factors in shaping the bacterial community compositions. Although spatial differences were observed, seasonal variation was the main determinant of bacterial diversity and community structure. Overall, our results show that anthropogenic pressures and seasonal changes are reflected in a dynamic microbial community with metabolic functions strongly shaped by human activity.},
}
@article {pmid42050886,
year = {2026},
author = {Fatima, R and Ud Din Shah, S and Hameed, A and Ditta, A and Saleemi, MK and Gill, A and Tarique, H},
title = {Microbiome-host interactions driving the transition from non-pregnant to pregnant states in a goat model.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag144},
pmid = {42050886},
issn = {1525-3163},
abstract = {Pregnancy in goats involves complex hormonal, metabolic, and immune shifts, and growing evidence suggests that the gut microbiome plays a key regulatory role in these physiological transitions, yet its specific role in guiding the shift from non-pregnant to pregnant states is still not clearly defined. This study investigated dynamic changes in the microbial community, biochemical markers, and metabolic profile shifts that influence host physiology during the transition from non-pregnant to pregnant states. The results revealed that significant changes in the abundance of microbial genera such as Ruminococcus, Bacteroides, and Lactobacillus were observed across groups. Alpha diversity metrics (Chao1, Shannon, Sobs) indicated substantial differences between groups, while Simpson diversity remained unaffected. Beta diversity analysis (PCoA, NMDS) revealed clear group separation, and pairwise PERMANOVA tests confirmed significant differences (P < 0.05). Heatmap and box plot analyses revealed distinct clustering of microbial profiles, and showed significant differences in genus abundance, including Bacteroides, Christensenella, and Prevotella_7 (P < 0.05). Moreover, significant variations in hematological parameters (RBC, HGB, MCV, MCH, MCHC, PLT, WBC) were noted, with distinct patterns between groups (P < 0.05). Correlation analysis identified strong associations between microbiota taxa (Lachnospira, p < 0.01; Oscillibacter, P < 0.001) and hematological markers. In addition, progesterone and estrogen hormones significantly increased in G1, G2 and G3 groups in response to control group (P < 0.01). Furthermore, antioxidant markers (SOD, CAT) were significantly elevated in G3 group, with a marked decrease in TAC as compared to control group (P < 0.05). FTIR analysis of plasma biomolecules revealed distinct functional group variations across the phases, indicating alterations in key metabolic components. LEfSe analysis identified microbial biomarkers specific to each group, with distinct taxa associated with each pregnancy stage. KEGG pathway analysis showed significant functional shifts, particularly in carbohydrate, amino acid, and energy metabolism. These findings suggest that microbial shifts, metabolic changes, and hormonal fluctuations are intricately linked and play a pivotal role in the reproductive transitions of Beetal goats. The study underpins the potential of microbiome analysis as a tool for improving reproductive health management in livestock.},
}
@article {pmid42050950,
year = {2026},
author = {Jia, Q and Jin, KJ and Liu, SQ and Zhang, YM and Meng, YL and Nie, H and Hu, S and Yang, F and Zhao, XC and Ye, J},
title = {[Research Progress on the Methodological System for Decomposition Stage Classification in Forensic Medicine].},
journal = {Fa yi xue za zhi},
volume = {42},
number = {1},
pages = {34-42},
doi = {10.12116/j.issn.1004-5619.2025.450906},
pmid = {42050950},
issn = {1004-5619},
mesh = {Humans ; *Postmortem Changes ; Algorithms ; *Forensic Medicine/methods ; Machine Learning ; *Forensic Pathology/methods ; Microbiota ; Metabolomics ; },
abstract = {Accurate classification of postmortem decomposition stages is a critical step in estimating the postmortem interval (PMI) and tracing the initial decomposition environment. Research on the decomposition staging methodological system is gradually shifting from empirical observation to the establishment of systems based on multidimensional quantitative indicators. This paper focuses on two key pathways, "macroscopic morphological evolution" and "microscopic molecular succession", and systema-tically reviews the evolutionary patterns and applicability of the decomposition staging system in three typical environmental media: surface exposure, burial, and aquatic systems. It also summarizes research progress in constructing stage classification models utilizing microbiome and metabolomic features. Furthermore, it highlights the integrated application of decomposition characteristic quantification techniques, multi-omics data integration, and machine learning algorithms in decomposition analysis systems. It analyzes the prospects and challenges of applying these approaches to build a standardized and practical decomposition staging system, aiming to provide theoretical support for establishing a decomposition staging system with high accuracy and strong adaptability to different environments.},
}
@article {pmid42051014,
year = {2026},
author = {Memon, FU and Ahmad, S and Mo, Q and Liu, S and Xie, X and Nabi, F and Huang, Z and Tettamanti, G and Tian, L},
title = {Probiotic-based fermentation of watermelon waste: Effects on bioconversion efficiency, microbial shifts, and expression profiles of black soldier fly larvae.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70280},
pmid = {42051014},
issn = {1744-7917},
support = {//Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology/ ; //Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; //Natural Science Foundation of Guangdong Province/ ; },
abstract = {Insects such as black soldier fly larvae (Hermetia illucens, BSFL) are efficient bioconverters whose growth and physiological performance are strongly influenced by diet composition, gut microbiota, and the molecular regulation. This study investigated how a probiotic-based fermentation strategy modulates larval physiology, microbiome dynamics, and gene expression when BSFL are reared on fermented watermelon waste. Watermelon waste was fermented for 14 d using a consortium of Bacillus subtilis, Enterococcus faecalis, and Aspergillus oryzae, resulting in a nutritionally enhanced substrate. BSFL fed on fermented diet exhibited significantly increased growth performance, biomass yield, and nutritional content of the insect biomass. Metagenomic analysis revealed marked enrichment of gut microbes belonging to genera known to include beneficial and commensal species (Enterococcus, Vagococcus, Carnobacterium, Tetragenococcus, and Blautia) along with a reduction in genera containing species previously associated with opportunistic or pathogenic traits (Mycobacterium, Pseudomonas, Morganella, Pedobacter, and Serpula), indicating diet-induced modulation of host-microbe interactions. Transcriptomic profiling highlighted an upregulation of key genes involved in growth and development (CK1, HIB, and PDK1), protein and fat biosynthesis (DVL, GSK3, and Lpin), and immune defense (PGRP-SA, Spz, Toll, and Cactus). Functional enrichment analysis further confirmed their participation in critical signaling pathways, including Hedgehog, Wnt, mTOR, Toll and Imd, and MAPK. Overall, this study demonstrates that probiotic fermentation improves nutrient utilization, regulates host-microbe interactions, and activates molecular pathways associated with growth and immune resilience in BSFL, providing new insights into the physiological and molecular basis of dietary adaptation in insects.},
}
@article {pmid42051097,
year = {2026},
author = {Kasthuri, S and Padmavathi, S and Jeevitha, M and Rajangam, J},
title = {Therapeutic Innovations in Parkinson's and Alzheimer's Disease: Molecular Mechanisms and Emerging Strategies.},
journal = {CNS &amp; neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273445849260403045802},
pmid = {42051097},
issn = {1996-3181},
abstract = {Parkinson's Disease (PD) and Alzheimer's Disease (AD) are still significant neurodegenerative disorders that have few disease-modifying therapies. In this review, recent advances are assessed based on the strength of evidence for major molecular targets and the therapeutic approaches that have been developed around those targets. Alpha-synuclein is a key target in PD, as indicated by genetic correlations, pathological distribution, and experimental evidence supporting its involvement in neuronal injury. Initial trials of alpha-synuclein antibodies and vaccines show evidence of target engagement, with yet-to-be-determined clinical outcomes. Interventions targeting gene-based dopamine synthesis restoration using AADC or multi-enzyme vectors have shown consistent biological effects, with clinical variability, and determining optimized delivery and patient selection is necessary. In AD, amyloid-beta- and tau-directed interventions have produced measurable changes in biomarkers, and some agents have demonstrated a slight deceleration of deterioration at an early stage of the disease. The experience with previous BACE inhibitors also demonstrates that excellent mechanistic rationale does not always translate into clinical efficacy in the case of interference with critical physiological processes by target modulation. Regenerative methods, such as stem-cell-based neuronal grafts in PD and neurotrophic factor gene delivery in AD, show potential to repair network function, but still pose issues regarding long-term stability, integration, and the complexity of the procedures. Lifestyle-driven interventions, control of the gut microbiome, and neuromodulation methods also remain of interest and can be included in the list of supportive strategies offered to complement molecular therapies. AI-based analytics and digital tools are helpful in the earlier detection, monitoring, and trial stratification. Taken together, existing evidence suggests that authenticated protein targets, neurotransmitter-targeted remedial strategies, and technology-enabled accuracy methods are the most promising approaches for the development of disease-modifying therapies in PD and AD.},
}
@article {pmid42051198,
year = {2026},
author = {Pan, Y and Xu, JF},
title = {Microbiome and its role in bronchiectasis.},
journal = {Therapeutic advances in respiratory disease},
volume = {20},
number = {},
pages = {17534666261444168},
doi = {10.1177/17534666261444168},
pmid = {42051198},
issn = {1753-4666},
mesh = {Humans ; *Bronchiectasis/microbiology/therapy/physiopathology/diagnosis ; *Dysbiosis/microbiology ; *Microbiota ; *Lung/microbiology/physiopathology ; *Gastrointestinal Microbiome ; Prognosis ; Severity of Illness Index ; Animals ; Mouth/microbiology ; Disease Progression ; },
abstract = {Bronchiectasis (BE) is a chronic respiratory disease characterized by damage to the bronchial wall structure and permanent dilation of the bronchi. The symptoms include a persistent cough, excessive production of purulent sputum, and recurrent hemoptysis. Dysbiosis of the microbiome plays a crucial role in the progression of BE. An increased abundance of pathogenic bacteria, along with viral and fungal infections, is closely associated with disease severity and clinical outcomes. Next-generation sequencing technology has significantly enhanced the sensitivity and resolution of the airway microbiome, providing powerful tools for a more detailed characterization of the microecology of BE. However, certain challenges still exist in clinical applications of this technology. In addition, extra-airway microbiomes, such as the gut and oral microbiome, may participate in airway inflammation and immune regulation through the gut-lung axis and oral-lung axis. In this review, we summarize the characteristics of microbiome dysbiosis in BE and highlight the potential value of related biomarkers in disease classification, severity assessment, and prognosis. We also provide an overview of recent treatment advancements. A deeper understanding of the microbiome's role in BE may facilitate early diagnosis and the optimization of individualized treatment strategies.},
}
@article {pmid42051260,
year = {2026},
author = {Liu, YN and Jia, SY and Zhou, LS and Tang, XJ and Ming, Z and Su, Y and Lin, JY},
title = {Paeoniflorin as a candidate disease-modifying therapy for diabetic peripheral neuropathy: mechanisms, exposure challenges, and translational priorities.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1751578},
pmid = {42051260},
issn = {1663-9812},
abstract = {Diabetic peripheral neuropathy (DPN) is the most common chronic complication of diabetes and remains largely treated with symptomatic analgesics (e.g., pregabalin, duloxetine) that do not reverse nerve fiber loss or demyelination, underscoring the need for disease-modifying therapies. Paeoniflorin (PF), a plant-derived monoterpene glycoside metabolite from Paeonia spp., shows multitarget activity relevant to DPN pathophysiology in preclinical studies, including activation of Nrf2/HO-1 antioxidant signaling, suppression of TLR4/NF-κB-driven neuroinflammation, support of neurotrophic/repair pathways (e.g., BDNF/TrkB) for axonal regeneration and remyelination, and modulation of microvascular pathways (e.g., HIF-1α/VEGF) linked to endoneurial perfusion. We critically appraise this evidence and highlight key translational constraints: very low oral bioavailability and poor intestinal permeability, extensive presystemic biotransformation (microbiome-mediated hydrolysis and CYP-mediated metabolism) with unresolved "active species" (parent PF versus metabolites), and limited DPN-relevant pharmacokinetics, particularly the lack of peripheral nerve/DRG exposure measurements aligned with pharmacodynamic endpoints. Although formulation and delivery approaches may improve exposure, PF-specific validation in DPN models is currently limited and should be distinguished from platform-level concepts. Finally, because DPN patients frequently experience polypharmacy, a clinically meaningful safety narrative requires systematic assessment of CYP/transporter-mediated drug-drug interaction potential. Priority next steps include integrated PK-PD studies with nerve/DRG distribution, metabolite-resolved exposure-activity linkage, PF-specific delivery validation using disease-modifying endpoints beyond pain behavior, and standardized DDI screening to support trial design.},
}
@article {pmid42051286,
year = {2026},
author = {Zeng, Y and Yang, L and Liu, H and Liao, H and Zhou, Y and Liu, J},
title = {Gut-Brain Connection: Deciphering Causal Pathways Between Gut Microbiota and Neuroimaging Profiles Through Mendelian Randomization.},
journal = {Food science &amp; nutrition},
volume = {14},
number = {},
pages = {e71820},
pmid = {42051286},
issn = {2048-7177},
abstract = {Recent research on the gut-brain axis (GBA) indicates that the gut microbiome can significantly influence brain structural and functional connectivity. However, the specific causal relationships between the gut microbiome and brain imaging-derived phenotypes (IDPs) of functional/structural connectivity, as well as how the gut microbiota influences mood and cognition, remain unclear. This study utilizes data from large-scale genome-wide association studies (GWAS) and employs a bidirectional Mendelian randomization (MR) approach to evaluate the causal effects between the gut microbiome and brain connectivity. We obtained data on 196 gut microbiome taxa from the MiBioGen consortium and acquired IDPs for seven resting-state networks (RSNs) from the UK Biobank (UKB). Subsequently, we conducted bidirectional MR analyses to explore their causal relationships. In the forward MR analysis, Ruminococcus torques, Eubacterium fissicatena, and Coprobacter exerted positive effects on the default mode network (DMN), whereas Terrisporobacter influenced the structural connectivity of the dorsal attention network (DAN). Conversely, Gammaproteobacteria inhibited the functional connectivity of the ventral attention network (VAN). Additionally, reverse MR analysis revealed that increased functional connectivity of the DAN was positively associated with the abundance of Alloprevotella. The enhanced functional connectivity of the VAN negatively impacted Alloprevotella, Catenibacterium, and Methanobacteria. Furthermore, the structural connectivity of the frontoparietal network (FPN) and somatomotor network (SMN) significantly reduced the abundance of Bacilli and Intestinibacter, respectively. This study utilized a bidirectional MR approach to establish causal evidence for the relationship between the gut microbiome and brain network connectivity, and support the bidirectional regulatory pattern of the GBA. These findings provide new insights into the potential roles of gut microbiota in emotional regulation, cognitive function, and neurodevelopment, and offer a theoretical basis for microbiome-based intervention strategies.},
}
@article {pmid42051335,
year = {2026},
author = {Li, B and Ren, Z and Li, H and Li, M and Zhong, H and Nie, Q and Chen, J and Wu, R and Zheng, JS and Deng, K and Cai, Y},
title = {Microbiota-metabolites interaction associated with glycemic improvement following a dietary herbal intervention in type 2 diabetes.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1793130},
pmid = {42051335},
issn = {2296-861X},
abstract = {BACKGROUND: Type 2 diabetes (T2D) is a global metabolic disorder characterized by chronic hyperglycemia and disruption of the gut microbiome. Nutritional and microbiota-targeted interventions have emerged as promising strategies for glycemic management, yet longitudinal clinical evidence integrating microbial and metabolic mechanisms remains limited. This study investigated microbiota-metabolites alterations during a standardized dietary herbal intervention (QingYun7, QY7) and explored their relationship with glycemic regulation across both animal study and clinical settings.<br><br>METHODS: The metabolic and microbial effects of QY7 were first evaluated in diabetic rats through measurements of blood glucose, and gut microbiota composition. Subsequently, a prospective cohort of 385 patients with T2D received QY7, with longitudinal monitoring of fasting, random, and 2-h postprandial glucose, gut microbiota, and serum metabolites across multiple time points. Fecal microbiota transplantation (FMT) from patients before and after intervention into antibiotic-treated mice was performed to evaluate the causal contribution of the gut microbiome to glycemic improvement. Mediation analyses were conducted to delineate potential pathways linking gut microbes, serum metabolites, and glucose outcomes.<br><br>RESULTS: In diabetic rats, QY7 administration significantly reduced blood glucose, and restored gut microbial composition. In the clinical cohort, the intervention was associated with rapid and sustained reductions in fasting, random, and postprandial glucose levels, accompanied by consistent remodeling of the gut microbiome and serum metabolite profile. FMT experiments demonstrated that microbiota derived from post-intervention patients conferred improved glycemic responses in recipient mice, supporting a causal role of gut microbiota in metabolic regulation. Serum metabolomic profiling revealed significant alterations, including enrichment of branched-chain amino acid related pathways. Mediation analyses identified key metabolites, phenyllactic acid, 3-methyl-2-oxobutanoic acid, and anandamide, as mediators linking specific bacterial taxa (Alistipes shahii and Limosilactobacillus mucosae) to fasting and postprandial glucose levels.<br><br>CONCLUSION: This study provides translational evidence that a dietary herbal intervention associated with glycemic improvement in T2D through microbiota-mediated metabolic reprogramming. Gut microbiome alterations induced by the intervention exerted causal effects on blood glucose regulation, with serum metabolites acting as potential key intermediaries. These findings highlight the mechanistic insight in nutrition-based microbiome modulation strategy in T2D.},
}
@article {pmid42051338,
year = {2026},
author = {Shahzad, M and Saidal, A and Ismail, M and Tariq, K and Melhem, AL and Iqbal, K and Khattak, MI and Ahmad, HA and Saeed, M and Ghani, M and Al Nabhani, Z and Andrews, SC},
title = {Dietary intake, nutritional status and healthcare characteristics of mothers and newborn infants in a prospective cohort study (CHAMP) from a malnutrition-endemic region of Pakistan.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1785862},
pmid = {42051338},
issn = {2296-861X},
abstract = {BACKGROUND: Dietary intake, nutritional status, healthcare access, and early-life exposures play a critical role in shaping infant growth and development. Recent evidence suggests that the impact is largely mediated by gut microbiome. The Child Health, Nutrition and Microbiome in Pakistan (the CHAMP study) is a longitudinal cohort study aiming to assess the bidirectional relationship between gut microbiome and infant growth and development in a cohort of children residing in malnutrition endemic areas of Pakistan.<br><br>OBJECTIVES: The current study report the baseline sociodemographic, dietary, healthcare, and nutritional characteristics of mother-infant dyads participating in the CHAMP study.<br><br>METHODS: Baseline data were collected from 70 mothers and 72 newborn infants recruited from rural communities in District Swat, Pakistan. Information on household socioeconomic status, maternal dietary intake, antenatal, delivery and postnatal care, infant feeding practices, morbidity, and anthropometric measurements was obtained using validated tools. Descriptive and sex-stratified analyses were conducted.<br><br>RESULTS: Households were socioeconomically disadvantaged, with low parental education, large family size, and mean household income substantially below the national minimum wage. Maternal utilization and quality of antenatal and postnatal care were suboptimal, including limited completion of recommended antenatal visits. Dietary quality was also poor, and none of the mothers met the recommended minimum dietary diversity for women. Among infants, morbidity was common, with nearly half experiencing diarrheal illness or respiratory infections. Exclusive breastfeeding reported only in 43.1% of infants. Anthropometric assessment revealed evidence of early growth faltering, with 35.4% of infants were low-length-for-age with higher prevalence among females.<br><br>CONCLUSION: These baseline findings highlight substantial socioeconomic vulnerability, poor maternal diet quality, gaps in maternal and infant healthcare, and early-life undernutrition in this rural Pakistani cohort. The study finding provides foundation for longitudinal analyses examining how these factors interact with gut microbiome development and child growth, informing and cost effective and culturally relevant intervention strategies.},
}
@article {pmid42051340,
year = {2026},
author = {Lee, S and Dubrof, S and Ahmed, I and Zhao, Q and Callaway, TR and Lourenco, J and Park, HJ},
title = {Maternal docosahexaenoic acid supplementation shapes offspring gut microbiota to modulate the gut-brain axis in a sow-piglet model.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1776896},
pmid = {42051340},
issn = {2296-861X},
abstract = {INTRODUCTION: Modification of maternal nutrition during the perinatal period represents an important window that may influence offspring neurodevelopment. Docosahexaenoic acid (DHA), a key omega-3 polyunsaturated fatty acid found in the brain, is reported to have beneficial effects on cognitive outcomes of infants. However, its specific effects on the shaping of gut microbiota to influence the piglet gut-brain axis remain to be elucidated.<br><br>METHODS: Using a sow-piglet model, this study aimed to investigate changes in offspring gut microbiota, intestinal barrier integrity, and their correlations with brain resting-state functional connectivity following maternal supplementation of DHA.<br><br>RESULTS: Piglets born to DHA-supplemented sows showed significant differences in microbial alpha- and beta-diversity compared to control piglets. Jejunal claudin-1 expression was upregulated in DHA piglets, and tight junction protein levels were positively correlated with specific microbial taxa. Furthermore, gut microbial diversity and specific taxa were significantly associated with functional brain networks.<br><br>DISCUSSION: Our findings demonstrate the role of maternal DHA supplementation in shaping offspring gut microbiome and gut integrity, potentially altering offspring brain function networks. Furthermore, these results underscore the importance of gut microbiota shaping through perinatal nutritional interventions as a means of programming the gut-brain axis in the early stages of life.},
}
@article {pmid42051348,
year = {2026},
author = {Liu, B and Zhang, Y and Deng, W and Zhou, YN and Cao, Y and Xiong, L and Shen, R and Lee, SM and Bian, J and Bian, Y},
title = {Dietary restriction as a potential neuroprotective intervention: a narrative review of its impact on neuroinflammation across neurodegenerative diseases and other neurological disorders.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1731416},
pmid = {42051348},
issn = {2296-861X},
abstract = {Dietary restriction (DR) involving chronic or intermittent calorie/nutrient reduction without malnutrition, delays neurological disease progression. Decades of research across in vitro models, animal studies, and clinical trials provide preclinical evidence for a potential role of DR in modulating multiple mechanisms underlying CNS disorders. Interactions between caloric intake, meal frequency, diet composition, and the gut microbiome regulate specific metabolic pathways governing cellular, tissue, and organ homeostasis as well as inflammatory processes during neurodegenerative and neurological diseases. In this review, we synthesize evidence on the role of DR in modulating neuroinflammation and related mechanisms within a selected set of neurodegenerative and neurological disorders, aims to provide a consolidated evidence base and perspective on the potential of DR as an adjunctive strategy for the future therapeutic investigations.},
}
@article {pmid42051417,
year = {2026},
author = {Stokes, CS and Türk, T and Lammert, F and Appenrodt, B},
title = {Comparison of Mucosal and Faecal Microbiomes in Patients With Cirrhosis.},
journal = {Gastroenterology research and practice},
volume = {2026},
number = {},
pages = {6847983},
pmid = {42051417},
issn = {1687-6121},
abstract = {OBJECTIVE: The colonic sigmoid mucosal microbiome is reportedly different from the faecal microbiome in patients with cirrhosis. This exploratory study is aimed at comparing the luminal and mucosal microbiome in patients with cirrhosis, with a specific focus on the proximal intestine.<br><br>METHODS: Mucosal and faecal samples were obtained from 12 patients with cirrhosis. The microbiome was quantified with V4 16S rRNA gene sequencing. Relative abundance, alpha and beta diversity were calculated, compared between the mucosal and faecal samples and correlated with stage of cirrhosis.<br><br>RESULTS: Faecal samples displayed lower microbial diversity than mucosal samples (Shannon diversity, p = 0.025) and the microbiome profiles differed significantly: Operational taxonomic units primarily of the phyla Firmicutes and Actinobacteria were more abundant in faecal samples, whereas biopsy samples contained units spanning all six phyla. Microbial composition of faecal samples were more similar to faecal samples from other patients rather than to the individual's corresponding biopsy sample (principal coordinate analysis, p = 0.004). At the family level, Lachnospiraceae, Erysipelotrichaceae and Enterobacteriaceae were significantly more abundant in faecal samples, whereas biopsy samples contained more Streptococcaceae (p = 0.011) and Prevotellaceae (p = 0.031). Faecal samples from patients in Child-Pugh Stage C contained less Bacteroidetes but significantly more Streptococcaceae than Stage B samples (p = 0.04); however, biopsy samples did not differ significantly.<br><br>CONCLUSIONS: This exploratory study in a small sample of patients with cirrhosis observed significant differences in the microbial signature of faecal versus biopsy samples from the proximal intestine. Future studies are needed to further investigate the relationship between different gastrointestinal microbial sites and cirrhosis.},
}
@article {pmid42051455,
year = {2026},
author = {Du, X and Su, H and Huang, Y and Liu, J and Li, Q and Yang, X and Tao, X and Li, R},
title = {Gut microbiome dysbiosis in PCOS: from pathogenesis to microbiome-targeted therapies.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1747766},
pmid = {42051455},
issn = {1664-2392},
mesh = {Humans ; *Polycystic Ovary Syndrome/microbiology/therapy/etiology/pathology ; *Dysbiosis/microbiology/therapy/complications ; *Gastrointestinal Microbiome/physiology ; Female ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; },
abstract = {(PCOS), one of the most common endocrine and metabolic disorders in women of reproductive age, has a complex pathogenesis that continues to be unraveled by ongoing research. The condition is defined by three key features: hyperandrogenemia, ovulatory dysfunction, and insulin resistance. Recent studies have highlighted the gut microbiome and its metabolites as crucial regulators in PCOS development. Evidence suggests that gut dysbiosis and intestinal barrier dysfunction play a pivotal role in the onset and progression of PCOS. This review comprehensively examines the central role of gut microbiota in PCOS pathogenesis, including shifts in microbial communities such as bacteria, fungi, and viruses, and their impact on critical metabolites like short-chain fatty acids, bile acids, and tryptophan metabolites, which modulate host metabolism and reproductive function. Furthermore, based on mechanistic insights, the review explores targeted gut microbiota interventions, systematically evaluating clinical evidence for dietary modifications, probiotic/prebiotic supplementation and fecal microbiota transplantation. These approaches provide novel perspectives for precision medicine in PCOS treatment. The findings not only deepen our understanding of PCOS pathogenesis but also establish a strong theoretical foundation for innovative microbiome-based therapeutics.},
}
@article {pmid42051461,
year = {2026},
author = {Wang, Q and Zhou, Z and Pang, L and Du, Y and Li, X and Dai, L},
title = {Gut microbiota in chronic kidney disease-mineral and bone disorder: shared mechanisms, disease-specific signatures, and therapeutic prospects.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1802845},
pmid = {42051461},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; *Chronic Kidney Disease-Mineral and Bone Disorder/microbiology/therapy/metabolism/pathology ; Fibroblast Growth Factor-23 ; Animals ; *Renal Insufficiency, Chronic/microbiology ; },
abstract = {Chronic Kidney Disease-Mineral and Bone Disorder (CKD-MBD) is a systemic syndrome characterized by mineral metabolism disorders and impaired bone homeostasis. Recent studies have indicated that gut microbiota dysbiosis is a key regulatory factor driving the development and progression of this disease. This review systematically summarizes the mechanisms by which gut microbiota acts in CKD-MBD through the "gut-kidney-bone axis": dysbiosis drives chronic low-grade inflammation by impairing the intestinal barrier and promoting endotoxin translocation; alterations in its metabolites (e.g., reduced short-chain fatty acids, accumulation of uremic toxins) and dysregulation of endocrine pathways (e.g., FGF23-Klotho axis, PTH) collectively exacerbate renal injury and abnormal bone metabolism. Additionally, in diseases such as CKD, rheumatoid arthritis (RA), osteoarthritis (OA), and osteoporosis (OP), gut microbiota exhibits the coexistence of "shared dysbiosis" and "disease-specific characteristics," which collectively contribute to chronic inflammation and metabolic disorders. Interventional strategies targeting gut microbiota have demonstrated the potential to regulate this axis and improve bone health, marking that the management of metabolic bone diseases and chronic kidney disease is entering the "era of microbiome medicine." This review aims to provide new insights into understanding the comorbidity mechanisms of the aforementioned diseases and lay a theoretical foundation for the development of microbiota-targeted therapeutic strategies.},
}
@article {pmid42051499,
year = {2026},
author = {Lee, AR and Choi, H and Lee, SY and Kang, HY and Moon, YM and Nam, SW and Lee, BI and Cho, ML},
title = {Overexpression of mitochondrial STAT3 protein improves colonic inflammation and fibrosis in inflammatory bowel disease by enhancing mitochondrial function.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1728341},
pmid = {42051499},
issn = {1664-3224},
mesh = {*STAT3 Transcription Factor/genetics/metabolism ; Animals ; *Inflammatory Bowel Diseases/metabolism/pathology/genetics ; Mice ; *Mitochondria/metabolism/genetics ; Fibrosis ; *Colon/pathology/metabolism/immunology ; Disease Models, Animal ; *Colitis/metabolism/pathology/genetics ; Gastrointestinal Microbiome ; Male ; Mice, Inbred C57BL ; Cytokines/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Inflammation ; },
abstract = {INTRODUCTION: The STAT3 protein is involved in mitochondrial functions such as the respiratory electron transport chain, regulation of cellular metabolism, and scavenging of reactive oxygen species. Inflammatory bowel disease (IBD) is associated with damaged intestinal cells and mitochondrial dysfunction due to the inflammatory environment of the intestine. Here, we studied the potential use of the Stat3 gene to induce STAT3 expression in mitochondria to help treat IBD.<br><br>METHODS: We transferred the Stat3 gene and examined its effects on the expression of proinflammatory cytokines and fibrosis markers, and mitochondrial function, in intestinal tissues via immunohistochemistry. The microbiomes of mice were also analyzed.<br><br>RESULTS: The gene increased the expression of mitochondrial STAT3 (mtSTAT3), which reduced the levels of iNOS and fibrosis factors (aSMA, COL1A1) as well as proinflammatory cytokines (IL-17, IL-6) in the colon. It also enhanced mitochondrial function in the colon, and in immune cells, and led to higher levels of the beneficial bacteria Lactobacillus reuteri and Akkermansia muciniphila in the intestine. Taken together, these changes helped alleviate colitis and protected against intestinal damage.<br><br>DISCUSSION: Stat3 gene transfer targeting mtSTAT3 expression ameliorates colitis, enhances mitochondrial function in the colon, and reduces inflammation via inhibition of the inflammatory response and necroptosis, offering a potential treatment for IBD.},
}
@article {pmid42051509,
year = {2026},
author = {Ali, S and Kuang, R and Abdelkarim, OF and Nawaz, AH and Rahim, MF and Wang, D and Asif, A and Zhu, M},
title = {Integrative transcriptome and microbiome analysis reveals ferroptosis-driven duodenal damage caused by Ochratoxin A in mice.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1804647},
pmid = {42051509},
issn = {1664-3224},
mesh = {Animals ; *Ferroptosis/drug effects/genetics ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Duodenum/drug effects/pathology/metabolism/microbiology ; *Ochratoxins/toxicity ; *Transcriptome ; Male ; Gene Expression Profiling ; Intestinal Mucosa/metabolism/drug effects/pathology ; Mice, Inbred C57BL ; },
abstract = {Ochratoxin A (OTA), a prevalent mycotoxin produced by fungal contaminants, poses a significant threat to intestinal health. That can induce ferroptosis, a regulated iron-dependent cell death by disrupting duodenal epithelium and gut microbiota homeostasis. We exposed mice to OTA (2 mg/kg body weight/day) for seven days and assessed duodenal damage using histological analysis, transmission electron microscopy (TEM), transcriptomics, quantitative real-time PCR (qRT-PCR), Western blotting, immunofluorescence, biochemical assays, and 16S rRNA sequencing of cecal contents. OTA markedly reduced body weight from day 2 onwards and significantly elevated serum lipopolysaccharides (LPS) (P<0.05), duodenal malondialdehyde (MDA), and iron levels compared to the control group. OTA significantly diminished duodenal antioxidant defenses, including glutathione, SOD, CAT, and total antioxidant capacity (T-AOC), and caused villus atrophy, crypt hyperplasia, and mitochondrial shrinkage with cristae loss, which are the hallmarks of ferroptosis. Transcriptomic analysis revealed 769 differentially expressed genes (DEGs), including 134 upregulated and 635 downregulated genes, with 26 overlapping ferroptosis-regulating genes (FerroDb). Among these, four key genes SLC7A11, GSTM1, CP, and SLC40A1 were downregulated, which are major regulators of redox and iron homeostasis, and were enriched in ROS/lipid metabolism pathways. Microbiome profiling showed augmented diversification, altered Bacteroidota abundance and enrichment of pathogenic microbiota (e.g., Oscillibacter and Barnesiella), linking ferroptosis with dysbiosis. These findings demonstrate that OTA induces duodenal ferroptosis through dual microbiota-duodenum axis, where microbial dysbiosis amplifies redox imbalance and iron homeostasis. Ferroptotic inhibitors may preserve the gut health in animals and humans exposed to fungal contaminants.},
}
@article {pmid42051515,
year = {2026},
author = {Zheng, QX and Wang, HW and Ge, L and Lin, Y and Gao, X and Zhu, Y and Huang, L and Jiang, XM},
title = {Influences of dietary intake on Chinese women with gestational diabetes mellitus by inhibiting gut microbiome on plasma metabolome.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1745459},
pmid = {42051515},
issn = {1664-3224},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Diabetes, Gestational/microbiology/blood/metabolism ; Adult ; *Metabolome ; China ; *Diet ; Prospective Studies ; Dysbiosis ; East Asian People ; },
abstract = {BACKGROUND: Lines of evidence indicate that microbiome and its derived metabolites are implicated in gestational diabetes mellitus (GDM) etiology through the regulation of insulin resistance and inflammatory responses, and pregnant women with GDM have significant gut dysbiosis and metabolic disturbance. Although the gut microbiota and gut metabolites in pregnant women with GDM are extensively studied, the trilateral relationship between diet, gut microbiota, and plasma metabolites in patients with GDM remains unclear. Therefore, the aim of this study was to systematically analyze the associations between diet, gut microbiome, and plasma metabolome among Chinese pregnant healthy controls and patients with GDM.<br><br>METHODS: The study is a prospective cohort study conducted at two maternal and child hospitals in China from 8 October 2021 to 31 December 2022. We compared the daily dietary intake, microbial compositions, and plasma metabolic signatures of 173 patients with GDM and 47 pregnant healthy individuals. A food frequency questionnaire was used to investigate the dietary intake of pregnant healthy controls and patients with GDM. 16S rRNA sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to sequence the gut microbiome and plasma metabolome, respectively.<br><br>RESULTS: We found that women with GDM had higher intakes of whole grains, red meat, poultry, and eggs compared with normal pregnant women. Women with GDM had lower amounts of Klebsiella, Lactiplantibacillus, and Sphingomonas, and higher amounts of Desulfovibrio; they also had higher amounts of D-mannose, D-ribose, homo-L-arginine, and norophthalmic acid in plasma. Moreover, whole grains negatively influenced Sphingomonas, Klebsiella, and Lactiplantibacillus; red meat had a negative influence on Sphingomonas; and eggs had a positive impact on Desulfovibrio; these gut microbiota affected D-mannose, D-ribose, homo-L-arginine, and norophthalmic acid.<br><br>CONCLUSION: Overall, this study provided information about the influences of dietary intake on Chinese women with GDM by inhibiting gut microbiome on plasma metabolome, and their interactions play vital roles in GDM pathogenesis. These findings may be useful for patients with GDM in terms of dietary counseling and glucose control during pregnancy.},
}
@article {pmid42051550,
year = {2026},
author = {Chakraborty, DK and Roy, T and Ngo, ST and Al-Chalabi, A and Al Khleifat, A},
title = {Gut microbiota and ALS: cause, consequence or correlation? - a systematic review.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1774417},
pmid = {42051550},
issn = {1662-4548},
abstract = {BACKGROUND: Gut microbiome disturbances have been proposed as contributors to amyotrophic lateral sclerosis (ALS), a multisystem neurodegenerative disorder characterised by motor neuron loss, extra-motor symptoms, and rapid progression. Mechanistic links between dysbiosis, epithelial and blood-brain barrier dysfunction, metabolic imbalance, and immune activation have been suggested, but causality remains unresolved. We conducted a systematic review to evaluate the evidence supporting microbiome involvement in ALS pathogenesis.<br><br>METHODS: We searched PubMed, Medline, Embase, Scopus, Semantic Scholar, and Google Scholar (Nov 23, 2025) for human and ALS-relevant animal studies assessing bacterial microbiota, gut or blood-brain barrier integrity, microbial metabolites, or immune pathways. No language or date restrictions were applied. Studies were screened according to predefined criteria, and quality was assessed using QUADAS-2. Owing to the heterogeneity of study designs and sequencing approaches, findings were synthesised narratively.<br><br>FINDINGS: 61 of 2,397 studies met inclusion criteria. Across human cohorts, ALS was consistently associated with reduced microbial diversity, shifts in key taxa, and disruption of microbial pathways regulating short-chain fatty acids, nicotinamide metabolism, and inflammatory signalling. Several mechanistic animal studies demonstrated that microbiota manipulation, through antibiotics, faecal microbiota transfer, or supplementation with protective taxa, modulated motor function, microglial activation, gut permeability, and survival, indicating that dysbiosis can influence disease trajectories. Conversely, longitudinal human data showed that dysbiosis often emerged alongside worsening physical function, gastrointestinal dysmotility, weight loss, and changes in dietary intake, suggesting secondary effects of disease progression. Integrative multi-omics studies linked microbial alterations with systemic cytokine profiles, metabolic stress pathways, and CNS immune phenotypes, reinforcing a bidirectional gut-brain axis. However, the predominance of cross-sectional designs and small sample sizes substantially limits causal inference.<br><br>INTERPRETATION: Current evidence supports a model in which gut dysbiosis interacts with ALS via barrier failure, metabolic disruption, and immune dysregulation, but does not establish dysbiosis as a primary cause of disease. Preclinical findings highlight microbiome-derived mechanisms with disease-modifying potential, yet human data largely indicate association rather than initiation. Clarifying temporal relationships will require longitudinal, multi-modal studies, integration with pre-symptomatic cohorts, and controlled interventional trials. Microbiome-targeted therapies remain a promising but unproven avenue for ALS.},
}
@article {pmid42051692,
year = {2026},
author = {Wang, LM and Chen, C and Danzheng, JC and Zhao, J},
title = {Gut microbiome in sepsis: from dysbiotic biomarker to precision and palliative decision-making.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1811304},
pmid = {42051692},
issn = {2296-858X},
abstract = {Sepsis is a major cause of mortality in critically ill patients, necessitating improved early detection, risk stratification, and individualized clinical decision-making. The gut microbiome actively regulates host immunity, metabolism, and barrier function, engaging in bidirectional interactions with sepsis progression. Evidence suggests that gut dysbiosis not only accompanies sepsis but may also accelerate it. Characteristic shifts, including reduced microbial diversity, expansion of opportunistic pathogens, and decreased short-chain fatty acid production, could offer early prognostic signals prior to clinical decline. Advances in multi-omics and computational analytics are enabling the translation of microbial signatures into actionable clinical insights, supporting phenotype-specific stratification in sepsis. Emerging microbiome-targeted interventions such as next-generation probiotics, synbiotics, metabolite supplementation, and fecal microbiota transplantation show potential for modulating host responses in a stage-specific manner. Within a precision medicine framework, microbiome-derived biomarkers may refine both critical care management and palliative decision-making. In advanced or refractory sepsis, these insights could help tailor treatment intensity, prioritize symptom control, and avoid non-beneficial therapeutic escalation. Realizing this potential will require prospective validation and standardized approaches to integrate microbiome data into personalized, goal-concordant sepsis care.},
}
@article {pmid42051745,
year = {2026},
author = {Urrutia, &#xcd;M and Plaza, N and Moraga, F and Griffiths-Sanhueza, C and Pérez-Reytor, D and Karahanian, E and Ramírez-Araya, S and Kinkead, A and Gómez, MP and Garcia, K},
title = {High intellectual ability and the gut-brain-sex steroids axis: a perspective on cognitive and emotional diversity.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1791778},
pmid = {42051745},
issn = {1664-042X},
abstract = {The gut-brain axis is a bidirectional communication network integrating neural, endocrine, immune, and metabolic signals that regulate neurodevelopment, cognition, and emotion. It contributes to neurotransmitter production, inflammatory regulation, and the microbial metabolism of sex steroids, processes that have been shown to modulate synaptic plasticity and emotional behavior in experimental and clinical contexts, although their specific relevance to high intellectual ability remains unknown. In this perspective, we propose that high intellectual ability could be explored as a heterogeneous construct, within which some individuals identified as having HIA may exhibit responses potentially associated with differential sensitivity to gut-brain-sex hormone interactions. We discuss that microbial modulation of steroid bioavailability and neuroactive metabolites may represent one hypothetical pathway through which variations in steroid bioavailability and neuroactive metabolites could intersect with cognitive performance and emotional intensity, traits frequently described in some individuals with HIA. Integrating evidence from neuroendocrinology, microbiome science, and cognitive neuroscience, we outline a conceptual framework linking microbial, hormonal, and neural processes. This model aims to stimulate empirical research examining how physiological variation across the gut-brain-sex hormone axis may underlie cognitive and emotional diversity in gifted subpopulations. Importantly, this framework is conceptual and extrapolates from converging evidence in microbiome science and neuroendocrinology, as direct empirical studies in high intellectual ability are currently lacking.},
}
@article {pmid42051940,
year = {2026},
author = {Sandra, F and Scania, AE and Dewi, NM and Ranggaini, D and Halim, J and Pakpahan, A and Lee, KH},
title = {Coevolution of Human Diet and Gut Microbiome: Implications for Nutrigenomics and Cross-Population Health.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {5597426},
pmid = {42051940},
issn = {1687-918X},
abstract = {The coevolution of the human diet and gut microbiome has played a pivotal role in shaping metabolic, immune, and epigenetic functions across human history. Dietary transitions from high-fiber ancestral patterns to modern ultraprocessed diets have markedly influenced microbial diversity and functionality, contributing to the emergence of chronic diseases such as obesity, Type 2 diabetes, and inflammatory conditions. Recognizing the significance of gut microbial patterns in humans, this review explores the coevolution of diet and gut microbiota, especially on how gut microbiota influences human gene regulation, and the implications of these interactions for personalized nutrition and global health strategies. Comparative insights across populations in different periods reveal that geography, dietary practices, and host genetics interact to shape distinct microbiome configurations and disease susceptibility. Therefore, implementing a nutrigenomics and nutrigenetics approach might provide a molecular framework to understand these interactions and to develop personalized nutrition strategies. Though several clinical implementations utilizing genomic data have been embedded in several countries, global implementation remains challenging due to population-specific genetic variability, cultural dietary preferences, cost limitations, and ethical considerations. Integrating microbiome and genetic data into clinical practice and public health policy offers a promising path to mitigate diet-related health disparities that is tailored to individual and population-level needs.},
}
@article {pmid42052124,
year = {2026},
author = {Liao, X and Liu, J and Pang, Z and Li, X and Jiang, D and Wang, J and Sun, Y and Pang, B},
title = {Pharmacodynamic Material Basis of the Components of Four Epimedium Species with Activities Against Hepatocellular Carcinoma Based on Biological Target Networks and Multi-Omics Analysis.},
journal = {Journal of hepatocellular carcinoma},
volume = {13},
number = {},
pages = {578719},
pmid = {42052124},
issn = {2253-5969},
abstract = {AIM: Epimedium plants are used in traditional Chinese medicine due to their medicinal properties and can be clinically used for the treatment of liver cancer.Using network pharmacology and HPLC, we identified a key anti-HCC complex, CMPLX (containing icariin and kaempferol), from four Epimedium species. In vitro and in vivo studies demonstrated that CMPLX suppresses HCC proliferation by downregulating p-Akt, p-PI3K, and Bcl-2 expression. Untargeted metabolomics and gut microbiome analysis revealed significant negative correlations between serum levels of lignin/kaempferol derivatives and Escherichia coli abundance. These findings highlight CMPLX as a promising candidate for HCC drug development.<br><br>PURPOSE: Investigate the pharmacodynamic material basis of the components of four Epimedium species with activities against hepatocellular carcinoma based on biological target networks and multi-omics analysis.<br><br>MATERIALS AND METHODS: We first screened four Epimedium extracts for anti-HCC activity using HepG2 cells. Shared bioactive compounds were identified through network pharmacology and HPLC, defining core target AKT1 and key complex CMPLX (icariin and kaempferol). Molecular docking/dynamics simulations confirmed CMPLX-AKT1 binding. In vitro assays (CCK-8, wound healing, colony formation, Annexin V/PI, Western blot) demonstrated CMPLX inhibits proliferation, migration, and induces apoptosis via PI3K/AKT/Bcl-2 pathway. In vivo validation in H22 tumor-bearing mice showed tumor suppression, corroborated by histology, serum metabolomics and gut microbiota analysis.<br><br>RESULTS: CMPLX suppressed hepatocellular carcinoma proliferation in vitro and in vivo. Mechanistically, it downregulated p-Akt, p-PI3K, and Bcl-2 expression, inhibiting growth and promoting apoptosis in HepG2 cells. Integrated multi-omics revealed CMPLX treatment elevated flavonoid/kaempferol derivatives while reducing Enterobacteriaceae_A/Escherichia abundance, with Marinifilaceae dominating the gut microbiota. Crucially, lignan/kaempferol derivatives showed significant negative correlation with Escherichia levels.<br><br>CONCLUSION: CMPLX demonstrated synergistic anti-HCC efficacy in vitro and in vivo. Multi-omics analysis revealed its modulation of tumor-related pathways and gut microbiota composition, collectively contributing to tumor suppression.},
}
@article {pmid42052326,
year = {2026},
author = {Shabibi, A and Basati, G and Zarif, BR and Davari, K and Rangin, A},
title = {Laboratory Analysis of Fecal Lactobacillus Strains and pH in Tobacco Smokers: A Comparative Study From a Developing Country.},
journal = {Health science reports},
volume = {9},
number = {5},
pages = {e72348},
pmid = {42052326},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Tobacco smoking is a major cause of preventable mortality globally, disproportionately impacting developing countries. While its systemic health effects are well-known, the influence of tobacco on gut microbiota-especially beneficial Lactobacillus species-remains poorly explored in resource-limited settings.<br><br>METHODS: This study examined fecal Lactobacillus composition and stool pH among 200 participants from western Iran, including cigarette smokers, hookah users, combined users, and non-smoking controls. Standard microbiological methods were employed: stool pH measurement, anaerobic culture on MRS agar, Gram staining, biochemical tests, phenotypic assays (acid/bile resistance, antibiotic susceptibility), and PCR sequencing of the 16S rRNA gene for species identification.<br><br>RESULTS: Results showed significantly elevated stool pH in tobacco users, particularly hookah smokers (p&#x2009;=&#x2009;0.001). Lactobacillus prevalence was markedly lower in all smoker groups compared to controls (p&#x2009;<&#x2009;0.001). Dominant species identified were L. casei, L. plantarum, and L. acidophilus, with control strains exhibiting greater acid and bile tolerance (p&#x2009;<&#x2009;0.05). Antibiotic resistance was common, notably to vancomycin (75%) and ampicillin (67%).<br><br>CONCLUSION: These findings indicate tobacco-associated gut dysbiosis characterized by increased stool pH and diminished Lactobacillus viability, potentially impairing gut barrier integrity. The study highlights the importance of clinical microbiological evaluation of smoking-related microbiota alterations, especially in populations with limited probiotic access.},
}
@article {pmid42052329,
year = {2026},
author = {Brar, GS and Sharma, A and Siddiqui, AJ and Sharma, L},
title = {Emerging Microbiome-Based Therapies for Skin Infections: From Probiotics and Prebiotics to Synthetic Microbiome Engineering.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {592685},
pmid = {42052329},
issn = {1178-6973},
abstract = {Skin infections are a major global health burden, made worse by the quick development of antimicrobial resistance (AMR) and the poor effectiveness of traditional antibiotic treatments for chronic and recurring diseases. The importance of the skin microbiome in preserving cutaneous homeostasis, pathogen exclusion, and immunological modulation is becoming more and more clear. Many infectious and inflammatory skin conditions have been linked to dysbiosis of the skin microbiota, which has led to a strategic reorientation from pathogen control to microbiome regulation. Probiotics, prebiotics, postbiotics, bacteriophages, microbiome transplants, and new methods in synthetic microbiome engineering are just a few of the recent advances in microbiome-based therapies in skin diseases that are covered in detail in this review. We go into the clinical effectiveness, safety issues, regulatory obstacles, and molecular underpinnings of various therapies. The promise of microbiome-based treatments to lower AMR, improve long-term effectiveness, and restore microbial balance is highlighted by comparison with traditional antibiotics. Lastly, future possibilities are examined that highlight the translational potential of microbiome-centred techniques in dermatology treatments, such as multi-omics integration, artificial intelligence-guided customisation, or synthetic microbial consortia.},
}
@article {pmid42052390,
year = {2026},
author = {Guo, Z and Feng, Y and Ren, Z and Wang, W and Huang, R and Zhao, J},
title = {Neurotransmitter-mediated gut-brain axis: a bibliometric analysis of research trends and knowledge structure.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771169},
pmid = {42052390},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut-brain axis constitutes a bidirectional network linking the gastrointestinal tract and central nervous system through neural, endocrine, metabolic, and immune pathways. Neurotransmitters play a central role in mediating this crosstalk, serving as intermediates through which the gut microbiota influences brain function. Although important mechanistic advances have been made, research on the neurotransmitter-mediated gut-brain axis remains fragmented across disciplines. This study aimed to provide a comprehensive bibliometric overview of this field.<br><br>METHODS: We conducted a bibliometric analysis of 788 publications retrieved from Web of Science, Scopus, and PubMed between 2005 and 2025. Using VOSviewer, CiteSpace, and Pajek, we analyzed publication trends, geographic distribution, institutional and author contributions, journal co-citations, and keyword evolution to characterize the knowledge structure and emerging themes of the field.<br><br>RESULTS: The results revealed three developmental phases: an exploratory phase (2005-2016) with limited output, a developmental phase (2017-2019) with moderate growth, and a rapid expansion phase (2020-2025) marked by exponential increases in publications driven by advances in microbiome and neurotransmitter research. China led in publication volume, while the United States and Ireland served as major hubs of collaboration. University College Cork showed the highest citation impact, with 10,935 citations from 28 publications (average citations per document = 390.54). John F. Cryan, Timothy G. Dinan, and Gerard Clarke were among the leading contributors, with Cryan ranking first in both publication output and citation count. Keyword and thematic analyses identified gut microbiota, serotonin, short-chain fatty acids, depression, and inflammatory bowel disease as core topics, reflecting a shift from mechanistic studies to disease-specific and neurotransmitter-targeted research. Highly cited studies focused on microbial regulation of neurotransmitters, neuroimmune signaling, and their implications for neurodevelopmental and neurodegenerative disorders.<br><br>DISCUSSION: This study provides the first comprehensive bibliometric overview of neurotransmitter-mediated gut-brain axis research, offering a macroscopic perspective on its evolution, core knowledge base, and emerging frontiers. Future research should integrate multidisciplinary approaches, apply omics technologies, and develop precision interventions targeting neurotransmitter pathways while considering individual microbial profiles, in order to translate mechanistic insights into therapeutic strategies for neuropsychiatric disorders.},
}
@article {pmid42052395,
year = {2026},
author = {Banerjee, A and Gupta, N and Koley, A and Kumar, MS and Saha, S and Balachandran, S},
title = {Microbial contamination and microbiome composition of fresh edible mushrooms: a critical review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1757755},
pmid = {42052395},
issn = {1664-302X},
abstract = {Fresh edible mushrooms have gained popularity as valuable dietary components, with global consumption steadily increasing due to their high nutritional and functional benefits. However, their constitutional characteristics make them especially vulnerable to microbial spoilage, potentially harming the fruiting bodies during cultivation and creating major challenges in harvesting, handling, and storage after harvest. This review highlights the types, sources, and impacts of microbial contamination in fresh edible mushrooms, with a focus on spoilage organisms. It explores the emerging field of mushroom microbiome research, highlighting the composition, diversity, and functional roles of microbial communities associated with 4 edible mushroom species (Agaricus sp., Pleurotus sp., Lentinula sp., and Flammulina sp). Studies employing high-throughput sequencing technologies to explore the microbial associations of edible mushrooms are discussed, providing deeper insights into these complex microbial ecosystems and their impacts on mushroom quality, shelf life, and safety. Bibliometric studies using VOSviewer over a 10-year period have uncovered global research trends, emerging focus areas, and identified gaps in the field. This review also discusses post-harvest control strategies and microbiome-targeted interventions to enhance microbial safety and extend shelf life. Edible mushrooms also contribute to the circular bioeconomy by converting agricultural residues into nutritious food. However, microbial contamination can compromise product quality and safety within this sustainable production system. Persistent knowledge gaps in understanding microbial dynamics and mushroom-microbiota interactions must be addressed to develop innovative, sustainable approaches to mushroom preservation and food safety management.},
}
@article {pmid42052398,
year = {2026},
author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC and Arsenault, RJ},
title = {Capturing the fungal diversity in manure, lagoons, troughs, and flies at a commercial dairy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1794875},
pmid = {42052398},
issn = {1664-302X},
abstract = {The microbiomes within dairy facilities that could serve as reservoirs for beneficial and pathogenic fungi have not been extensively explored. Though fungi can cause food safety and animal health issues, they also represent species contributing to bovine digestion and environmental nutrient cycling. This study investigated whether fungal communities from specific elements at a working dairy differed between cross-vent or flow-through, free stall barn management systems and defined the possible pathogen locations. Shotgun metagenomics was carried out on manure, lagoons, troughs, and fly samples from the barns. The diversity of species was not significantly affected by management systems, except between lagoon communities. Flies carried the highest number of unique fungal species and the most abundant potential mammalian pathogens, but there was a lack of overlapping pathogen profiles between flies and the other dairy components. Thus, it remains unclear whether the species are being efficiently exchanged between these different components of the dairy environment, mechanically or biologically. Manure harbored the most opportunistic pathogenic species, lagoons harbored the most plant pathogens and beneficial species, and troughs had the most innocuous or understudied species. The results allow dairy managers to consider advantageous management systems and focus on fungal mitigation efforts at appropriate locations within the dairy.},
}
@article {pmid42052400,
year = {2026},
author = {Xie, J and Zhang, J and Zhang, L and Chen, X},
title = {Exercise prescription for mood and cognition: targeting the microbiota-gut-brain axis through short-chain fatty acids.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1740680},
pmid = {42052400},
issn = {1664-302X},
abstract = {Scientific study has extensively corroborated the advantageous impacts of exercise on mood, cognitive function, and stress resilience. Nonetheless, the fundamental biological mechanisms underpinning these effects have yet to be thoroughly integrated. This review advocates for and substantiates an integrated model focused on the "Exercise-Gut Microbiome-Short-Chain Fatty Acids (SCFAs)-Brain Function" axis. Consistent physical exercise alters the gut microbiota, enhancing Short-Chain Fatty Acid (SCFA)-producing populations, which is associated with markedly elevated bioavailability of key metabolites (acetate, propionate, and butyrate). Rather than detailing exhaustive molecular pathways here, we emphasize that these SCFAs facilitate gut-brain communication through multiple synergistic routes, including receptor-mediated neuroendocrine signaling, epigenetic modulation of neuroplasticity, and the attenuation of systemic neuroinflammation. Current human observational and interventional data strongly support an associative link between exercise-induced SCFA fluctuations and improved mental health outcomes. Crucially, we propose the novel "Exercise × Fiber Synergy" hypothesis: exercise primes the intestinal ecological niche for efficient substrate-utilizing bacteria, while adequate fermentable dietary fiber provides the necessary raw materials. Synergistically, this combination optimizes SCFA production to maximize cognitive and emotional benefits. To transition this framework into clinical practice, future research must prioritize 2 × 2 factorial designs (Exercise × Fiber) with dynamic kinetic measurements, paving the way for microbial phenotype-oriented precision exercise and personalized nutritional interventions to enhance public mental health.},
}
@article {pmid42052590,
year = {2026},
author = {Alebouyeh, M and Aminzadeh, M and Pourmand, MR and Bahiraee, M and Mirbagheri, SZ and Bakhtiari, R},
title = {Culturable bacteria in the gastric tissue and diversity of antimicrobial resistance in adults with gastritis.},
journal = {Caspian journal of internal medicine},
volume = {17},
number = {1},
pages = {143-151},
pmid = {42052590},
issn = {2008-6164},
abstract = {BACKGROUND: Despite growing knowledge in microbiome studies data about the diversity of cultivable bacteria and their drug resistance patterns in patients with gastritis are scant.<br><br>METHODS: Two gastric biopsies of 171 symptomatic patients were collected and examined by histological and microbiological methods. Viable bacteria were characterized using conventional techniques, and antimicrobial susceptibility of the isolates was detected.<br><br>RESULTS: Acute gastritis, chronic gastritis, and peptic ulcers were detected in 3.5%, 86.5%, and 5.8% of the patients, respectively. Culturable bacteria were isolated from 71.3% of the patients, including Helicobacter pylori (H. pylori) (26.9%), Staphylococcus epidermidis (19.8%), Micrococcus (1.1%), Streptococcus viridans (S. viridans) (13.4%), Enterococcus faecalis (E. faecalis) (4.6%), Staphylococcus aureus (S. aureus) (1.7%), and Group D Streptococcus (7.1%). Single infection and coexistence of two and three types of bacteria were detected in 43.2%, 15.2%, and 5.2% of the patients, respectively. An odd ratio of 4.4 was measured for Staphylococcus spp. in patients with acute gastritis (P-value = 0.08). E-test results showed intermediate resistance to penicillin in 66.6% of the S. aureus isolates, while resistance to vancomycin was detected only in the S. viridans (30.4%). Resistance to linezolid was detected in 100%, 17.4%, and 16.7% of E. faecalis, S. viridans, and group D Streptococci isolates, respectively. A high frequency of resistance to penicillin, clindamycin, linezolid, erythromycin, and tetracycline was detected in S. epidermidis strains.<br><br>CONCLUSION: Our results highlighted the importance of Gram-positive bacteria in the etiology of gastritis. Resistance of these bacteria to different classes of antibiotics should be considered in the clinical setting.},
}
@article {pmid42052722,
year = {2026},
author = {Qiao, S and Fan, S and Xu, J and Xu, Z and Peng, C and Qu, J and Bing, Z and Zhou, S and Shen, S and Xu, G and Zhao, Y and Wang, T},
title = {Gut Mycobiota-Associated Tryptophan Catabolites Protect Against Metabolic Dysfunction-Associated Steatotic Liver Disease.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e14830},
doi = {10.1002/advs.202514830},
pmid = {42052722},
issn = {2198-3844},
support = {T2341015//National Natural Science Foundation of China/ ; 32271182//National Natural Science Foundation of China/ ; 82273011//National Natural Science Foundation of China/ ; 82302934//National Natural Science Foundation of China/ ; 2024300382//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Accumulating evidence suggests that the intestinal microbiota participates in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD) through microbiota-host interaction. However, the beneficial role of commensal mycobiota in MASLD progression remains poorly understood. By comparing the gut microbiome differences, we demonstrated that the deficiency of Caspase Recruitment Domain-containing protein 9 (CARD9), an adaptor protein for a microbiota recognition receptor, exacerbated high-fat diet (HFD)-induced MASLD in a gut fungi-dependent manner. CARD9 deficiency reduced the abundance of Saccharomyces cerevisiae (S. cerevisiae), which was a probiotic alleviating MASLD progression. S. cerevisiae promoted a significantly greater abundance of 5-hydroxyindoleacetic acid (5-HIAA) in the intestine through Toll-like receptor 1 (TLR1), which reduced body weight in mice and alleviated MASLD phenotypes via the "gut-liver" axis. Particularly, 5-HIAA directly binds to aryl-hydrocarbon receptor (AhR) and stimulates its nuclear translocation, subsequently inducing fatty acid oxidation via carnitine palmitoyltransferase 1A (CPT1A) and acyl-CoA oxidase 1 (ACOX1) transactivation. MASLD patients exhibited decreased levels of S. cerevisiae and 5-HIAA, and S. cerevisiae effectively reduced hepatic steatosis and improved glucose homeostasis in patients with MASLD. In summary, our findings identified a novel pathway of fungi-S. cerevisiae stimulating intestinal 5-HIAA production and indicated that S. cerevisiae and 5-HIAA might alleviate MASLD progression, highlighting that the mycobiota-dependent gut-liver axis was a promising target for the prevention of MASLD.},
}
@article {pmid42052831,
year = {2026},
author = {Li, Y and Gao, H and Liao, Z and Chen, Z and Song, Z and Xiong, W and Dai, Y and Li, W and Luan, S},
title = {Metagenomic Analysis Reveals Gut Microbiota Features in Membranous Nephropathy.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {4},
pages = {48982},
doi = {10.31083/FBL48982},
pmid = {42052831},
issn = {2768-6698},
support = {JCYJ20240813153002004//Shenzhen Foundation of Science and Technology/ ; JCYJ20250604191024032//Shenzhen Foundation of Science and Technology/ ; 2025A1515012512//Guangdong Basic and Applied Basic Research Foundation/ ; 2022041//Shenzhen Longhua District Healthcare Institutions Scientific Research Project/ ; //Key Medical Discipline Construction Fund of Shenzhen Longhua District/ ; JZ2025107//Guangdong Yiyang Healthcare Charity Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, Membranous/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; *Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {BACKGROUND: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut-renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported.<br><br>METHODS: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated.<br><br>RESULTS: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 &#xb1; 0.12, suggesting promising discriminatory potential that warrants further validation.<br><br>CONCLUSION: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.},
}
@article {pmid42052832,
year = {2026},
author = {Byun, AS and Kwok, PCL and Chan, HK and Vitetta, L},
title = {The Gut-Lung Axis, Epigenetics and Respiratory Disease.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {4},
pages = {48743},
doi = {10.31083/FBL48743},
pmid = {42052832},
issn = {2768-6698},
mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; *Lung/microbiology ; Prebiotics ; Probiotics/therapeutic use ; Animals ; *Respiratory Tract Diseases/microbiology ; },
abstract = {The first and second phases of the human microbiome project provided a view of mucosal surfaces and the skin of humans that mapped an abundant and complex ecosystem (microbiota) that is composed of bacteria (bacteriobiota), fungi (mycobiota), viruses (virobiota), enteric phages, archaea, protists, and helminths. Intestinal dysbiosis describes an adverse shift in microbial homeostasis in the gut that enhances intestinal epithelial permeability, translocating toxins that may lead to endotoxemia. Numerous intestinal and extra-intestinal illnesses have been linked to gut dysbiosis, including inflammatory bowel disease, infections, food allergies, asthma, diabetes, obesity, multiple sclerosis, autism, periodontitis, and colorectal cancer. The gut-lung axis is a bidirectional communication network between the lungs and the intestines mediated by bacterial elaborated products (e.g., butyrate), immune cells and neural pathways influencing health and disease at both sites. This review has focused on the gut-lung axis and the role that probiotics, prebiotics and postbiotics may play on the amelioration of respiratory symptoms that may result from viral and/or bacterial lung infections. Clinicians have for some time focused on treating inflammatory lung disorders such as asthma and chronic obstructive pulmonary disease by encouraging beneficial effects on the intestinal microbiome through the gut-lung axis with orally administered probiotics and pre- and/or postbiotics. The purpose is to restore gut microbial homeostasis. Developing novel delivery platforms to administer probiotics directly to the airways or as adjunctive systemic modulators is a plausible and increasingly supported hypothesis, with careful strain selection, formulation to preserve viability, targeted delivery, and rigorous safety and efficacy testing before clinical use. It is posited that such adjunctive treatments may significantly influence the lung microbiota epigenome by positively impacting the balance of microorganisms within the lung, restoring eubiosis and consequently health.},
}
@article {pmid42052843,
year = {2026},
author = {Yusuf, K and Attard, TM and Al-Kasspooles, M and Umar, S},
title = {An Emerging Approach to IBD Treatment: Personalized Nutrition Through Gut Microbiome Optimization.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {4},
pages = {47779},
doi = {10.31083/FBL47779},
pmid = {42052843},
issn = {2768-6698},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/diet therapy/microbiology/therapy ; *Precision Medicine/methods ; Diet ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract characterized by relapsing and remitting disease activity. Despite decades of research, a definitive cure for IBD remains elusive, as cycles of remission and flare-ups mark the disease course and often relies on long-term pharmacologic and supportive strategies. Increasing evidence indicates that diet and nutrition play an important role in modulating the outcomes of IBD. Although a wide range of dietary interventions has been explored, no universally effective approach has been established. Investigations have also proven that different dietary interventions can significantly affect clinical outcomes by altering gut microbial composition. This review explores a novel approach to IBD management by integrating gut microbiome modulation into personalized patient diets. The review examines various dietary interventions commonly used in IBD treatment and their impact on the gut microbiome composition. Furthermore, the study proposes a framework for creating personalized nutrition based on individual microbiome profiles. Finally, the review discusses the potential of personalized nutrition as a long-term therapeutic strategy for IBD management, offering insights into its feasibility and implications for patient care.},
}
@article {pmid42053308,
year = {2026},
author = {Bojang, E and Sheriff, L and Morris, E and Rouvray, S and Fu, MS and Wellings, C and Abdissa, K and Stavrou, V and Clark, C and Southam, AD and Dunn, WB and Bending, D and Hombrebueno, JR and Jacobsen, I and Dimeloe, S and Hall, RA and Drummond, RA},
title = {Vancomycin disrupts mitochondrial morphology and function and impairs macrophage fungal killing.},
journal = {mBio},
volume = {},
number = {},
pages = {e0058026},
doi = {10.1128/mbio.00580-26},
pmid = {42053308},
issn = {2150-7511},
abstract = {Vancomycin is a widely prescribed antibiotic used in the treatment of gram-positive bacterial infections. We previously showed that this antibiotic disrupted protective antifungal immune responses via microbiome dysbiosis, enhancing susceptibility to invasive candidiasis. Antibiotics are an independent risk factor for developing this life-threatening fungal infection, but whether microbiota-independent mechanisms also drive this association is not clear. Here, we show that vancomycin directly impairs macrophage responses to Candida albicans, the main causative agent of invasive candidiasis. Vancomycin-treated macrophages were less able to kill C. albicans despite normal phagocytosis rates and were hyper-inflammatory and more likely to die during infection. Using a fluorescently labeled vancomycin, we observed vancomycin uptake by macrophages in vivo and within close proximity to the mitochondrial outer membrane. Vancomycin treatment led to a significant depolarization, reduced respiratory capacity, and a hyper-fragmented morphology of mitochondria, as well as increased cellular ROS production. Taken together, this work demonstrates direct effects of vancomycin on mammalian immune cells, helping us to understand the pro-inflammatory effects of this drug and how it promotes susceptibility to life-threatening fungal infection.IMPORTANCEAntibiotics are widely prescribed drugs used to treat bacterial infections; however, their use may increase the likelihood of developing life-threatening fungal infections in vulnerable patients. Candida albicans is a commensal fungus in humans but may cause serious disease in patients with defined risk factors, including antibiotic exposure. We find that the antibiotic vancomycin significantly impairs the ability of macrophages to kill C. albicans yeast. Vancomycin-induced defects in fungal killing were associated with changes to mitochondria in antibiotic-exposed macrophages, which also exhibited enhanced oxidative stress and reduced survival during fungal infection. This work identifies a direct mechanism by which antibiotics may impair antifungal immunity.},
}
@article {pmid42053319,
year = {2026},
author = {Fulcher, MR and Tritz, A and Beauchamp, V and Wu, CA},
title = {Wavyleaf basketgrass (Oplismenus undulatifolius) invasion is associated with changes in soil microbial communities.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0089525},
doi = {10.1128/msphere.00895-25},
pmid = {42053319},
issn = {2379-5042},
abstract = {UNLABELLED: Introduced invasive plants can alter the composition of resident soil microbial communities, which may disrupt ecosystem function and facilitate continued invasion success. Wavyleaf basketgrass (Oplismenus undulatifolius) is a high-risk, non-native invasive plant currently confined to the Mid-Atlantic United States but with the potential to colonize forest understory across the eastern United States. In this study, we characterized soil microbial communities from locations spanning the invaded range using amplicon sequencing to understand the impacts of wavyleaf basketgrass establishment on resident soil microbiomes. We compared the diversity and structure of microbial communities from invaded and uninvaded forest soils, as well from wavyleaf basketgrass rhizospheres. Invasion by wavyleaf basketgrass was associated with an increase in fungal diversity within sampling locations but a decrease in diversity across sampling locations. Changes in the relative abundance of specific sequence variants indicated a small number of resident microbes may be amplified in wavyleaf basketgrass rhizospheres. Finally, fungal alpha diversity was correlated with soil chemistry variables in uninvaded plots but not in invaded plots, and increased plant ground cover attributed to wavyleaf basketgrass invasion was positively correlated with fungal diversity. Together, these patterns suggest that wavyleaf basketgrass recruits diverse microbial associates from the environment, homogenizes soil microbiomes across invaded locations, and overrides existing environmental selection pressures exerted by soil chemistry profiles. Ongoing expansion of the species' invaded range may produce similar impacts in new environments.<br><br>IMPORTANCE: Understanding whether and how microbial communities are altered by plant invasion provides important information about the impact of introduced species on natural resources, nutrient cycling, and biodiversity that influence subsequent land management and ecosystem restoration decisions. We document biotic homogenization of resident soil microbes across geographically disparate locations following a relatively recent plant invasion. We further provide evidence suggesting microbial community changes are linked to the enrichment of specific taxa from the invasive plant's rhizosphere and possible buffering of these communities against other environmental selective pressures.},
}
@article {pmid42053321,
year = {2026},
author = {Okyere, L and Di Fulvio, A and Gaulke, CA},
title = {Long-term culture of germ-free zebrafish using gamma-irradiated feeds.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0035326},
doi = {10.1128/msystems.00353-26},
pmid = {42053321},
issn = {2379-5077},
abstract = {Host-associated microbiota play important roles in modulating key host functions, including digestion, nutrient acquisition, immunity, and xenobiotic metabolism. Disruption of these communities is linked to numerous diseases and health defects, though causal mechanisms underpinning these associations remain unclear in most cases. Gnotobiotic zebrafish provide a scalable low-cost in vivo model that is increasingly used to resolve causality in host-microbiota interactions. However, reliance on live diets and autoclaved diets limits the use of gnotobiotic zebrafish to early life stages where body systems and microbial communities are incompletely developed. As a result, many important host-microbiota interactions may be unable to be studied in this model system. Here, we tested a simple method for long-term husbandry of gnotobiotic zebrafish using gamma-irradiated chow diets and evaluated effects on growth, gene expression, and microbial community composition. In conventionally reared animals, gamma-irradiated diets did not affect growth or survival and only modestly impacted microbial community composition and diversity. In contrast, germ-free zebrafish maintained on sterile irradiated diets for 55 days post-fertilization were smaller, weighed less, and exhibited aberrant gene expression profiles relative to controls. These genes were enriched for pathways related to immune response, xenobiotic metabolism, organ development, liver function, and lipid metabolism, with many expression patterns linked to the abundance of specific microbial taxa. Together, these findings establish a practical protocol for long-term maintenance of gnotobiotic zebrafish and extend the utility of this model to study microbiome-dependent effects on host physiology and development beyond early larval stages of life.IMPORTANCEWhile the gnotobiotic zebrafish have been a powerful model for interrogation of host-microbiota interactions, their use has been limited to early life stages due to complications of long-term husbandry. To address this limitation, we developed a simple protocol that enables rearing germ-free zebrafish well beyond larval stages. Germ-free fish exhibit physiological and developmental defects that mirror those described in mammalian counterparts supporting a conserved role for microbiota in vertebrate development and physiology. Our protocol provides a method to investigate microbial influences on adaptive immunity, metabolism, and chronic disease processes in zebrafish not possible with current methodologies. Given the rapid and simple methods for gnotobiotic derivation and the large number of transgenic animal lines available for zebrafish, we anticipate this model will accelerate mechanistic discovery of microbial impacts on host health.},
}
@article {pmid42053337,
year = {2026},
author = {Wutke-Ostręga, J and Szul, M and Pluta, D},
title = {Eradicating hyperandrogenism? Hormonal changes following Helicobacter pylori eradication in women with polycystic ovary syndrome: an observational case series.},
journal = {Endokrynologia Polska},
volume = {77},
number = {2},
pages = {107-111},
doi = {10.5603/ep.110428},
pmid = {42053337},
issn = {2299-8306},
mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/complications/blood ; Adult ; *Helicobacter Infections/drug therapy/complications/blood ; *Hyperandrogenism/blood/drug therapy/complications ; *Helicobacter pylori ; Sex Hormone-Binding Globulin/metabolism/analysis ; Testosterone/blood ; Young Adult ; Androgens/blood ; Dehydroepiandrosterone Sulfate/blood ; Anti-Mullerian Hormone/blood ; },
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is a heterogeneous endocrine disorder in which hyperandrogenism represents a centralpathophysiological feature. Increasing attention has been directed toward chronic inflammatory factors that may modulate androgenexcess. Helicobacter pylori (H. pylori) infection is a prevalent chronic bacterial infection associated with systemic low-grade inflammation.However, its potential relationship with androgen-related hormonal parameters in PCOS remains poorly explored.<br><br>MATERIAL AND METHODS: This observational mini case series included seven women with PCOS diagnosed according to the Rotterdam criteriaand confirmed active H. pylori infection. Hormonal parameters including total testosterone, androstenedione, dehydroepiandrosteronesulfate (DHEAS), sex hormone-binding globulin (SHBG), anti-M&#xfc;llerian hormone (AMH), and free androgen index (FAI) were assessedduring active infection and after confirmed eradication. No hormonal contraception, antiandrogens, metformin, incretin-based therapies,or inositol supplements were used during the study period.<br><br>RESULTS: Following successful H. pylori eradication, consistent changes in androgen-related parameters were observed. Median DHEAS,androstenedione, and total testosterone concentrations decreased, while SHBG levels increased. Consequently, the free androgen indexdecreased in all patients. AMH levels showed a downward trend after eradication. Due to the descriptive nature of the study, no inferentialstatistical analyses were performed.<br><br>CONCLUSIONS: In this observational case series, H. pylori eradication was associated with coherent changes in androgen-related hormonal parameters and reduced androgen bioavailability in women with PCOS. Although causality cannot be established, these findings suggestthat chronic infection-related inflammation may influence the androgenic milieu in PCOS.},
}
@article {pmid42053342,
year = {2026},
author = {Mehta, N and Guzzetta, V and Liu, KH and Webster, AS and Adelman, MW and Fitts, EC and Jones, DP and Kraft, CS and Woodworth, MH and Collins, JM},
title = {High-resolution metabolomic analysis of stool reveals expanded biomarkers of C. difficile colitis and insights into pathophysiology.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0282625},
doi = {10.1128/spectrum.02826-25},
pmid = {42053342},
issn = {2165-0497},
abstract = {Clostridioides difficile infection (CDI) is facilitated by gut microbiome disruption and associated metabolic disturbances. While many prior studies have focused on the microbial composition of CDI stool, fewer have explored the fecal metabolome using untargeted high-resolution metabolomics (HRM). To characterize the metabolic phenotype of CDI, we performed untargeted HRM on stool samples from 55 CDI patients and 72 healthy controls. CDI was associated with marked alterations in stool metabolites, mapping to 14 significantly dysregulated pathways, including tryptophan metabolism, bile acid metabolism, short-chain fatty acid metabolism, and fatty acid oxidation. These findings suggest that CDI is associated with a distinct fecal metabolic milieu that may promote inflammation, impair colonization resistance, and facilitate C. difficile replication. Our results corroborate previous studies and support further investigation of the role of microbial and immune signaling in CDI as well as metabolic biomarkers and therapeutic targets.IMPORTANCEAs we learn more about the essential role of gut microbes in human health and disease, there is an effort to identify and characterize stool biomarkers that distinguish patients with microbiome-associated disease from healthy individuals. Clostridioides difficile infection contributes to excess healthcare burden and is tightly linked to disruption of the gut microbiome (usually by use of antimicrobials). We compared the metabolome of healthy stool and C. difficile-infected stool to identify metabolites that correlate with disease and may support the development of improved diagnostic tests for C. difficile infection. In comparing these two groups, we found chemical pathways that strongly correlate with disease and others more associated with healthy stool, including bile acid biosynthesis, tryptophan metabolism, and carnitine activation.},
}
@article {pmid42053606,
year = {2026},
author = {Koch, H and Lessard, B and Escobar-Correas, S and Thurman, JH and Paten, AM and Morgan, MJ},
title = {A Comparative Survey of Soldier Fly (Stratiomyidae) Larval Gut Microbiomes Across Five Subfamilies Reveals Novel Bacterial Diversity and a "Wild Core" in Hermetia illucens.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02760-z},
pmid = {42053606},
issn = {1432-184X},
}
@article {pmid42053608,
year = {2026},
author = {Çağatay, NS and Dageri, A and Saruhan, I and Tuncer, C and Guz, N},
title = {Diversity and Composition of the Microbiome Associated with Adult of the Green Shield Bug Palomena prasina (Hemiptera: Pentatomidae).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02779-2},
pmid = {42053608},
issn = {1432-184X},
support = {Project number: 116O328//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; },
}
@article {pmid42053737,
year = {2026},
author = {Jasrotia, P and Chandra, P and Singh, A and Kashyap, PL and Sharma, SK},
title = {Symbiont dominance and microbiome dysbiosis in wheat-aphid revealed through 16 S rRNA gene amplicon sequencing analysis.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42053737},
issn = {1573-0972},
mesh = {*Triticum/parasitology/microbiology ; Animals ; *Aphids/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; *Symbiosis ; *Dysbiosis/microbiology ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Biodiversity ; },
abstract = {Insect herbivory represents a major biotic stress that leads to significant losses in crop yield and quality worldwide. Aphids, in particular, damage wheat (Triticum aestivum L.), a staple crop that provides nearly 20% of the global protein and caloric intake, and also harbor diverse bacterial symbionts that can influence plant health. In this study, 16 S rRNA gene amplicon sequencing was used to characterize the bacterial communities associated with healthy and aphid-infested wheat plants. Alpha-diversity indices, including Simpson, Shannon, Chao1, and ACE, revealed statistically significant variation (P < 0.05) in bacterial richness and diversity across the samples. Richness estimates ranged from 101.25 to 137.2 (Chao1) and 106.04 to 139.37 (ACE), while diversity metrics ranged from 0.428 to 1.243 for the Shannon index, with Faith's phylogenetic diversity varying from 1.27 to 1.48 and Pielou's evenness from 0.626 to 0.740. In healthy wheat plants, Spirodela accounted for approximately 4% of the bacterial community, whereas about 95% of taxa remained unclassified. In contrast, aphid-infested wheat plants contained 3% Spirodela, 7% Buchnera, and 89% unclassified taxa. The aphid microbiome itself was strongly dominated by Buchnera (86%), followed by Pseudomonas (2%) and other minor taxa (1%), with approximately 10% remaining unclassified. The pronounced abundance of Buchnera in both aphids and infested wheat plants highlights its essential nutritional role and its long-standing obligate endosymbiotic association with aphids. Overall, these findings provide new insights into wheat-aphid-microbiome interactions and establish a foundation for developing microbiome-informed pest management strategies.},
}
@article {pmid42053754,
year = {2026},
author = {Goyal, O and Aggarwal, A and Goyal, MK and Mehta, V and Mahajan, R and Gupta, Y and Singh, A and Sood, A},
title = {Prevalence, clinical significance and predictors of small intestinal bacterial overgrowth and elevated fecal calprotectin in refractory irritable bowel syndrome: Insights from a prospective cross-sectional study.},
journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42053754},
issn = {0975-0711},
abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is a common disorder with multi-factorial pathophysiology. Emerging evidence suggests a role of low-grade mucosal inflammation in IBS. Small intestinal bacterial overgrowth (SIBO), which has symptoms similar to IBS, may be misdiagnosed as IBS. Data on the prevalence of SIBO and elevated fecal calprotectin (FCP) levels in IBS patients remains sparse and conflicting. We aimed at determining the prevalence and clinical significance of SIBO and elevated FCP in patients with refractory IBS.<br><br>METHODS: This prospective cross-sectional study enrolled refractory IBS patients (Rome-IV criteria). SIBO was diagnosed using the glucose&#xa0;hydrogen breath test and FCP levels &#x2265; 50 &#x3bc;g/g were considered elevated. Clinical evaluation was performed using standardized&#xa0;questionnaires: IBS Symptom Severity Scale (IBS-SSS) and IBS Quality of Life (IBS-QoL).<br><br>RESULTS: &#xa0;Of 209 patients screened, 148 with refractory IBS were enrolled (mean age 35.8&#x2009;&#xb1;&#x2009;11.9&#xa0;years; 66.1% male). SIBO was detected in 46 (31.1%) and elevated FCP in 41 (27.7%) patients, with the highest prevalence in the IBS-D group (37.1% and 33.3%, respectively). Patients who were SIBO and/or FCP-positive had a longer duration of symptoms, higher IBS symptom burden and poorer QoL. Multi-variate analysis identified bloating (aOR&#x2009;=&#x2009;4.59) and the IBS-SSS (aOR&#x2009;=&#x2009;1.20) as independent predictors of SIBO.<br><br>CONCLUSIONS: Approximately one-third of patients with refractory IBS, particularly those with IBS-D, have SIBO and/or elevated FCP. This subset&#xa0;of patients demonstrates a higher symptom burden and poorer QoL, emphasizing the crucial need for accurate diagnosis and&#xa0;personalized treatment. Incorporating non-invasive biomarkers (SIBO testing and FCP) into the management of refractory IBS may&#xa0;optimize patient care.},
}
@article {pmid42053902,
year = {2026},
author = {Dai, T and Chen, AX and Chow, EWL and Pang, LM and Li, J and Verma, CS and Oehlers, SH and Wang, Y and Li, N},
title = {A Cationic Supramolecule With Potent Antifungal Activity, Single-Species Selectivity, and Strong Synergy With Echinocandins.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e75480},
doi = {10.1002/advs.75480},
pmid = {42053902},
issn = {2198-3844},
support = {//A*STAR Infectious Diseases Labs/ ; OFYIRG24jan-0051//National Medical Research Council Open-Fund Young Individual Research Grant/ ; C233312014//A*STAR Career Development Fund/ ; SRIS_JRG_2001//Skin Research Institute of Singapore Joint Research Grant (SRIS_JRG_2001)/ ; },
abstract = {Claiming 3.8 million lives annually, fungal pathogens represent a major health threat, where Candida species are the leading cause with >40% mortality rates. Despite rising prevalence of life-threatening fungal species/strains, progress in developing new antifungal agents remains limited. Here, we report a new synthetic membrane-active cationic supramolecule Gua-SMACS-16 that exhibits high antifungal potency and selectivity for Candida tropicalis (MIC = 0.4-0.8 µM) without affecting other phylogenetically close species in the Candida genus, non-Candida fungal, or common opportunistic bacterial species in the human microbiome. Gua-SMACS-16 exerts its activity by disrupting the cytoplasmic membrane, while its C. tropicalis selectivity is attributed to the species' low cell wall β-glucan level, which fails to block the supramolecule entry. It also exhibits minimal toxicity to mammalian cells and zebrafish embryos, suggesting a high clinical translation potential. Moreover, an ultra-strong synergy was observed between Gua-SMACS-16 and caspofungin, a clinical antifungal drug inhibiting 1,3-β-glucan synthase, reducing their MICs by orders of magnitude against all tested Candida species including the intractable C. auris. Together, this work highlights the importance of cell wall glucan for membrane-active antifungal amphiphiles, provides a novel design principle for species-specific antifungal agents, and uncovers a new approach to developing synergizers for combination antifungal therapy.},
}
@article {pmid42054100,
year = {2026},
author = {Mellor, SA and Bloomfield, SJ and Palau, R and Savva, GM and Wain, J and Mather, AE},
title = {Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.},
journal = {Microbial genomics},
volume = {12},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001705},
pmid = {42054100},
issn = {2057-5858},
mesh = {Animals ; *Metagenomics/methods ; *Food Microbiology ; Chickens/microbiology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; *Meat/microbiology ; Cattle ; Sheep ; Salmon/microbiology ; United Kingdom ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Swine ; },
abstract = {Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.},
}
@article {pmid42054198,
year = {2026},
author = {Côrtes, J and Trindade Filho, JCS and Rogatto, SR},
title = {The emerging role of the microbiome in bladder cancer: prognostic implications and treatment response.},
journal = {Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas},
volume = {59},
number = {},
pages = {e15526},
pmid = {42054198},
issn = {1414-431X},
mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/therapy/pathology ; *Microbiota/physiology ; Prognosis ; Risk Factors ; },
abstract = {Bladder cancer (BCa) is a histologically and molecularly heterogeneous disease and is one of the leading causes of cancer death globally. The main risk factors are sex (with incidence 3 to 4 times higher in men), tobacco usage, occupational exposure to carcinogens, and persistent infections, such as those caused by Schistosoma haematobium. Urine and the bladder were recently confirmed to be non-sterile, prompting investigations into the urinary and intratumoral microbiomes and their roles in tumor stage, prognosis, and therapy response. In this context, the role of the urinary and intratumoral microbiome in bladder carcinoma is among the most promising areas in translational uro-oncology. Recent evidence demonstrates the presence and diversity of microbial communities in both urine and bladder cancer tissue, with patterns associated with tumor stage and prognosis. Chronic inflammation, genotoxin production, altered carcinogen metabolism, and modulation of the immune microenvironment are biological processes that provide a rationale for the functional role of these microorganisms in the bladder. Furthermore, microbial profiles have been correlated with responses to intravesical therapies (such as BCG - Bacillus Calmette-Guérin) and, potentially, with systemic immunotherapies. The microbiome can help identify predictors of treatment response and potential adjuvant interventions, and offers a non-invasive, translational pathway for diagnosis and surveillance. This review summarizes current evidence on the microbiome in bladder cancer patients and its prognostic and therapeutic potential.},
}
@article {pmid42054627,
year = {2026},
author = {Braun, AE and Hesami, H and Deng, M and Hasler, JS and Bukavina, L and Handorf, E and Abbosh, PH},
title = {Association Between Antibiotic Therapy and Treatment Effectiveness in Patients With Renal Cell Carcinoma Receiving Immune Checkpoint Inhibitors or Tyrosine Kinase Inhibitors.},
journal = {JCO oncology practice},
volume = {},
number = {},
pages = {OP2500963},
doi = {10.1200/OP-25-00963},
pmid = {42054627},
issn = {2688-1535},
abstract = {PURPOSE: It has been theorized that antibiotic therapy (ABT) affects response to immune checkpoint inhibition (ICI) by inducing dysbiosis of the gut microbiome (GM). To investigate the association between ABT and real-world overall survival (rwOS)/progression-free survival (rwPFS) in patients with metastatic renal cell carcinoma (mRCC) receiving ICI versus tyrosine kinase inhibitors (TKIs).<br><br>METHODS: In total, 5,237 patients with mRCC from a nationwide electronic health record-derived deidentified database who received ICI or TKI first-line after diagnosis were included. ABT exposure was stratified by exposure (yes or no), timing (before v after treatment initiation v none), excretion modes (hepatic v renal excretion v none), and administration routes (oral v intravenous v none). Three-month landmark Kaplan-Meier estimation and log-rank tests were used to compare rwOS/rwPFS among ABT groups. Multivariable Cox proportional hazards models with time-varying coefficients investigated the association between rwPFS, rwOS, ABT, and treatment modality.<br><br>RESULTS: ABT exposure was negatively associated with rwOS/rwPFS in both ICI (rwOS [23.9 v 33.6 months, P = .029]; rwPFS [8.8 v 11.6 months, P < .001]) and TKI (rwOS [17.4 v 26.2 months, P < .001]; rwPFS [8.0 v 9.7 months, P < .001]) recipients. For ICI patients only, a negative correlation between ABT after treatment initiation (rwOS, P = .003, rwPFS <0.001) and oral administration route (rwOS P = .004, rwPFS P = .001) was identified. In time-varying Cox proportional models, the effect of ABT on rwPFS beyond 12 months was only statistically significant in ICI patients (ICI, hazard ratio [HR], 1.67, P = .013; TKI, HR, 0.95; P = .7).<br><br>CONCLUSION: In our observational study, we identified a potential unique and complex association between ABT and rwOS/rwPFS in patients with mRCC receiving ICI. We found a negative correlation between ABT use after treatment initiation or via the oral route on oncologic outcomes in ICI patients. Moreover, there appears to be an ICI-specific negative association of ABT on rwPFS beyond 1 year. Our findings are associative, but they emphasize the importance of antibiotic stewardship in this space.},
}
@article {pmid42054761,
year = {2026},
author = {Liu, Y and He, P and He, P and Li, X and Ahmed, A and Tang, G and Tang, P and Di, Y and Zhou, Y and Hu, D and Li, Y and Wu, Y and Munir, S and He, Y},
title = {Cross-kingdom synthetic microbial consortium controls citrus Huanglongbing and root rot by modulating the rhizosphere microbiome and plant defense.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128528},
doi = {10.1016/j.micres.2026.128528},
pmid = {42054761},
issn = {1618-0623},
abstract = {The synergistic occurrence of citrus Huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus (CLas) and root rot severely threatens the global citrus industry. In this study, field surveys were conducted across nine major citrus-producing regions in seven provinces of China. Highly pathogenic strains, Phytophthora nicotianae CR62 and Fusarium solani CR15, were selected as targets for screening Trichoderma strains for mycoparasitic activity. Compatibility and metabolic cross-feeding with the HLB-controlling strain Bacillus subtilis L1-21 enabled the construction of a cross-kingdom SynCom. Pot experiments evaluated plant growth promotion and root rot control, while high-throughput sequencing (16S rRNA/ITS) elucidated the regulatory mechanisms of rhizosphere microbiomes. The results showed that HLB and root rot co-occurred widely in the field, with oomycetes (Phytophthora spp. and Pythium spp.) accounting for 65.22% of root rot pathogens. P. nicotianae and F. solani exhibited the highest pathogenicity, whereas no significant correlation was detected between the root rot disease index and CLas titer. Targeted screening showed that T. asperellum NY-1 exerted more than 60% inhibition against root rot pathogens and exhibited high compatibility with B. subtilis L1-21. Moreover, the cell-free filtrate of NY-1 significantly reshaped the global metabolic profile of L1-21, primarily by modulating amino acid and energy metabolism, as well as ABC transporter pathways, thereby comprehensively altering its cellular metabolic activities. Importantly, the SynCom NL significantly promoted plant growth and increased rhizosphere urease and sucrase activities after 90 days of treatment. SynCom NL enriched beneficial microbes (Bacillus, Sphingomonas, Trichoderma, Humicola), suppressed pathogens (Fusarium, Penicillium, Neocosmospora), and activated root defense enzymes (SOD, CAT, PAL, PPO), boosting root protection and achieving 92.86 ± 8.25% root rot control. Overall, the Trichoderma-Bacillus cross-kingdom SynCom targeting the HLB-root rot disease complex provides a technical foundation for integrated biocontrol and sustainable citrus production.},
}
@article {pmid42043192,
year = {2026},
author = {Knap-Wielgus, W and Knap, A and Pietrzak, B and Suchońska, B and Wielgoś, M},
title = {A Role of the Lower Genital Tract Microbiome in Promoting Cervical Intraepithelial Neoplasia: A Premalignant Precursor of Cervical Cancer-A Literature Review.},
journal = {Viruses},
volume = {18},
number = {4},
pages = {},
pmid = {42043192},
issn = {1999-4915},
mesh = {Humans ; Female ; *Microbiota ; *Uterine Cervical Dysplasia/microbiology/virology/pathology ; *Uterine Cervical Neoplasms/microbiology/virology/pathology ; Papillomavirus Infections/complications/virology/microbiology ; Dysbiosis/microbiology ; *Vagina/microbiology/virology ; Papillomaviridae ; Lactobacillus ; },
abstract = {The cervicovaginal microbiome (CVMB) is pivotal in maintaining the homeostasis of the lower female genital tract and has emerged as a significant modulator of cervical carcinogenesis. Although persistent infection with high-risk human papillomavirus (HR-HPV) is a prerequisite for the development of cervical intraepithelial neoplasia (CIN) and subsequent cervical carcinoma, it remains insufficient alone to drive oncogenesis. Accumulating evidence suggests that alterations in the CVMB composition profoundly impact HPV persistence, local immune responses, and disease progression. A vaginal microbiota dominated by Lactobacillus species, most notably Lactobacillus crispatus, correlates with low microbial diversity, robust immune regulation, and facilitated HPV clearance. Conversely, microbial dysbiosis-characterized by Lactobacillus depletion and a concomitant proliferation of anaerobic taxa, typical of Community State Type (CST) IV and Lactobacillus iners-dominated profiles-is strongly associated with chronic inflammation, oxidative stress, epithelial barrier compromise, and an elevated risk of CIN progression. This review synthesizes current evidence regarding the multifaceted interactions among the cervicovaginal microbiome, HPV pathogenesis, immune dysregulation, and oxidative stress in the etiology of CIN. Elucidating these intricate host-microbiome dynamics may precipitate the discovery of novel microbiome-derived biomarkers, ultimately informing innovative prophylactic and therapeutic interventions for cervical cancer.},
}
@article {pmid42043303,
year = {2026},
author = {Böswald, LF and Zeyner, A and Santo, MM and Wensch-Dorendorf, M and Sünder, A and Popper, B and Siegert, W},
title = {Feeding Laboratory Mice: Comparing a Standard Versus a Purified Diet - Marked Effects on Digestive Physiology.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.70063},
pmid = {42043303},
issn = {1439-0396},
abstract = {Diet composition and processing have a major impact on its utilisation by the animal, as is known from farm and pet animal species. This includes effects on energy and nutrient digestibility, the intermediary metabolism, and the intestinal microbiome, with all the resulting impacts. For laboratory animals, data is scarce on influencing factors on diet digestibility. In experiments using special diets, either standard diets are used for the control group, or purified control diets. The aim of the present study was to compare a standard diet and a purified control diet (both pelleted) fed ad libitum to C57BL/6J mice and to investigate the potential effect on body weight development, feed conversion, energy and nutrient digestibility and indicators of intestinal fermentation (pH, short-chain fatty acids). Thus, 21 mice each were fed the standard diet (STD) and the purified diet (PD). Results showed a significantly higher apparent digestibility of gross energy and the crude nutrients in group PD (p < 0.001). The weight of the filled cecum and colon was significantly lower in group PD than STD (p < 0.001; p < 0.01). The pH of ingesta was significantly higher in stomach, cecum and colon of group PD (p < 0.0001), likely influenced by the significantly lower concentration of total short-chain fatty acids measures in cecum and colon of PD mice. The high apparent digestibility of the PD implied a lower influx of fermentable substrate into the hindgut, resulting in lower concentrations of microbial metabolites and altered pH milieu.},
}
@article {pmid42043563,
year = {2026},
author = {Chatterjee, S and Dutta, S and Ghosh, J and Saha, S and Mondal, M and Sarkar, J and Mondal, N and Ghosh, W},
title = {Warming responses, antibiosis potentials, and ecological implications of cryo-adapted copiotrophs from a Trans-Himalayan lake-desert ecosystem.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043563},
issn = {1432-072X},
support = {Intramural Faculty Grant//Bose Institute/ ; },
}
@article {pmid42043564,
year = {2026},
author = {Niu, YJ and Liu, LB and Yang, ZD and Xu, CJ and Zhao, TK and Chen, LL and Wang, QQ and Sun, B and Kim, S},
title = {The antimicrobial arsenal of endophytes in Lilium pumilum: active components of Fusarium tricinctum and antifungal mechanisms.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043564},
issn = {1432-072X},
support = {No. 22267011//National Natural Science Foundation of China/ ; 2023-RC-43//The project of the Bureau of Science and Technology of Lanzhou/ ; Y20220198//The Science and Technology Plan Project of Wenzhou, China/ ; 2025CXZX-608//The Gansu Provincial Department of Education: Graduate Student 'Innovation Star' Project/ ; No. 2022CYZC-29//The Industrial Support Plan Project of Colleges and Universities in Gansu Province/ ; },
mesh = {*Fusarium/isolation &amp; purification/metabolism/physiology/chemistry ; Botrytis/drug effects ; *Endophytes/isolation &amp; purification/metabolism/chemistry/physiology ; *Lilium/microbiology ; Plant Diseases/microbiology/prevention &amp; control ; Rhizoctonia/drug effects ; *Antifungal Agents/pharmacology ; Soil Microbiology ; Rhizosphere ; Ascomycota/drug effects ; Antibiosis ; Hypocreales ; },
abstract = {The microbiome of Lilium pumilum represents a valuable resource for developing sustainable biocontrol strategies. This study investigated the potential of these microorganisms to serve as major plant pathogen-antagonistic strains. In this study, 38 strains (18 fungi and 20 actinobacteria) were isolated from L. pumilum and its rhizosphere soil. Among these, the endophytic fungus Z-SD-LJ-2 (Fusarium tricinctum) exhibited remarkable broad-spectrum antifungal activity against five tested plant pathogens, with inhibition rates of 68.07-89.42% and half maximal effective concentration (EC50) values of 16.58-30.97 µg mL[- 1]. Notably, its performance surpassed the commercial fungicide azoxystrobin against Fusarium oxysporum and Botrytis cinerea. Concurrently, the rhizosphere-derived strain Z-SDTR-2 (Purpureocillium lilacinum) demonstrated potent inhibition against Rhizoctonia solani, Sclerotinia sclerotiorum, and Botrytis cinerea, with all inhibition rates exceeding 80% and EC50 values of 17.17-21.80 µg mL[- 1]. Activity-guided isolation from Z-SD-LJ-2 led to the identification of enniatin B as the most active compound, exhibiting EC50 values of 13.78-26.81 µg mL[- 1]. Further studies revealed that enniatin B induces apoptosis in the pathogens by triggering reactive oxygen species (ROS) accumulation and causing mitochondrial dysfunction. In pot experiments, the fermentation broth of Z-SD-LJ-2 (2 × 10[3] mg L[- 1]) effectively controlled lily wilt, reducing the disease index to 30% (14.3% lower than azoxystrobin) and achieving a preventive efficacy of 72.6% (18% higher than the control). Additionally, the treatment promoted lily growth, increasing plant height by 4.4% and stem thickness by 8.71% compared to the control, underscoring its dual-function potential as a novel, effective biopesticide for sustainable agricultural practices.},
}
@article {pmid42043853,
year = {2026},
author = {Pucci, N and Mende, DR},
title = {bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilization.},
journal = {Microbial genomics},
volume = {12},
number = {4},
pages = {},
pmid = {42043853},
issn = {2057-5858},
mesh = {Humans ; *Milk, Human/metabolism/microbiology ; *Glycoside Hydrolases/genetics/metabolism ; *Polysaccharides/metabolism ; *Bifidobacterium/genetics/enzymology/metabolism ; *Molecular Sequence Annotation/methods ; Bacterial Proteins/genetics/metabolism ; Software ; },
abstract = {Human milk glycan (HMG) metabolism, especially by bifidobacteria, is crucial for infant gut colonization and healthy microbiome development. Bifidobacterial species and even strains are highly variable in their ability and in their enzymatic repertoire for HMG metabolism. The enzymes involved in HMG metabolism often have many non-HMG-related homologues, necessitating fine-grained annotation for accurate assessment of bifidobacterial HMG metabolic capabilities. However, current annotation tools provide only broad glycoside hydrolase (GH) (sub)family classifications. Here, we present bifidoAnnotator, a tool for fine-grained annotation and visualization of bifidobacterial GH genes involved in HMG utilization. bifidoAnnotator leverages MMseqs2 (Many-against-Many sequence searching) to map protein sequences against a manually curated database of over 22,000 bifidobacterial GH proteins, organized into 13 families and 108 functional clusters, each assigned a validation status (i.e. experimentally validated, putative or hypothetical). The tool performs hierarchical annotation at family and cluster levels, identifying consistently annotated protein variants rather than just broad family assignments, and generates publication-ready heatmaps for comparative analysis. Benchmarking on a gold standard dataset demonstrated that bifidoAnnotator has superior performance (95.9% precision, 100% recall) compared with six established tools and is an order of magnitude faster than the most accurate competitor. bifidoAnnotator's superior performance and computational efficiency represent a meaningful advance in high-throughput genomic annotation workflows, enabling detailed characterization of strain-level functional diversity in bifidobacterial HMG metabolism.},
}
@article {pmid42043859,
year = {2026},
author = {Patel, RA and Harke, SN},
title = {A decade of evidence linking gut microbiome dysbiosis to depression: a computational meta-analysis of mechanistic pathways: 2014-2024.},
journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/15622975.2026.2660311},
pmid = {42043859},
issn = {1814-1412},
abstract = {OBJECTIVES: The gut microbiome-gut-brain axis (MGBA) has been associated in the pathophysiology of depression; however, the expanding literature remains fragmented across metabolic signalling, immune-inflammatory pathways, stress physiology and dysbiosis outcomes.<br><br>METHODS: Abstracts were retrieved from bibliographic databases (Lens.org, PubMed, DOAJ, Europe PMC) for studies published between 2014 and 2024 investigating associations between the gut microbiome and depression using 16S rRNA sequencing. Following text preprocessing, Latent Dirichlet Allocation (LDA) was applied to identify latent thematic topics. Topic proportions were subsequently embedded using principal component analysis (PCA), t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation and projection (UMAP).<br><br>RESULTS: Topic modelling revealed distinct interconnected thematic domains within the gut microbiome depression literature, encompassing metabolic and short chain fatty acid pathways, immune inflammatory mechanisms, stress and hypothalamic pituitary adrenal (HPA) axis regulation, probiotic and interventional work, microbial diversity and compositional metrics, neurochemical and neuroplasticity, developmental cohorts, and sequencing- or methodology-focused research.<br><br>CONCLUSIONS: Computational synthesis indicates that research on the gut microbiome depression axis is structured around multiple convergent mechanistic themes. This thematic landscape highlights dominant areas of mechanistic focus, providing a conceptual framework to guide future experimental design, mechanistic validation and translational research.},
}
@article {pmid42043941,
year = {2026},
author = {Qu, W and Shi, X and Xu, X and Liu, C and Ding, L and Song, M and Xu, Z and Xu, Y and Mo, F and Ruan, J and Timko, MP and Fan, L and Zheng, S and Jiang, W and Wang, Y and Shen, Y},
title = {BACON: decoding the dynamic social networks of complex microbial communities at single-cell resolution.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {42043941},
issn = {1477-4054},
support = {82402729//National Natural Science Foundation of China/ ; 32200073//National Natural Science Foundation of China/ ; 32250710678//National Natural Science Foundation of China/ ; LQ23H200003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021R01012//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2024C03005//Pioneer' R&amp;D programs of Zhejiang Province/ ; 2024SSYS0022//Key Research and Development Program of Zhejiang/ ; LR23H200002//Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholar/ ; },
mesh = {*Quorum Sensing ; Humans ; *Single-Cell Analysis ; *Gastrointestinal Microbiome ; *Microbiota ; Escherichia coli/genetics ; Bacillus subtilis/genetics ; *Computational Biology/methods ; Pseudomonas aeruginosa/genetics ; },
abstract = {Microbial communities function as dynamic societies where intercellular communication governs collective behaviors. However, mapping these interaction networks has remained a fundamental challenge in microbiology. This study aims to decode the social networks of complex bacterial communities at single-cell resolution by developing BACON, a computational framework that infers quorum sensing-mediated communication from single-microbe transcriptomic data. The approach combines a curated database of signaling systems with a statistical model that quantifies communication strength through coordinated expression of signal synthesis and receptor genes. Validation in model systems demonstrated BACON's precision in reconstructing density-dependent communication trajectories in Bacillus subtilis and capturing rapid network reorganization in Escherichia coli under antibiotic stress, revealing distinct sender-receiver subpopulations. Applied to human gut microbiomes, BACON unveiled diurnal fluctuations in cross-species signaling that transcend enterotype boundaries and uncovered conserved metabolic specialization in signal-responsive bacteria. In a clinical context, analysis of an ICU patient's gut microbiome revealed how Pseudomonas aeruginosa establishes a self-reinforcing communication circuit that upregulates virulence pathways. This work provides a unified framework for analyzing bacterial social interactions across diverse ecosystems. It opens new avenues for understanding microbial sociology, combating antimicrobial resistance, and engineering synthetic communities.},
}
@article {pmid42044092,
year = {2026},
author = {Bloemendaal, M and Mulder, D and Gudden, J and Heikamp-de Jong, I and Ioannou, A and Belzer, C and Emile Natasha, E and Edwin Thanarajah, S and Aatsinki, AK and van Gelder, MMHJ and Arias Vasquez, A},
title = {Development of the gut microbiota throughout the first year of life and its association with socio-emotional development into childhood.},
journal = {Developmental neuroscience},
volume = {},
number = {},
pages = {1-27},
doi = {10.1159/000552189},
pmid = {42044092},
issn = {1421-9859},
abstract = {Introduction Early life is a critical window for the development of many bodily systems, including the gut microbiota and the central nervous system, that are inter-connected through the gut-brain-axis. These early life gut-brain-axis connections are often studied through cross-sectional cohorts, limiting insights into temporal developmental trajectories. This longitudinal cohort study assessed whether gut microbial development over the first year of life is associated with socio-emotional development into childhood. Methods The PRIDE (PRegnancy and Infant DEvelopment) BIOME study (n=81, n=42 males) is a focus cohort within the larger prospective PRIDE Study. Gut microbiome was measured 5 times throughout the first year of life (at 2, 4, 6, 9 and 12 months through V4 16S rRNA sequencing) and socio-emotional development 8 times over 4.5 years, between 6 months and 5 years through the Ages and Stages Questionnaire: Social-Emotional (ASQ-SE). We related the development of the gut microbiota of infants throughout their first year of life with their socio-emotional development into childhood, the latter modelled as a slope per individual (ASQ slope). We assessed effects of time, ASQ slope and its interaction with time on microbial community measures alpha and beta diversity, as well as taxonomy, using linear mixed-effects models and PERMANOVA, correcting for sex, birth weight, gestational age and sequencing depth. Results Expected developmental patterns on the gut microbiota over the first year of life were observed, including increased alpha diversity and clustering of beta diversity before and after solid food introduction. Interestingly, ASQ slope was a significant predictor of beta diversity (F(1,394)=25.90, p=0.001) and Bifidobacterium abundance across the first year of life (b= -0.745, SE= 0.24, pFDR= 0.023). Moreover, we observed a temporal association between ASQ slope and Eggerthella abundance (ASQ slope × timepoint interaction, b=0.709, SE=0.21, pFDR=0.009). That is, Eggerthella abundance decreased across the group, but not in "late concern" infants, with concern about socio-emotional development at more recent timepoints. Discussion This study shows that genera Bifidobacterium and Eggerthella, known to be altered in mental health conditions such as autism spectrum disorder and depression, are already linked to socio-emotional development during early life. Hence, this work contributes to the identification of gut microbial candidates relevant for preventive screening of healthy gut-brain development and microbiota-targeted interventions.},
}
@article {pmid42044128,
year = {2026},
author = {Zhou, Y and Trujillo-González, A and Nicol, S and Huerlimann, R and Sarre, SD and Gleeson, D},
title = {Diet and gut microbiome of skipjack tuna (Katsuwonus pelamis) as indicators of environmental changes.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346882},
pmid = {42044128},
issn = {1932-6203},
mesh = {Animals ; *Tuna/microbiology/physiology ; *Gastrointestinal Microbiome ; *Diet ; Pacific Ocean ; *Climate Change ; Ecosystem ; Food Chain ; },
abstract = {Understanding the relationship between environmental changes and marine ecosystem dynamics is crucial, especially under the influence of climate events such as the El Niño Southern Oscillation (ENSO). The diet and gut microbiome of marine predators have the potential to efficiently, timely, and reliably indicate impacts of environmental and ecosystem changes, especially with the assistance of high-throughput sequencing (HTS) technology. This study investigated the gut content and microbiome of skipjack tuna (Katsuwonus pelamis) collected in the central Pacific Ocean during a transitional period of ENSO phases, shifting from a strong La Niña phase to a weak El Niño phase, aiming to evaluate the impacts of ENSO and other environmental factors on marine food webs and microbiome dynamics of skipjack tuna. While prey diversity was unaffected by ENSO events, skipjack tuna exhibited high diversity and opportunistic foraging patterns, with fish as the primary prey. In contrast, gut microbiome diversity was affected by ENSO events and Southern Oscillation Index (SOI). Five microbiome families (Fusobacteriaceae, Bacillaceae, Propionibacteriaceae, Beijerinckiaceae, and Comamonadaceae), which are associated with immune system functionality and nutritional provisioning of the host, displayed the most significant abundance changes between ENSO phases. A random forest model showed potential for ENSO phase classification based on the abundances of these five families, achieve high accuracy in internal validation, though the performance of external validation was mixed due to storage and sampling period differences. This study highlights the potential of skipjack tuna gut microbiome as indicators of rapid environmental changes, while acknowledging that the short sampling period requires longer-term validation across multiple ENSO cycles.},
}
@article {pmid42044527,
year = {2026},
author = {Rabasco, JT and Bolyen, E and Caporaso, JG and Sapers, H and Callahan, BJ},
title = {Identify contaminants with decontam on the QIIME 2 Framework.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0126125},
doi = {10.1128/mra.01261-25},
pmid = {42044527},
issn = {2576-098X},
abstract = {Here, we present the integration of the decontam method for contaminant identification and a supplemental approach for identifying the source of contaminants in sequencing data within the QIIME 2 Framework for microbiome data science. We demonstrate its use in a tutorial based on the QIIME 2 "Moving Pictures Tutorial" data.},
}
@article {pmid42044645,
year = {2026},
author = {Shoemark, A and Johnson, ED and Shuttleworth, M and Schwiening, M and Hull, R and Stobo, J and Abo-Leyah, H and Finch, S and Pollock, J and Huang, JTJ and Richardson, H and Perea, L and McIntosh, E and Cant, E and Galloway, R and Choi, H and de Soyza, A and Spinou, A and Ringshausen, FC and Lorent, N and Mallia, P and Johnston, SL and Gierlinski, M and Goeminne, P and Loebinger, MR and Hua Gao, Y and Chotirmall, SH and Dhar, R and Haworth, C and Altenburg, J and Blasi, F and Polverino, E and Shteinberg, M and Strickson, S and Cipolla, D and Teper, A and Fernandez, C and Shih, VH and Mange, K and Singanayagam, A and Aliberti, S and Sibila, O and Long, MB and Chalmers, JD},
title = {Azurocidin-1 as a mediator of bronchiectasis severity, epithelial defence, and target of dipeptidyl peptidase-1 inhibition: an international, multicohort study.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(25)00334-0},
pmid = {42044645},
issn = {2213-2619},
abstract = {BACKGROUND: Dipeptidyl peptidase-1 (DPP1) inhibitors prevent the activation of neutrophil serine proteases and reduce exacerbations in people with bronchiectasis. We previously identified a novel effect of DPP1 inhibitors in reducing the neutrophil pseudoenzyme azurocidin-1 (AZU1). The aim of this study was to investigate the role of AZU1 in the pathophysiology of bronchiectasis.<br><br>METHODS: Sputum AZU1 concentrations were analysed in multiple cohorts. These consisted of two observational cohorts of patients with bronchiectasis (EMBARC BRIDGE cohort 1 and cohort 2) and a cohort of patients with chronic obstructive pulmonary disease (COPD; TARDIS COPD cohort) to correlate AZU1 with disease severity and exacerbations. A rhinovirus challenge study was used to investigate AZU1 concentrations during experimental exacerbation in COPD, people who smoke, and controls. A post-hoc analysis of the phase 2 WILLOW trial of brensocatib versus placebo was used to assess the effect of DPP1 inhibition on airway AZU1.<br><br>FINDINGS: Higher AZU1 sputum concentration was associated with increased bronchiectasis disease severity index (p<0&#xb7;0001), decreased percentage predicted forced expiratory volume in 1 second (r=-0&#xb7;4662, p<0&#xb7;001), and increased exacerbation frequency (p<0&#xb7;0019; EMBARC cohort 1, n=197). AZU1 was associated with radiological severity (Reiff score), symptoms (quality of life bronchiectasis respiratory symptom score), and bacterial infection (sputum microbiology and 16S microbiome alpha diversity; highest levels of AZU1 were found in airway samples with Pseudomonas aeruginosa; p<0&#xb7;0001; EMBARC cohort 2, n=144). Bronchiectasis patients with bacterial and viral exacerbations had increased concentrations of AZU1 (p=0&#xb7;0003; n=96). These findings were extended to COPD, in which AZU1 was related to COPD severity (COPD cohort, n=101), and in patients with COPD challenged with rhinovirus A16, AZU1 was increased at day 9 post-challenge (p<0&#xb7;001; n=9). In-vitro AZU1 impaired ciliary function and epithelial integrity, suggesting a mechanism by which AZU1 drives disease pathogenesis. In a post-hoc analysis of the WILLOW trial, AZU1 was the most downregulated protein with brensocatib treatment (brensocatib 10 mg, n=71; brensocatib 25 mg, n=73; and placebo, n=71). Over 24 weeks, AZU1 was significantly reduced by DPP1 inhibition (p<0&#xb7;0001).<br><br>INTERPRETATION: AZU1 was identified as a novel marker of disease severity in bronchiectasis, associated with bacterial infection and exacerbation, and targeted by DPP1 inhibition.<br><br>FUNDING: EMBARC3 and Insmed.},
}
@article {pmid42044680,
year = {2026},
author = {Maitan Santos, B and Estellé, J and Ramayo-Caldas, Y and Chadi, S and Barone, M and Chain, F and Kropp, C and Bridigi, P and Langella, P and Martín, R},
title = {Sex modulates the long-term effects of delivery mode on microbiota-gut barrier crosstalk and colitis susceptibility in mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2658276},
doi = {10.1080/19490976.2026.2658276},
pmid = {42044680},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Mice ; Disease Susceptibility ; *Colitis/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Sex Characteristics ; Sex Factors ; *Cesarean Section/adverse effects ; *Intestinal Mucosa/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Sexual dimorphism and mode of delivery are key determinants of gut physiology and microbiota development and may differentially affect predisposition to gut-related diseases. Cesarean section delivery markedly shapes early-life microbiota, predisposing individuals to higher risk of immune and metabolic comorbidities later in life. Although both sex and delivery mode are known to influence gut barrier-microbiota crosstalk, whether delivery mode modulates or counter-regulates sex-specific features of this interaction remains, to our knowledge, largely unexplored. Here, we investigated how sex impacts gut barrier-microbiota crosstalk shaped by delivery mode across development until adulthood by reanalyzing existing data. Using a preclinical mouse model, we combined gut barrier analyses with differential abundance and co-occurrence network approaches (LinDA and NetMoss). We found that the impact of CSD on gut barrier-microbiota crosstalk is partially dependent on sex and life stage. During the first days of life, delivery mode dictates immune imprinting and microbial network topology, with only limited sex effects. However, trajectories diverged with age, with CSD males exhibiting colitis reoccurrence in adulthood. By applying integrative strategies to stratify data by sex and development, our study uncovers short- and long-term sex-dependent gut barrier and microbial signatures. These findings reveal that delivery mode might program sex-specific host-microbiota trajectories with consequences for gut health and disease susceptibility, highlighting the need to consider sex and early-life microbial imprinting in future microbiome-targeted interventions.},
}
@article {pmid42044685,
year = {2026},
author = {Kooima, P and Oesterle, DA and Hematti, Y and Kay, DM and McFarlane, K and Roberts, JL},
title = {Gut microbiota depletion alters functional recovery and bone healing following fracture in mice.},
journal = {Bone},
volume = {},
number = {},
pages = {117907},
doi = {10.1016/j.bone.2026.117907},
pmid = {42044685},
issn = {1873-2763},
abstract = {Bone fracture pain evolves dynamically with tissue repair, yet current analgesic strategies are limited by adverse effects and concerns regarding impaired healing. The gut microbiome is an established regulator of pain and inflammation; however, its contribution to post-fracture recovery remains unclear. We tested whether antibiotic-induced microbiota depletion alters functional recovery and behavior after femoral fractures. Young female C57BL/6J mice received a broad-spectrum oral antibiotic cocktail or control water for two weeks prior to femoral fracture and were assessed longitudinally over 28 days after fracture. Microbiota depletion was associated with prolonged deficits in hindlimb loading and zone clearance performance, and continuous home-cage monitoring revealed decreased vertical rearing activity and voluntary wheel-running, collectively indicating sustained functional and motivational impairment. Despite a hypoinflammatory systemic and intestinal phenotype, microbiota-depleted mice exhibited elevated ipsilateral lumbar DRG expression of Ngf and Cxcl1 at Day 7 post-fracture alongside suppressed DRG Il10. NGF immunoreactivity was also elevated in the ipsilateral lumbar DRG of microbiota-depleted mice at the same timepoint. Microarchitectural analysis of fracture callus were suggestive of delayed secondary fracture healing. Together, these findings indicate that antibiotic-induced microbiota depletion was associated with altered inflammatory, behavioral, and skeletal responses after fracture. These results identify the gut microbiome as a potential contributor to the integrated pain-healing response to skeletal injury.},
}
@article {pmid42044842,
year = {2026},
author = {Al-Awadi, AA and Grove, JI and Bawden, S and Vijay, A and Valdes, AM and Gowland, P and Taylor, MA and Aithal, GP},
title = {The effect of a two-week low glycaemic index, higher fibre diet versus high glycaemic index diet on body composition, ectopic lipids, inflammatory biomarkers, gastrointestinal hormones and gut microbiota in Metabolic dysfunction-associated Steatotic Liver Disease (MASLD): A pilot randomized cross-over study.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {103306},
doi = {10.1016/j.clnesp.2026.103306},
pmid = {42044842},
issn = {2405-4577},
abstract = {Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) is a global health concern. Low glycaemic index (LGI) diets, which tend to be naturally higher in dietary fibre, may reduce liver fat, blood glucose, and gut microbiota imbalance arresting MASLD progression. We hypothesized that in patients with MASLD, an LGI diet, meeting estimated energy requirements, would reduce liver fat more than a high GI (HGI) diet, despite matched energy (isoenergetic) and macronutrient content. To test this, a 2×2 randomized cross-over trial was undertaken involving 7 participants with MASLD randomised (1:1 ratio) to a 2-week either high GI (HGI) or LGI diet followed by a 4-week wash-out period and then the opposite diet. The impact of the LGI diet on liver fat content, measured using Magnetic Resonance Spectroscopy ([1]H-MRS) liver-related blood biomarkers, appetite (using subjective visual analogue scales) and gut microbiome composition was identified. Relative liver fat fraction was markedly reduced following the LGI diet (8.57%).Observations in the LGI group coincided with changes in blood glycaemic biomarkers, including a significant reduction in HOMA-IR (-1.78, p=0.043). Additionally, the LGI diet resulted in significant reductions in body weight (-1.2 kg, p=0.018) and body mass index (-0.38 Kg/m[2], p=0.017), as well as increased pre-meal appetite scores during the middle of the diet period and decreased interleukin 6; IL-6 (-0.9 pg/mL) and glucagon (-13.7 pg/mL) levels (all p<0.05). In agreement with previous work in healthy participants, this study suggests that LGI diets reduce liver fat in patients with MASLD and may be an important factor in preventative care. REGISTRATION: This trial was registered on the website of ClinicalTrials.gov, number NCT04415632.},
}
@article {pmid42044997,
year = {2026},
author = {Sanyaolu, L and Ahmed, H and Santer, M and Jones, S and Hayward, G},
title = {Update to the management of recurrent urinary tract infections in women aged 16 years and older.},
journal = {Drug and therapeutics bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1136/dtb.2025.000042},
pmid = {42044997},
issn = {1755-5248},
abstract = {Recurrent urinary tract infections (rUTIs) are a burdensome condition affecting approximately 6% or 1.7 million women in the UK. UTIs are also a common reason for antibiotic use, with UK data demonstrating that they are the second most common reason for antibiotic prescribing after respiratory tract infections. UTIs also result in significant healthcare costs, with hospital admissions alone estimated to have cost the National Health Service in England over £600 million from 2023 to 2024. This review provides an up-to-date overview of the management of rUTIs, focusing on the updated 2024 National Institute for Health and Care Excellence guidance, which recommends a stepwise approach starting with behavioural measures, then progressing to non-antibiotic and finally antibiotic prevention. It also compares the guidance with international recommendations and outlines the current evidence on pathogenesis, diagnostic approaches and treatment options, including behavioural measures, non-antibiotic interventions (eg, vaginal oestrogen and methenamine hippurate) and antibiotic prophylaxis. Key challenges in primary care are discussed, such as diagnostic uncertainty, patient dissatisfaction and antimicrobial resistance (AMR). Emerging research in point-of-care testing, the urinary microbiome and novel therapies is also highlighted. This review aims to support safe prescribing, improve patient satisfaction and mitigate AMR by promoting antimicrobial and diagnostic stewardship in the management of rUTIs.},
}
@article {pmid42045370,
year = {2026},
author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB},
title = {Author Correction: Unbinned contigs expand known diversity in the global microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-026-02354-y},
pmid = {42045370},
issn = {2058-5276},
}
@article {pmid42045408,
year = {2026},
author = {Kutuzova, S and Piera Líndez, P and Danielsen, LS and Nielsen, KN and Olsen, NS and Riber, L and Gobbi, A and Forero-Junco, LM and Erdmann Dougherty, P and Westergaard, JC and Browne, PD and Christensen, S and Hestbjerg Hansen, L and Nielsen, M and Nybo Andersen, J and Rasmussen, S},
title = {Improving metagenome binning by integrating intrinsic features and taxonomy.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42045408},
issn = {1546-1696},
support = {NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 7076-00129B//Innovationsfonden (Innovation Fund Denmark)/ ; },
abstract = {A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. State-of-the-art binning methods use coabundance and sequence-based motifs such as tetranucleotide frequencies, whereas taxonomic labels derived from alignment based classification have not been widely used. Here we propose TaxVAMB, a metagenome binning tool based on semisupervised bimodal variational autoencoders, combining tetranucleotide frequencies and contig coabundances with taxonomic information. TaxVAMB outperformed all other binners on CAMI2 human microbiome datasets, returning on average 29% more high-quality assemblies than the next best binner, and performed on par with the best binners on short-read datasets. On a human gut long-read dataset, TaxVAMB recovered 29% more high-quality bins. In a typical single-sample setup, TaxVAMB on average returns 83% more high-quality bins compared to VAMB. Lastly, TaxVAMB binned incomplete genomes better than any other tool, returning on average 300% more high-quality bins of incomplete genomes than the next best binner.},
}
@article {pmid42045433,
year = {2026},
author = {Reisinger, SN and Kong, G and van de Garde, N and Muhammad, A and Adithya, P and Lu, D and Kiridena, P and Gubert, C and Dabscheck, G and Payne, JM and Hannan, AJ},
title = {Gut microbiome alterations are sex-dependently associated with brain abnormalities in a mouse model of Neurofibromatosis type I.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {42045433},
issn = {1476-5578},
abstract = {Neurofibromatosis type 1 (NF1) is a genetic condition presenting with variable symptomatology, however most individuals will demonstrate cognitive and behavioural difficulties, including autism. Using a heterozygous germline knockout mouse model of NF1 (Nf1 +/-), we performed in-depth behavioural evaluations encompassing learning and memory, stereotypy, social interaction, anxiety- and depression-like behaviour. Anatomical and functional studies of the brain and gastrointestinal tract were followed by the first investigation of gut microbiota composition (via full-length 16S rRNA sequencing) in a Nf1 +/- mouse model. The cognitive and autism-like behavioural phenotype seen in Nf1 +/- mice was accompanied by a striking increase in relative brain size which is highly relevant to clinical NF1. Furthermore, brain size was correlated with behaviour, supporting a potential mechanistic link. Nf1 +/- mice showed significant alterations in gut microbiota composition vs. Nf1 +/+ wild-type controls, with males additionally showing significant changes to species abundance of the Clostridium and Blautia genera, and the Lachnospiraceae family, findings which partially overlap with those in preclinical and clinical autism. Composition of associated functional pathways was not globally altered, however +/- mice showed significant changes in a pyrimidine deoxynucleotide biosynthesis pathway. In male Nf1 +/- mice, we also identified a genotype-specific host-microbial signature, pointing towards a mechanistic link between gut microbiome composition and brain size. These findings significantly expand our understanding of brain and behavioural abnormalities in this preclinical model of NF1 and, importantly, have uncovered the gut microbiome as a highly promising new area of research and a potential therapeutic target for these symptom clusters.},
}
@article {pmid42045512,
year = {2026},
author = {Moghadam, Z and Doraghi, M and Fallahizadeh, S and Badeenezhad, A and Alinehjad, N and Parseh, I},
title = {Enhanced phytoremediation of crude oil-contaminated soil using Cynodon dactylon with nutrient and mixed liquid suspended solids amendments.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50261-3},
pmid = {42045512},
issn = {2045-2322},
support = {98065//Behbahan Faculty of Medical Sciences/ ; },
}
@article {pmid42045563,
year = {2026},
author = {Mai, H and Wang, Y and Zhu, Y and Zhao, Y and Chen, Y and Hoeher, L and Al-Maskari, R and Luo, J and Erturk, A},
title = {Whole-mouse immunolabeling at cellular resolution for comprehensive 3D atlases.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {42045563},
issn = {1750-2799},
abstract = {Mapping complex biological systems and tracking disease progression at high resolution across the entire mammalian body has remained technically challenging. Here, to address this, we present wildDISCO (immunolabeling of wild-type mice and DISCO clearing), a comprehensive protocol for whole-body immunolabeling, optical clearing and imaging of mice at cellular resolution using standard IgG antibodies. This protocol optimizes tissue permeabilization using cyclodextrin as a potent enhancer of cholesterol extraction and membrane permeabilization, enabling deep antibody penetration across all organs. We detail procedures for sample preparation, tissue decolorization and decalcification, whole-body immunostaining, clearing, and subsequent 3D imaging, virtual reality visualization and whole-mouse atlas construction. The method allows comprehensive mapping of neuronal, vascular, lymphatic and immune systems, as well as systemic studies in disease models, including cancer and microbiome-host interaction studies. We anticipate that wildDISCO will serve as a broadly applicable platform for generating whole-body cellular atlases, enabling systems-level investigations of health and disease. Only standard immunohistochemistry facilities are required, but successful implementation may require initial technical training, particularly for researchers with limited prior experience in tissue clearing or 3D imaging workflows. From start to finish, the procedure takes 4 weeks.},
}
@article {pmid42045628,
year = {2026},
author = {Snir, A and Schwarzman, P and Wainstock, T and Sheiner, E},
title = {Offspring long-term infectious morbidity following pregnancies with cervical cerclage.},
journal = {Archives of gynecology and obstetrics},
volume = {313},
number = {1},
pages = {},
pmid = {42045628},
issn = {1432-0711},
mesh = {Humans ; Female ; *Cerclage, Cervical/adverse effects/statistics &amp; numerical data ; Pregnancy ; Retrospective Studies ; Adult ; Premature Birth/prevention &amp; control ; Kaplan-Meier Estimate ; Proportional Hazards Models ; Infant, Newborn ; *Uterine Cervical Incompetence/surgery ; Incidence ; Young Adult ; },
abstract = {INTRODUCTION: Cervical cerclage is an acceptable procedure in women with cervical insufficiency and is known to be effective in the prevention of preterm delivery. However, limited data exist regarding long-term health outcomes among offspring exposed to cerclage during pregnancy. Since the presence of a foreign body during pregnancy may change the vaginal microbiome, we aimed to study whether a cervical cerclage is associated with long-term infectious morbidity of the offspring.<br><br>STUDY DESIGN: A retrospective population-based cohort study was performed at a tertiary medical center, including all singleton deliveries between the years 1991-2021. Long-term infectious morbidity was compared among offspring after pregnancies with and without cervical cerclage. The diagnoses of infectious morbidities were defined based on ICD-9 codes as recorded in community clinics and hospitalization files. A Kaplan-Meier survival curve was utilized to evaluate the cumulative incidence. A Cox proportional hazards model was used to control for confounders.<br><br>RESULTS: Out of 356,356 offspring included in the analysis, 0.4% (n&#x2009;=&#x2009;1416) were following pregnancies with cervical cerclage. Unadjusted analyses demonstrated no significant difference in total infectious morbidity between the groups (OR 1.0, 95% CI 0.9-1.1; p&#x2009;=&#x2009;0.369, Table 1). Kaplan-Meier analysis showed no difference in cumulative incidence (log-rank test P-value&#x2009;=&#x2009;0.19, Fig.&#xa0;1). In the primary analysis, cerclage was not associated with long-term infectious morbidity. However, in a secondary model, after adjustment for confounders including gestational age, obesity and diabetes, cerclage exposure was associated with a modest reduction in the risk of long-term infectious morbidity (adjusted HR 0.9, 95% CI 0.87-0.99, p&#x2009;=&#x2009;0.036).<br><br>CONCLUSION: In this large population-based cohort, cervical cerclage was not associated with increased long-term infectious morbidity in offspring. A modest association with reduced infectious morbidity was observed after adjustment for confounding factors. These findings should be interpreted cautiously given the observational design and potential residual confounding.},
}
@article {pmid42045676,
year = {2026},
author = {Wood, GV and Liddicoat, C and Robinson, JM and Breed, MF},
title = {Restoring soil and sediment microbiomes in the Anthropocene.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42045676},
issn = {1740-1534},
abstract = {Soil and sediment microbiomes have a central role in biogeochemical cycling, climate regulation and ecosystem resilience. However, they are increasingly degraded by land use change, pollution and climate change. Despite their foundational roles in ecosystems, these microbiomes remain under-represented in ecosystem restoration science, practice and policy. Improving the integration of microbiomes across the restoration science-practice-policy nexus is essential for achieving more effective and resilient restoration outcomes. Without this, global restoration risks neglecting the microbial foundations of functional ecosystems and long-term resilience. In this Review, we synthesize the current state of knowledge of soil and sediment microbiome restoration. We describe the major anthropogenic stressors that are degrading these microbiomes, highlighting the linked and context-dependent nature of these impacts, and evaluate existing strategies to restore them. To improve restoration effectiveness, we propose a research workflow that encompasses baseline establishment, degradation diagnostics, designing and testing interventions, research methodology selection and best practice principles. We also outline key theoretical frameworks and propose future research priorities to help soil and sediment microbiome restoration to move towards a predictive, theory-led discipline.},
}
@article {pmid42045695,
year = {2026},
author = {da Silva, JB and Câmara, PEAS and Rosa, LH and Oliveira, VM},
title = {Disentangling bacterial diversity and biogeography in snow-covered regions.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42045695},
issn = {1573-0972},
abstract = {UNLABELLED: This study investigated the bacterial diversity of snow-inhabiting microbial communities across multiple geographic locations, including Antarctic and temperate regions. Using high-throughput sequencing of the 16S rRNA gene from Antarctic snow samples and comparisons with publicly available datasets from other cold regions worldwide, we assessed patterns of taxonomic diversity and the influence of geographic and environmental factors on snow bacterial communities. Our results revealed that bacterial communities from Martel Inlet (King George Island) exhibited lower diversity compared to other Antarctic sites, likely influenced by the geographic characteristics. In contrast, snow microbial communities from temperate regions such as Austria, Quebec, and Iceland showed higher diversity, potentially driven by overlapping environmental conditions including temperature range, snow dynamics, and seasonal variability. Network analyses revealed distinct interaction patterns among regions, with more dynamic and competitive microbial networks observed in Maritime Antarctic environments, while continental snow ecosystems exhibited more compartmentalized and stable network structures. Overall, our findings highlight the combined influence of geographic distance and environmental conditions in shaping microbial diversity and ecological interactions in snow ecosystems across different regions of the globe.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11274-026-04918-w.},
}
@article {pmid42045813,
year = {2026},
author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , },
title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05101-9},
pmid = {42045813},
issn = {1471-2180},
}
@article {pmid42045958,
year = {2026},
author = {Huang, J and Chen, Z and Wang, M and Yang, C and Wang, A and Chen, Y},
title = {Efficacy and safety of fecal microbiota transplantation in reducing recurrence of colorectal adenomas after endoscopic resection: study protocol for a multicenter, open-label, randomized, no-treatment-controlled trial.},
journal = {Trials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13063-026-09740-1},
pmid = {42045958},
issn = {1745-6215},
support = {C2401027//Shenzhen Medical Research Fund/ ; },
abstract = {BACKGROUND: Endoscopic resection is the standard treatment for colorectal adenoma (CRA), a key precursor to colorectal cancer (CRC). However, a high rate of recurrence post-procedure poses a significant challenge for long-term CRC prevention. Growing evidence suggests gut microbial dysbiosis contributes to adenoma development and recurrence. This trial will test the hypothesis that restoring a healthy gut microbiome with fecal microbiota transplantation (FMT) can reduce the recurrence of CRA after endoscopic resection.<br><br>METHODS: This protocol describes a multicenter, open-label, randomized, no-treatment-controlled trial that will enroll 466 participants with CRA following endoscopic resection. Participants will be randomly assigned in a 1:1 ratio to receive either FMT or no treatment (control). The FMT intervention consists of an initial colonoscopic infusion and oral capsules, followed by oral maintenance capsules at months 3, 6, and 9. The primary outcome is the rate of CRA recurrence at the 12-month follow-up colonoscopy. Key secondary outcomes include the incidence of all polypoid lesions, changes in the gut and mucosal microbiota composition, the incidence of CRC, and a comprehensive assessment of adverse events to evaluate safety.<br><br>DISCUSSION: This trial is designed to provide high-quality evidence on the efficacy and safety of FMT for preventing CRA recurrence. The findings may support a novel, microbiome-based strategy for the secondary prevention of CRC and provide mechanistic insights into the role of the gut microbiota in colorectal carcinogenesis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT06205862. Registered on 16 January, 2024. https://clinicaltrials.gov/study/NCT06205862.},
}
@article {pmid42045979,
year = {2026},
author = {Deng, Y and Chen, R and Gao, X and Wu, H and He, N and Hu, N and Zhang, W and Chen, L and Zheng, X and Jiang, J},
title = {Tissue-resident Limosilactobacillus reuteri modulates intratumoral arachidonic acid metabolism to enhance CD8[+] T cell-mediated anti-PD1 response.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08170-6},
pmid = {42045979},
issn = {1479-5876},
}
@article {pmid42046041,
year = {2026},
author = {Thomas, LF and Panaretos, C and Scott, MA and Valeris-Chacin, R and Cook, WE},
title = {Distinct host-pathogen and microbiome responses of aoudad (Ammotragus lervia) and bighorn sheep (Ovis canadensis) following exposure to Mycoplasma ovipneumoniae with or without co-exposure to leukotoxigenic Pasteurellaceae.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05375-1},
pmid = {42046041},
issn = {1746-6148},
}
@article {pmid42046057,
year = {2026},
author = {Hsu, CY and Abdelgawwad El-Sehrawy, AAM and Alshkarchy, SS and Abdul, AS and Ganesan, S and Gupta, PK and Sharma, R and Nayak, PP and Ebrahimpour, A and Khazaei, Y},
title = {Innovative approaches in the treatment of hematologic malignancies: the role of CRISPR-engineered microbiomes along the gut-immune axis in immunotherapy development.},
journal = {Cancer cell international},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12935-026-04316-0},
pmid = {42046057},
issn = {1475-2867},
}
@article {pmid42046285,
year = {2026},
author = {Miyamoto, S and Yoshimoto, S and Katsumata, N and Mutoh, N and Iwabuchi, N and Odamaki, T and Asaoka, D and Machida, S},
title = {Bifidobacterium longum BB536 is associated with improvements in gastrointestinal symptoms and odor-related metabolites in microbiota-defined subgroups of male athletes consuming a high-protein diet: exploratory randomized double‑blind placebo‑controlled trial.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {23},
number = {1},
pages = {2664664},
doi = {10.1080/15502783.2026.2664664},
pmid = {42046285},
issn = {1550-2783},
mesh = {Humans ; Male ; Double-Blind Method ; *Gastrointestinal Microbiome ; *Probiotics/administration &amp; dosage ; *Bifidobacterium longum ; Adolescent ; *Odorants ; Feces/microbiology/chemistry ; *Diet, High-Protein/adverse effects ; Young Adult ; Athletes ; Volatile Organic Compounds/analysis ; *Gastrointestinal Diseases ; Whey Proteins/administration &amp; dosage ; },
abstract = {BACKGROUND: High‑protein diets are widely used by athletes but may disturb the gut environment and increase production of odor‑related metabolites. Probiotic supplementation has been proposed as a strategy to support gastrointestinal function under such dietary stress. This study aimed to explore the effects of Bifidobacterium longum BB536 on gastrointestinal symptoms, gut microbiota, and odor‑related metabolites in male athletes consuming a high‑protein diet.<br><br>METHODS: In an exploratory, randomized, double&#x2011;blind, placebo&#x2011;controlled trial, 60 healthy male athletes (mean age: 18.62&#x2009;&#xb1;&#x2009;0.75 years; mean BMI: 22.35&#x2009;&#xb1;&#x2009;1.80&#x2009;kg/m[2]) consumed a whey protein supplement (70 g/day) together with either BB536 (46 billion CFU/day, as measured at the start of the intervention) or placebo for 4 weeks. Gastrointestinal symptoms, gut microbiota composition, skin&#x2011;emitted volatile compounds, and fecal metabolites were assessed. Subgroup analyses based on responder status and baseline enterotype were conducted post hoc to generate hypotheses regarding microbiota&#x2011;dependent responses.<br><br>RESULTS: In the overall cohort, no significant between&#x2011;group differences were observed across gastrointestinal outcomes, gut microbiota indices, or metabolite profiles. Within the BB536 group, diarrhea&#x2011;related scores improved from baseline. Post hoc analyses suggested that increases in Faecalibacterium were evident among responders. Enterotype&#x2011;based patterns also emerged: individuals with Ruminococcus&#x2011;dominant microbiota showed higher skin&#x2011;emitted short&#x2011;chain fatty acids after BB536 intake, whereas those with Faecalibacterium&#x2011;dominant microbiota exhibited reductions in odor&#x2011;related metabolites, including methyl mercaptan and ammonia. Corresponding fecal metabolite shifts were modest.<br><br>CONCLUSION: BB536 supplementation was associated with improvements in diarrhea&#x2011;related symptoms and odor&#x2011;related metabolites in specific microbiota&#x2011;defined subgroups. As these findings did not extend to the full cohort, they should be interpreted as exploratory and hypothesis&#x2011;generating. Baseline gut microbiota composition may influence probiotic responsiveness, warranting confirmatory trials with prespecified endpoints.},
}
@article {pmid42046303,
year = {2026},
author = {Sun, S and He, Y and Deng, Y and Wang, J},
title = {Urinary Microbiome Characteristics in Kidney Transplant Recipients and Their Clinical Implications: A Narrative Review.},
journal = {Annals of transplantation},
volume = {31},
number = {},
pages = {e952286},
doi = {10.12659/AOT.952286},
pmid = {42046303},
issn = {2329-0358},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Microbiota ; Dysbiosis/microbiology ; *Urinary Tract/microbiology ; Graft Rejection/microbiology ; Transplant Recipients ; Urinary Tract Infections/microbiology ; *Urine/microbiology ; },
abstract = {High-throughput sequencing has overturned the long-standing "sterile urine" paradigm and revealed a low-biomass yet clinically informative urinary tract microbiota. In kidney transplant recipients, immunosuppression, perioperative instrumentation, and antibiotic exposure can reshape urinary microbial communities; however, reported signatures remain heterogeneous across cohorts and methodologies. This narrative review synthesizes evidence on: (1) baseline urobiome patterns and major determinants of inter-individual variability, (2) post-transplant drivers of dysbiosis, and (3) associations between urobiome dynamics and key transplant outcomes, including urinary tract infection (UTI), acute rejection (AR), and chronic allograft dysfunction such as interstitial fibrosis and tubular atrophy (IF/TA). Across studies, dysbiosis commonly manifests as reduced diversity, depletion of putatively protective taxa, and enrichment of opportunistic pathogens; several longitudinal cohort studies further suggest that microbiome shifts can precede clinical events, supporting a potential window for risk stratification and early surveillance. We also summarize translational research directions, including integration of urinary microbial profiles with host biomarkers and multi-omics readouts, as well as microbiome-sparing strategies (antimicrobial stewardship, targeted probiotics/synbiotics, and dietary modulation). Finally, we highlight methodological challenges unique to low-biomass urine samples - especially contamination control, negative controls, and transparent reporting - that are essential for improving reproducibility and enabling clinical implementation. This review aims to provide an up-to-date, clinically oriented synthesis of the post-transplant urobiome and to propose methodological and translational priorities for future research and implementation.},
}
@article {pmid42046343,
year = {2026},
author = {Jiang, L and Li, T and Wu, J and Lau, HCH and Wong, CC and Zhou, X and Cheung, AHK and Wei, Q and Ren, J and Zhang, X and Li, Q and Nie, Y and Yu, J},
title = {Dietary nitrate drives gastritis by modulating gastric microbiota and metabolites.},
journal = {Cancer biology &amp; medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0679},
pmid = {42046343},
issn = {2095-3941},
support = {2023ZD0501400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 82472896//National Natural Science Foundation of China/ ; 3133344//Strategic Seed Funding Collaboration Research Scheme CUHK/ ; 3135509//Strategic Impact Enhancement Fund CUHK/ ; 3134277//Impact Case for RAE CUHK/ ; },
abstract = {OBJECTIVE: Dietary nitrate has been increasingly recognized as a potential carcinogen associated with gastritis. In this study the mechanistic role of a high-nitrate diet (NaD) in driving gastritis was elucidated with a focus on modulation of the gastric microbiota composition and metabolomic profiles.<br><br>METHODS: Animals were randomly assigned to two dietary intervention groups using a C57BL/6 mouse model: a NaD containing 7.5% nitrate; or a standard normal diet (ND). Gastric microbiota composition was characterized based on full-length 16S rRNA sequencing and gastric metabolite profiles were analyzed using high-performance liquid chromatography-mass spectrometry (HPLC/MS). Finally, the roles of the microbiome and metabolites in gastritis development were validated using the human gastric epithelial cell line (GES-1), as well as conventional and germ-free mouse models.<br><br>RESULTS: NaD induced gastritis in conventional mice compared to ND-fed mice. In addition, NaD incited the infiltration of macrophages and neutrophils with elevated levels of inflammatory cytokine genes (IL-17a, Ccl20, Cxcl5, IL-6, and Ccl2). A significant shift in the composition of the gastric microbiota occurred with an increase in pathogenic bacteria (Enterococcus gallinarum, Prevotella timonensis, and Mycobacterium gordona) and a decrease in probiotics (Roseburia hominis, Clostriduim scindens, and Faecalibacterium prausnitzii). Furthermore, NaD induced alterations in the metabolic profile, marked by an elevated level of 5-hydroxyindoleacetate (5-HIAA), a key downstream metabolite of the tryptophan metabolic pathway. Notably, 5-HIAA also upregulated the levels of inflammatory cytokines in the human gastric epithelial GES-1 cell line. In addition, both E. gallinarum colonization and 5-HIAA exposure significantly increased inflammatory responses in conventional and germ-free mouse models.<br><br>CONCLUSIONS: NaD drives gastritis in mice by inducing gastric microbial dysbiosis and metabolomic dysregulation with elevated 5-HIAA.},
}
@article {pmid42046474,
year = {2026},
author = {Allaham, S and Mohamed, S and Yusuf, M and Abdillahi, A},
title = {Early-Life Viral Lower Respiratory Tract Infections and Their Impact on Childhood Asthma: Molecular Endotypes and Prevention Strategies.},
journal = {Pediatric allergy, immunology, and pulmonology},
volume = {},
number = {},
pages = {2151321X261445781},
doi = {10.1177/2151321X261445781},
pmid = {42046474},
issn = {2151-3228},
abstract = {Background: Early-life viral lower respiratory tract infections (LRTIs), particularly those caused by respiratory syncytial virus (RSV) and human rhinovirus (HRV), are major contributors to pediatric morbidity and are strongly linked to asthma. RSV causes about 3.6 million hospitalizations and 100,000 deaths annually in children under 5, mainly in low- and middle-income countries. RSV peaks in infancy, while HRV has more impact later in childhood. Mechanisms include viral epithelial injury, genetic susceptibility (e.g., 17q21 variants), and environmental factors (e.g., allergic sensitization). Together, these raise asthma risk. Diagnosis is difficult due to overlapping presentations and reliance on molecular tests. Preventive strategies include maternal RSV vaccination, long-acting monoclonal antibodies such as nirsevimab and palivizumab, and pediatric vaccine candidates. Strategies to limit allergic sensitization may lower HRV-related asthma risk. Long-term effects include persistent wheeze and asthma, making early life a crucial window for prevention.Methods: This review summarizes current evidence on the epidemiology, mechanisms, and long-term impact of early viral LRTIs.Results: It highlights molecular and immunological endotypes of virus-induced asthma and explores the influence of genetic, epigenetic, and microbial factors. Emerging diagnostic tools and preventive strategies-including vaccines, monoclonal antibodies, environmental interventions, and microbiome-targeted therapies-are also discussed as means to reduce the global pediatric asthma burden and improve respiratory health.},
}
@article {pmid42046516,
year = {2026},
author = {Chowdhury, I and Massay, R and Stubbs, A},
title = {Food additives, emulsifiers, microplastics, and ultra-processed foods in rheumatic disease pathogenesis.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOR.0000000000001161},
pmid = {42046516},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: Dietary patterns have changed significantly over time, with ultra-processed foods now comprising a large proportion of daily energy intake in many countries. Ultra-processed foods (UPFs) contain numerous additives and may also increase exposure to processing- and packaging-related contaminants that could influence immune function. This review summarizes why UPFs have drawn growing attention and evaluates their potential relevance to autoimmune inflammation, with a focus on rheumatoid arthritis (RA) and related disorders.<br><br>RECENT FINDINGS: Population studies suggest that higher UPF intake is associated with an increased risk of RA after adjustment for obesity and lifestyle factors. Experimental and translational studies suggest that components common in UPF-rich diets (e.g., emulsifiers, thickeners, synthetic colorants, added sugars, excess sodium, and some nonnutritive sweeteners), as well as microplastic exposures, may disrupt gut barrier integrity, remodel the microbiome, and promote low-grade inflammation. These mechanisms overlap with pathways implicated in RA and systemic inflammation, including dysregulation of Treg/Th17 balance, loss of mucosal tolerance, endotoxemia, and innate immune activation.<br><br>SUMMARY: Overall, evidence supports biologically plausible mechanisms and epidemiologic associations linking UPF-rich dietary patterns to immune dysregulation relevant to rheumatic disease, but direct RA-specific interventional and mechanistic clinical data remain limited. Dietary exposures may represent modifiable risks; however, stronger longitudinal studies with validated RA phenotyping and pragmatic dietary interventions are needed before firm clinical recommendations can be made.},
}
@article {pmid42046678,
year = {2026},
author = {Dayrit, G and Mabrok, M and Chaiyapechara, S and Rodkhum, C},
title = {Habitat-structured fungal mycobiomes at the water-gill interface of farmed red tilapia in Central Thailand: An internal transcribed spacer rRNA amplicon sequencing study.},
journal = {Veterinary world},
volume = {19},
number = {3},
pages = {1196-1214},
pmid = {42046678},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Tilapia aquaculture is rapidly expanding across Southeast Asia and plays a critical role in regional food security. While bacterial microbiomes of farmed fish have been widely investigated, the fungal component of aquatic microbial communities remains poorly characterized, particularly at the biologically important interface between rearing water and fish gills. Fungi may influence fish health, environmental microbial ecology, and occupational exposure risks within aquaculture systems. This study aimed to characterize fungal mycobiomes associated with rearing water and gills of clinically healthy red tilapia (Oreochromis spp. hybrids) cultured in Central Thailand using internal transcribed spacer (ITS) rRNA amplicon sequencing and to determine how habitat type, farming system, and environmental variables shape fungal community structure.<br><br>MATERIALS AND METHODS: Samples were collected from ten tilapia farms located in five provinces of Central Thailand, representing two aquaculture systems: open river cages and closed earthen ponds. A total of 27 rearing water samples and 30 composite gill samples were analyzed. Fungal DNA was extracted and the ITS1 region was amplified and sequenced using the Illumina MiSeq platform. Sequence processing and amplicon sequence variant inference were performed in QIIME2 using the DADA2 pipeline. Alpha diversity indices and beta diversity analyses were used to evaluate community structure, while multivariate statistical approaches assessed the influence of habitat type, geographic location, farming style, and physicochemical water parameters.<br><br>RESULTS: Fungal communities displayed considerable taxonomic diversity and differed significantly between habitats. Rearing water samples exhibited significantly higher alpha diversity than gill-associated communities. Dominant genera included Cladosporium, Candida, Aspergillus, Fusarium, and Rhodotorula. Gill communities were relatively enriched in Candida and Fusarium, whereas rearing water contained higher abundances of Cladosporium and Rhodotorula. Beta diversity analyses demonstrated significant effects of sampling source, province, and farming system on fungal community composition. Environmental parameters such as pH, nitrate concentration, and ionic strength were associated with variations in fungal diversity, particularly in rearing water. Several detected genera included taxa with known opportunistic pathogenic potential for fish and humans.<br><br>CONCLUSION: This study provides the first ITS-based baseline characterization of fungal mycobiomes associated with red tilapia aquaculture systems in Central Thailand. Distinct fungal assemblages occur at the water-gill interface, with environmental conditions and aquaculture practices influencing community composition. The presence of opportunistic fungal genera highlights the importance of incorporating fungal community monitoring into aquaculture biosecurity and One Health surveillance frameworks to support sustainable fish production, environmental health, and occupational safety.},
}
@article {pmid42046684,
year = {2026},
author = {Dehghan, H and Moghaddaszadeh-Ahrabi, S and Hashemzadeh-Farhang, H and Shahbazi, P and Nobari, B},
title = {Synergistic effects of Ferula asafoetida extract and condensed tannins from raisin pomace on in vitro cecal fermentation kinetics and nutrient digestibility in horses.},
journal = {Veterinary world},
volume = {19},
number = {3},
pages = {905-919},
pmid = {42046684},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The equine hindgut depends on microbial fermentation for efficient nutrient utilization but remains vulnerable to dysbiosis, hindgut acidosis, and suboptimal fiber digestion. Growing restrictions on antibiotic and synthetic feed additives have increased interest in natural phytogenic compounds. Medicinal plant extracts and condensed tannins are promising candidates to modulate microbial activity, improve fermentation efficiency, and enhance nutrient digestibility. This study aimed to investigate the individual and combined effects of hydroalcoholic extract of Ferula asafoetida and condensed tannins extracted from raisin pomace on equine cecal fermentation parameters and nutrient utilization using in vitro gas production and batch culture techniques.<br><br>MATERIALS AND METHODS: A 2 &#xd7; 2 factorial in vitro design was used with four treatments: control (C; basal diet only), F. asafoetida extract (A; 30 mg), condensed tannins from raisin pomace (G; 50 mg), and their combination (A &#xd7; G). Fecal inoculum was collected from four healthy 14-month-old Arabian geldings adapted for 14 days to a forage-based maintenance diet. Fermentation kinetics were evaluated over 120 h using the in vitro gas production technique and fitted to the Gompertz model. Parallel batch cultures measured pH, ammonia-nitrogen (NH3-N), and apparent disappearances of dry matter (DM), crude protein (CP), acid detergent fiber (ADF), and neutral detergent fiber (NDF). Data were analyzed using PROC GLM in SAS with Tukey-Kramer post-hoc tests (p < 0.05).<br><br>RESULTS: Cumulative gas production at 120 h was significantly higher in G (340.5 mL) and A &#xd7; G (340.3 mL) than in C (228.8 mL) (p < 0.01), with faster fermentation rates and shorter lag times (p < 0.01). Terminal pH values remained stable (6.33-6.40) across treatments with no indication of acidosis. NH3-N concentrations were elevated in G (26.0 mg/dL) and A &#xd7; G (25.5 mg/dL) compared with C (24.5 mg/dL) (p < 0.01). Apparent digestibility improved markedly: DM increased from 64.5% (C) to 70.3% (G), CP from 60.3% (C) to 66.9% (G), with parallel positive trends observed for ADF and NDF (p < 0.01).<br><br>CONCLUSION: Supplementation with F. asafoetida extract and condensed tannins from raisin pomace, especially in combination, enhanced fermentation efficiency, accelerated substrate degradation, and improved nutrient digestibility while maintaining stable pH in an in vitro equine cecal model. These findings indicate strong potential for these phytogenic compounds as sustainable natural feed additives to optimize equine hindgut function. In vivo validation, dose optimization, and long-term microbiome studies are recommended to confirm practical efficacy and safety in horses.},
}
@article {pmid42046757,
year = {2026},
author = {Gao, RY},
title = {Targeting gut immunity as a therapy for steatotic liver disease.},
journal = {eGastroenterology},
volume = {4},
number = {2},
pages = {e100404},
pmid = {42046757},
issn = {2976-7296},
}
@article {pmid42046871,
year = {2026},
author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q},
title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.},
journal = {Journal of Zhejiang University. Science. B},
volume = {27},
number = {4},
pages = {375-389},
pmid = {42046871},
issn = {1862-1783},
support = {2021YFA0805904//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Mice ; Germ-Free Life ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Metagenomics ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Mice, Inbred C57BL ; Female ; },
abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.},
}
@article {pmid42046931,
year = {2026},
author = {Zhang, F and Lard, ML and Khachatryan, L and Guo, C and Sandifer, A and Villafuerte, NM and Nde, DB and Cook, RL and Cormier, SA and Richmond-Bryant, J},
title = {Shifts in soil microbiome surrounding a thermal treatment facility for hazardous waste: the hidden impact of environmentally persistent free radicals.},
journal = {Environmental science. Processes &amp; impacts},
volume = {},
number = {},
pages = {},
pmid = {42046931},
issn = {2050-7895},
abstract = {The disposal of hazardous materials from Superfund sites often involves thermal treatment (TT), generating environmentally persistent free radicals (EPFRs). While substantial evidence links EPFR exposure to negative health outcomes, its effects on the soil microbiome remain underexplored. Since the mid-1980s, a TT facility in Colfax, LA, has employed open-burn and open-detonation to process hazardous waste. In 2023, we collected soil samples from 13 residential sites within a 17-km radius of the TT facility and analyzed microbial communities and EPFR content. Our findings revealed a distinct microbial community near the TT facility (within 5-km), characterized by reduced bacterial abundance and increased fungal presence. Soil EPFR concentrations ranged from 0.81 × 10[16]-4.39 × 10[16] spins per g with g-factor values of 2.0033-2.0040, indicating a mixture of carbon-centered radicals with adjacent oxygen and oxygen-centered radicals. Correlation analysis identified bacterial taxa, particularly Alpha-proteobacteria and Actinobacteria, positively associated with EPFR abundance. In vitro tests showed that laboratory generated EPFRs more strongly inhibited bacterial growth than fungal growth, though some bacterial isolates from the study sites exhibited resistance to EPFR exposure. The differences in microbial responses to EPFR exposure may contribute to the shifts in microbial communities near the TT facility. Our study advances the understanding of EPFR impacts on the soil microbiome and suggests potential long-term effects on environmental and community health.},
}
@article {pmid42047038,
year = {2026},
author = {Marsh, EB and Lavretsky, H and Kasparian, NA and Pike, NA and Doyle, KP and Aggarwal, NT and Fullerton, HJ and Ivy, AS and Dlamini, N and , },
title = {Brain Health Across the Life Span: A Framework for Future Studies: A Scientific Statement From the American Heart Association.},
journal = {Stroke},
volume = {},
number = {},
pages = {},
doi = {10.1161/STR.0000000000000518},
pmid = {42047038},
issn = {1524-4628},
abstract = {The concepts of brain health (ie, optimal functioning of the brain across cognitive, emotional, and behavioral domains throughout life) and cognitive resilience (ie, the ability of the brain to recover after an insult) have become increasingly important as the population ages. Previous research has called attention to vascular risk factors underlying cerebrovascular disease, as well as modifiable variables that contribute to premature aging and cognitive dysfunction. In this scientific statement, we focus on the role of nonvascular physical and psychologic variables that affect brain health across the life span. We provide a broad overview of influences such as chronic medical conditions, inflammation, environmental exposures, and socioeconomic drivers that affect the developing brain, along with factors including sleep quality, the gut microbiome, and mental health that contribute to neurodegeneration. We also review the varying strength of evidence supporting biologic mechanisms and mitigating strategies that may help optimize resilience, with the goal of providing a framework for future studies.},
}
@article {pmid42047173,
year = {2026},
author = {Zhang, N and Wang, Z and Yang, F and Liu, T and Ji, D},
title = {The causality between gut microbiota and ectopic pregnancy based on genome-wide association: A Mendelian randomization study.},
journal = {African journal of reproductive health},
volume = {30},
number = {8},
pages = {66-75},
doi = {10.29063/ajrh2026/v30i8.7},
pmid = {42047173},
issn = {1118-4841},
mesh = {Humans ; Pregnancy ; Female ; *Gastrointestinal Microbiome/genetics ; *Pregnancy, Ectopic/genetics/microbiology ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; Blood Proteins ; },
abstract = {Ectopic pregnancy represents a prevalent gynecological emergency with incompletely characterized pathophysiology, creating substantial clinical challenges in timely diagnosis and effective management. The causal interplay between gut microbiota and ectopic pregnancy, particularly through plasma proteomics mediation, remains undefined. We derived Gut microbiota GWAS data (n=412) from the Dutch Microbiome Project meta-analysis and Ectopic pregnancy data from IEU OpenGWAS and FinnGen project. The results revealed nine kinds of gut microbiotas demonstrating causal associations with ectopic pregnancy risk. A total of 67 plasma proteins causally impact the risk of ectopic pregnancy. In addition, three kinds of gut microbiotas were mediated by 25 kinds of plasma proteins on ectopic pregnancy. Microbiota enriched in L.rhamnose.degradation.I affected ectopic pregnancy through 22 kinds of plasma proteins. This study establishes causal relationships between specific gut microbial pathways and ectopic pregnancy risk, mediated through distinct plasma protein signatures, providing directions for clinical interventions and future research.},
}
@article {pmid42047214,
year = {2026},
author = {Mingolelli, G and Bashatwah, RM and Jurek, MJ and Chauvin, IM and Orjala, J and Riley, AP and Burdette, JE and Henke, MT},
title = {The Human Gut Microbiome Metabolizes Diverse Bioactive Coumarins via α,β-Unsaturated Lactone Reduction.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.6c00329},
pmid = {42047214},
issn = {1520-6025},
abstract = {The gut microbiome can influence drug efficacy through the direct metabolism of bioactive molecules. Despite numerous high-throughput screens for drug-microbiome interactions, the gut microbial metabolism of many bioactive compounds and its impact on treatment efficacy remain uncharacterized. We chose to investigate coumarins, which are a large class of bioactive natural products and chemical scaffolds for synthetic drugs. The core of the class, 1,2-benzopyrone, is metabolized by the microbiome to yield 3,4-dihydrocoumarin and melilotic acid via α,β-unsaturated lactone reduction. To explore the scope of this pathway, we screened a structurally diverse group of 12 bioactive coumarins using semitargeted LC-MS/MS metabolomics and ex vivo cultures of human feces. The culturable gut microbiome can reduce the α,β-unsaturated lactone of isocoumarin, simple, furano, pyrano, and prenylated coumarins with an unsubstituted 3,4-alkene bond. In a monoculture screen of microbiome isolates, we determined that 11 species could metabolize multiple coumarins through this pathway. Further, we demonstrate the direct coumarin-reducing capability of N-ethylmaleimide reductase from Escherichia coli. Finally, gut microbial metabolites of methoxsalen had diminished cytotoxicity against melanoma cancer cells compared to the parent drug. In summary, the human gut microbiome utilizes a single metabolic pathway to modulate the bioactivities of many coumarins.},
}
@article {pmid42047238,
year = {2026},
author = {Cardoso, A and Naghibi, M and Climent, E and Rodenes-Gavidia, A and Lamelas, A and Llobregat, L and Martínez-Blanch, J and Friedman, D and Vijayakumar, V and Day, R},
title = {Effects of Live and Heat-Treated Bifidobacterium longum CECT 7347 in Adults With Allergic Rhinitis: A Randomised, Double-Blind, Placebo-Controlled Trial.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70360},
pmid = {42047238},
issn = {1398-9995},
support = {//Archer Daniels Midland/ ; IDI-20170876//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
abstract = {BACKGROUND: Allergic rhinitis (AR) is an increasingly common chronic inflammatory condition of the nasal mucosa. While conventional anti-allergy treatments are widely used, they can come with side effects and are not always effective. As a result, AR remains a significant concern for many millions of people worldwide, affecting quality of life and social functioning.<br><br>OBJECTIVE: To investigate clinical evidence for the role of probiotics and postbiotics in reducing AR symptoms.<br><br>METHODS: In this single-centre, randomized, double-blind, placebo-controlled clinical trial, 72 adults aged 18-60&#x2009;years with moderate-severe AR, taking first-line medication, were studied. The primary outcome of the trial was to determine the effects of supplementation with the probiotic Bifidobacterium longum CECT 7347 (PRO) and the heat-treated postbiotic of the same strain (POST) on symptoms associated with AR as assessed using the Combined Symptom and Medication Score (CSMS). The secondary outcomes of the study assessed the effects of the interventions over: quality of life (rhinitis quality of life questionnaire [RQLQ]), systemic immune response, local immune response, and faecal microbiota composition.<br><br>RESULTS: Statistically significant reduction in total CSMS after 8&#x2009;weeks of supplementation was observed in the POST group compared to placebo control (CON) (p&#x2009;=&#x2009;0.022), showing on average a 0.6 greater reduction than placebo (CI: 0.09-1.12), equivalent to a 33.15% greater reduction&#xa0;and exceeding the World Allergy Organization's threshold for minimal clinically significant efficacy.<br><br>CONCLUSION: POST intake for 8&#x2009;weeks was associated with a statistically significant reduction of total CSMS compared to placebo. There was also improvement in RQLQ parameters when compared to baseline. PRO intake for 8&#x2009;weeks resulted in non-significant beneficial effects on AR-related symptoms.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT05208528.},
}
@article {pmid42047389,
year = {2026},
author = {Adeniji, A and Wassie, M and Madebo, MP and Liang, G},
title = {Harnessing plant-exuded prebiotics as a next-generation strategy for sustainable agriculture.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70275},
pmid = {42047389},
issn = {1744-7909},
support = {//Yunnan Provincial Foreign Experts Project/ ; },
abstract = {Global agriculture urgently needs sustainable strategies to boost crop productivity while reducing environmental impact. Harnessing plant-exuded bioactive metabolites, such as polyphenols, flavonoids, and organic acids, as natural prebiotics offers a powerful yet underexploited avenue for modulating rhizosphere microbiomes. These prebiotics complement existing microbial inoculants by leveraging the plant's own chemistry to selectively recruit beneficial microbes, thereby enhancing disease suppression, nutrient acquisition, and soil health more reliably than introduced consortia, which often fail due to ecological instability. However, translating this promise into practice is hampered by the profound complexity of the soil-root-microbe interface. This review establishes a conceptual framework that positions plant prebiotics as actionable tools for precision microbiome engineering. We summarize the biosynthetic pathways and mechanisms through which these specialized metabolites stimulate specific beneficial microbial functions. Building on this synthesis, we introduce the PRE-DDV pipeline (decode-design-validate), a closed-loop strategy integrating multi-omics profiling, synthetic community design, and iterative field validation. To enable commercial-scale field application, we critically examine key translational considerations: Identifying scalable plant sources (including native flora and agro-industrial byproducts), advancing formulation and precision delivery to ensure stability and targeted release, and assessing the economic feasibility, environmental sustainability, and regulatory frameworks governing industrial-scale production. Together, these contributions position prebiotics within a concrete pathway that bridges biological mechanisms and practical scalability, transforming them from a promising concept into a practical cornerstone of sustainable, climate-resilient agriculture.},
}
@article {pmid42047396,
year = {2026},
author = {Yuan, W and Feng, Z and Zhang, W and Liu, Y and Zhou, Y and Qin, Y and Bai, Y and Zhu, H and Yao, Q},
title = {Keystone taxa of phyllosphere microbiome confer resistance to citrus bacterial canker in pomelo via multiple mechanisms.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70273},
pmid = {42047396},
issn = {1744-7909},
support = {//National Key Research and Development Program of China/ ; },
abstract = {Citrus bacterial canker (CBC) is a globally important citrus disease caused by Xanthomonas citri subsp. citri (Xcc). Increasing evidence shows that the plant microbiome is crucial for host growth performance and health maintenance, among which the keystone taxa stand out due to their indispensable roles in microbiome homeostasis. However, how keystone taxa in the phyllosphere microbiome contribute to disease resistance remains unclear. In this study, we characterized the phyllosphere bacterial community of pomelo across an annual cycle and found that amino acids in leaves were the main drivers of the bacterial community structure. Meanwhile, five OTUs were identified as keystone taxa. A total of 587 phyllosphere bacterial strains were isolated, among which six strains belonging to Methylobacterium, Sphingomonas, Massilia, and Paenibacillus were identified as the corresponding keystone strains. We further constructed a consortium with these six strains to test its role in controlling CBC in planta. Network analysis reveals that consortium inoculation increased the phyllosphere bacterial community stability, whereas Xcc inoculation decreased it. However, dual inoculation of the consortium and Xcc restored community stability compared to the control. Interestingly, the inoculated keystone strains, if not all, still appeared as keystone taxa in the microbiomes of the control, consortium inoculation, and dual inoculation treatments, but not in the Xcc-inoculated treatment. Moreover, the consortium inoculation significantly increased the defense-related enzyme activities such as PPO, POD, and PAL in leaves, suggesting a triggered plant immune response. In vitro assays indicated that these keystone strains showed either antagonistic activity against Xcc or siderophore-producing activity. Finally, the consortium inoculation significantly reduced the disease index by 78% in planta. Taken together, these results suggest that the keystone taxa of the phyllosphere microbiome can confer disease resistance to the host via multiple mechanisms, especially by maintaining phyllosphere microbiome homeostasis.},
}
@article {pmid42047468,
year = {2026},
author = {Liu, Z and Huang, R and Sun, T and Zhu, L},
title = {Probiotic supplementation during pregnancy for vaginal microbiota improvement and pathogen clearance: A systematic review and meta-analysis.},
journal = {Acta obstetricia et gynecologica Scandinavica},
volume = {},
number = {},
pages = {},
doi = {10.1111/aogs.70234},
pmid = {42047468},
issn = {1600-0412},
support = {2025-I2M-XHZY-037//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 2025-I-PY-010//the Independent Research Fund of the State Key Laboratory of Complex, Severe, and Rare Diseases/ ; 82530054//the National Natural Science Foundation of China/ ; },
abstract = {INTRODUCTION: Pregnancy is associated with susceptibility to vaginal dysbiosis, including Group B Streptococcus (GBS), bacterial vaginosis (BV), and vulvovaginal candidiasis (VVC). Probiotic supplementation has emerged as a potential strategy to restore vaginal microecology, yet its effectiveness during pregnancy remains uncertain.<br><br>MATERIAL AND METHODS: To evaluate whether probiotic supplementation during pregnancy increases the likelihood of clearance of GBS colonization, BV, and VVC. We systematically searched PubMed, Embase, Cochrane CENTRAL, and Web of Science from inception to 16 April 2025. Eligible studies were randomized or non-randomized studies comparing probiotic supplementation with placebo or no treatment in pregnant women, reporting outcomes related to vaginal microbiota, pathogen decolonization, or infection resolution. Two reviewers independently screened studies and extracted data. Randomized controlled trials (RCT) were evaluated using the Cochrane ROB-1 tool, and the single non-RCT was assessed using ROBINS-I. Meta-analyses were performed for co-primary outcomes, with subgroup analyses by timing, comparator type (placebo-controlled vs. no-treatment control), and duration of intervention.<br><br>RESULTS: Eighteen studies (n&#x2009;=&#x2009;3705) were included. For the co-primary outcomes, a statistically significant increase in the odds of GBS decolonization was observed (OR 1.38, 95% CI 1.08-1.76; I[2]&#x2009;=&#x2009;2%). This association was no longer statistically significant in analyses restricted to RCTs (OR&#x2009;=&#x2009;1.28, 95% CI 0.93-1.76; I[2]&#x2009;=&#x2009;9%) and remained non-significant when further restricted to placebo-controlled RCTs (OR&#x2009;=&#x2009;1.32, 95% CI 0.94-1.85; I[2]&#x2009;=&#x2009;31%). No significant effects were found for BV (OR 0.91) or VVC (OR 0.65). An exploratory pooled analysis across infection types showed no significant overall improvement in infection clearance (OR 1.13, 95% CI 0.94-1.36; I[2]&#x2009;=&#x2009;16%). Subgroup analysis indicated greater efficacy in interventions initiated during the third trimester or lasting &#x2264;4&#x2009;weeks, though interaction tests were not significant.<br><br>CONCLUSIONS: Probiotic supplementation during pregnancy may increase the likelihood of GBS decolonization. However, this association was not statistically significant in sensitivity analyses restricted to randomized and placebo-controlled trials. No consistent benefit was observed for BV or VVC. Standardized probiotic regimens and harmonized diagnostic frameworks are needed.},
}
@article {pmid42047508,
year = {2026},
author = {Li, H and Fei, Y and Zhao, W},
title = {The Control of Canine Halitosis By Sugar Cane Polyphenols: Effects and Potential Mechanisms.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c00022},
pmid = {42047508},
issn = {1520-5118},
abstract = {Halitosis in companion animals lacks safe, effective long-term solutions. This study evaluated sugar cane polyphenols (SP) as an oral deodorizer for dogs using acute and 30 day intervention trials. Efficacy was evaluated by sensory scoring, volatile profiling, microbiome analysis, and mechanistic assays. Oral malodor was significantly reduced in both the acute (0-120 min) spray test and the 30 day SP intervention, accompanied by decreases in volatile sulfur compounds and indole. Mechanistic evidence indicated that SP interacts with odorants through noncovalent interactions and reduces protein surface hydrophobicity. Molecular simulations further supported competitive occupation of hydrophobic and aromatic protein binding regions by SP. Meanwhile, salivary β-glucosidase activity was inhibited in a concentration-dependent manner. SP exposure was also associated with reduced abundances of odor-associated oral taxa, such as Porphyromonas and Fusobacterium. These findings support SP as a food-grade strategy for controlling canine halitosis, with translational relevance to oral care applications.},
}
@article {pmid42047567,
year = {2026},
author = {Seeram, D and Park, H and Abrams, JA and Uhlemann, AC and Freedberg, DE},
title = {Vancomycin-resistant Enterococcus often spreads from hospitalized patients into the local environment and less often spreads from the environment into patients.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag240},
pmid = {42047567},
issn = {1537-6613},
abstract = {BACKGROUND: Uncertainty remains about how gut-based organisms such as vancomycin-resistant Enterococcus (VRE) are spread within the local hospital environment. We hypothesized that, in the medical intensive care unit (ICU), VRE is spread predominantly patient-to-environment rather than environment-to-patient.<br><br>METHODS: Medical ICU patients with sepsis and receiving broad-spectrum antibiotics were sampled via deep rectal swabs at ICU admission and on ICU days 3, 7, 14, and 30. Corresponding ICU room environmental samples were taken at the same timepoints. All samples were analyzed with 16S sequencing and selective culture, and VRE isolates were genetically characterized via whole genome sequencing (WGS).<br><br>RESULTS: There were 680 samples gathered from 90 unique patients and their ICU rooms. 47/90 (52%) patients and 36/90 (40%) rooms showed VRE colonization at one or more timepoint. On 16S sequencing, Enterococcus relative abundance was enriched in room samples when the room housed a VRE positive patient (0.63% VRE(+) vs. <0.01% VRE(-), p<0.01). In a network analysis, patient and room Enterococcus were connected for VRE positive but not VRE negative patients. WGS identified 23 genetically distinct clusters of VRE. There were 3 events when distinct clusters appeared first in the patient gut and then in the room and 3 events when clusters appeared simultaneously in the gut and room; in no cases was a cluster first detected in the room.<br><br>CONCLUSIONS: We detected three events when spread of genetically distinct VRE clusters from hospitalized patients into their local ICU environment but no reverse events. Effectiveness of infection prevention might be increased by gut-targeting interventions.},
}
@article {pmid42047611,
year = {2026},
author = {Capone, K and Kuller, J and Durand, DJ and Tierney, NK and Lund, C},
title = {Exploration of Changes in the Human Skin Microbiome by Mode of Birth and Following First Bath.},
journal = {Pediatric dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/pde.70219},
pmid = {42047611},
issn = {1525-1470},
support = {UL1 TR000004/TR/NCATS NIH HHS/United States ; //Johnson &amp; Johnson Consumer Inc./ ; },
abstract = {BACKGROUND/OBJECTIVES: Microbes colonize the skin soon after birth, and the skin microbiome changes over time. However, the effects of bathing and hygiene products on the infant skin microbiome are not well studied. This randomized, single-center trial analyzed the skin microbiome in neonates born vaginally or via cesarean section (c-section), before and after their first bath with or without a mild baby cleanser.<br><br>METHODS: One hundred healthy full-term neonates were randomized to baths with water alone or with mild baby cleanser, stratified by delivery mode. Volar forearm swabs of neonates (before and after first bath) and their mothers were analyzed by 16S rRNA metagenomic sequencing.<br><br>RESULTS: At birth, neonates born vaginally had greater overall richness of the skin microbiome versus those born via c-section. Vaginally delivered neonates had similar species richness as their mothers, while neonates delivered via c-section had much lower species richness. Shannon diversity was similar regardless of birth mode, but community structure varied. Species richness was similar before and after bath in vaginally delivered neonates, but those born via c-section had higher species richness after their first bath and showed larger changes in community structures, compared with the vaginal group. Whether water alone or baby cleanser was used for the first bath did not greatly affect skin microbiome composition.<br><br>CONCLUSIONS: The mode of birth had the largest effect on the skin microbiome composition, richness, and structure. Neonates born via c-section showed the largest post-bath changes in the skin microbiome, while the use of water or baby cleanser had little effect.},
}
@article {pmid42047845,
year = {2026},
author = {Pereira-Rodrigues, A and Gonçalves, A and Alves, IN and Mendes, CS and Silva, C and Campos, J and Sampaio-Maia, B and Falcão-Pires, I and Araujo, R},
title = {Metabolic and gut microbiota effects of ketogenic diet and exogenous ketone salts in a rat model of metabolic syndrome.},
journal = {European journal of nutrition},
volume = {65},
number = {4},
pages = {},
pmid = {42047845},
issn = {1436-6215},
}
@article {pmid42048286,
year = {2026},
author = {Yan, Q and Yu, X and Wei, J and Fang, C and Zhao, J and Li, X and Fu, Y and Li, X},
title = {Shewanella oneidensis Metabolically Engineered with Prussian Blue for Synergistic Tumor Microenvironment Remodeling and Photodynamic Breast Tumor Elimination.},
journal = {ACS biomaterials science &amp; engineering},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsbiomaterials.6c00087},
pmid = {42048286},
issn = {2373-9878},
abstract = {Microorganism-based tumor therapy has attracted increasing interest due to the intrinsic tumor tropism and metabolic plasticity of certain bacterial species. However, their therapeutic efficacy is often hindered by insufficient metabolic activity within the tumor microenvironment and safety concerns associated with systemic administration. Here, we develop a biohybrid system, termed Ce6@PB@MR-1, to enhance the intrinsic tumor-targeting behavior of chlorin e6 (Ce6) and lactate-metabolizing capability of Shewanella oneidensis MR-1 (MR-1) through engineered material-microbe coupling. In this system, Prussian blue (PB) is metabolically precipitated onto the MR-1 surface during anaerobic respiration, forming an electron-mediating interface in which PB functions as an efficient exogenous electron acceptor to strengthen respiratory electron flux and accelerate the lactate metabolism of MR-1. The PB coating simultaneously attenuates bacterial immunogenicity, enabling the improved in vivo persistence and safety of MR-1. Furthermore, bioconjugated Ce6 enables 660 nm-triggered photodynamic therapy to induce immunogenic cell death and activate antitumor immune responses. In vivo, the biohybrid system achieves durable tumor eradication accompanied by a marked remodeling of the tumor microenvironment. This work establishes a metabolically assisted material-microbe hybridization framework that expands microbial functionality and offers a versatile strategy for developing safe and effective microbe-based cancer therapies.},
}
@article {pmid42048337,
year = {2026},
author = {Bernal Hernández, N and Rodríguez Cabal, HA and Pino, NJ and Ramírez Restrepo, S and Múnera Porras, LM},
title = {Metagenomic and taxonomic profiling of phyllosphere bacteria from Mangifera indica in response to urban air pollutants in Medellín, Colombia.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347959},
pmid = {42048337},
issn = {1932-6203},
mesh = {Colombia ; *Mangifera/microbiology ; *Bacteria/genetics/classification/drug effects ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Air Pollutants/metabolism ; Microbiota/genetics ; *Metagenome ; Phylogeny ; Cities ; },
abstract = {Urban trees and their phyllosphere-associated microbiota constitute a promising nature-based solution for mitigating urban air pollution. In this study, we characterized the taxonomic composition, diversity patterns, and functional potential of bacterial communities inhabiting the phyllosphere of Mangifera indica in two urban sites of Medellín, Colombia, with contrasting pollution levels and across two time points, analyzing a total of 12 samples. We integrated 16S rRNA gene amplicon sequencing, performed on the Illumina MiSeq platform, with shotgun metagenomic sequencing generated on the Illumina NovaSeq 6000 platform to assess community structure and the presence of genes involved in the degradation of airborne organic pollutants. Bacterial assemblages were dominated by Pseudomonadota (Proteobacteria), Actinomycetota, and Bacteroidota, with genera such as Methylobacterium, Pseudomonas, and Serratia consistently prevalent. Alpha diversity was higher in the highly polluted downtown, while beta diversity was shaped primarily by temporal variation. Functional annotation of metagenome-assembled genomes (MAGs) uncovered genes encoding complete aromatic hydrocarbon degradation pathways, including naphthalene, toluene, xylenes, and benzoate. Both ortho- and meta-cleavage routes for catechol degradation were detected, with temporal shifts in pathway dominance linked to changes in the abundance of key degraders taxa. These results reflect genetic potential for xenobiotic degradation within the M. indica phyllosphere microbiota, modulated by environmental conditions. Our findings highlight the ecological role of phyllosphere bacteria as contributors of inferred functional capacity relevant to atmospheric bioremediation and supports their integration into microbiome-informed green infrastructure strategies.},
}
@article {pmid42048459,
year = {2026},
author = {He, D and Zhou, Y and Li, M and Wang, M and Yu, W and Shao, C and Singh, SK and Gu, M and Wang, Y and Yuan, J and Wu, X and Zheng, S and Xie, Y and Chen, L and Morcillo, RJL and Yang, Y and Vílchez, JI and Zhang, JL and Miao, Y and Macho, AP and Zhang, H},
title = {Perception of a bacterial quorum sensing signal activates a tripartite plant immune strategy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {18},
pages = {e2532423123},
doi = {10.1073/pnas.2532423123},
pmid = {42048459},
issn = {1091-6490},
mesh = {*Quorum Sensing ; *Arabidopsis/immunology/microbiology/genetics ; *Pseudomonas aeruginosa/physiology ; Arabidopsis Proteins/metabolism/genetics ; *Plant Immunity ; Signal Transduction ; Protein Serine-Threonine Kinases/metabolism/genetics ; Plant Diseases/microbiology/immunology ; Acetophenones/metabolism ; Plant Roots/microbiology/immunology ; Disease Resistance ; },
abstract = {Bacterial quorum sensing (QS) signals an increasing threat during pathogenesis. How plants deploy timely defenses through QS perception is poorly understood. Here, we report that Arabidopsis thaliana perceives 2'-aminoacetophenone (2'-AA), a volatile QS signal from Pseudomonas aeruginosa, and mounts a multilayered defense. This response comprises BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-dependent intracellular immunity, extracellular quorum quenching through the release of acetic acid, and ecological remodeling of the root microbiome to suppress Pseudomonas. Our findings demonstrate that plants can translate the detection of a specific bacterial QS molecule into a coordinated, preemptive disease resistance strategy.},
}
@article {pmid42048700,
year = {2026},
author = {Aycan, M and Fakhet, D and Picazo, PJ and Bodur, S and Nagano, H and Asiloglu, R and Aranjuelo, I and Mitsui, T},
title = {Plant-microbiome interactions are associated with enhanced salinity tolerance and methane emissions in rice.},
journal = {Plant physiology and biochemistry : PPB},
volume = {234},
number = {},
pages = {111324},
doi = {10.1016/j.plaphy.2026.111324},
pmid = {42048700},
issn = {1873-2690},
abstract = {Salinity is a severe environmental stressor that reduces crop performance, alters soil microbial communities, and influences greenhouse gas emissions such as methane (CH4). Climate change is expected to further increase salinity globally. Although plants have evolved physiological and molecular mechanisms to cope with salinity, the role of plant-microbiome interactions in salinity tolerance and their link to CH4 emissions remain poorly understood. Here, we investigated the interactions among plant salinity tolerance, rhizobiome, and CH4 emission under salinity stress. We used salt-tolerant and salt-sensitive rice genotypes grown in nutrient-poor paddy field soil and nutrient-rich commercial nursery soil under climate-controlled greenhouse conditions with salinity stress until harvesting. Salt-sensitive genotypes exhibited decreases in early biomass and gas exchange due to salinity stress under nutrient-rich nursery soil. However, salinity effects were mitigated by plant-microbiome interactions, which improved plant growth performance. Rhizosphere microbiome analysis revealed that Rhizobacteria, including Cyanobacteria, were associated with plant development and salinity tolerance. Salinity altered methanogenic archaeal communities, especially Methanobacteria and Methanocellia, with salt-tolerant genotypes releasing more CH4 during stress. Gas exchange and antioxidant enzyme activity were positively correlated with CH4 emissions, suggesting an association between improved physiological performance under salinity and microbial methanogenesis. Gene expression profiling revealed a significant upregulation of hormone- and ion-transport-related genes in paddy soil, which may be associated with stress tolerance, microbial activity, and CH4 emissions. This study proposes a mechanistic framework that links plant salinity tolerance, rhizosphere microbial dynamics, and methane production, illustrating how these interconnected processes shape plant performance and the environmental outcomes. These findings emphasize the necessity of balancing agricultural productivity with CH4 emissions and soil resilience under climate-induced stress.},
}
@article {pmid42048934,
year = {2026},
author = {Gaafar, AM and Stolberg-Mathieu, G and Roager, HM and La Barbera, G},
title = {A validated chiral LC-MS/MS method for enantioselective quantification of aromatic lactic acids in human faeces.},
journal = {Journal of chromatography. A},
volume = {1779},
number = {},
pages = {466997},
doi = {10.1016/j.chroma.2026.466997},
pmid = {42048934},
issn = {1873-3778},
abstract = {Bifidobacterium, a key genus of the infant gut microbiome, produces d- and l- enantiomers of aromatic lactic acids that may influence early-life immune development through stereochemistry-dependent biological activity. No validated analytical methods currently enable their accurate enantio‑separation and quantification in human biological samples. We report the first validated, targeted, liquid chromatography-mass spectrometry method using a chiral column for the enantioselective separation and quantification of d- and l- forms of phenyllactic acid (PLA), 4-hydroxyphenyllactic acid (4OH-PLA), and indolelactic acid (ILA) in faecal samples. The method achieves baseline separation of all enantiomers within 10 min, with resolution values of 2.66 (PLA), 1.77 (4OH-PLA), and 2.42 (ILA). Solid-phase extraction reduces matrix effects (>80 %) and improves analyte recovery (>80 %). Limits of quantification range from 2.9 to 6.7 ng mL[-1], and calibration curves show excellent linearity (R[2] > 0.99). Inter- and intra-day precision expressed as %RSD are < 15 % for most analytes. The method was successfully applied to infant faecal samples, enabling sensitive and stereospecific quantification of aromatic lactic acids, thus establishing a foundation for exploring the biological relevance of these enantiomers in infant health.},
}
@article {pmid42049031,
year = {2026},
author = {Wong, O and Zheng, Z and Wang, M and Cao, A and Chan, FKL and Ng, SC and Su, Q},
title = {Microbiome biomarkers in autism spectrum disorder: Toward prediction, diagnosis, and prognosis.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102780},
doi = {10.1016/j.xcrm.2026.102780},
pmid = {42049031},
issn = {2666-3791},
abstract = {Autism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. This review outlines mechanistic insights from preclinical and clinical studies to illustrate how microbial disturbances affect neurodevelopment. It examines the evolution of biomarker research from early 16S rRNA sequencing to advanced shotgun metagenomics incorporating functional integration, multi-omics, and genomic variants. Such advancements enhance diagnostic accuracy and generalizability. Although clinical causal evidence remains indirect, these microbial signatures show potential for early diagnosis, presymptomatic risk prediction, and tailored therapies. Key challenges include prospective validation in diverse cohorts, specificity testing against comorbidities, and addressing clinical heterogeneity. By summarizing methodological gaps and providing future guidance, this review aims to bridge mechanistic research and clinical practice to improve outcomes across the spectrum.},
}
@article {pmid42049134,
year = {2026},
author = {Gajendiran, TY and Ganamurali, N and Sabarathinam, S},
title = {The host-steroid-microbiome axis: Microbial remodeling of steroid scaffolds and its implications for metabolic and endocrine disorders.},
journal = {Drug discovery today},
volume = {},
number = {},
pages = {104683},
doi = {10.1016/j.drudis.2026.104683},
pmid = {42049134},
issn = {1878-5832},
abstract = {Steroids, chemically conserved yet functionally diverse, integrate metabolic, endocrine and microbial networks. Beyond host hormones acting via specific receptors, the gut microbiome edits steroid scaffolds, yielding metabolites that reshape systemic signaling. We introduce the host-steroid-microbiome axis, framing steroids as holobiont currencies coordinating metabolism, immunity and endocrine balance. This continuum links endogenous steroidogenesis, microbial transformations (via hydroxysteroid dehydrogenases, sulfatases and β-glucuronidases) and host receptor modulation (farnesoid X, TGR5, estrogen, androgen and glucocorticoid receptors), impacting bile acid signaling, glucose/lipid metabolism and hormone-related diseases. Steroidomics, multiomics, cryo-EM, artificial intelligence (AI) modeling and digital twins illuminate these interactions, enabling precision endocrinology informed by the microbiome, diet and genetics. A roadmap unites microbial ecology, steroid chemistry and AI for therapeutic targeting.},
}
@article {pmid42049248,
year = {2026},
author = {Jose, A and Apewokin, S and Ollberding, NJ and Duan, Q and Trannguyen, J and Prisco, SZ and Thenappan, T and Hemnes, AR and Elwing, JM},
title = {Lactobacillus Is Associated With Disease in Pulmonary Arterial Hypertension: A Prospective Cohort Study.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70161},
doi = {10.1002/cph4.70161},
pmid = {42049248},
issn = {2040-4603},
support = {K23HL16497/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; 2022 Research Award//Team Phenomenal Hope/ ; },
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; *Lactobacillus/physiology ; Prospective Studies ; Middle Aged ; *Pulmonary Arterial Hypertension/microbiology/physiopathology ; Adult ; Aged ; *Hypertension, Pulmonary/microbiology ; Ventricular Dysfunction, Right ; },
abstract = {BACKGROUND: Gut dysbiosis and gut-derived metabolites have been linked to pulmonary arterial hypertension. However, associations between specific microbes, and corresponding metabolites, with pulmonary arterial hypertension disease severity is limited.<br><br>METHODS: This was a prospective cohort study of patients with pulmonary arterial hypertension undergoing right heart catheterization, with pulmonary artery blood subject to nuclear magnetic resonance metabolomics, and simultaneous stool sample shotgun metagenomics. Validation of metabolite levels with disease severity was done in an independent cohort of pulmonary arterial hypertension patients with blood samples from right heart catheterization testing.<br><br>RESULTS: The presence of Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients was associated with less severe pulmonary hemodynamics and echocardiographic right ventricular dysfunction. Higher threonine levels were associated with more favorable pulmonary hemodynamic characteristics in both prospective and independent validation cohorts of pulmonary arterial hypertension patients.<br><br>CONCLUSIONS: Detectable Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients are associated with more favorable pulmonary hemodynamic and right ventricular characteristics. Circulating gut-derived metabolites may also be involved. Further investigation into the relationship between gut microbial Lactobacillus, circulating metabolites, disease severity, and clinical outcomes in pulmonary arterial hypertension may be warranted.},
}
@article {pmid42049393,
year = {2026},
author = {Iorra, FQ and Loebens, LAS and Auler, A and Nascimento, ECT and Schaan, BD and Bock, PM},
title = {Effects of Weight Loss Interventions on Gut Microbiota-Derived Metabolites Linked to Cardiometabolic Health: A Systematic Review and Meta-Analysis.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70151},
doi = {10.1111/obr.70151},
pmid = {42049393},
issn = {1467-789X},
support = {//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {BACKGROUND: Gut microbiota-derived metabolites are emerging as potential mediators between obesity and cardiometabolic conditions. While weight loss interventions modify microbiota composition, their effects on systemic microbial metabolites remain unclear.<br><br>OBJECTIVE: To evaluate the effect of weight loss interventions on circulating levels of key gut-derived metabolites in individuals with overweight or obesity, through a systematic review and meta-analysis.<br><br>METHODS: Searches were performed in MEDLINE, EMBASE, and The Cochrane Library up to July 17, 2024. We included intervention studies in individuals with overweight/obesity undergoing weight loss strategies, with measurement of serum lipopolysaccharides (LPSs), trimethylamine N-oxide (TMAO), secondary bile acids, short-chain fatty acids (SCFAs), or indole derivatives. Meta-analysis used the standardized mean difference (SMD) with a random-effects model, stratified by intervention type (non-surgical or surgical).<br><br>RESULTS: Sixty-seven studies were included. Non-surgical interventions were associated with reduced TMAO (n&#x2009;=&#x2009;8 studies; SMD: -0.56; 95% CI -0.90 to -0.22; I[2]&#x2009;=&#x2009;74.7%), but not LPS (n&#x2009;=&#x2009;10 studies; SMD: -0.11; 95% CI -0.58 to 0.35; I[2]&#x2009;=&#x2009;91.2%). Surgical interventions were associated with decreased LPS (n&#x2009;=&#x2009;7 studies; SMD: -0.47; 95% CI -0.80 to -0.14; I[2]&#x2009;=&#x2009;78.8%), and increased TMAO (n&#x2009;=&#x2009;8 studies; SMD: 0.49; 95% CI 0.08 to 0.90; I[2]&#x2009;=&#x2009;81.8%) and secondary bile acids (n&#x2009;=&#x2009;13 studies; SMD: 0.48; 95% CI 0.30 to 0.66; I[2]&#x2009;=&#x2009;58.8%). Evidence on SCFAs and indole derivatives was limited.<br><br>CONCLUSION: Weight loss strategies have distinct effects on gut microbiota-derived metabolites, underscoring the complexity of microbiota-host interactions and the potential for personalized approaches to obesity treatment.},
}
@article {pmid42049453,
year = {2026},
author = {Voyiatzis, I and Vatsellas, G and Valakos, D and Stavropoulos, G and Lamia, A and Stamatogianni, C and Athanasiadis, E and Anagnostopoulos, AK and Alexiou, L},
title = {Effects of a Greek Yoghurt-based Complex on the Human Facial Skin Microbiome.},
journal = {In vivo (Athens, Greece)},
volume = {40},
number = {3},
pages = {1852-1863},
doi = {10.21873/invivo.14339},
pmid = {42049453},
issn = {1791-7549},
mesh = {Humans ; *Yogurt/microbiology ; *Microbiota/drug effects/genetics ; Female ; Male ; Adult ; Middle Aged ; *Skin/microbiology/drug effects ; Aged ; *Face/microbiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Skin Microbiome ; },
abstract = {BACKGROUND/AIM: Natural ingredient-containing complexes are used in dermo-cosmetics to ameliorate facial characteristics, yet human experimental approaches and trials demonstrating their efficacy remain limited. This study assessed the effects of a Greek yoghurt-based complex on the human facial skin microbiome.<br><br>MATERIALS AND METHODS: Thirty-one volunteers (27 females, 4 males; 20-65 years) with stressed facial skin and 15 volunteers (10 females, 5 males) with balanced skin were enrolled in a 28-day clinical study. At baseline, skin swabs were collected from both groups. Participants with stressed skin were treated in a split-face design with a yoghurt-based complex applied to the right cheek and placebo to the left cheek for 28 days, with follow-up sampling on days 7, 14, and 28. Bacterial DNA was analyzed by 16S rRNA gene amplicon sequencing. Bioinformatic analyses assessed microbial composition, diversity, and relative abundance. Baseline differences between skin types and treatment effects versus placebo were evaluated over time.<br><br>RESULTS: A lowered microbiota diversity was observed in "stressed" facial skin, compared to the "balanced" group, on day 0. The four most abundant microbiota genera were Corynebacterium, Propionibacterium, Staphylococcus and Actinomyces spp. A significant difference in the relative abundance of these species was noted in the two groups (stressed vs. balanced) at baseline, as well as a consistent increase in mean bacterial diversity after intervention with the yogurt-based complex.<br><br>CONCLUSION: A gradual restoration of the skin's microbial balance essential for a healthy skin function and appearance, was noted following the yoghurt-based complex application.},
}
@article {pmid42049487,
year = {2026},
author = {El-Assaad, F and El-Omar, EM},
title = {Gut-peritoneal-multisystem axis in endometriosis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337490},
pmid = {42049487},
issn = {1468-3288},
}
@article {pmid42049488,
year = {2026},
author = {Lan, K and Bai, D and Yuan, L and Luo, H and Jin, J and Li, SC and Wu, LF and Sun, XS and Liu, SL and Chen, QY and Mai, HQ and Liu, YX and Tang, LQ},
title = {Metagenomic identification of gut microbiome signatures for accurate diagnosis and prognostic prediction of Epstein-Barr virus-associated nasopharyngeal carcinoma.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338223},
pmid = {42049488},
issn = {1468-3288},
abstract = {BACKGROUND: Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. The gut microbiome can influence outcomes of viral infections but the potential links among the gut microbiome, EBV infection and NPC remain unclear.<br><br>OBJECTIVE: To characterise gut microbiome alterations in EBV-associated NPC, evaluate microbiome-based diagnostic performance (alone and in combination with EBV markers), and explore associations between microbial features, EBV DNA burden, prognosis and the tumour microenvironment.<br><br>DESIGN: We conducted a large-scale shotgun metagenomic study including 516 patients with EBV-associated NPC and 263 healthy controls. Microbiome dysbiosis, functional pathways and associations with plasma EBV DNA were assessed. Species-level markers were used to build a random forest classifier for NPC diagnosis, and performance was evaluated alone and in combination with EBV-specific markers. Survival analyses were performed to identify microbial features associated with NPC-related mortality and relationships with an immune-suppressive tumour microenvironment were explored.<br><br>RESULTS: NPC was characterised by gut microbiome dysbiosis, including depletion of short-chain fatty acid-producing species and reduced butanoate metabolism, which were significantly associated with plasma EBV DNA. A random forest classifier based on species-level markers distinguished NPC from controls with an area under the curve (AUC) of 0.917; performance improved to an AUC of 0.984 when combined with EBV-specific markers. Specific microbial species were associated with NPC-related mortality and prognostic microbial features were linked to an immune-suppressive tumour microenvironment.<br><br>CONCLUSION: EBV-associated NPC is associated with distinct gut microbiome and functional alterations that correlate with plasma EBV DNA. Microbial markers show strong diagnostic potential, particularly when integrated with EBV-specific markers, and prognostic microbial features may be linked to an immune-suppressive tumour microenvironment, supporting a potential role of the gut microbiome in NPC tumourigenesis.},
}
@article {pmid42049541,
year = {2026},
author = {Yang, M and Liu, T and Qin, Y and Cai, R and Yang, X and Tang, C},
title = {Role of gut microbiota modulation in preventing and treating sarcopenia in patients with liver cirrhosis: A narrative review.},
journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajg.2026.03.005},
pmid = {42049541},
issn = {2090-2387},
abstract = {Sarcopenia, a common and serious complication in patients with liver cirrhosis, is associated with high morbidity and mortality. Accumulating evidence highlights the gut-liver-muscle axis as a key regulatory pathway underlying muscle wasting in cirrhosis, with disruptions in the gut microbiome taking center stage. This review systematically summarizes the mechanisms by which gut microbiota dysregulation contributes to sarcopenia in cirrhosis, examining how compromised intestinal integrity, inflammatory responses, and disrupted metabolism of key compounds, such as short-chain fatty acids, branched-chain amino acids, and bile acids, play pivotal roles in this pathological process. We also critically examine the scientific evidence supporting approaches that target gut microbiome health, aiming to provide a comprehensive and up-to-date overview for clinicians and researchers.},
}
@article {pmid42049610,
year = {2026},
author = {Barrientos, G and Fahlbusch, FB and Conrad, ML},
title = {Microbes, molecules, and the maternal-fetal interface: rethinking the gut-placenta axis.},
journal = {Trends in immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.it.2026.03.010},
pmid = {42049610},
issn = {1471-4981},
abstract = {Placental biology is increasingly framed through a signaling paradigm in which maternal microbiome-derived mediators-rather than microbial colonization-affect the function of the interface. This review synthesizes evidence that circulating microbial signals, including short-chain fatty acids, tryptophan-derived indoles, bile-acid-linked ligands, microbe-associated molecular patterns, and bacterial extracellular vesicles, are associated with placental vascular development, immune regulation, nutrient transport, and endocrine programs-processes central to pregnancy outcomes. We integrate mechanistic insights from gnotobiotic and supplementation models with limitations of human evidence and identify key translational gaps. The current evidence supports a model in which maternal microbial ecology shapes a network of circulating mediators that converge on interlinked placental pathways essential for placental function and fetal development.},
}
@article {pmid42049611,
year = {2026},
author = {Gurumurthy, G and Gurumurthy, J and Gurumurthy, S and Reynolds, L and Thachil, J},
title = {Dysbiosis and immunothrombosis - How platelets and the gut microbiome interact.},
journal = {Blood reviews},
volume = {},
number = {},
pages = {101395},
doi = {10.1016/j.blre.2026.101395},
pmid = {42049611},
issn = {1532-1681},
abstract = {Platelets are classically recognised for their role in haemostasis and thrombosis. They are now increasingly recognised as modulators of the immune system, referred to as immunothrombosis, and are thought to be closely associated with the gut microbiome. The gut microbiome shapes platelet phenotype through receptor-mediated sensing of microbial ligands and circulating metabolite-driven priming. Dysbiosis and barrier disruption increase systemic exposure to microbial-associated molecular patterns (MAMPs) which, in turn, engage platelet and vascular pattern-recognition receptors. Prothrombotic metabolites such as trimethylamine N-oxide has also been shown to modulate platelet activation by amplifying calcium-dependent activation and downstream inflammatory crosstalk. Other metabolites, such as phenylacetylglutamine, have been shown to increase platelet activation through adrenergic receptor-mediated pathways. In contrast, short-chain fatty acids may reduce this thromboinflammatory platelet phenotypes through anti-inflammatory signalling and potential effects on megakaryopoiesis and platelet reactivity. Therapeutic options that target these pathways between platelets and the microbiota have been explored. Examples include dietary modifications and microbiome-based interventions. Yet, whilst promising, significant gaps remain in understanding the long-term impacts of these strategies on platelet behaviour and overall disease outcomes.},
}
@article {pmid42049674,
year = {2026},
author = {Velarde-Salcedo, AJ and Serrato-Alemán, O and Barba-de la Rosa, AP},
title = {Food-Derived Peptides: Neuropeptides and the Diet-Microbiome-Brain Axis.},
journal = {Annual review of food science and technology},
volume = {17},
number = {1},
pages = {79-101},
doi = {10.1146/annurev-food-053124-011258},
pmid = {42049674},
issn = {1941-1421},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neuropeptides/metabolism/chemistry ; *Brain/physiology/metabolism ; *Diet ; *Peptides/chemistry/metabolism ; Animals ; Dietary Proteins/metabolism ; },
abstract = {Food-derived peptides are short chains of amino acids encrypted in the proteins of several plant sources. Several functions of food-derived peptides, or bioactive peptides (BPs), such as antioxidant, antihypertensive, antidiabetic, antiobesity, and antimicrobial, have been well studied. However, at the beginning of the twenty-first century, due to stressful situations such as prolonged aging and pandemic diseases, the study of BPs with the potential to mitigate the impact of anxiety, cognitive impairment, and the progression of neurodegenerative diseases has received increased attention. Classical processes such as enzymatic hydrolysis, fermentation, the use of probiotics, and the simulation of gastrointestinal digestion are used to release BPs. Heating, high pressure, and in silico design are methods proposed to obtain novel peptides. In addition, gut microbiota play a key role in the metabolism of dietary proteins; therefore, through cross-kingdom communication, the diet-gut-brain axis is a fundamental mechanism in maintaining health status that is only just beginning to be understood. Furthermore, attention is being paid to small peptides, or noncoding peptides, which can be found in dietary foods, as new players capable of modulating the diet-gut-brain axis.},
}
@article {pmid42049694,
year = {2026},
author = {Joung, JY and Choi, HS and Oh, NS},
title = {Emerging Roles of Postbiotics in Gut-Brain-Microbiome Axis Modulation and Neurobiological Pathways of Chronic Stress-Related Brain Dysfunction.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2603010},
doi = {10.4014/jmb.2603.03010},
pmid = {42049694},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Stress, Psychological/microbiology/physiopathology ; Animals ; *Brain/physiopathology ; Dysbiosis ; Hypothalamo-Hypophyseal System ; Probiotics ; Pituitary-Adrenal System ; *Brain-Gut Axis ; },
abstract = {Chronic psychological stress disrupts the gut-brain-microbiome axis (GBMA) through gut dysbiosis, intestinal and blood-brain barrier disruption, hypothalamic-pituitary-adrenal (HPA) axis dysregulation, and neuroinflammation, collectively impairing neurotransmitter signaling and neuroplasticity. Addressing these interconnected pathological processes requires therapeutic strategies capable of acting across multiple nodes of the GBMA simultaneously. Postbiotics, defined as preparations of inanimate microorganisms and/or their components that confer a health benefit on the host, have emerged as promising candidates for restoring GBMA homeostasis under chronic stress. Key postbiotic classes, including short-chain fatty acids, tryptophan metabolites, GABA-related compounds, heat-killed bacteria, and bacterial extracellular vesicles, attenuate neuroinflammation, reinforce barrier integrity, normalize neurotransmitter balance, and promote brain-derived neurotrophic factor (BDNF)-dependent neuroplasticity. Preclinical evidence has consistently demonstrated behavioral and neurochemical improvements following postbiotic administration, and limited clinical data suggest preliminary reductions in cortisol, inflammatory biomarkers, and stress-related symptom severity. However, clinical translation remains constrained by the absence of standardized postbiotic characterization and limited mechanistic data from human trials. This review provides an integrated account of the neurobiological pathways by which chronic stress disrupts the GBMA and examines the emerging roles of postbiotics in modulating these pathways, with the goal of informing future postbiotic-based strategies for chronic stress-related brain dysfunction.},
}
@article {pmid42039801,
year = {2026},
author = {Hanlon, M and Van Beeck, W and Wei, L and Tosta, I and Liao, R and Marco, ML and DiCaprio, E},
title = {Consumer knowledge and motivations for consumption of fermented foods.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1789825},
pmid = {42039801},
issn = {1664-302X},
abstract = {Non-alcoholic fermented foods (FFs) are a popular food group with consumers; however limited studies exist evaluating the motivations for consuming FFs and the frequency of consumption. To begin to address this gap in knowledge, we developed an online survey to assess participant familiarity with different types of fermented products, determine consumption frequency, and gain insight into the motivation for consumption. A total of 751 participants completed the survey. Yogurt was the most frequently identified fermented food (n = 658; 87.62% of respondents). Participants reported consuming fermented cereal grains (n = 307; 46.17%), fruits and vegetables (n = 281; 42.26%), dairy products (n = 204; 39.70%), soy/rice products (n = 250; 37.60%) and fermented meats (n = 204; 30.68%). Reported daily consumption was highest for categories of fermented cereal and dairy products, compared to the other categories which typically were consumed on a weekly or monthly basis. The primary motivator for consumption was taste (n = 337; 50.68%) compared to health benefits (n = 235; 35.34%) and cultural reasons (n = 80; 12.03%). The most highly selected health benefits associated with FF consumption were "improved gut microbiome" (n = 513; 77.14%), "digestive benefits" (n = 508; 76.39%), and "probiotic" (n = 458; 68.87%). Participants associated health benefits with all fermented products listed in the survey. Therefore, consumers may assume that all fermented foods confer the same health benefits. The motivations for consumption (sensory attributes, health benefits, cultural reasons) did not vary when individuals were asked to respond for FFs as a broad category versus specifically for non-alcoholic, fermented fruits and vegetables. This suggests that consumers view FFs similarly regardless of the starting ingredients and fermentative process involved.},
}
@article {pmid42039807,
year = {2026},
author = {Liu, X and Tang, W and Li, C and Jiao, Y and Bai, Y and Xiang, L and Wu, Z},
title = {Vaginal microbiota in assisted reproduction: determinants, dynamics, and impact on clinical outcomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1770446},
pmid = {42039807},
issn = {1664-302X},
abstract = {The vaginal microbiota (VMB), predominantly composed of Lactobacillus genus, plays a crucial role in maintaining female reproductive health through acid production, immune modulation, and protection against pathogens. However, substantial inter-individual variability exists in its composition and stability. In assisted reproduction, the vaginal microenvironment is increasingly recognized as an important factor influencing embryo implantation and pregnancy outcomes. Emerging evidence suggests that the composition and dynamics of the vaginal microbiome are not only predictive biomarkers but also potential regulatory targets influencing assisted reproduction outcomes. This review outlines vaginal microbial community types, key behavioral and host-related determinants, and their links to ART outcomes. We also discuss current limitations, including methodological heterogeneity, unclear causal mechanisms, and the lack of standardized intervention strategies. Finally, we highlight the need for longitudinal and multi-omics studies to support the clinical translation of vaginal microbiome research in reproductive medicine.},
}
@article {pmid42039826,
year = {2026},
author = {Gini, C and Tiezzi, F and Jiang, J and Byrd, MH and Wen, H and Johnson, JS and Brito, LF and van Vliet, S and Maltecca, C},
title = {Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797687},
pmid = {42039826},
issn = {1664-302X},
abstract = {BACKGROUND: Heat stress (HS) can disrupt the gut microbiome, yet most livestock studies rely on taxonomic summaries that overlook the ecological structure of microbial communities. Enterosignatures (ES) as latent, co-occurring microbial assemblages learned from metagenomic data, offer a framework to capture these dynamics but have scarcely been applied in livestock HS research.<br><br>METHODS: Shotgun metagenomes were obtained from 25 lactating sows, belonging to two genetic lines (TOL, n = 13; SEN, n = 12), which were divergently selected based on genomic breeding values (GEBVs) for heat tolerance, and exposed to HS conditions. Results were decomposed using non-negative matrix factorization (NMF), yielding 8 taxonomic (T-ES) and 5 functional (F-ES) subcommunities. Functional profiles (based on KEGG Orthology, KOs) were mapped to metagenome-assembled genomes (MAGs) to integrate metabolic attributes within each ES.<br><br>RESULTS: Temporal shifts dominated T-ES variation, with limited genetic-line effects. T-ES 1 (p = 5.42 &#xd7; 10[-4], Cohen's d = 0.723) and T-ES 7 (p = 0.007, Cohen's d = 0.303) showed increases from day 4 to day 14. Despite modest overall genetic line effects, TOL animals progressively transitioned toward phylogenetically diverse and balanced communities, whereas SEN animals shifted toward imbalanced states characterized by enrichment of taxa with pathobiont potential or single-taxon dominance. Other T-ES displayed small to moderate effects, and T-ES 8 showed a potentially noteworthy genetic line-specific effect size at late lactation (Cohen's d = 0.960; 95% CI: -1.80 to -0.10), though omnibus tests were non-significant (p = 0.757), and the wide confidence interval underscores substantial uncertainty at this sample size. No F-ES reached statistical significance (p > 0.05); moderate effect sizes (up to d = 0.638) suggest possible functional restructuring warranting investigation in larger cohorts.<br><br>CONCLUSION: This work presents the first use of ES to track microbiome responses to HS in lactating sows. ES revealed latent taxonomic and functional subcommunities with clear temporal reorganization, offering insights not detectable with standard clustering or diversity metrics. Although genetic-line effects were modest, several ES showed biologically relevant shifts, supporting ES as a hypothesis-generating exploratory framework for linking microbial ecology to physiological adaptation under HS conditions, while warranting validation in larger, controlled trials.},
}
@article {pmid42039832,
year = {2026},
author = {Sola, L and Candeliere, F and Busi, E and Raimondi, S and Amaretti, A and Rossi, M},
title = {A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761627},
pmid = {42039832},
issn = {1664-302X},
abstract = {INTRODUCTION: Clostridia is a major microbial class in the human gut, crucial for fermenting undigested carbohydrates and proteins, which produce short-chain fatty acids essential for gut health and immune balance. This study revised the taxonomic classification and phylogeny of all the species of intestinal Clostridia catalogued in the Unified Human Gastrointestinal Genome database using a whole-genome approach and assessed butyrate and propionate producing species.<br><br>METHODS: A total of 1,897 Clostridia species, including those with recognised binomial nomenclature and those lacking formal taxonomic classification, were retrieved and reclassified using GTDB-Tk. Their phylogeny was determined by identifying, concatenating, and aligning the 120 ubiquitous single-copy proteins defined in the GTDB. Average amino acid identity (AAI), percentage of conserved proteins (POCP), and phylogenetic relationships were used to organize the species into genera and families. The presence of enzymes belonging to the biosynthetic pathways for butyrate and propionate production was investigated in all genomes with the tool GapSeq.<br><br>RESULTS: Reclassification of the genomes resulted in 404 recognised species and 1,493 species lacking formal taxonomic classification. Oscillospirales and Lachnospirales encompassed most of the species. The pathways leading to butyrate and propionate production were analyzed in their entirety, revealing 519 species as potential butyrate producers, 257 as potential propionate producers and 77 capable of producing both. To assess the abundance of each species, 151 faecal metagenomes of healthy subjects were profiled, indicating that butyrate producing Clostridia accounted on average for 28.0% of each microbiome.<br><br>CONCLUSIONS: This study offers a comprehensive overview of intestinal Clostridia diversity, emphasising their role in gut ecosystems and their potential for butyrate and propionate production.},
}
@article {pmid42039839,
year = {2026},
author = {Chonnacháin, CN and Gibney, ER and Feeney, EL and Rooney, M and O'Connor, A and Noronha, N and Crispie, F and Cotter, PD and FitzGerald, JA},
title = {Unmelted, melted, and deconstructed Cheddar cheese: effects on the gut microbiome from a human dietary intervention study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1702111},
pmid = {42039839},
issn = {1664-302X},
abstract = {INTRODUCTION: Cheddar cheese is a nutritionally dense food matrix containing nutrients and bioactives with the potential to influence gut microbial characteristics. Food matrices influence nutrient absorption and digestibility, therefore the dairy matrix may affect gut microbial responses to dairy food intake. This research aims to identify gut microbial responses to Cheddar cheese consumption, considering aspects of the dairy matrix.<br><br>METHODS: Secondary analysis was conducted on a subset (n = 69) of participants' data collected during a 6-week parallel 3-armed intervention study. Interventions involved daily consumption of one of the following: (A) 120 g unmelted Cheddar cheese; (B) 120 g melted Cheddar cheese; (C) butter (49 g), calcium caseinate powder (30 g), and Ca supplement (500 mg). Demographics, anthropometry, dietary intake and fecal samples were collected at baseline (V1) and post-intervention (V2). Fecal samples underwent 16S rRNA gene sequencing, followed by bioinformatic processing and statistical analysis.<br><br>RESULTS: At V1, 52% were female, mean age was 58.2 &#xb1; 5.4 years, with no significant differences between groups or timepoints. Following sequencing, 12,098 unique bacterial taxa in total were identified. Under a False Discovery Rate (FDR) cutoff of 0.1, Dorea (W = 0.568, FDR = 0.079) and Erysipelotrichaceae UCG-003 (W = 0.887, FDR = 0.097) were significantly increased from V1 to V2 in the unmelted cheese group. At V2, Bacteroides was differentially more abundant in the unmelted cheese group, relative to the melted group (W = 0.587, FDR = 0.034). Bacterial alpha diversity (Shannon, Simpson) significantly increased in the unmelted cheese group only from V1 to V2 (p < 0.05). Beta diversity analysis showed a significant group effect considering both timepoints (F = 1.505, p < 0.01). Considering V2 only, Principal Coordinate Analysis showed the unmelted group clustered more closely relative to the other groups, although the effect was not significant.<br><br>DISCUSSION: Unmelted Cheddar cheese modulated the gut microbiome by increasing alpha diversity and abundance of several fermenting bacteria. Overall community structure also became more similar following consumption of unmelted cheese, relative to the other groups. Heating cheese and altering its physical structure disrupts the dairy matrix, potentially influencing downstream gut-nutrient interactions and subsequent gut microbial response.},
}
@article {pmid42039844,
year = {2026},
author = {Duff, AF and Bailey, MT},
title = {Abnormal intestinal microbial colonization in prenatally stressed offspring is related to lung and intestinal cytokine expression.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1813467},
pmid = {42039844},
issn = {1664-302X},
abstract = {INTRODUCTION: Prenatal stress (PNS) is associated with deleterious effects on childhood health and wellbeing. Among these consequential health repercussions, PNS-exposed children are at increased risk for acquiring early-life infections, with respiratory infections frequently reported. Stress-induced perturbations in the maternal microbiome during pregnancy represent a key link between stress in utero and aberrant offspring development and can drive abnormal pioneer colonization of offspring microbiomes.<br><br>METHODS: Using a mouse model of PNS, we aimed to understand the extent to which these early-life intestinal microbial perturbations are related to intestinal and lung cytokine gene expression. The intestinal microbiome alongside intestinal and lung tissue gene expression were assessed over the first five weeks of life in PNS-exposed offspring to characterize basal cytokine differences in relation to intestinal microbial composition.<br><br>RESULTS: In addition to significant changes in microbiome diversity and differential abundance, PNS offspring exhibited significant differences in ileal and lung cytokines characterized by overall increased interferon and proinflammatory gene signatures. PNS-associated microbiome changes also correlated to gene expression in both the ileum and lung. Finally, PNS-associated cytokine differences were not observed in MyD88[-/-] offspring which lack the ability to initiate inflammatory responses through microbially-stimulated toll-like receptor signaling.<br><br>CONCLUSION: These findings suggest that PNS-mediated changes in the early-life microbiome are linked to respiratory and ileal immune development and the microbe-immune interactions are MyD88 pathway-dependent.},
}
@article {pmid42039845,
year = {2026},
author = {Muscò, A and Tarracchini, C and Rizzo, SM and Viappiani, A and Ventura, M and Turroni, F},
title = {Exploring the molecular crosstalk between the sex steroids drospirenone and ethinylestradiol with vaginal lactobacilli.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1725887},
pmid = {42039845},
issn = {1664-302X},
abstract = {INTRODUCTION: The vaginal microbiota, dominated by the genus Lactobacillus spp., plays a crucial role in maintaining vaginal homeostasis and protecting against infection through lactic acid production, antimicrobial compound secretion and competitive exclusion of pathogens. Although hormonal fluctuations are known to influence microbial composition, the molecular mechanisms underlying these interactions remain largely unexplored. The aim of this study was to investigate the direct effects of the synthetic sex hormones drospirenone and ethinylestradiol, key components of hormonal contraceptives, on representative vaginal Lactobacillus species.<br><br>METHODS: Representative Lactobacillus species associated with different vaginal Community State Types (CSTs) were exposed to drospirenone and ethinylestradiol under simulated vaginal conditions. Lactobacilli responses were assessed using growth assays and RNA-seq transcriptome profiling to evaluate species-specific transcriptional changes following hormonal exposure.<br><br>RESULTS: Among the tested strains, Lactobacillus crispatus PRL2021 showed the most pronounced transcriptomic modulation. In this strain, hormone treatment led to the upregulation of genes involved in cell wall biosynthesis, amino acid and carbohydrate metabolism, and stress adaptation. Specifically, expression of the histidine kinase gene sasA_1, part of a two-component regulatory system potentially involved in environmental sensing, was induced. Additionally, the ribBA and ribE genes, predicted to be involved in riboflavin biosynthesis and associated with antioxidant defense and mucosal protection, were upregulated.<br><br>CONCLUSION: These findings demonstrate that drospirenone and ethinylestradiol can directly modulate bacterial gene expression, revealing a previously underinvestigated molecular crosstalk between host endocrine signals and the vaginal microbiota. This interaction may contribute to the maintenance of vaginal eubiosis and has potential implications for the development of microbiome-targeted strategies to support women's health. Further studies are needed to elucidate the broader functional consequences of hormone-microbiota interactions and their clinical relevance.},
}
@article {pmid42039849,
year = {2026},
author = {Weng, N and Pinela, E and Shakeri Yekta, S and Moestedt, J and Westerholm, M},
title = {Interplay of iron and sulfur with syntrophic propionate oxidation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798413},
pmid = {42039849},
issn = {1664-302X},
abstract = {In anaerobic environments, different chemical forms of iron and sulfur influence microbial community composition and functions. This study employs mesophilic and thermophilic ammonia-tolerant syntrophic propionate-oxidizing (SPO) cultures to investigate how different iron and sulfur species influence propionate oxidation, as well as downstream syntrophic acetate oxidation and methanogenesis. Elevated concentrations of both Fe[3+] and Fe[2+] species strongly inhibited SPO activity and suppressed propionate oxidation by the mesophilic culture. In contrast, FeSO4 addition to the thermophilic SPO culture markedly enhanced propionate oxidation and methane formation. Notably, neither Na2SO4 nor FeCl2 alone produced comparable stimulation, suggesting that the observed response was driven by a synergistic effect of Fe[2+] and SO4 [2-] on the SPO microbial network. Following Fe[2+] amendment of thermophilic cultures, a bacterium associated with the glycine cleavage pathway became enriched. Subsequently, with the onset of syntrophic propionate and acetate oxidation, the SPO candidate "Candidatus Thermosyntrophopropionicum ammoniitolerans," a syntrophic acetate-oxidizing bacterium affiliated with the family Thermacetogeniaceae, and a hydrogenotrophic methanogen affiliated with the genus Methanothermobacter increased in relative abundance. Overall, the study demonstrates that predicting the outcomes of iron amendments to the anaerobic microbiome demands careful consideration of the prevailing iron and sulfur chemical speciation and their relative molar concentrations, as these factors drive divergent microbial responses under mesophilic and thermophilic conditions. The outcomes support developing targeted strategies to optimize anaerobic digestion and enhance renewable methane yields in high-ammonia biogas systems.},
}
@article {pmid42039890,
year = {2026},
author = {Feng, F and Choi, J and Ahn, D and Truong, TMT and Yim, KJ and Kim, HJ and Jung, MY and Lee, HW and Kim, DS and Kang, I},
title = {Marine-derived extracts of Peyssonnelia caulifera Okamura and Meristotheca papulosa demonstrate differential efficacy in modulating obesity-related metabolic skewing revealed by integrative analysis of extract metabolomics and microbiome profiles.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1749413},
pmid = {42039890},
issn = {2296-861X},
abstract = {This study investigated the anti-obesity efficacy of Peyssonnelia caulifera Okamura extract (PCE) and Meristotheca papulosa extract (MPE) in a high-fat diet (HFD)-induced obese mouse model. Both extracts improved hyperinsulinemia, adipocyte hypertrophy, and adipose/hepatic inflammation. PCE significantly reduced fasting glucose and hepatic triglyceride levels, while MPE effectively normalized colonic histopathology. Both extracts restored tight junction protein expression and mitigated gut barrier disruption. At the phylum level, both supplementations decreased Bacteroidota and increased Verrucomicrobiota; At the genus level, MPE significantly enriched Lachnospiraceae NK4A136, Dubosiella, Faecalibaculum, and Ruminococcaceae NK4A214, while PCE showed modest, non-significant increase. PCE more potently suppressed LPS-induced cytokines expression and adipogenesis than MPE in vitro. UPLC-QTOF-MS revealed distinct metabolite fingerprints for each extract, and correlation analysis linked key metabolites (e.g., carnitine, valyl isoleucine) to inflammatory and metabolic indices. These findings identify PCE and MPE confer metabolic benefits in HFD-induced obesity through coordinated effects on gut, hepatic, and adipose tissue responses, with PCE showing superior efficacy.},
}
@article {pmid42040226,
year = {2026},
author = {Francomano, E and Aci, MM and Mosca, S and Mohamed, NZ and Agosteo, GE and Li Destri Nicosia, MG and Malacrinò, A and Schena, L},
title = {Plant health in the era of global changes, holobiont biology, and microbiome-based solutions.},
journal = {Horticulture research},
volume = {13},
number = {4},
pages = {uhaf364},
pmid = {42040226},
issn = {2662-6810},
abstract = {Agriculture faces unprecedented challenges due to climate change, increasing food demand, and resource scarcity, which needs sustainable and innovative solutions. This review explores the emerging paradigm of holobiont biology (host and its microbiome as biological unit) in the context of emerging plant health challenges driven by global changes. We highlight three critical challenges: the rise of complex plant syndromes, the emergence and re-emergence of plant diseases, and the consequences of dysbiotic plant microbiomes. We discuss how microbiome-based strategies can enhance plant resilience, reduce reliance on agrochemicals, and foster sustainable agriculture. Integrating these strategies with advanced frameworks, such as holo-omics and machine learning, opens avenues for microbiome-based solutions to address agricultural challenges in the era of global changes, ensuring resilient crop systems and planetary health.},
}
@article {pmid42040306,
year = {2026},
author = {Yang, R and Zhu, J and Zhang, Y and Liu, Y and Li, Z and Zhang, H and Li, Q and Wang, X and Chen, X and Chen, D and Liu, Q},
title = {Organic amendments boost maize yield (Zea mays L.) in karst soils via a hierarchical process driven by soil phosphorus enhancement and microbial-mediated nutrient cycling.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1782544},
pmid = {42040306},
issn = {1664-462X},
abstract = {INTRODUCTION: Sustainable food production in fragile karst landscapes requires moving beyond input-intensive agriculture.<br><br>METHODS: This study investigated how long-term organic amendments affected maize yield, using a 15-year field trial on karst yellow soil. Integrating soil analysis, metagenomics, and causal modeling, revealed that adding farmyard manure or bio-organic fertilizer to mineral NPK increased yield by 12.08% and 11.48%, respectively, and improved key soil properties, most notably available phosphorus.<br><br>RESULTS: Organic inputs shifted the soil microbiome toward copiotrophic taxa and enriched genes for organic matter decomposition and phosphorus mobilization. However, statistical modeling revealed that these biological changes did not directly drive yield. Instead, the primary pathway was hierarchical: amendments first enhanced the soil's chemical habitat, which then directly boosted crop growth while simultaneously shaping the microbial community and its functional potential. The interaction of soil, microbes, and genes together explained 81% of the yield variation.<br><br>DISCUSSION: Our findings demonstrate that in phosphorus-limited karst soils, organic amendments act foremost as soil conditioners. Microbial processes, though crucial, are secondary mediators that translate improved soil conditions into efficient nutrient cycling. Therefore, sustainable intensification in these vulnerable agroecosystems should prioritize managing soil health over directly targeting microbial processes.},
}
@article {pmid42040322,
year = {2026},
author = {Tong, J and Li, Y and Zhang, Y and Zhang, P and Wang, K and Zou, Q and Shen, S},
title = {Genotype-matched mapping reveals consistent regional flavour signatures and rhizosphere microbial correlates in spring-flush Yunnan large-leaf tea.},
journal = {Food chemistry: X},
volume = {35},
number = {},
pages = {103869},
pmid = {42040322},
issn = {2590-1575},
abstract = {Microbial correlates of tea terroir are often confounded by cultivar. Using eight SNP-confirmed genotype-matched pairs large-leaf tea cultivar pairs across Menghai and Pu'er, we tested whether rhizosphere communities covary with flavour chemistry during the spring flush. Under genotype control, the volatile Signature Index (VSI) was consistently higher in Menghai in all pairs, with a β-caryophyllene detection/non-detect contrast (7/8 detected in Pu'er vs 0/8 in Menghai). Non-volatiles chemistry showed a two-tier response: EGCG increased in Menghai, whereas nitrogen-associated taste allocation varied by pair. Bulk soil nitrogen and enzyme activities did not directly explain leaf patterns, while bacterial and fungal communities showed significant regional separation and cross-kingdom concordance. Within this strict genotype-matched framework, the results identify spring-flush regional flavour signatures and their microbial correlates as association-level patterns, providing candidate targets for subsequent mechanistic study.},
}
@article {pmid42041114,
year = {2026},
author = {Chen, J and Liang, T and Xu, X and Yu, X and Li, Z and Zheng, X and Liu, Y and Yang, S and Meng, Z and Zhou, Y and Ye, C and Tu, H and Cao, G and Chen, H and Chen, L and Li, B and Nie, Y and Sun, S and Zhang, Y and Lu, Y and Zhang, X and Yu, G and Lv, Y and Jia, H and Deng, Z and Pei, N and Shi, Y and Yang, Y},
title = {Characterization of the intrahepatic microbiome in patients with HBV-Related end-stage liver disease.},
journal = {Virulence},
volume = {},
number = {},
pages = {2665492},
doi = {10.1080/21505594.2026.2665492},
pmid = {42041114},
issn = {2150-5608},
abstract = {BACKGROUND: Dysregulated microbiota is a hallmark of end-stage liver disease (ESLD). This study aimed to elucidate the intrahepatic microbiome in hepatitis B virus (HBV)-related ESLD.<br><br>METHODS: We collected liver tissue samples from patients undergoing liver transplantation due to decompensated cirrhosis (DC) (n&#x2009;=&#x2009;20) or acute-on-chronic liver failure (ACLF) (n&#x2009;=&#x2009;24), as well as 18 samples from donors. Metatranscriptomic sequencing was performed to profile liver microbiome and transcriptome.<br><br>RESULTS: 2208 bacterial species were detected across 13 phyla and 165 genera. Metatranscriptomic profiling revealed that Proteobacteria and Actinobacteria dominated the intrahepatic microbiome, with Escherichia coli and Pseudomonas most prevalent across groups. Principal coordinate analysis showed distinct microbial community structures among donors, DC, and ACLF patients. Compared with donors, both groups exhibited increased abundance of Bacteroides heparinolyticus, Moraxella osloensis, and Gardnerella vaginalis, while ACLF patients were further enriched with Alcaligenes faecalis and Burkholderia insecticola, and DC patients had higher B. heparinolyticus. Most taxa originated from the gut, with additional oral- and respiratory-derived species. Despite similar abundance between groups, E. coli in ESLD displayed marked functional activation, including nutrient acquisition systems and virulence factors linked to adhesion, invasion, and toxin production. Integrated host - microbiome analysis revealed taxa-specific associations with impaired hepatic metabolic, immune, and structural integrity.<br><br>CONCLUSION: This study delineates the compositional and functional reprogramming of the intrahepatic microbiome in patients with ESLD and its coupling with liver metabolic, immune, and structural pathways. These findings suggest the intrahepatic microbiome as a promising therapeutic target for ESLD.},
}
@article {pmid42041249,
year = {2026},
author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS},
title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.},
journal = {mBio},
volume = {},
number = {},
pages = {e0286825},
doi = {10.1128/mbio.02868-25},
pmid = {42041249},
issn = {2150-7511},
support = {F32 AI186285/AI/NIAID NIH HHS/United States ; L40 HD116358/HD/NICHD NIH HHS/United States ; R01 AI153332/AI/NIAID NIH HHS/United States ; R21 AI186346/AI/NIAID NIH HHS/United States ; },
abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.},
}
@article {pmid42041258,
year = {2026},
author = {Nieciecki, V and Seitz, VA and Burcham, ZM and Otto, K and Cantrell, K and Kirkland, J and Ackermann, G and Knight, R and Lynne, A and Metcalf, JL and Bucheli, S},
title = {Insects shape the cadaver decomposition microbiome and postmortem interval estimation accuracy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0068125},
doi = {10.1128/msystems.00681-25},
pmid = {42041258},
issn = {2379-5077},
abstract = {The breakdown and recycling of carrion is a crucial ecological process that largely relies on a community of necrophagous insects and microbes. Recent work has shown that a specialized microbial network, likely dispersed throughout the environment by insects, assembles during cadaver decomposition to break down flesh regardless of climate and geography. Because of their broad distribution and successional nature, decomposer microbes have been used in machine learning models to predict the postmortem interval (PMI) of human remains, an important contribution to the field of forensics. How factors such as an indoor environment, which alters insect activity, impact the composition of microbial communities decomposing human remains is unclear. Here, we investigate the effects of enclosed shelter on microbial community assembly and successional patterns during human decomposition and provide important considerations for PMI modeling. Compared to outdoor cadavers, we show that indoor cadavers experienced delayed colonization of key decomposer microbes over the course of decomposition due to restricted insect access. Consequently, machine learning models trained on outdoor cadavers frequently underestimated the PMI of cadavers decomposing indoors. Delayed colonization by blow fly maggots (Diptera: Calliphoridae) was correlated with higher PMI prediction errors, suggesting that insects are an important source of microbial decomposers that drive PMI model predictions. Incorporating microbial data from indoor cadavers and insect activity into PMI models significantly improved prediction capabilities for both indoor and outdoor decomposition environments. Ultimately, we demonstrate the important role insects play in the maintenance and distribution of microbes that help to recycle vertebrate remains.IMPORTANCEMicrobes are critical for the decomposition and recycling of organic matter. Recently, microbiome-based models have shown promising performance in estimating the postmortem interval (PMI). However, many deaths occur indoors, yet no studies have investigated the impact of enclosed shelter on the cadaver microbiome in a controlled setting. Here, cadavers were decomposed indoors, and we found that blow fly maggots serve as an important source of decomposer taxa that significantly alter the cadaver microbiome following infestation. Notably, PMI estimation models trained on outdoor data sets failed to accurately predict the PMI when insect colonization was delayed. We show that incorporating 16S rRNA amplicon data from cadavers decomposing indoors, along with environmental variables, significantly improves PMI estimates, suggesting a microbiome-based forensic tool may be feasible across decomposition environments. Importantly, this research demonstrates the critical ecological role insects play in the dispersal of specialized microbes that are involved in the breakdown and recycling of vertebrate remains.},
}
@article {pmid42041314,
year = {2026},
author = {Ma, H and Zhang, L and Wang, L and Yang, Z and Liu, J and Sun, H and Ge, S and Quan, C},
title = {Antibiotic Mechanisms and Resistance: Molecular Insights and Therapeutic Strategies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041314},
issn = {2079-6382},
support = {2022020332-JH2/1013//Applied Basic Research Project of Liaoning Provincial Science and Technology Department/ ; LJKMZ20220401//Basic scientific research projects of Liaoning Provincial Department of Education/ ; },
abstract = {Antibiotic resistance is a critical global health threat, already causing over 1.27 million deaths annually and projected to exceed 10 million by 2050. This crisis is compounded by stagnation in novel antibiotic discovery, highlighting the need for mechanism-based innovation. Here, we provide an integrative framework linking antibiotic mechanisms of action, bacterial resistance pathways, and emerging therapeutic strategies. Antibiotics are systematically categorized by their molecular targets, cell wall synthesis, membrane integrity, nucleic acid replication, protein synthesis, and metabolic pathways, while resistance mechanisms are outlined in parallel, including enzymatic degradation, target modification, efflux, and permeability barriers. We further highlight novel approaches such as structure-guided drug design, synergistic combinations, nanoparticle delivery, and artificial intelligence-driven discovery. Precision medicine and microbiome modulation are also emphasized as next-generation interventions. By bridging molecular mechanisms with translational strategies, this review outlines opportunities to guide antibiotic innovation and advance precision therapies against the escalating threat of antimicrobial resistance.},
}
@article {pmid42041360,
year = {2026},
author = {Hashim, NT and Babiker, R and Rahman, MM and Mohammed, R and Padmanabhan, V and Islam, MS and Elsheikh, M and Abduljalil, SMA and Mahmoud, G and Chaitanya, NCSK and Siriwardena, BSMS and Ahmed, A and Gismalla, BG},
title = {Targeting Bacterial Infections in Periodontal Disease: From Conventional Antibiotics to Next-Generation Therapeutics.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041360},
issn = {2079-6382},
abstract = {Periodontitis is a highly prevalent chronic inflammatory disease with significant oral and systemic consequences, including associations with cardiovascular disease, diabetes, and adverse pregnancy outcomes. Although mechanical debridement remains the cornerstone of therapy, adjunctive antibiotic use is increasingly limited by antimicrobial resistance, biofilm-associated tolerance, pharmacokinetic constraints, and disruption of the commensal microbiome, leading to inconsistent outcomes and disease recurrence. This review highlights the mechanistic limitations of conventional antibiotic therapies in periodontitis and critically examines emerging next-generation therapeutic strategies aimed at overcoming these challenges. Specifically, it explores antimicrobial peptides, quorum sensing inhibitors, nanotechnology-based drug delivery systems, host modulation approaches, and microbiome-targeted therapies, with emphasis on their molecular mechanisms, clinical relevance, and translational potential. By integrating microbial, host, and pharmacological perspectives, this review provides a comprehensive framework for advancing precision-guided periodontal therapy and supports the shift toward targeted, sustainable, and personalized treatment strategies.},
}
@article {pmid42041380,
year = {2026},
author = {Alvaro, ME and Caserta, S and Martino, EA and Skafi, M and Bruzzese, A and Amodio, N and Lucia, E and Olivito, V and Labanca, C and Mendicino, F and Vigna, E and Morabito, F and Gentile, M},
title = {Gut Microbiota and Acute Myeloid Leukemia: State of the Art, Clinical Signals, and Translational Opportunities.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041380},
issn = {2079-6382},
abstract = {Acute myeloid leukemia (AML) remains a highly morbid malignancy in which outcomes are constrained not only by disease refractoriness and relapse, but also by therapy-related toxicity-particularly infections, mucosal injury, and delayed hematopoietic reconstitution. The gut microbiota has emerged as a potentially modifiable layer of host vulnerability and resilience during AML treatment. Microbiome disruption is detectable already at diagnosis, even in antibiotic-naïve patients, and is often characterized by reduced community diversity, depletion of anaerobic taxa linked to short-chain fatty acids (SCFAs) production, and enrichment of pathobiont-associated profiles. During induction, cytotoxic therapy and antimicrobials precipitates diversity loss, domination events, and persistent shifts beyond discharge. Clinically, the most consistent translational signal is the association between baseline or early-treatment microbiome features and infectious outcomes, while emerging data suggest that diagnosis-time microbiome structure may also relate to hematologic recovery kinetics. Mechanistic models converge on pathways linking barrier integrity, microbial metabolites (notably butyrate and other SCFAs), immune calibration, and inflammatory translocation of microbial products. These insights support hypotheses: antimicrobial stewardship may preserve microbiome function; ecosystem repair strategies such as autologous fecal microbiota transfer (A-FMT) are feasible and can restore community structure; and metabolite or nutritional interventions merit evaluation in immunocompromised hosts. Regimen-specific microbiome effects and microbiome-drug interactions suggest that treatment choice could have downstream microbiome-mediated consequences. We synthesize evidence, outline interventional concepts, and define methodological priorities for next-generation trials assessing causality and clinical benefit. Progress will require longitudinal sampling, multi-omic integration (metabolomics, resistomics, and barrier/inflammatory biomarkers), and interventional designs linking microbiome dynamics to clinically meaningful outcomes.},
}
@article {pmid42041382,
year = {2026},
author = {Malinoski, L and Silva, GG and Rodrigues, LKI and Carneiro, LF and Gomes, MP},
title = {How Glyphosate and Its Derivatives Influence Antimicrobial Resistance Emergence and Transmission: A One Health Perspective.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041382},
issn = {2079-6382},
support = {302226/2022-2//National Council for Scientific and Technological Development/ ; SUS2025831000005//Funda&#xe7;&#xe3;o Arauc&#xe1;ria/ ; },
abstract = {Background/Objectives: Glyphosate-based formulations are globally pervasive pollutants increasingly recognized as potential contributors to antimicrobial resistance (AMR) in environmental microbiomes. Although glyphosate is designed to inhibit plant 5-enolpyruvylshikimate-3-phosphate synthase, it also affects microbial metabolism, stress response, and genetic exchange. This review synthesizes the pathways through which glyphosate, its metabolite aminomethylphosphonic acid (AMPA), and commercial mixtures influence resistance-associated phenotypes and the dissemination of antibiotic resistance (ABR). Methods: A critical synthesis of the literature was conducted to evaluate the mechanistic and ecological interactions between glyphosate exposure and bacterial resistance in soil, aquatic, and host-associated microbiomes. Results: Experimental evidence showed that sublethal glyphosate exposure induced oxidative stress, altered membrane permeability, activated multidrug efflux pumps, and promoted tolerance phenotypes that could modify antibiotic susceptibility. It also enhances mutation rates and horizontal gene transfer processes associated with the emergence of resistance under controlled conditions. At the community level, glyphosate exposure is associated with microbiome restructuring and enrichment of resistance determinants, often without major shifts in overall diversity of the microbiome. These effects have been reported at environmentally relevant concentrations, although the evidence remains largely derived from laboratory and mesocosm studies. Conclusions: Glyphosate acts as both a biochemical modulator of resistance-related phenotypes and an environmental selective pressure that shapes microbial communities. Its widespread use and environmental persistence position it as a context-dependent contributor to the emergence and dissemination of AMR through interacting mechanistic and ecological pathways. Integrating AMR endpoints into pesticide risk assessments and surveillance frameworks is warranted, in addition to expanded field-based validation.},
}
@article {pmid42041383,
year = {2026},
author = {Dahdah, M and Ettouil, Y and Issa, H and Koussih, L and Almutairi, MH and Rouabhia, M and Semlali, A},
title = {Evaluation of the Antifungal Activity of the Polyphenol Formulation Viroelixir Against Candida albicans.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041383},
issn = {2079-6382},
abstract = {UNLABELLED: Candida albicans (C. albicans) is an opportunistic fungal pathogen capable of causing a wide range of infections, including mucosal and systemic candidiasis. In the oral cavity, fungi represent a minor component of the microbiome but can significantly contribute to morbidity, particularly under conditions of dysbiosis or immunosuppression. Treatment remains challenging due to increasing multidrug resistance. This study investigates the in vitro antifungal potential of Viroelixir, a standardized polyphenol blend derived from green tea and pomegranate and enriched in catechins (including epigallocatechin gallate, EGCG), ellagitannins (notably punicalagin), ellagic acid, and flavonoids, with particular focus on its potential anti-virulence mechanisms.<br><br>METHODS: The effect of Viroelixir on C. albicans growth was assessed using MTT assay, optical density measurements, colony formation, carbohydrate quantification, and pH variation analysis. Biofilm formation, morphological transition, ROS production, necrosis, virulence gene expression, adhesion, and host immune responses were also evaluated.<br><br>RESULTS: Viroelixir significantly inhibited C. albicans growth and reduced colony formation compared with untreated controls. The formulation also inhibited biofilm formation and markedly reduced pseudohyphal development, reaching up to 94% reduction under specific treatment conditions. Flow cytometry analysis showed an increase in dead fungal cells, reaching approximately 88% following exposure to Viroelixir at the highest tested concentration. In addition, Viroelixir reduced the transcript levels of several virulence-associated genes, including SAP1-SAP9 and EAP1. In epithelial cell co-culture models, pre-treatment of C. albicans with Viroelixir reduced fungal adhesion and attenuated epithelial inflammatory responses, including IL-6, IL-8, and hBD-2 production, and was associated with reduced activation of the TLR4-NF-&#x3ba;B signaling pathway.<br><br>CONCLUSIONS: These findings suggest that the antifungal and anti-virulence effects observed may be associated with the polyphenolic compounds present in the Viroelixir formulation, highlighting its potential as a promising in vitro antifungal candidate against C. albicans.},
}
@article {pmid42041444,
year = {2026},
author = {Gu, BC and Jiang, GY and Tseng, CH and Chen, YJ and Wu, CY and Lin, ZX and Yeh, ZW and Wu, CC},
title = {Rapid Electrochemical Profiling of Fecal Short-Chain Fatty Acids Using Esterification/Dissociation Fingerprints and Artificial Neural Networks.},
journal = {Biosensors},
volume = {16},
number = {4},
pages = {},
pmid = {42041444},
issn = {2079-6374},
support = {112-2221-E-005-087//National Science and Technology Council/ ; 113-2622-E-005-005//National Science and Technology Council/ ; 113-2221-E-005-058//National Science and Technology Council/ ; 114-2221-E-005-047-MY2//National Science and Technology Council/ ; },
mesh = {*Neural Networks, Computer ; *Feces/chemistry ; *Fatty Acids, Volatile/analysis ; Humans ; Esterification ; *Electrochemical Techniques ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome ; *Biosensing Techniques ; },
abstract = {Short-chain fatty acids (SCFAs) are key biomarkers of gut microbiota activity; however, routine quantification in fecal samples relies largely on chromatography, which is instrument-intensive and throughput-limited chromatography techniques. Herein, we present a rapid machine-learning-assisted electroanalysis platform for SCFAs profiling that integrates a disposable three-electrode planar gold chip with voltammetric fingerprinting and artificial neural network (ANN)-based signal decoupling. To generate orthogonal chemical information and improve the discrimination of structurally similar species, a dual pretreatment strategy combining acid-catalyzed esterification and alkaline dissociation was employed prior to electrochemical analyses. Differential pulse voltammetry (DPV) and cyclic voltammetry (CV) were employed to acquire high-dimensional fingerprints, from which current-, potential-, and area-based descriptors were extracted using a cross-information feature strategy. A hierarchical modeling framework improved total SCFAs prediction by incorporating ANN-predicted propionate and butyrate concentrations as auxiliary inputs. While linear calibration was achievable in standard mixtures, direct linear models performed poorly in real fecal matrices due to strong sample-dependent matrix interference. In contrast, the ANN captured nonlinear relationships among multifeature inputs and suppressed matrix effects. Validation against gas chromatography-mass spectrometry in an independent fecal test cohort (n = 30) demonstrated excellent agreement and low prediction errors, with mean absolute error/root mean square error values of 0.063/0.072 mM (propionic acid), 0.029/0.034 mM (butyric acid), and 0.135/0.202 mM (total SCFAs). The DPV/CV acquisition requires only minutes per sample, whereas pretreatment takes 1~3 h depending on the target route but can be performed in parallel for batch processing; thus, overall throughput is determined mainly by batch pretreatment rather than per-sample instrument time. This electrochemical-ANN workflow provides a portable, high-throughput alternative to chromatography for fecal SCFAs profiling in clinical screening and microbiome research.},
}
@article {pmid42041525,
year = {2026},
author = {Bertoni, G and Ristori, S and Monti, D},
title = {Immunosenescence and Inflammaging as Drivers of Neurodegeneration: Cellular Mechanisms, Neuroimmune Crosstalk, and Therapeutic Implications.},
journal = {Cells},
volume = {15},
number = {8},
pages = {},
pmid = {42041525},
issn = {2073-4409},
support = {DM 1557 11.10.2022//Next Generation EU/ ; },
mesh = {Humans ; *Immunosenescence/immunology ; *Neurodegenerative Diseases/immunology/pathology/therapy ; *Inflammation/immunology/pathology ; Animals ; *Aging/immunology ; *Neuroimmunomodulation ; },
abstract = {Aging is accompanied by profound alterations in immune function, termed immunosenescence, and by a chronic, low-grade inflammatory state known as inflammaging. These processes are increasingly recognized as central drivers of age-related neurodegenerative diseases, including Alzheimer's Disease, Parkinson's Disease, Amyotrophic Lateral Sclerosis and Multiple Sclerosis. In the central nervous system, senescent microglia and astrocytes lose their homeostatic and neuroprotective functions, while systemic immune aging and blood-brain barrier dysfunction further amplify neuroinflammation and impair protein aggregate clearance. This sustained pro-inflammatory environment promotes synaptic dysfunction, neuronal loss and cognitive decline. Here, we synthesize current knowledge of the mechanistic links among immunosenescence, inflammaging, and neurodegeneration, highlighting innate and adaptive immune dysregulation, mitochondrial impairment, and failed resolution pathways. We further discuss emerging therapeutic strategies, including senolytics, immunoceuticals, microbiome-based interventions and advanced drug delivery systems, aimed at restoring immune homeostasis and enhancing brain resilience. By integrating mechanistic and translational insights, this review provides a framework for developing novel interventions to target immune aging in neurodegenerative diseases.},
}
@article {pmid42041582,
year = {2026},
author = {Chandra, H and Yadav, B and Kuhnell, D and Langevin, S and Biesiada, J and Medvedovic, M and Yadav, JS},
title = {Exosomal microRNAs from Alveolar Macrophages Reveal a Protective Role of the Lung Microbiome Against Oncogenic Signaling During PAH Exposure.},
journal = {Cells},
volume = {15},
number = {8},
pages = {},
pmid = {42041582},
issn = {2073-4409},
support = {P30ES006096//NIH /NIEHS/ ; },
mesh = {Animals ; *MicroRNAs/metabolism/genetics ; *Exosomes/metabolism/genetics/drug effects ; *Macrophages, Alveolar/metabolism/drug effects ; Mice ; *Lung/microbiology/drug effects ; Signal Transduction/drug effects ; *Microbiota/drug effects ; Benzo(a)pyrene/toxicity ; Receptors, Aryl Hydrocarbon/metabolism ; Mice, Inbred C57BL ; *Polycyclic Aromatic Hydrocarbons/toxicity ; *Carcinogenesis/drug effects/genetics ; Lung Neoplasms/genetics ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs), such as benzo[a]pyrene (B[a]P), are major risk factors for lung cancer and other diseases, acting through the aryl hydrocarbon receptor (AHR). Alveolar macrophages (AMs) help regulate the lung microenvironment by responding to inhaled toxicants and resident microbiota. Although small extracellular vesicles (sEVs, aka exosomes) released by AMs mediate intercellular communication and immune responses, the influence of lung microbiota on sEV biogenesis and the mechanisms underlying sEV dysregulation during PAH exposure remain unknown. Here, we investigated the interplay between AMs, B[a]P, and lung microbiota, focusing on sEV-associated miRNAs (exo-miRNAs). Murine AMs (MH-S) were exposed to varying B[a]P concentrations in the presence or absence of murine lung microbiota with or without an AHR antagonist. sEVs from each condition were characterized and profiled for miRNA. Distinct miRNA signatures emerged: high-dose B[a]P enriched miRNAs linked to cancer progression, whereas lung microbiota alone or with low-dose B[a]P induced tumor-suppressor miRNAs that limit proliferation and metastasis and promote apoptosis, an effect enhanced by AHR antagonism. Lung microbiota appeared to counteract high-dose B[a]P by modulating tumor-suppressive exo-miRNAs. This study demonstrates that lung microbiota-induced exo-miRNAs critically shape AM-derived sEV-miRNA signaling during PAH exposure. The identified exosomal miRNAs could serve as important exposure biomarkers and therapeutic targets for mitigating B[a]P-induced toxicity and cancer development.},
}
@article {pmid42041649,
year = {2026},
author = {Cheng, AY and Zheng, FM and Chen, J and Chu, CH},
title = {Addressing Research Gaps in Early Childhood Caries: A Comprehensive Review.},
journal = {Dentistry journal},
volume = {14},
number = {4},
pages = {},
pmid = {42041649},
issn = {2304-6767},
support = {17104123//Research Grant Council General Research Fund/ ; },
abstract = {Background: Early childhood caries (ECC) is one of the most common chronic diseases in children and remains unevenly distributed across populations. It is associated with pain, impaired function, and long-term health consequences. Although advances have been made in understanding its aetiology and prevention, important gaps in evidence limit progress in prevention, early detection, and equitable care. Objective: To examine current evidence on ECC and identify key research gaps across biological, behavioral, social, and health system domains. Methods: This narrative review draws on peer-reviewed literature addressing ECC epidemiology, pathogenesis, risk factors, diagnosis, management, and service delivery. The literature was examined to identify areas where evidence is limited, inconsistent, or insufficient to inform clinical practice and public health policy. Results: Research on ECC remains uneven across levels. Longitudinal evidence linking microbiome dynamics, host susceptibility, and lesion progression is limited, restricting causal understanding. Genetic and epigenetic contributions are incompletely defined, particularly in diverse populations. Although socioeconomic gradients are well established, integrative models connecting structural determinants with biological mechanisms are scarce. Emerging diagnostic tools, including biomarkers and artificial intelligence, lack robust evidence demonstrating improved clinical or behavioral outcomes. Implementation research addressing scalability, cost-effectiveness, and equity impact is underdeveloped, especially in low-resource settings. Long-term systemic and developmental consequences of ECC remain insufficiently characterized. Conclusions: Addressing ECC requires integrated and equity-oriented research frameworks that bridge biological, social, diagnostic, and implementation domains. Clarifying these gaps is essential to inform coherent prevention strategies and reduce persistent disparities in child oral health.},
}
@article {pmid42041656,
year = {2026},
author = {Abbinante, A and Barile, G and Antonacci, A and Basso, M and Pascale, F and Bartolomeo, N and Agneta, MT and D'Albis, G and Corsalini, T and Capodiferro, S and Corsalini, M},
title = {Probiotics and Ozonated Olive Oil to Maintain Oral Eubiosis in Stage I and II Periodontitis Patients: A Randomized Triple-Blind Clinical Trial.},
journal = {Dentistry journal},
volume = {14},
number = {4},
pages = {},
pmid = {42041656},
issn = {2304-6767},
abstract = {Background: Researchers are now focusing on new and less invasive therapies to improve the domiciliary maintenance phase of periodontitis. Ozonated olive oil as an alternative to common local antiseptics and the assumption of probiotics to maintain a eubiotic oral microbiome show promising results. However, the literature is still limited on this topic. This RCT aims to investigate the clinical benefits of combining ozonated olive oil products (mouthwash and toothpaste) with probiotics on oral health status in patients with stage I and II periodontitis following the active phase of therapy. Methods: The study followed a triple-blind RCT design. Patients with stage I and II periodontitis were enrolled and randomly assigned to three groups: group A (placebo), group B (effective ozonated olive oil mouthwash and toothpaste), and group C (combined protocol with effective ozonated olive oil and probiotics). Clinical assessment was performed at the first visit and after 30 days, considering Full-Mouth Plaque Score (FMPS), Full-Mouth Bleeding Score (FMBS), and Probing Pocket Depth (PPD). Results: The FMPS percentages showed a significative reduction (p = 0.0002) of 24%, 33%, and 62% observed in group A, group B, and group C, respectively. Also, the FMBS percentages were significantly decreased (p < 0.0001): -15%, -20%, and -49% observed in group A, group B, and group C, respectively. The mean PPD showed significant differences (p < 0.0001): -0.10 mm, -0.40 mm, and -1.10 mm observed in group A, group B, and group C, respectively. Overall, group C showed the best improvement among the considered clinical indexes. Conclusions: The findings of this clinical trial support the use of a combined regime of the antimicrobial and anti-inflammatory effects of ozonated olive oil and the modulation of the oral microbiome of probiotic supplements as an adjunctive domiciliary strategy for patients affected by stage I and II periodontitis.},
}
@article {pmid42041792,
year = {2026},
author = {Lee, S and Welch, CB and Zinka, K and Evans, M and Park, HJ and Lozada-Fernandez, VV and West, FD},
title = {Distinct Gut Microbiome Characteristics Associated with Mental Health Symptoms of Healthy Adults.},
journal = {Brain sciences},
volume = {16},
number = {4},
pages = {},
pmid = {42041792},
issn = {2076-3425},
support = {HATCH #GEO001002//Georgia Experimental Agricultural Station/ ; },
abstract = {Background/Objectives: Mental health conditions, including stress, anxiety, depression, and sleep problems, represent a significant health concern globally. Mounting evidence suggests a link between mental health and the gut microbiome via the gut-brain axis. However, discrepancies in human microbiome data exist due to the heterogeneity in study design and analytical approaches. Thus, this study aimed to explore the gut microbial characteristics associated with self-reported mental health symptoms using multiple analytical methods. Methods: A total of 44 healthy adults, defined as individuals without any major chronic medical conditions, were assessed for mental health symptoms using self-reported questionnaire data. To evaluate gut microbial characteristics, stool samples were collected at six time points over 28 days and underwent 16S rRNA gene sequencing. Differential abundance was assessed via ANCOM-BC, and a random forest classifier was implemented to rank features important for the classification of mental health symptoms. Participants who did not report anxiety, stress, depression, or sleep problems served as the reference group for microbiome comparisons. Results: The proportion of participants with self-reported mental health symptoms was 11.4% (stress), 27.3% (depression), 31.8% (anxiety), and 15.9% (sleep problems). Participants reporting mental health symptoms showed differences in gut microbiome composition compared to asymptomatic participants, including variation in alpha- and beta-diversity. Differential analysis identified specific taxa with higher or lower relative abundance in participants reporting specific mental health symptoms. Random forest feature ranking identified partially overlapping taxa across methods, suggesting candidate associations warranting further investigation. Conclusions: These exploratory findings suggest that self-reported mental health symptoms in otherwise healthy adults are associated with differences in the gut microbiome. The taxa identified in this study represent candidates for validation in larger, independent cohorts.},
}
@article {pmid42041827,
year = {2026},
author = {Day, R and Friedman, D and Cardoso, A and Naghibi, M and Pont, A and Martinez-Blanch, J and Lamelas, A and Chenoll, E and Kakilla, C and Rea, K and Vijayakumar, V},
title = {A Randomised, Double-Blind, Placebo-Controlled Trial of Probiotic and Postbiotic Strains in Healthy Adults with Self-Reported Anxiety: Effects on Mood, Vitality, Quality of Life and Perceived Stress.},
journal = {Brain sciences},
volume = {16},
number = {4},
pages = {},
pmid = {42041827},
issn = {2076-3425},
support = {N/A//Archer Daniels Midland (United States)/ ; },
abstract = {Background: Subclinical psychological symptoms-such as low mood, perceived stress, and poor sleep-affect a large portion of the population and can impair quality of life despite remaining below clinical thresholds. The gut-brain axis has emerged as a promising target for interventions that support emotional and psychological resilience. Probiotics and postbiotics are gaining attention for their potential to modulate mood and stress via microbiome-related mechanisms, but human evidence remains limited, particularly in non-clinical populations. Objectives: We aimed to assess the effects of a two-strain combination of live microorganisms alongside a two-strain combination of heat-treated inactivated microorganisms on outcomes associated with anxiety, mood, perceived stress, and quality of life in healthy adults experiencing mild stress. Methods: This study was conducted in two parts. In Part I, a randomized, double-blind, placebo-controlled study, 100 participants were randomized to receive either a blend of live microorganisms (Bifidobacterium longum CECT 7347 and Lactobacillus rhamnosus CECT 8361) or an identical placebo once daily for 12 weeks. In Part II, a pilot feasibility study, a subset of eight placebo non-responders from Part I received the heat-inactivated preparation of the same bacterial strains in a 6-week trial extension phase. For Parts I and II, the primary outcome was the change in the Hamilton Anxiety Rating Scale (HAM-A). Secondary outcomes included measures of mood (Beck Depression Inventory (BDI); Patient Health Questionnaire-9 (PHQ-9)), stress (state and trait anxiety inventory (STAI); Perceived Stress Scale (PSS)), sleep (Pittsburgh Sleep Quality Index (PSQI)), quality of life (36-item Short Form Survey (SF-36)), gastrointestinal symptoms (Gastrointestinal Symptom Rating Scale (GSRS)), salivary cortisol and microbiome modulation. Results: In Part I, there were no significant effects of the live blend on the HAM-A, indicating that the primary endpoint was not met. In addition, no significant effects were seen on the STAI or PSS scores when compared to the placebo. However, participants consuming the live blend trended toward a reduction in total PHQ-9 scores compared to placebo (p = 0.089), whilst preliminary exploratory analyses suggested an improvement in anhedonia (p = 0.045). Furthermore, there was a significant improvement in the vitality domain of the SF-36 compared to placebo (p = 0.017). On microbiome analysis, it was noted that consumption of the live blend was linked to the preservation of butyrate-producing bacteria, particularly members of the Pseudoflavonifractor genus and the Clostridium SGB6179 species. Furthermore, the abundance of B. longum species was found to be inversely associated with the total PSS Scores. In Part II, supplementation with the inactivated preparation resulted in significant within-group improvements for the vitality (p = 0.006) and social functioning (p = 0.010) domains of the SF-36 and improvements in PSS scores compared to baseline (p = 0.050). Conclusions: Supplementation with either the dual-strain live or inactivated formulations was associated with significant improvements in the vitality domain of the SF-36, whilst participants receiving the inactivated formulation demonstrated lower perceived stress and improved social functioning compared to baseline. Overall, the findings from this pilot study suggest that these two biotic consortia are well-tolerated and may be associated with improvements in measures of vitality in individuals with subclinical psychological symptoms. The subtle observations detected for stress and anhedonia suggest that further well-powered trials are needed to better characterize these findings, potentially in populations with greater baseline symptomatology.},
}
@article {pmid42041878,
year = {2026},
author = {Carlone, J and Ribeiro, &#xc1;CDS and Parisi, A and Giampaoli, S and Fasano, A},
title = {Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
pmid = {42041878},
issn = {2079-7737},
abstract = {The growing interest in the role of the gut microbiome in athletic performance has led to the application of various sequencing technologies in this field. This review critically examines the sequencing methodologies used in microbiome studies on physical performance and sport, comparing their advantages, limitations, and applicability. In particular, the focus is on 16S metabarcoding and shotgun metagenomics, evaluating how these methodological approaches influence the interpretation of results in sports contexts. Close attention is directed toward technical challenges, methodological biases, and future perspectives, including emerging technologies and multi-omics approaches. This review aims to bridge the gap between methodological rigor and sports-specific applicability, providing evidence-based methodological guidance to support researchers in designing robust athlete microbiome studies and translating sequencing-derived findings into concrete applications for performance and sports health.},
}
@article {pmid42041903,
year = {2026},
author = {Dogra, S and Arukha, AP and Koul, B and Rabbee, MF},
title = {Redox Reprogramming of the Diseased Liver by Dietary Flavonoids: From Molecular Signalling to Gut-Liver Crosstalk.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
pmid = {42041903},
issn = {2079-7737},
abstract = {Liver diseases, including fatty liver, hepatitis, and cirrhosis, remain major global health challenges due to their disruption of metabolic homeostasis and detoxification processes. Redox imbalance plays a central role in liver disease progression by promoting inflammation, hepatic stellate cell activation, mitochondrial dysfunction, and fibrogenesis. Although flavonoids have historically been considered direct reactive oxygen species (ROS) scavengers, emerging evidence indicates that their biological effect at physiological concentrations are primarily mediated through modulation of intracellular redox signalling rather than simple radical neutralisation. This review highlights flavonoids as redox-modulating agents capable of restoring hepatic redox homeostasis through coordinated regulation of molecular pathways. Mechanistically, flavonoids activate the Nrf2-Keap1 axis to enhance endogenous antioxidant defences, including heme oxygenase-1 and glutathione biosynthesis enzyme, while suppressing NF-κB-mediated pro-inflammatory signalling and modulating MAPK and PI3K/Akt pathways. They also regulate mitochondrial redox balance, supporting mitophagy, metabolic adaptation, and cellular resilience to oxidative stress. In addition, flavonoid biotransformation by the gut microbiome improves intestinal barrier integrity, reduces endotoxin-driven hepatic inflammation, and contributes to gut-liver crosstalk. Collectively, these mechanisms position dietary flavonoids as multi-target redox modulators with promising therapeutic potential in chronic liver disease, although further studies are needed to improve their bioavailability and clinical translation.},
}
@article {pmid42041913,
year = {2026},
author = {Wang, T and Wang, Z and Yang, X and Zhang, L},
title = {From Microbial Ecology to Functional Components in Microbe-Host Interactions.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
pmid = {42041913},
issn = {2079-7737},
support = {82370785//National Natural Science Foundation of China/ ; tscy20190612//TaiShan Industrial Experts Program/ ; tshw20120206//TaiShan Scholars Program of Shandong Province/ ; },
abstract = {Microbiome research is shifting from a focus on "whole microorganisms" to an emphasis on microbial functional components. This review systematically describes how the effects of microbial communities on the host are mediated by bioactive functional components released by microbes. These components primarily exert their effects through interactions with host Pattern Recognition Receptors (PRRs) and metabolic sensing receptors, thereby regulating host immune, metabolic, and barrier function networks. The biological effects of these functional components are highly context-dependent. Under homeostasis, metabolites such as SCFAs and bile acids promote mucosal immune tolerance and maintain epithelial barrier integrity. However, the same signals can become deleterious under dysbiosis, driving inflammation and contributing to colorectal tumorigenesis. Mechanistic dissection of individual components, such as lipopolysaccharide (LPS), is now propelling a transition in clinical translation from whole-microbe-based interventions toward component-oriented diagnostics and therapeutics. Component-oriented diagnostics and therapeutics use defined microbial molecules rather than whole microorganisms. Microbial nucleic acids (e.g., HPV DNA), metabolites (e.g., SCFAs), and proteins can serve as biomarkers for disease risk, diagnosis, and prognosis. Therapeutic strategies include targeted modulation of beneficial components, neutralization of harmful molecules, and engineered microbial delivery.},
}
@article {pmid42041929,
year = {2026},
author = {Ma, Y and Hu, Y and Zhang, J and Sun, Q and Wang, H and Liu, X and Tian, W and Wang, W and Ma, X and Shao, D and Liu, K and Li, B and Qiu, Y and Ma, Z and Li, Z and Wei, J},
title = {The Gut Microbiome and Metabolome of Domestic Cats Were Altered by the Oral Administration of Complex Probiotics.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
pmid = {42041929},
issn = {2079-7737},
abstract = {Probiotics are commonly applied to maintain the balance of gut microbiota and regulate the intestinal metabolic function of companion animals. In the present study, complex probiotics (Bacillus coagulans SNZ-1969, Bacillus subtilis, and Bacillus licheniformis) were added into the basal diet of domestic cats to investigate their influence on the intestinal microbiome and metabolic characteristics. Results revealed that the alpha diversity of the gut microbiota in the probiotic group was enhanced when compared to the control group. The beta diversity of the gut microbiota was also altered by the oral consumption of the complex probiotics. Compared to the control group, the relative abundance of beneficial microbes (such as Clostridium, Bacteroides, Phocaeicola, and Ruminococcus) in the probiotic group was enhanced, while the relative abundance of opportunistic pathogens (such as Escherichia, Gallibacter, Corynebacterium) was decreased. Additionally, the intestinal metabolic characteristics of domestic cats were also changed. The metabolomic analysis identified 408 differential metabolites between the two groups, and the KEGG function pathway analysis proved that the dominant pathway related to the differential metabolites were the amino acid metabolism, lipid metabolism, carbohydrate metabolism, energy metabolism, endocrine system, digestive system, immune system, and other metabolic pathways. Spearman's correlation analysis revealed that the beneficial microbes had positive correlations with the differential metabolites. In conclusion, the current study demonstrated that oral administration of complex probiotics could regulate overall health and well-being in domestic cats through modulating the gut microbiome and metabolic characteristics.},
}
@article {pmid42042209,
year = {2026},
author = {Guryanova, SV and Belogurova-Ovchinnikova, OY and Ovchinnikova, TV},
title = {Human and Marine Host Defense Peptides for Healthy Skin.},
journal = {Marine drugs},
volume = {24},
number = {4},
pages = {},
pmid = {42042209},
issn = {1660-3397},
support = {22-14-00380-P//Russian Science Foundation/ ; },
mesh = {Humans ; *Aquatic Organisms/chemistry ; *Skin/drug effects/metabolism ; Animals ; Skin Aging/drug effects ; *Antimicrobial Peptides/pharmacology ; *Biological Products/pharmacology ; Wound Healing/drug effects ; *Antimicrobial Cationic Peptides/pharmacology ; Immunity, Innate ; *Peptides/pharmacology ; },
abstract = {The skin serves as the first line barrier of innate immunity, protecting the body from external influences and maintaining its homeostasis. Exogenous and endogenous stress factors alter the structure and functional properties of the skin. The search for compounds capable of counteracting these processes has allowed the identification of peptides as promising ingredients of products for medicinal and cosmetic applications. This review comprehensively examines the mechanisms of action and dermatological applications of two distinct classes of natural products-endogenous human peptides and those derived from marine organisms. Human peptides exhibit numerous biological functions, including antimicrobial and immunomodulatory ones, as well as promoting antioxidant protection and wound healing. Microbiome-associated peptides are an underestimated but powerful regulator of skin aging through immunomodulation, inflammation control, barrier function maintenance, and selection of the proper microbial community. Peptides from marine organisms exhibit significant structural diversity and a broad spectrum of biological activity, including regenerative effects and effects on antibiotic-resistant microorganisms. This review summarizes current data obtained from in vitro, ex vivo, and clinical studies demonstrating a broad potential of peptides for maintaining skin health. Both peptide classes represent powerful, targeted strategies for innovative dermatological interventions aimed at promoting skin rejuvenation, protection, and overall homeostasis.},
}
@article {pmid42042323,
year = {2026},
author = {Granata, G and Petrosillo, N},
title = {Newer Therapeutics to Selectively Kill Clostridioides difficile and Restore the Microbiome.},
journal = {Infectious disease reports},
volume = {18},
number = {2},
pages = {},
pmid = {42042323},
issn = {2036-7430},
abstract = {BACKGROUND: The antibiotic ibezapolstat and the live biotherapeutic product live-JSLM are promising future approaches for treating Clostridioides difficile infection. Ibezapostat is a highly specific antibiotic for Clostridioides difficile, with minimal impact on the intestinal flora. Live-JSLM is designed to restore healthy intestinal microbiota, thus preventing recurrence of Clostridioides difficile infection. In this narrative review, we reviewed available data on ibezapostat and live-JSLM, considering that they are prototypes of two distinct, unique mechanisms of action against Clostridioides difficile.<br><br>METHODS: Data sources: PubMed and SCOPUS databases were searched from 1 January 2012 to 15 November 2025. Original articles reporting data on ibezapolstat and live-JSLM were included.<br><br>RESULTS: 31 studies were included. When compared to conventional anti-Clostridioides difficile antibiotics, ibezapolstat had a similar level of effectiveness and minimal impact on the gut microbiota. The available data confirm live-JSLM safety and efficacy in restoring the gut microbiota following the conclusion of the standard anti-Clostridioides difficile antibiotic regimen.<br><br>CONCLUSIONS: The results on ibezapolstat efficacy are promising, but require confirmation in larger patient populations through double-blind, randomised phase III trials. In the near future, an integrated approach may enhance the management of Clostridioides difficile infection: starting with highly specific antibiotics, i.e., ibezapolstat, followed by microbiome-based therapies such as live-JSLM.},
}
@article {pmid42042338,
year = {2026},
author = {Jiang, H and Xu, H and Meng, Z and Hao, K and Yang, Y and Zhao, Y and Yao, Q and Li, M},
title = {Field Root-Associated Microbiome Characteristics of Astragalus membranaceus and Its Transcriptomic Response to Purpureocillium lilacinum BP2-7 Treatment.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {4},
pages = {},
pmid = {42042338},
issn = {2309-608X},
support = {[2022ZD01]//Inner Mongolia Natural Science Foundation/ ; },
abstract = {Astragalus membranaceus suffers severe yield and quality losses due to root rot caused by Fusarium solani. To address this, we analyzed the root-associated microbial communities of healthy and diseased plants in northwest China using high-throughput sequencing. Combining community analysis with pot experiments and transcriptomic profiling, we elucidated the molecular mechanisms by which the biocontrol fungus Purpureocilliu lilacinum BP2-7 suppresses root rot. Root rot reshaped root-associated microbial structure, affecting fungal diversity more than bacterial diversity. The antagonistic effect of P. lilacinum BP2-7 against F. solani reached 71.43% in plate assays and 63.7% control efficacy in pot experiments, representing the first report of P. lilacinum application for managing root rot in A. membranaceus. Transcriptomic analysis revealed that P. lilacinum BP2-7 promotes the transition of plants from a damaged to a recovering state by modulating translation and metabolic processes, and enhancing protein homeostasis, while moderately downregulating defense-related responses to alleviate pathogen-induced excessive defense mechanisms. Additionally, twenty candidate genes involved in the direct inhibition of F. solani were identified, suggesting a role in enhancing host resistance. This study supports eco-friendly biocontrol strategies and advances understanding of plant-microbe interactions for managing soil-borne diseases in other important crops.},
}
@article {pmid42042377,
year = {2026},
author = {Yang, Y and Jiang, H and Yang, X and Hao, K and Zhao, Y and Yao, Q and Li, M},
title = {Characterization of Penicillium halotolerans with Antagonistic Activity Against Fusarium Root Rot in Astragalus membranaceus.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {4},
pages = {},
pmid = {42042377},
issn = {2309-608X},
support = {2022ZD01//Inner Mongolia Natural Science Foundation Project/ ; KJJYZX2026080//2026 Special Project of Surplus Funds in Natural Sciences, Inner Mongolia Normal University/ ; },
abstract = {Astragalus membranaceus is an important perennial medicinal plant whose roots constitute its primary medicinal organ; however, its cultivation is severely constrained by root rot caused by Fusarium oxysporum. This study aimed to characterize differences in the rhizosphere microbiome between healthy and diseased plants, identify antagonistic microorganisms from healthy rhizosphere soils, and investigate their suppressive effects on F. oxysporum and the associated host metabolic responses. High-throughput sequencing was used to compare bacterial and fungal communities in the rhizospheres of healthy and diseased plants. Microorganisms were isolated from healthy rhizosphere soils and screened for antagonistic activity against F. oxysporum, followed by validation in pot experiments. Metabolomic analysis was further conducted to assess host metabolic responses to microbial treatment. Root rot disease significantly altered the dominant composition of rhizosphere microbial communities and was associated with reduced fungal diversity and lower bacterial richness in diseased soils. Co-occurrence network analysis revealed increased complexity in bacterial networks and strengthened positive correlations among fungal taxa under diseased conditions. A total of 81 microbial strains were isolated from healthy rhizosphere soils, among which Penicillium halotolerans exhibited the strongest inhibitory activity against the mycelial growth of F. oxysporum. Pot experiments further supported its suppressive effect on Astragalus root rot. Metabolomic analysis indicated that P. halotolerans treatment was associated with changes in host metabolic profiles related to energy metabolism, defense-associated protein synthesis, and nutrient uptake. Overall, this study identified P. halotolerans as a fungal strain with antagonistic activity against F. oxysporum and provided initial evidence for its association with the suppression of Astragalus root rot. These findings offer candidate microbial resources and mechanistic insights for understanding rhizosphere-associated disease suppression in Astragalus membranaceus.},
}
@article {pmid42042414,
year = {2026},
author = {Wu, H and Ji, C and Dong, K and Wang, R and Gao, L and Luo, W and Liu, J},
title = {Dietary p-Coumaric Acid Modulates Non-Core Gut Microbiota and Sucrose Solution Consumption in Apis cerana.},
journal = {Insects},
volume = {17},
number = {4},
pages = {},
pmid = {42042414},
issn = {2075-4450},
support = {22539C//Chongqing Municipal Fiscal Fund Project/ ; cstc2021jscx-gksbX0009//Key Project of Special Focus on Technological Innovation and Application Development/ ; CARS-44-SYZ12//Modern Agroindustry Technology Research System/ ; 25403//Chongqing Academy of Animal Science/ ; },
abstract = {As the predominant native pollinator across Asia, Apis cerana is essential for the maintenance of biodiversity and agricultural productivity. The gut microbiota of honeybees plays a central role in host nutrition, detoxification, and immune function. p-Coumaric acid, a widespread phenolic acid enriched in pollen and nectar, has been reported to promote honeybee health by prolonging lifespan and increasing the expression of detoxification-related genes, hence improving tolerance to pesticides. Its influence on gut microbial communities, however, remains insufficiently characterized in A. cerana. This study evaluated the effects of dietary p-coumaric acid on survival, sucrose solution consumption, and gut microbiome composition in A. cerana workers using absolute quantification sequencing. Bees were provided sucrose solutions containing p-coumaric acid at concentrations of 41.0, 82.0, and 164.0 mg/L for durations of 5 and 10 days. The results indicated no effect on survival but revealed time-dependent changes in sucrose solution consumption. p-Coumaric acid exposure altered the abundance of non-core bacterial taxa, including Bombella and Apilactobacillus, whereas the core gut microbiota (Lactobacillus, Gilliamella, Snodgrassella, Apibacter, and Bifidobacterium) remained stable. These results suggest that p-coumaric acid modulates sucrose solution consumption and selectively influences non-core gut bacteria without disrupting survival or core microbiota stability, underscoring its role in regulating host-microbe interactions in honeybees.},
}
@article {pmid42042549,
year = {2026},
author = {Alagiakrishnan, K and Halverson, T and Olivares, DVF and Sadowski, CA},
title = {New Personalized Medicine Model for Medication Management.},
journal = {Journal of personalized medicine},
volume = {16},
number = {4},
pages = {},
pmid = {42042549},
issn = {2075-4426},
abstract = {When using traditional approaches, such as pharmacokinetics and pharmacodynamics, the entire cellular or molecular response to drugs in the body cannot be fully ascertained or established. The oral medication process involves pharmacokinetics, followed by oral microbiomics and then gut microbiomics and pharmacodynamics. Recently, there has been increasing interest in the role of genetics (pharmacogenetics and pharmacogenomics) in both humans and microbiomes, as well as omics alterations (e.g., epigenetic, transcriptomic, proteomic, and metabolomic alterations as a consequence of drug exposure), which can help to ascertain the cellular responses to medications. Both the efficacy and toxicity of a drug are influenced by these factors. To assess these at an individual level, an integrative Personalized Medicine Model may be needed to help with medication management. Two example application cases for SSRIs and statins demonstrate the clinical usefulness of such a model, which can guide clinicians during drug selection and dosing to reduce reliance on trial-and-error, thus potentially improving patient outcomes and safety. Integrating this framework into practical clinical workflows requires the capture, analysis, and translation of multi-omics data in order to realize decision support protocols and actionable drug recommendations. This review also discusses IT requirements and different stakeholder roles. Although the proposed model can guide the treatment of diseases at the individual patient level, further research is still needed before it can be implemented as part of drug development research, clinical care, and healthcare delivery systems.},
}
@article {pmid42042803,
year = {2026},
author = {Akhtar, MS and Zaman, W},
title = {From Gut to Shot: Microbiome-Guided Strategies to Improve Vaccine Responses in Food Animals.},
journal = {Vaccines},
volume = {14},
number = {4},
pages = {},
pmid = {42042803},
issn = {2076-393X},
abstract = {Vaccine performance in livestock and poultry often varies under field conditions. Conventional explanations, such as handling errors, cold-chain failures, or antigen mismatch do not fully account for inconsistent immunogenicity and durability. Increasing evidence suggests that the gut microbiome acts as an upstream regulator of vaccine responses through microbial structural signals and metabolites that shape antigen presentation, B-cell metabolism, and inflammatory tone. Early life microbiome disruption can impair antibody responses to multiple vaccines, highlighting a plausible causal role for dysbiosis in suboptimal vaccine efficacy. Microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), can influence B-cell differentiation and antibody production through metabolic and epigenetic pathways. However, these effects are dose- and context-dependent, highlighting the need for controlled translation rather than generalized assumptions that higher SCFA levels are beneficial. This review synthesizes microbiome-immunometabolism pathways relevant to vaccine responses in food animals and assesses practical nutritional and microbiome-targeted strategies, such as amino acids, trace minerals, organic acids, phytogenics, and postbiotics, that may modulate these pathways to improve outcomes. We also propose field-deployable biomarker panels that combine immune readouts with inflammation- and microbiome-linked metabolite proxies to stratify likely responders, monitor intervention effects, and improve trial comparability. Finally, we outline translational study designs that connect microbiome shifts to protective immune endpoints and performance outcomes, enabling evidence-based integration of microbiome-informed strategies into vaccination programs for poultry, with broader conceptual relevance to other food animals.},
}
@article {pmid42042831,
year = {2026},
author = {Alturaiki, W},
title = {The Role of Lung Microbiota in Shaping Host Immunity and Mucosal Vaccine Responses.},
journal = {Vaccines},
volume = {14},
number = {4},
pages = {},
pmid = {42042831},
issn = {2076-393X},
support = {R-2026-x2//Majmaah University/ ; },
abstract = {Respiratory infections remain a leading cause of morbidity and mortality worldwide, highlighting the urgent need to better understand host defense mechanisms in the respiratory tract. Recent advances in sequencing technologies have challenged the traditional view of the lungs as sterile organs and revealed the presence of a distinct, low-biomass microbial community known as the lung microbiota. These microbial populations interact closely with airway epithelial cells and immune cells to maintain respiratory homeostasis and regulate host immune responses. In healthy lungs, microbial communities dominated by Firmicutes, Bacteroidetes, and Proteobacteria contribute to immune regulation through interactions with innate and adaptive immune pathways. Microbiota-derived signals are detected by pattern recognition receptors, activating signaling pathways that regulate cytokine production, immune cell recruitment, and T-cell differentiation. In the respiratory mucosa, microbial stimulation can also induce epithelial and antigen-presenting cells to produce B-cell activating factor (BAFF) and a proliferation-inducing ligand (APRIL), which promote immunoglobulin A (IgA) class-switch recombination and support mucosal antibody responses. During pulmonary infection, disruption of microbial communities can lead to dysbiosis that amplifies inflammatory responses, impairs epithelial barrier integrity, and increases susceptibility to secondary bacterial infections. In addition to local microbial interactions, the gut-lung axis represents a key communication pathway linking intestinal microbiota with respiratory immunity through microbial metabolites such as short-chain fatty acids (SCFAs) and immune signaling networks. This review summarizes current insights into microbiota-immune crosstalk in the lung during pulmonary infection and discusses how these interactions may inform mucosal vaccine development. A deeper understanding of host-microbiota interactions may enable microbiome-informed vaccines and therapeutic strategies to improve protection against respiratory diseases.},
}
@article {pmid42042833,
year = {2026},
author = {Vaughan, E and Gilbert, A and Shi, B and Perkins, GB and Wu, H and Chadban, S},
title = {The Role of the Gut Microbiota and Uraemic Toxins in Vaccine Responsiveness Among People Receiving Maintenance Haemodialysis.},
journal = {Vaccines},
volume = {14},
number = {4},
pages = {},
pmid = {42042833},
issn = {2076-393X},
abstract = {Background: Patients with kidney failure requiring dialysis experience a high burden of vaccine-preventable diseases, and vaccine hypo-responsiveness is a key contributor. Uraemic toxins and gut dysbiosis are potential causes of hypo-responsiveness. Aim: This study aimed to determine whether uraemic toxin concentrations or gut dysbiosis are associated with vaccine response in haemodialysis patients. Methods: This was a single centre, observational cohort study of maintenance dialysis patients receiving a conventional 2-dose primary COVID-19 vaccination course. Demographic, clinical and vaccination data were collected from the eMR. Vaccine response (Elecsys Anti-SARS-CoV-2 immunoassay), serum uraemic toxin concentrations (indoxyl sulphate, p-cresyl sulphate, and trimethylamine N-oxide by liquid chromatography), and stool microbiome (16S rRNA gene sequencing) were measured 8 weeks after the second dose of vaccine. Results: Forty participants (43% female, mean age 66 years; 59% Caucasian) were included, 70% of whom were classified as a vaccine responder. Antibiotic exposure, prednisolone use and lymphopenia were significantly associated with hypo-responsiveness. Microbiome profiling identified differences in beta diversity between responders and non-responders, positively correlated with short-chain fatty acid producers (Parabacteriodes) and negatively with pathobionts (Escherichia/Shigella). Differential abundance analysis identified lower levels of Tyzzerella, Gemmiger, and Hungatella and higher levels of Turicibacter in vaccine responders. Total uraemic toxin burden and individual toxin concentrations did not differ between responders and hypo-responders (all p > 0.05). Stratification by low versus high/very high toxin burden groupings was not associated with response (p > 0.99). Conclusions: Differences in gut microbial composition were observed between vaccine responder groups, while uraemic toxin concentrations were not associated with vaccine responsiveness. These findings suggest gut microbiota composition may contribute to vaccine hypo-responsiveness in individuals receiving dialysis and warrant further investigation in larger mechanistic studies.},
}
@article {pmid42042856,
year = {2026},
author = {Tian, Y and Wu, L and Xie, X and Gu, J and Zhang, S and Chen, H and Zhang, B and Deng, X and Wang, X and Jiang, Y and Zhong, Y and Chen, W},
title = {Burkholderia spp. from HLB-Escape Rhizosphere Suppress Candidatus Liberibacter asiaticus Titers and Induce Defense Responses in Citrus.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c18038},
pmid = {42042856},
issn = {1520-5118},
abstract = {Citrus Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease, with no effective control strategies currently available. This study investigated the contribution of the rhizosphere microbiome to HLB resistance by comparing bacterial communities associated with symptomatic and escape trees. Escape trees harbored distinct microbial communities, with notable enrichment of Paraburkholderia spp. Among over 300 isolates, four Burkholderia strains (G23, G24, G25, and G29) exhibited strong inhibitory activity against CLas-related bacteria and close phylogenetic affiliation with Burkholderia theae XITOU. Genomic analyses revealed genes associated with environmental adaptation and host interaction. All four strains suppressed CLas proliferation and induced defense-related gene expression in citrus. Notably, strain G24 significantly reduced CLas titers, alleviated disease symptoms, and promoted plant recovery under field conditions, highlighting its potential as a microbial strategy for HLB management.},
}
@article {pmid42042868,
year = {2026},
author = {Zhou, D and Huang, Y and Li, F and Liu, Q and Wang, X and Wei, Q and Chen, J and Liu, Z and Huang, Y},
title = {Correlation Between Gut Microbiota and Plasma Metabolites in a Mouse Model for Post-Traumatic Stress Disorder.},
journal = {Metabolites},
volume = {16},
number = {4},
pages = {},
pmid = {42042868},
issn = {2218-1989},
support = {CSTB2022NSCQ-MSX0163//Natural Science Foundation of Chongqing (General Program)/ ; },
abstract = {BACKGROUND: The gut microbiota and plasma metabolites have been shown to contribute to the etiology of post-traumatic stress disorder (PTSD). The relationship between the gut microbiome and plasma metabolome in PTSD is poorly understood. This study aims to integrate the gut microbiome data and plasma metabolome data to elucidate microbial-metabolite associations specific for PTSD in a mouse model.<br><br>METHODS: A PTSD mouse model was induced by single prolonged stress and electric foot shock (SPS&amp;S). We sequenced the gut microbiota composition by 16S rRNA gene sequencing and used ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) for the plasma metabolomic profiling to explore the association between the gut microbiota and the plasma metabolites in mice with PTSD.<br><br>RESULTS: The PTSD mice exhibited robust anxiety-like behaviors, significantly elevated plasma IL-1&#x3b2; and TNF-&#x3b1;, and profound gut dysbiosis characterized by a marked depletion of Muribaculaceae and Akkermansia and expansion of the Lachnospiraceae_NK4A136_group. The plasma metabolomics identified 24 significantly dysregulated metabolites, including upregulated L-arginine, palmitic acid, and oleic acid, and downregulated uridine. The pathway enrichment analysis revealed coordinated perturbations in arginine biosynthesis, pyrimidine metabolism, unsaturated fatty acid biosynthesis, and glycerophospholipid metabolism. Critically, genus-level correlation analysis uncovered biologically coherent associations. The Muribaculaceae abundance showed strong negative correlations with L-arginine and palmitic acid and positive correlations with L-glutamine and thymidine.<br><br>CONCLUSIONS: This study provides an exploratory investigation into the association network between the gut microbiota and the plasma metabolites in a PTSD mouse model, offering preliminary insights into potential microbe-metabolite interactions in PTSD.},
}
@article {pmid42042900,
year = {2026},
author = {Ferrier, L and Dogra, SK and Vu, LD and Kanellopoulos, AK and Poppe, J and Biehl, L and Baudot, A and Van den Abbeele, P},
title = {Age-Specific Ex Vivo Modulation of Gut-Brain Axis-Associated Metabolites by Galacto-Oligosaccharides and Nutrient Blends in Early Childhood.},
journal = {Metabolites},
volume = {16},
number = {4},
pages = {},
pmid = {42042900},
issn = {2218-1989},
abstract = {Background: Gut microbiome-derived metabolites, particularly short-chain fatty acids (SCFA) and tryptophan derivatives, are central mediators of the gut-brain axis. This ex vivo study assessed how nutritional interventions impact such metabolites during early life, a critical period for neurodevelopment. Methods: The effects of galacto-oligosaccharides (GOS), nutrient blends (vitamins, minerals and amino acids) and their combinations were evaluated in the gut microbiomes of infants (2-4 months, n = 6) and young children (2-3 years old, n = 6) using the ex vivo SIFR[®] technology. Results: Baseline microbiome composition was age-dependent, with infants displaying lower α-diversity and greater interpersonal variability. After ex vivo incubation, nutrient blends increased the propionate/butyrate ratio and branched-chain fatty acids in young children and elevated several B-vitamins and amino acid-derived metabolites, including indole-3-carboxaldehyde, imidazoleacetic acid and pipecolinic acid. Combining nutrient blends with GOS exhibited potential synergistic effects on propionate (infants) and 2-hydroxyisocaproic acid (HICA, both age groups). GOS strongly stimulated Bifidobacteriaceae and increased metabolites linked to bifidobacterial metabolism like acetate, HICA, N-acetylated amino acids, aromatic lactic acids and acetylagmatine; in young children, butyrate and γ-aminobutyric acid (GABA) also increased. Conclusions: Combinations of GOS with nutrient blends impacted microbiome-derived metabolites associated with the gut-brain axis, with potential synergistic increases of metabolites with emerging roles in neurodevelopment, including GABA, acetylagmatine and HICA. Despite shared bifidogenic effects, differences between age groups indicate that microbiome maturity may influence responses to nutritional intervention. Future clinical studies are needed to determine whether these metabolite changes translate into neurodevelopmental benefits in vivo.},
}
@article {pmid42042904,
year = {2026},
author = {Liu, S and Wang, M and Sun, X and Jia, Z and Huang, K},
title = {A Dual-Target Microbial Therapeutic Strategy for Treating Metabolic Diseases: Complementary Mechanisms and Clinical Prospects of Lactiplantibacillus plantarum and Akkermansia muciniphila.},
journal = {Metabolites},
volume = {16},
number = {4},
pages = {},
pmid = {42042904},
issn = {2218-1989},
support = {KJQN202401144//Chongqing Municipality Education Commission/ ; },
abstract = {Metabolic diseases, including obesity, type 2 diabetes, and their related complications, have emerged as major global public health challenges. Increasing evidence indicates that gut microbiota dysbiosis contributes to disrupted metabolic homeostasis, chronic low-grade inflammation, and progression of metabolic disorders. Among candidate microbiome-based interventions, Lactiplantibacillus plantarum (L. plantarum) and Akkermansia muciniphila (A. muciniphila) have attracted particular attention because they regulate host metabolism through partially distinct yet potentially complementary mechanisms. L. plantarum has been associated with modulation of appetite-related hormones, adipose tissue remodeling, reinforcement of intestinal barrier function, and attenuation of inflammatory signaling. A. muciniphila has been linked to strengthening of the mucus barrier, production of beneficial metabolites, and improvement in immune and metabolic homeostasis. However, current evidence remains fragmented across strain-specific studies, heterogeneous formulations, and predominantly single-strain experimental designs, and direct comparative evidence for combined administration is still limited. This review synthesizes current epidemiological, mechanistic, preclinical, and clinical evidence on L. plantarum and A. muciniphila, with emphasis on their physiological traits, gut ecological adaptability, pathway-based metabolic effects, and translational challenges in obesity, type 2 diabetes, and related complications. We further highlight the ecological rationale for their functional complementarity and discuss priorities for future combination studies and precision implementation. Overall, the available literature supports functional complementarity and possible additive metabolic benefits, but synergistic effects in humans remain unconfirmed. A clearer understanding of strain identity, active therapeutic entities, delivery strategies, and host context will be essential for advancing this dual-target microbial strategy toward clinically meaningful applications.},
}
@article {pmid42043039,
year = {2026},
author = {Lauriola, M and Valkenburg, S and Dejongh, S and Zadora, W and Krukowski, H and Evenepoel, P and Raes, J and Farré, R and Glorieux, G and Meijers, B},
title = {Kidney Function Modulates Gut Microbial Metabolism.},
journal = {Toxins},
volume = {18},
number = {4},
pages = {},
pmid = {42043039},
issn = {2072-6651},
support = {860329//European Union's Horizon 2020 research and innovation program/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/metabolism/microbiology/physiopathology ; *Colon/microbiology/metabolism ; Male ; Tryptophan/metabolism ; Feces/microbiology/chemistry ; *Kidney/physiopathology ; Fatty Acids, Volatile/metabolism ; Indoles/metabolism ; Kynurenine/metabolism ; Rats ; Amino Acids/metabolism ; Fermentation ; Rats, Wistar ; Cresols/metabolism ; *Bacteria/metabolism ; },
abstract = {Growing evidence suggests that chronic kidney disease (CKD) profoundly disrupts gut microbiome and its activity. This study explores how CKD affects colon microbial metabolism, focusing on (1) the representativeness of fecal metabolomics, (2) saccharolytic and proteolytic fermentation metabolites, and (3) the gut microbiome's role in the partitioning of tryptophan in its metabolic pathways. Tryptophan's main metabolic pathways include the indolic and the kynurenine pathways, which lead, respectively, to the formation of indoxyl sulfate and kynurenine, both contributing to uremic toxicity. Using a rat model of CKD, we evaluated whether fecal concentrations of microbial compounds, on which most studies are based, reflect the colonic concentrations in contact with the gut mucosa. Thus, we quantified the concentration and content of amino acids, indole, p-cresol, and also short-chain fatty acids, in different colon sections. We demonstrated that CKD promotes increased proteolytic fermentation and an augmented tryptophan partitioning into both the indolic and kynurenine pathways. Depletion of the indolic pathway obtained upon antibiotic treatment leads to a further enhancement of the kynurenine pathway.},
}
@article {pmid42043109,
year = {2026},
author = {Sun, J and Kuang, S and Yang, H},
title = {Physiological Stress Signatures of Waterborne Glyphosate Exposure in Apostichopus japonicus: Insights for Aquatic Ecotoxicology.},
journal = {Toxics},
volume = {14},
number = {4},
pages = {},
pmid = {42043109},
issn = {2305-6304},
support = {2023YFE0106200//the National Key R&amp;D Program of China/ ; },
abstract = {Glyphosate is a widely used herbicide with increasing concern regarding its non-target impacts in coastal ecosystems and mariculture species. Here, we profiled acute physiological stress signatures of waterborne glyphosate exposure in the sea cucumber Apostichopus japonicus, integrating measured exposure concentrations, tissue residues, digestive and oxidative/innate immune biomarkers, and gut microbiota. After 24 h exposure, measured waterborne glyphosate confirmed the intended gradient (0.09 ± 0.02, 1.26 ± 0.09, and 4.49 ± 1.12 mg/L for low-, medium-, and high-dose treatments, respectively), and overt stress phenotypes with mortality occurred only at the high dose (36.67%), enabling separation of high-dose survivors (HS) and high-dose dead (HD) for downstream analyses. Tissue measurements showed low/background levels in controls, with compartment-specific distribution: the respiratory tree exhibited higher burdens at the medium dose, whereas coelomic fluid showed the highest burdens in HS at the 24 h endpoint. Functionally, most intestinal digestive enzymes were unchanged, but trypsin activity was consistently suppressed across exposed groups (p < 0.05). In coelomic fluid, oxidative stress responses were evident, with elevated MDA (L and M), reduced CAT (L, M, and HS), and reduced GSH-PX in HS (all p < 0.05), while SOD, GR, and lysozyme showed no significant changes. Gene sequencing of 16S rRNA (n = 3 per group) revealed significant shifts in community diversity/evenness (Shannon p = 0.0497; Simpson p = 0.0484) and beta diversity (PCo1 = 30.08%, PCo2 = 26.30%; PERMANOVA F = 1.816, p = 0.008), with LEfSe indicating discriminative taxa associated with exposure/outcomes. Collectively, these multi-level endpoints define an acute glyphosate stress signature in A. japonicus, linking internal dose distribution to oxidative disruption, impaired intestinal proteolysis, and microbiome restructuring.},
}
@article {pmid42043130,
year = {2026},
author = {Huang, L and Fu, S and Du, S and Feng, Y},
title = {Functional Portability of a Hyperaccumulator-Derived Core Microbiome: Enhancing Cadmium Phytoextraction in Brassica juncea L. Through Molecular Reprogramming.},
journal = {Toxics},
volume = {14},
number = {4},
pages = {},
pmid = {42043130},
issn = {2305-6304},
support = {LQN26D010019//Zhejiang Province Natural Science Foundation/ ; 42507020//National Natural Science Foundation of China/ ; },
abstract = {Soil cadmium (Cd) contamination is a persistent threat to global food security, requiring sustainable in situ remediation strategies. While hyperaccumulating plants possess specialized traits for metal extraction, their low biomass limits large-scale application. This study investigates the potential of a core endophytic synthetic community (SynCom-NS)-characterized by heavy metal tolerance and growth-promoting traits, originally derived from the hyperaccumulator Sedum alfredii-by assessing its ability to modulate the remediation phenotype of a high-biomass non-host crop, Brassica juncea. Pot experiments revealed that SynCom-NS root-zone application significantly alleviated Cd toxicity, increasing total fresh weight by 82% and chlorophyll content by 33%. Crucially, the consortium bypassed the "growth-dilution" trade-off, facilitating a 4.07-fold increase in shoot Cd accumulation. Multi-omics analysis demonstrated a systemic modulation of the host's defense machinery, marked by a >3-fold surge in glutathione (GSH) levels and the induction of phenylpropanoid biosynthesis for cell wall reinforcement. SynCom-NS application also mediated tissue-specific regulation of the key metal transporter HMA4, upregulating its expression in roots to accelerate long-distance translocation while downregulating it in shoots. These findings demonstrate that specialized core microbiomes function as potent bio-inoculants, offering a promising biological strategy for engineering high-efficiency phytoremediation systems.},
}
@article {pmid42026051,
year = {2026},
author = {Newton, DP and Ho, PY and Huang, KC},
title = {The network structure of cross-feeding impacts microbial community diversity under growth-inhibiting stresses.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71097-5},
pmid = {42026051},
issn = {2041-1723},
support = {RM1 GM135102/GM/NIGMS NIH HHS/United States ; F32 GM143859/GM/NIGMS NIH HHS/United States ; },
abstract = {Perturbations such as dietary shifts and drug treatment can reduce gut microbiome diversity, with negative consequences for host health, yet predicting diversity responses remains challenging because microbial species interact through multiple mechanisms. While nutrient competition and cross-feeding both influence microbiota assembly, environmental stresses such as antibiotics are typically studied experimentally in monoculture, and most theoretical frameworks consider nutrient competition alone. To investigate how these processes jointly shape community structure, we develop a consumer-resource model that incorporates nutrient competition, growth-inhibiting stress, and metabolite cross-feeding with a unified framework spanning varied cross-feeding architectures. For three-species communities, coexistence during narrow-spectrum growth inhibition is maximized by cyclic cross-feeding networks, whereas fully connected cross-feeding networks maximize coexistence during broad-spectrum growth inhibition. However, the benefits of cyclic cross-feeding depend strongly on community size and stress targeting: in communities with more than six species and six resources, cyclic networks can destabilize coexistence. These results are robust to inefficient leakage, dead-end metabolites, and embedding in larger communities, and large communities generalize to random leakage architectures in which connectivity determines the response to stress. Together, this framework shows that cross-feeding network architecture can fundamentally reshape how microbial communities respond to growth-inhibiting stresses.},
}
@article {pmid42026082,
year = {2026},
author = {Human, ZR and Štursová, M and Odriozola, I and Větrovský, T and Howe, A and Navrátilová, D and López-Mondéjar, R and Žifčáková, L and Brabcová, V and Mundra, S and Thoen, E and Morgado, L and Fiore-Donno, AM and Bonkowski, M and Adamczyk, B and Kohout, P and Lipton, MS and Calhoun, S and LaButti, K and Lipzen, A and Keymanesh, K and Tejomurthula, S and Pennacchio, C and Grigoriev, IV and Martin, F and Kauserud, H and Baldrian, P},
title = {Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07163-w},
pmid = {42026082},
issn = {2052-4463},
support = {240859//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; },
abstract = {Coniferous forest soils represent a globally important carbon sink, where the microbiome is essential for carbon flux between tree roots, rhizosphere, litter and soil. Soil habitats, such as roots, rhizosphere, bulk soil and litter differ in physicochemical properties and composition of highly specialized microbial communities, whose activity reflects the seasonality of temperature and tree activity of these mid- to high-latitude biomes. Here we present a multi-omic dataset encompassing 160 samples collected from four coniferous forest soil habitats in the Czech Republic and Norway, sampled in early summer, late summer, early winter and late winter that characterize the composition, genomic potential and activity of tree roots and microbiome. For each sample, we provide metabarcoding-based composition of bacterial, fungal and eukaryotic communities, results of shotgun DNA sequencing (metagenomes) and shotgun RNA sequencing (metatranscriptomes) illustrating the functional potential and activity within habitats. This dataset enables analyses of the temporal variation of taxonomic composition, functional potential and transcription across seasons in a temperate and boreal coniferous forest.},
}
@article {pmid42026105,
year = {2026},
author = {Abd-Elgwad, AFA and Bakr, SA and Sabra, EA and Khorshed, MM and Metwally, HM and Rabee, AE},
title = {Rumen bacteria, feed utilization, and milk production of Damascus goats fed different levels of azolla meal.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42026105},
issn = {2045-2322},
abstract = {UNLABELLED: Azolla could be a promising alternative feed as it is a rich source of nutrients and bioactive compounds that can modulate rumen microbiota and improve animal productivity. This study evaluated the effects of inclusion dietary Azolla (Azolla pinnata) as a partial replacement of concentrate feed mixture (CFM) on rumen bacteria, nutrient digestibility, and milk production in lactating Damascus goats. Thirty-two goats were assigned to four groups (n = 8): a control group (C), A10, A20, and A30 to receive 0, 10%, 20%, and 30% of Azolla as a replacement of CFM, respectively. Microbial diversity increased in Azolla-fed goats, with enrichment of phylum Firmicutes in Azolla-supplemented groups C=13.36%, A10= 31.09%, A20= 25.15%, and A30= 29.85%. Fiber-degrading bacterial genera such as Prevotella, Ruminococcus, and Christensenellaceae R-7 group. .Crude protein digestibility was declined in supplemented groups and was found in order 74.76>69.11>68.24>63.93 %. Total volatile fatty acids (TVFA) and the concentration of acetate, propionate, and butyrate were higher in supplemented groups (p < 0.01). Fat-corrected milk (FCM) was higher in A20 (1139 mL/head) compared to other groups (C=992, A10=1050, A30=888 mL/head and feed efficiency followed the same trend (p < 0.05). Azolla could replace 20% of CFM in goats’ diet, and it is a viable alternative feed resource, particularly under challenges associated with the availability of conventional concentrate mixtures.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-38113-6.},
}
@article {pmid42026253,
year = {2026},
author = {Plaza-Florido, A and Carrera-Bastos, P and Pérez-Prieto, I and Fiuza-Luces, C and Radom-Aizik, S and Del Pozo Cruz, B and Franceschi, C and López-Soto, A and López-Otín, C and Lucia, A},
title = {The long-lived immune system of centenarians.},
journal = {Nature reviews. Immunology},
volume = {},
number = {},
pages = {},
pmid = {42026253},
issn = {1474-1741},
abstract = {Centenarians - individuals aged 100 years or older - constitute a biologically distinct human population that achieves exceptional longevity while frequently retaining functional independence and avoiding major age-related diseases or postponing their onset. Despite their advanced age, many centenarians show relatively preserved immune function and resistance to conditions linked to immunosenescence and chronic low-grade inflammation (inflammageing). These features are especially pronounced in semi-supercentenarians (105-109 years) and supercentenarians (≥110 years), whose immune profiles often resemble those of much younger individuals. In this Review, we explore how centenarians modulate key hallmarks of immune ageing across innate and adaptive immune compartments. We discuss evidence that they limit the pathological effects of inflammageing, potentially through reduced NLRP3 inflammasome activation, enhanced autophagy and a tempered senescence-associated secretory phenotype. Omics studies further reveal transcriptomic, epigenetic and microbial signatures consistent with preserved immune function, including youth-like gene expression patterns in circulating immune cells and beneficial shifts in gut microbiome composition. Together, these findings suggest that centenarians achieve longevity through coordinated adaptations that maintain immune homeostasis and disease resistance and may inform strategies to enhance healthspan in ageing societies.},
}
@article {pmid42026383,
year = {2026},
author = {Owen, EAM and Griffiths, RI and Golyshin, PN and Chernikova, TN and Kurr, M},
title = {Patterns in Marine Fungal Diversity and Community Structure on Native Versus Invasive Macroalgae at a Local Geographic Scale.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02781-8},
pmid = {42026383},
issn = {1432-184X},
support = {81280//European Regional Development Fund (ERDF)/ ; 81280//European Regional Development Fund (ERDF)/ ; },
}
@article {pmid42026467,
year = {2026},
author = {Luo, C and Yao, H and Xian, Y and Yang, T and Xiao, X and Ying, L and Xu, J and Luo, X and Qiu, D and Liu, Y and Liu, B and Li, F},
title = {Functional remodeling of the gut microbiome and metabolome in primary idiopathic male infertility.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05064-x},
pmid = {42026467},
issn = {1471-2180},
support = {2024NSFSC0647//Sichuan Provincial Science and Technology Support Program/ ; 24SYJS01//Health Commission of Sichuan Province Medical Science and Technology Program/ ; SCU2025J4183//the Fundamental Research Funds for the Central Universities/ ; },
}
@article {pmid42026475,
year = {2026},
author = {Jia, L and Ren, S and Zhang, J and Ma, J and Yu, Z and Sun, N and Li, B and Zhang, X and Liang, B},
title = {Apple replant disease resistance in different apple rootstocks evaluated using microbiomic and metabolomic analyses.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08844-9},
pmid = {42026475},
issn = {1471-2229},
support = {HBCT2024150205//Hebei Agriculture Research System/ ; 21326308D-02-03//Key Research and Development Project of Hebei Province/ ; C2024204214//Natural Science Foundation of Hebei Province/ ; BJK2022012//Science and Technology Project of Hebei Education Department/ ; },
}
@article {pmid42026738,
year = {2026},
author = {Cao, B and Zhou, X and Cao, X and Shi, J and Liu, C and Yuan, B},
title = {Application of Gut Microbiota in the Treatment and Efficacy Evaluation of Tic Disorders: A Systematic Review.},
journal = {Journal of child and adolescent psychopharmacology},
volume = {},
number = {},
pages = {10445463261445906},
doi = {10.1177/10445463261445906},
pmid = {42026738},
issn = {1557-8992},
abstract = {OBJECTIVE: To systematically review existing evidence on the role of gut microbiota in the pathogenesis of tic disorders (TD) and to assess the therapeutic potential of microbiome-targeted interventions such as probiotics and fecal microbiota transplantation in the management of TD.<br><br>METHODS: A comprehensive search was conducted in PubMed, Web of Science, EMBASE, and The Cochrane Library (up to May 26, 2025). The review followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 guidelines and was registered in PROSPERO (CRD420251067880).<br><br>RESULTS: Eleven studies were included, with four focusing on gut microbiome-based therapies and seven studies with gut microbiota and its metabolites as outcome indicators. At the genus level, children with TD exhibited specific alterations in gut microbiota: increased abundance of Bacteroides, Faecalibacterium, and Ruminococcus, alongside decreased levels of Bifidobacterium and Prevotella. This functional dysbiosis may trigger neuroinflammation via disrupted short-chain fatty acid metabolism and impaired intestinal barrier function, ultimately disturbing the glutamate and &#x3b3;-aminobutyric acid neurotransmitter balance and leading to dysfunction in the cortico-striato-thalamo-cortical circuit. Meanwhile, probiotics as an intervention have been consistently reported to alleviate tic symptoms, although clinical evidence remains limited.<br><br>CONCLUSION: Gut microbiota may contribute to TD pathogenesis via immune modulation and neurotransmitter metabolism. While microbiota-based strategies show promise, heterogeneity and methodological limitations in current studies necessitate further high-quality research to validate mechanisms and support clinical application.},
}
@article {pmid42026776,
year = {2026},
author = {Hu, S and Miao, Z and Xiao, C and Fu, Y and Zheng, J and Hu, W and Zheng, JS},
title = {Gut microbiome and pregnancy complications: emerging evidence and mechanistic insights.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2661417},
doi = {10.1080/19490976.2026.2661417},
pmid = {42026776},
issn = {1949-0984},
mesh = {Humans ; Pregnancy ; Female ; *Gastrointestinal Microbiome ; *Pregnancy Complications/microbiology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Animals ; },
abstract = {The gut microbiome undergoes significant alterations during pregnancy. Perturbations in these microbial communities are increasingly associated with a range of pregnancy complications, including miscarriage, gestational diabetes mellitus, preeclampsia, preterm birth, and fetal growth restriction, among others. This review synthesizes current evidence on the dynamic changes in the maternal gut microecosystem including bacterial, fungal, and viral communities throughout gestation and examines its relationships with various pregnancy complications. We also summarize the underlying mechanisms driving these interactions, focusing on metabolic regulations involving short-chain fatty acids, bile acids, indoles, sex hormones, intestinal barrier integrity, and the modulation of maternal immune responses essential for fetal tolerance. Additionally, we discuss the lasting impact of the maternal microbiome on offspring health via vertical transmission and developmental programming. This review provides a conceptual framework that integrates mechanistic insights with clinical findings, with the goal of informing future research and supporting the development of microbiome-based interventions to improve maternal and neonatal health outcomes.},
}
@article {pmid42026801,
year = {2026},
author = {Klümpen, L and Mantri, A and Donkers, A and Seel, W and Stoffel-Wagner, B and Coenen, M and Schmid, M and Weinhold, L and Grein, F and Newels, P and Bedarf, J and Wüllner, U and Stehle, P and Simon, MC},
title = {Calorie-restricted oat diet is associated with zonulin and short-chain fatty acid response in metabolic syndrome: a randomized controlled trial.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2662687},
doi = {10.1080/19490976.2026.2662687},
pmid = {42026801},
issn = {1949-0984},
mesh = {Humans ; *Avena/metabolism ; *Metabolic Syndrome/diet therapy/microbiology/metabolism/blood ; Haptoglobins ; Male ; *Fatty Acids, Volatile/metabolism/blood ; Middle Aged ; Female ; *Protein Precursors/blood ; Gastrointestinal Microbiome ; Adult ; *Cholera Toxin/blood ; *Caloric Restriction ; Permeability ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; },
abstract = {Oats are associated with positive effects on gut health, but human studies are largely lacking. Therefore, we investigated the effects of two different oat diets on gut permeability makers in individuals with metabolic syndrome, each in a randomized, controlled parallel design. Participants either consumed 3 × 100 g oatmeal/d for 2 d or an adapted control diet, or they integrated 1 × 80 g oatmeal/d into their habitual diet for 6 weeks or maintained it unchanged. Serum zonulin decreased upon 2-d calorie-restricted oat diet compared to baseline, while plasma butyric acid increased compared to the control (n = 27). Zonulin reduction correlated inversely with changes in short-chain fatty acids (SCFAs), particularly valeric and butyric acids, which were associated with shifts in microbial composition. During the 6-week isocaloric oat diet, these parameters remained stable (n = 22). Our data suggests that alterations in microbiome and related effects on SCFAs upon a short-term calorie-restricted diet with high-dose oats are contributing factors to changes in gut permeability markers. Thus, an intense oat intake might be a suitable and feasible approach to improve obesity-related intestinal barrier dysfunction in metabolic syndrome.German Clinical Trials Register: 07/28/2020, identifier: DRKS00022169.},
}
@article {pmid42026803,
year = {2026},
author = {Zhang, F and Hu, K and Sun, C and Chen, R and Ni, G and Liu, X and Wei, L and Su, R},
title = {Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2662690},
doi = {10.1080/19490976.2026.2662690},
pmid = {42026803},
issn = {1949-0984},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome/genetics/drug effects ; *Neoplasms/drug therapy/microbiology ; Deep Learning ; Biomarkers, Tumor/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; Metagenomics ; },
abstract = {Targeting programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) with immune checkpoint inhibitors (ICIs) has improved survival across multiple cancer types, but the variability in patient response highlights the need for better predictive biomarkers. Existing studies rely on taxonomic abundance derived from reference genome databases, limiting the discovery and functional interpretation of uncharacterized microbes. Here, we integrated metagenomic data from multiple ICI-treated cohorts spanning diverse cancer types and geographic regions and developed a deep learning model, named BioP-VAE, that incorporates biological prior knowledge via protein sequence embeddings and uses gene-level microbial abundance features as input. Gene-level microbial abundance outperformed taxonomy abundance in predicting both ICI response and 12-month progression-free survival (PFS). In patients receiving combination immune checkpoint blockade (CICB), BioP-VAE achieved a mean AUC of 0.89 in intracohort and 0.88 in cross-cohort evaluation. Notably, in the monotherapy-treated intracohorts, BioP-VAE achieved a mean AUC of 0.97. Feature attribution analysis revealed key microbial genes. Additionally, we identified distinct predictive microbial signatures via age-stratified analysis, suggesting that host age may modulate microbiome‒immune interactions. Importantly, this is the first large-scale study to evaluate gene-level microbial abundance features for ICI response prediction across multiple cancer types by deep learning. Our findings demonstrate that incorporating biological prior knowledge into deep learning models can improve the discovery of microbial biomarkers that can be generalized across cancer types and treatment settings, offering a novel strategy for patient stratification in immunotherapy.},
}
@article {pmid42026999,
year = {2026},
author = {Dantas Alves, JS and De Oliveira Melo, NC and Toscano, AE and Manhães-De-Castro, R and Fraga Filho, CX and Cruz Neto, JPR and De Brito Alves, JL and Muniz, GS},
title = {Ketogenic diet modulates gut microbiota composition in an experimental model of cerebral palsy.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/1028415X.2026.2656403},
pmid = {42026999},
issn = {1476-8305},
abstract = {BACKGROUND: Cerebral palsy (CPa) is a neurodevelopmental disorder often accompanied by gastrointestinal dysfunction and dysbiosis of the gut microbiota (GM). The ketogenic diet (KD) has demonstrated neuroprotective and anti-inflammatory properties in neurological diseases, yet its effects on GM in CPa remain poorly understood.<br><br>OBJECTIVE: This study aimed to evaluate the impact of KD on the GM composition in an experimental model of CPa.<br><br>METHODS: Male Wistar rats were assigned to four groups (n&#x2009;=&#x2009;10) according to healthy status and KD intervention: healthy control (C), healthy ketogenic diet (K), cerebral palsy (P), and cerebral palsy with ketogenic diet (PK). CPa was induced by perinatal anoxia and sensorimotor restriction, and, from postnatal day 25-65, animals received a standard or a KD. Body weight, food, and energy intake were monitored. Fecal samples were collected at day 65 for 16S rRNA sequencing and bioinformatics analyses.<br><br>RESULTS: The CPa condition was associated with reduced body weight, decreased food intake, and marked alterations in GM composition, characterized by increased abundance of Proteobacteria, Enterobacteriaceae, and Escherichia-Shigella, along with reduced levels of Bifidobacterium and Lactobacillus. KD intervention in animals with CPa was associated with coordinated shifts in GM structure, including reduced representation of taxa linked to inflammatory profiles and increased abundance of short-chain fatty acid-producing bacterial groups, such as members of the Lachnospiraceae and Ruminococcaceae families.<br><br>CONCLUSION: Overall, these findings suggest that modulation of GM may contribute to the neuroprotective and anti-inflammatory effects of the KD, highlighting GM as a potential therapeutic target for CPa-associated comorbidities.},
}
@article {pmid42027256,
year = {2026},
author = {Lu, S and Xia, Y and Sun, Q and Sun, Y and Chen, R and Jin, H and Zhang, J and Liu, W and Huang, J},
title = {Characterization of the Gut Virome in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {581751},
pmid = {42027256},
issn = {1178-7031},
abstract = {OBJECTIVE: The dysbiosis of the gut microbiota is a well-known correlate in the pathogenesis of inflammatory bowel disease (IBD). However, the microbiome characteristics of patients with IBD who also have non-alcoholic fatty liver disease (NAFLD) are understudied, particularly the potential pathogenic mechanisms of the gut virome.<br><br>MATERIALS AND METHODS: In this study, we conducted a comprehensive gut virome correlation study, along with serum metabolomics analysis, by performing virus-like particle (VLP) and metagenomic sequencing on fecal samples from patients with inflammatory bowel disease and non-alcoholic fatty liver disease (IBD-NAFLD) and NAFLD (MASLD) controls without gastrointestinal diseases.<br><br>RESULTS: The results showed that changes in the fecal virome were associated with IBD-NAFLD (MASLD), particularly with an increase in the abundance of Caudovirales in IBD-NAFLD (MASLD) patients. Subsequent analysis of the gut virome identified Bacteroides as the top predicted host for the viruses. Additionally, we identified the pathways involved in all differential metabolites through KEGG annotation analysis, with the highest correlation being the galactose metabolism pathway.<br><br>CONCLUSION: In conclusion, by using a customized integrated gut virome catalog tailored for IBD, we revealed the fundamental changes in the gut virome of IBD-NAFLD (MASLD) patients. This study is the first to uncover the specificity of the gut virome in IBD-NAFLD (MASLD) patients and predict Bacteroides as a potential host, suggesting a microbial signature primarily influenced by intestinal inflammation.},
}
@article {pmid42027356,
year = {2026},
author = {Ulijn, GA and Išerić, E and van de Loo, AJAE and Garssen, J and Engen, PA and Naqib, A and Green, SJ and Keshavarzian, A and Verster, JC},
title = {Immune fitness and biomarkers of immune function: Relationships with the oral and gut microbiome composition.},
journal = {Brain, behavior, &amp; immunity - health},
volume = {54},
number = {},
pages = {101239},
pmid = {42027356},
issn = {2666-3546},
abstract = {BACKGROUND: Immune fitness refers to the body's capacity to respond to health challenges, such as infections, by activating an appropriate immune response. The aim of the current study was to investigate the relationship between oral and gut microbiota community structure and immune fitness scores.<br><br>METHODS: Stool and saliva samples were collected to assess compositions of both oral and gut microbiota. Immune fitness was assessed with a single-item scale ranging from 0 (very poor) to 10 (excellent). Additionally, saliva samples were analyzed to measure the concentrations (pg/ml) of pro-inflammatory biomarkers interleukin (IL)-1&#x3b2;, IL-6, IL-8, and tumor necrosis factor-alpha (TNF-&#x3b1;). Spearman's correlations were computed between microbiota abundance, immune fitness, and salivary biomarker levels. Bootstrapping was used to adjust for the relatively small sample size in the correlation analysis.<br><br>RESULTS: A total of 29 healthy participants (15 males; 14 females) enrolled in the study, with a mean age of 21.1 years old. Analysis of the salivary microbiota revealed significant negative correlations between self-reported immune fitness scores and the relative abundances of putative oral proinflammatory genera Selenomonas (r&#xa0;=&#xa0;-0.610), and Lachnospiraceae uncultured (r&#xa0;=&#xa0;-0.501). In the fecal microbiota, immune fitness scores showed a significant positive correlation with the relative abundance of putative beneficial butyrate-producing genus Lachnoclostridium (r&#xa0;=&#xa0;0.513), and significant negative correlations with commensal gut bacterial genera Colidextribacter (r&#xa0;=&#xa0;-0.582) and Lachnospiraceae FCS020 group (r&#xa0;=&#xa0;-0.504).<br><br>CONCLUSION: Self-reported immune fitness is associated with the oral and gut microbiota community. The findings demonstrate the importance of microbiota in immune function and support the use of self-assessment scales to evaluate immune fitness.},
}
@article {pmid42027463,
year = {2026},
author = {Drago, L and De La Motte, LR},
title = {The eye's coral reef: toward a planetary-health agenda for ocular-microbiome stewardship.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1816460},
pmid = {42027463},
issn = {1664-302X},
abstract = {Coral reefs and the human ocular surface represent ecologically distinct yet structurally comparable microbial ecosystems in which resilience depends on finely regulated host-microbe interactions. In coral reef science, microbial shifts precede visible bleaching and ecosystem collapse, enabling the development of predictive stress indices such as Degree Heating Weeks (DHW). Comparable principles are emerging in host-associated, low-biomass microbiomes, where subtle perturbations may trigger disproportionate functional consequences. Here, we propose a systems-level conceptual framework linking coral reef holobionts and the ocular surface as sentinel ecosystems governed by cumulative stress, threshold dynamics, and microbial instability. We introduce two heuristic constructs-the Cumulative Desiccating Load (CDL) and the Ocular Dysbiosis Sentinel Index (ODSI)-to frame dysbiosis as a trajectory of resilience loss driven by cumulative perturbations. Aging-related conditions such as age-related macular degeneration are discussed as examples of microbial and metabolic senescence within the human holobiont, conceptually paralleling coral reef decline under chronic sublethal stress. By integrating environmental and host-associated microbiome research within a planetary-health perspective, this article advances a resilience-oriented systems framework applicable across biological scales.},
}
@article {pmid42027582,
year = {2026},
author = {Giudice, A and Brescia, C and Morano, D and Viglietto, G and Luzza, F and Amato, R and Spagnuolo, R},
title = {Th17/treg balance in Inflammatory Bowel Disease: the role of microbial, and genetic regulators in disease modulation.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1774790},
pmid = {42027582},
issn = {2296-634X},
abstract = {Inflammatory Bowel Disease (IBD) is a chronic condition characterized by persistent mucosal inflammation driven by complex interactions among the gut microbiome, host immune genetics, and cellular metabolism. Emerging evidence highlights the central role of the Th17/Treg cell balance in maintaining intestinal immune tolerance, which is tightly regulated by microbe-derived metabolites and host metabolic pathways. In IBD, microbial dysbiosis and altered metabolite profiles disrupt this equilibrium, favoring pro-inflammatory responses. Moreover, genetic variants affecting immune regulation modulate individual susceptibility and disease course. Understanding how microbiome modulation, metabolic reprogramming, and genetic predisposition converge in IBD pathogenesis opens new avenues for precision medicine. This minireview discusses recent advances in this field, emphasizing novel microbiome-targeted strategies, metabolic interventions, and personalized immunomodulatory therapies aimed at restoring Th17/Treg homeostasis. Integrating microbiome, metabolome, and immunogenetic profiling may ultimately guide tailored treatments and improve long-term outcomes in IBD.},
}
@article {pmid42027687,
year = {2026},
author = {Wu, H and Yu, M and Huang, S and Peng, Y and Wei, G and Huang, C},
title = {The Gut-Brain Axis as a Mediator of Environmental Endocrine Disruptors in Attention-Deficit/Hyperactivity Disorder: A Systematic Review and Mechanistic Synthesis.},
journal = {Biological psychiatry global open science},
volume = {6},
number = {3},
pages = {100717},
pmid = {42027687},
issn = {2667-1743},
abstract = {The rising global prevalence of attention-deficit/hyperactivity disorder (ADHD) underscores the importance of environmental factors, particularly environmental endocrine-disrupting chemicals (EEDs), whose mechanistic links to ADHD remain unclear. The gut-brain axis, a key modulator of neurodevelopment, is susceptible to EEDs and is altered in ADHD, suggesting a potential mediating pathway. Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and PROSPERO registration (CRD420251152480), we systematically searched PubMed, Web of Science, and Embase (January 2014-July 2025) for studies on EEDs, gut microbiota, and ADHD. Data from 127 included studies (observational, experimental, interventional) were narratively synthesized to evaluate the gut-brain axis as a mediator. We found 1) consistent epidemiological associations between prenatal/childhood EED exposure (e.g., phthalates, bisphenol A, pesticides) and increased ADHD risk; 2) a distinct gut microbial signature in ADHD featuring reduced alpha diversity, elevated Firmicutes/Bacteroidetes ratio, depletion of beneficial taxa (Lactobacillus, Bifidobacterium), and impaired short-chain fatty acid (SCFA) production; 3) evidence that EED exposure induces convergent gut dysbiosis; and 4) interventional studies indicating that modulating the microbiota (via probiotics, synbiotics, fecal microbiota transplantation) can ameliorate ADHD-related behaviors. These findings support a novel mechanistic model wherein EEDs disrupt gut microbiota homeostasis, thereby contributing to ADHD pathogenesis via immune-inflammatory, microbial metabolite (e.g., SCFA), and neuroendocrine pathways along the gut-brain axis. This review synthesizes evidence positioning the gut-brain axis as a critical mediator linking EED exposure to ADHD. It proposes a unifying etiological framework and highlights the microbiome as a promising target for preventive and therapeutic strategies. Future longitudinal and intervention studies are needed to establish causality.},
}
@article {pmid42027746,
year = {2026},
author = {Alibrahim, MN and Carbone, A and Gloghini, A},
title = {Predictors of sensitivity to immune therapies in classic Hodgkin lymphoma.},
journal = {Blood neoplasia},
volume = {3},
number = {2},
pages = {100207},
pmid = {42027746},
issn = {2950-3280},
abstract = {Immune checkpoint blockade, particularly programmed cell death protein 1 inhibition, has redefined the management of classic Hodgkin lymphoma (cHL), achieving unprecedented efficacy in relapsed/refractory settings. Yet, durable benefit is not universal, because mechanisms of primary and acquired resistance remain incompletely understood. This review integrates current knowledge on predictors of sensitivity to immune therapies in cHL across clinical, biological, and technological dimensions. Established predictors, including disease burden, previous treatment exposure, CD30 intensity, programmed death-ligand 1 (PD-L1)/PD-L2 copy number gains, and loss of major histocompatibility complex expression, offer valuable but incomplete prognostic information. Tumor microenvironmental features such as macrophage polarization, T-cell exhaustion, and immune spatial organization further refine response prediction, whereas circulating biomarkers such as soluble PD-L1, circulating tumor DNA kinetics, and cytokine profiles provide noninvasive insights. Molecular and cellular pathways underlying resistance encompass genetic and epigenetic alterations, immune editing, and adaptive checkpoint upregulation. Emerging predictive frameworks, spanning multiomics and spatial profiling, radiomics, artificial intelligence, and microbiome-host cross talk, promise to enhance precision in patient stratification. Finally, the review outlines key challenges and research priorities for translating these multidimensional biomarkers into clinical trials and practice. A unified predictive framework integrating clinical, molecular, and computational indicators may ultimately enable personalized immunotherapy and overcome resistance in cHL.},
}
@article {pmid42028017,
year = {2026},
author = {Xie, J and Deng, S and Zhang, X and Zhang, L and Jia, X},
title = {From dysbacteriosis to ecological remodeling: A new breakthrough in microbial treatment of inflammatory bowel disease.},
journal = {iScience},
volume = {29},
number = {5},
pages = {115483},
pmid = {42028017},
issn = {2589-0042},
abstract = {Inflammatory bowel disease (IBD) is a group of chronic and recurrent inflammatory conditions of the gastrointestinal tract, arising from complex interactions among genetic susceptibility, environmental factors, immune dysregulation, and alterations in the gut microbiota. Increasing evidence suggests that gut microbiota dysbiosis is closely associated with IBD pathogenesis and disease progression, providing a promising target for microbiome-oriented therapeutic strategies. However, due to the multi-factorial and dynamic nature of microbial alterations in IBD, single-intervention approaches often show limited efficacy and durability. On this basis, this review highlights emerging strategies based on engineered microbial ecosystems, which aim to systematically modulate microbial composition and function, reinforce intestinal barrier integrity, and regulate host immune responses. While these approaches hold significant potential, their therapeutic value should be interpreted in the context of current preclinical and early clinical evidence, and further validation is required to determine their long-term efficacy and safety in patients with IBD.},
}
@article {pmid42028131,
year = {2026},
author = {Radhamanalan, G},
title = {Postbiotics and phage synergy in precision oral microbiome engineering: systems biology strategies targeting Streptococcus mutans in dental caries.},
journal = {Frontiers in molecular biosciences},
volume = {13},
number = {},
pages = {1766853},
pmid = {42028131},
issn = {2296-889X},
abstract = {Dental caries continues to represent a major global public health concern and arises from complex ecological shifts within oral biofilms. The dominance of Streptococcus mutans, in combination with broader microbial imbalance and interactions involving the oral virome, plays a central role in disease progression. Although established preventive measures such as fluoride therapy and mechanical plaque control reduce enamel demineralization and microbial load, they do not comprehensively address dysbiosis, virulence regulation, or host-microbial signaling dynamics. Postbiotics are non-viable microbial products or metabolic derivatives with biological activity, are gaining attention as targeted modulators of the oral ecosystem. These agents include organic acids, exopolysaccharides, bacteriocins, and structural components derived from inactivated probiotic cells. Through diverse mechanisms, postbiotics can reduce acidogenic potential, weaken extracellular matrix integrity within biofilms, disrupt bacterial communication systems, and modulate mucosal immune pathways. Such effects may limit colonization efficiency and pathogenic behavior of S. mutans while preserving commensal balance. Emerging strategies propose combining postbiotics with bacteriophage-based approaches, immunomodulatory platforms, and innovative delivery systems such as nanoformulations and bioadhesive matrices to improve site-specific efficacy. Advances in multi-omics technologies, systems biology modeling, and artificial intelligence-driven diagnostics further support the development of personalized interventions tailored to individual microbial signatures. In addition, postbiotic-mediated modulation of viral-bacterial interactions and horizontal gene exchange may contribute to restoring ecological stability and reducing antimicrobial resistance dissemination. This review integrates current knowledge on postbiotic-driven regulation of the oral microbiome and virome and examines their potential role in precision-oriented caries management. Addressing translational challenges, including formulation stability, safety evaluation, regulatory pathways, and comprehensive virome profiling, will be critical for future clinical application.},
}
@article {pmid42028145,
year = {2026},
author = {Chen, Y and Zhang, L and Wang, T and Pan, X and Chen, D and Liu, J},
title = {Characteristics of CD4[+]T-cell reduction and pulmonary infections in critically ill immunocompromised patients.},
journal = {Journal of intensive medicine},
volume = {6},
number = {2},
pages = {157-165},
pmid = {42028145},
issn = {2667-100X},
abstract = {BACKGROUND: The CD4[+]T-cell count is a key indicator for evaluating immunosuppression. Infections significantly influence the survival and prognosis of critically ill patients. This study aims to systematically evaluate the association between reduced CD4[+] T-cell counts and lung infections in immunosuppressed ICU patients, offering clinical evidence to guide the management of lung infections in this population.<br><br>METHODS: This retrospective, single-center study included 40 immunocompromised patients admitted to the ICU from January 1, 2021, to June 30, 2023. All participants underwent metagenomic next-generation sequencing. Patients with suspected lung infections based on their CD4[+]T-cell counts were divided into mild (350/&#xb5;L<CD4[+]T-cell count<500/&#xb5;L), moderate (200 /&#xb5;L<CD4[+]T-cell count &#x2264; 350/&#xb5;L), and severe (CD4[+]T-cell count &#x2264;200/&#xb5;L) groups. Microecological analysis was performed on each group. Intergroup comparisons were conducted for 28-day mortality, hospital length of stay, and ICU length of stay.<br><br>RESULTS: Amang these forty immunosuppressed patients, 8 were assigned to the mild group, 16 to the moderate group, and 16 to the severe group. Streptococcus pneumoniae was almost all distributed in moderate patients (75.0%), while severe patients had a higher proportion of fungi detected (25.7%). Respiratory microbiome analysis identified Acinetobacter baumannii, Human alphaherpesvirus 1, and Klebsiella pneumoniae as the most abundant species. Although no significant difference in the alpha diversity index was found among the groups, index values were lower in the severe group than in the moderate group. Beta diversity analysis showed that the microbial community structure did not significantly differ among the three groups. A total of 27 microbial markers were obtained, with multiple streptococcal species showing enrichment in moderate group and Candida tropicalis in severe group. By day 28, four patients (50.0%) in the mild group had died compared with six (37.5%) in the moderate group and nine (56.3%) in the severe group. There were no significant difference in the duration of ICU or hospital stays.<br><br>CONCLUSIONS: This study on ICU-admitted immunocompromised patients identified the prevalent pathogens and microbiome features associated with pulmonary infections, as well as their relationship with CD4[+]T-cell depletion. These findings are valuable for optimizing clinical diagnosis and treatment strategies and may contribute to improving patient outcomes.},
}
@article {pmid42028273,
year = {2026},
author = {Taha, H and Al-Shalalfeh, M and Khalil, A and Khasawneh, Y and Abu Ata, A and AbuEin, H and Issa, A and Alhawamdeh, T and BaniMustafa, M and Al-Sabbagh, MQ and Jönsson, L},
title = {Mode of birth and risk of inflammatory bowel disease in offspring: an updated systematic review and meta-analysis.},
journal = {Frontiers in reproductive health},
volume = {8},
number = {},
pages = {1776110},
pmid = {42028273},
issn = {2673-3153},
abstract = {BACKGROUND: Cesarean section (CS) rates continue rising worldwide, raising concerns about long-term offspring health consequences, including inflammatory bowel disease (IBD). This systematic review and meta-analysis evaluate the association between CS and risk of IBD, Crohn's disease (CD), and ulcerative colitis (UC).<br><br>METHODS: PubMed, Scopus, CENTRAL, and Web of Science were searched through June 2025. Eligible studies included observational cohorts and case-control studies reporting CS vs. vaginal delivery (VD) and IBD outcomes. Data extraction and risk of bias assessment were performed independently. Pooled relative risks (RRs), hazard ratios (HRs), and odds ratios (ORs) were calculated using fixed or random-effects models. Subgroup analyses and publication bias assessment were conducted.<br><br>RESULTS: Twenty-two studies comprising over 13 million births were included. Unadjusted analyses showed no association between CS and IBD (RR: 0.98, 95% CI: 0.88-1.08), CD (RR: 0.99, 95% CI: 0.88-1.12), however, an inverse association was observed for UC (RR: 0.82, 95% CI: 0.72-0.95). Regional variation was observed, with CS associated with reduced IBD risk in Denmark, Switzerland, and Norway, but increased risk in Germany and Australia. Adjusted analyses consistently demonstrated no association: IBD (HR: 1.14, 95% CI: 0.99-1.30; OR: 0.91, 95% CI: 0.65-1.25), CD (HR: 1.07, 95% CI: 0.90-1.28; OR: 1.11, 95% CI: 0.98-1.26), and UC (HR: 0.96, 95% CI: 0.87-1.05; OR: 1.05, 95% CI: 0.86-1.27). No publication bias was detected.<br><br>CONCLUSION: Across over 13 million births, delivery mode was not associated with IBD, CD, or UC risk. Despite biologically plausible mechanisms linking CS to altered microbiome patterns, epidemiological evidence does not support CS as an independent IBD risk factor. These findings provide reassurance for clinical counseling regarding CS and long-term IBD risk.<br><br>https://www.crd.york.ac.uk/PROSPERO/view/CRD420251237413, PROSPERO CRD420251237413.},
}
@article {pmid42028293,
year = {2025},
author = {Rourke-Funderburg, AS and Francisco, VA and Nelson, DJ and Goncalves, KL and Haselton, FR and Elsamadicy, E and Locke, AK},
title = {Investigating microbiota and biochemical changes in vaginal fluid toward point-of-care microbial monitoring using surface-enhanced Raman spectroscopy.},
journal = {Biophotonics discovery},
volume = {2},
number = {4},
pages = {042102},
pmid = {42028293},
issn = {3005-4745},
abstract = {SIGNIFICANCE: Vaginal health is maintained by the vaginal microbiome, and dysbiosis of this community can have lifelong negative consequences for women. Current clinical techniques for detecting bacteria in the vagina rely on subjective visual and microscopic analysis or untimely microbial culturing. Surface-enhanced Raman spectroscopy (SERS), a biochemical fingerprinting technique, shows potential for filling this gap as it can identify bacterial species and strains.<br><br>AIM: In this study, SERS was used to investigate biochemical changes in vaginal fluid when common vaginal bacteria were present and absent. Subsequently, the performance of a portable Raman spectrometer to detect these biochemical changes was evaluated.<br><br>APPROACH: Vaginal fluid was collected from participants attending routine gynecology exams, and SERS spectra were collected using a Raman microscope and a portable spectrometer. Partial least squares, peak intensity, and peak ratio analysis were used to investigate biochemical differences. Quantitative polymerase chain reaction was performed for characterization of Lactobacillus iners, Lactobacillus crispatus, Gardnerella vaginalis, and Streptococcus agalactiae content.<br><br>RESULTS: Gardnerella vaginalis presence was characterized by a significant increase in protein and lipid-related features and a decrease in organic acid peaks. The presence of Lactobacillus iners was represented by increased organic acid peaks and a reduction of protein, amino acid, and polysaccharide-related features. Similar trends with little loss of significance were observed when comparing the performance of a Raman microscope and a portable spectrometer.<br><br>CONCLUSION: We highlight the feasibility of SERS for detecting differences in bacterial species presence in vaginal fluid and showcase the potential for clinical translation.},
}
@article {pmid42028862,
year = {2026},
author = {Shanmugam, G and Singh, CD and Thiruvengadam, R and Thiruvengadam, M and Morozov, V and Kolesnikov, R and Alkaladi, A and Saleh, R and Shariati, MA},
title = {Emerging Therapeutic Strategies in Oral Cancer: Epigenetic, Mitochondrial and Immunotherapy Approaches.},
journal = {Journal of cellular and molecular medicine},
volume = {30},
number = {8},
pages = {e71107},
pmid = {42028862},
issn = {1582-4934},
mesh = {Humans ; *Mouth Neoplasms/therapy/genetics/immunology/pathology ; *Epigenesis, Genetic/drug effects ; *Mitochondria/drug effects/metabolism/genetics ; *Immunotherapy/methods ; Tumor Microenvironment/drug effects ; Animals ; },
abstract = {Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer and poses treatment challenges owing to genetic, epigenetic and environmental factors. Conventional treatments, including surgery, chemotherapy and radiation therapy, often have limitations in terms of efficacy and tolerability. Advances in epigenetic therapies such as DNA methyltransferase and histone deacetylase inhibitors offer promising avenues for reversing abnormal gene expression in OSCC. Mitochondria-targeted therapies leverage metabolic disruption and reactive oxygen species modulation to induce apoptosis. Immunotherapy, particularly with immune checkpoint inhibitors and cancer vaccines, enhances the immune response against cancer cells. This review explores the interplay between the tumour microenvironment and oral microbiome in OSCC progression and treatment response. Additionally, RNA interference therapy and nanoparticle-based drug delivery systems enable targeted therapeutic strategies, reduce off-target effects and improve efficacy. Although these approaches show potential, challenges in clinical translation remain. The integration of precision medicine with innovative drug delivery systems can significantly improve patient outcomes in oral cancer management.},
}
@article {pmid42028897,
year = {2026},
author = {Wang, S and He, H and Zhang, S and Tian, L and Lu, Q and Mai, B and Adrian, L and Dolfing, J and Xu, G},
title = {Decoding Microbial Reductive Dechlorination of 209 Polychlorinated Biphenyl Congeners through Experiment-Aided Quantum Chemistry and Machine Learning.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16226},
pmid = {42028897},
issn = {1520-5851},
abstract = {Polychlorinated biphenyls (PCBs) persist globally as legacy pollutants with a complex structural diversity that complicates the understanding of their microbial conversion processes and remediation. In this study, high-throughput enzymatic assays, quantum chemical calculations, and machine learning were integrated to elucidate the reductive dechlorination pathways and reactivity of all 209 PCB congeners. By coupling Hirshfeld charge analysis with empirically derived steric effects, 98.3% accuracy was achieved in predicting dechlorination pathways across diverse Dehalococcoides isolates and enrichment cultures containing distinct organohalide-respiring bacteria. Furthermore, XGBoost models incorporating electronic, steric, and physicochemical descriptors were developed to quantify the dechlorination reactivity of PCBs, revealing that the steric effect-corrected Hirshfeld charge and PCB solubility primarily control microbial reductive dechlorination potential. The model successfully captured the observed trends in the dechlorination reactivity of PCBs across multiple dechlorinating cultures and predicted that 11 of the 12 dioxin-like PCB congeners were susceptible to microbial reductive dechlorination, highlighting intrinsic microbial detoxification potential under anaerobic conditions. This integrative framework unveils the first full picture of microbial dechlorination pathways and reactivity for the entire PCB family, providing mechanistic insight into how molecular properties dictate halogen removal. The findings advance the predictive understanding of organohalide respiration and offer a roadmap for designing microbiome-based bioremediation strategies for persistent halogenated pollutants like PCBs.},
}
@article {pmid42028948,
year = {2026},
author = {Joncour, G and Saghbini, S},
title = {[Cutaneous pre- and probiotics: Modulating the axillary microbiome to control body odors].},
journal = {Medecine sciences : M/S},
volume = {42},
number = {4},
pages = {398-401},
doi = {10.1051/medsci/2026062},
pmid = {42028948},
issn = {1958-5381},
mesh = {*Probiotics/administration &amp; dosage/therapeutic use ; Humans ; *Microbiota/drug effects/physiology ; *Axilla/microbiology ; *Odorants/prevention &amp; control/analysis ; *Skin/microbiology ; *Prebiotics/administration &amp; dosage ; Administration, Cutaneous ; },
}
@article {pmid42028995,
year = {2026},
author = {Liu, M and Du, M and Xi, Z and Tastambek, KT and Bao, Y and Song, X and Zhou, A and Wang, Y},
title = {Bacillus aerius synergizes with coal gangue to enhance Medicago sativa growth via soil microbiome and gene regulation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0026826},
doi = {10.1128/aem.00268-26},
pmid = {42028995},
issn = {1098-5336},
abstract = {UNLABELLED: The extensive accumulation of coal gangue poses significant environmental threats through water contamination, soil degradation, and atmospheric pollution, necessitating the urgent development of ecological utilization strategies. This study elucidates the mechanistic basis by which the thermophilic bacterium Bacillus aerius (B. aerius) enhances plant growth in coal gangue-amended sandy soils. Through integrated analysis of nutrient dynamics, phytohormonal activities, soil enzymatic profiles, and metagenomic functional profiling, we demonstrate significant synergy between coal gangue and B. aerius. When applied together in sandy soils, the germination rate, plant height, root length, and fresh biomass of Medicago sativa (alfalfa) increased by 1.18-2.06 times. The levels of soil nitrogen, phosphorus, and potassium also significantly increased, resulting in notable improvements in soil fertility. The bacterial treatment enhanced the activities of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various soil enzyme activities while also optimizing the microbial community structure and increasing the abundance of beneficial bacteria, including Bacillus. Metagenomic analysis revealed the upregulation of growth-promoting genes such as acdS, nifK, and phnG, which collectively drive plant growth through multiple pathways, including enhanced soil nutrient availability, hormone regulation, soil enzyme activities, and nutrient cycling. Collectively, this work deciphers molecular-scale bacteria-gangue synergism, providing a theoretical foundation for sustainable coal gangue utilization and ecological restoration of degraded soils.<br><br>IMPORTANCE: The accumulation of coal gangue poses significant environmental challenges, necessitating the development of eco-friendly utilization strategies. This study demonstrates that the thermophilic bacterium Bacillus aerius acts synergistically with coal gangue to promote alfalfa growth in sandy soils while improving soil fertility. The combined treatment enhanced plant morphological traits, soil nutrient availability, beneficial microbial communities, and associated biological activities, with these effects supported by molecular evidence. As the first study to verify this growth-promoting mechanism, our findings address a critical knowledge gap and provide a theoretical foundation for the sustainable utilization of coal gangue in the ecological restoration of degraded soils.},
}
@article {pmid42029022,
year = {2026},
author = {Bornbusch, SL and Muletz-Wolz, CR},
title = {Applying microbial ecology frameworks to microbial therapies for wildlife.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0059825},
doi = {10.1128/msystems.00598-25},
pmid = {42029022},
issn = {2379-5077},
abstract = {Microbial ecology is increasingly incorporated into human and animal medicine via the study and purposeful manipulation of host-associated microbiomes. Microbial therapies-treatments with the aim of beneficially modulating microbiomes-are a burgeoning area of research and industry. These microbial therapies include prebiotic dietary items, live probiotics, and whole microbiota transplants (e.g., fecal microbiota transplants). Although microbial therapies for humans and domestic animals are now widely produced for commercial use and application, evidence supporting the efficacy of commercial microbial therapies is mixed. We suggest that microbial therapies are most effective when paired with concepts from ecology and rigorous empirical research. This is particularly relevant for the development and use of microbial therapies in wildlife animal species, in which we see large-scale variation in microbial communities across hosts of varying ecologies. Identifying and developing microbial therapies that can simultaneously be accessible and effective in a variety of hosts poses a novel challenge for microbial ecologists, animal scientists, and human and animal medical professionals. In addition to pre- and probiotics, we suggest that whole microbiota transplants provide a method of microbial supplementation that may better align with species-specific microbial ecology. Moving forward, emerging methods used in human medicine such as machine learning, network analysis, and microbiome engineering using high-throughput culturomics will likely be key to identifying and applying functionally relevant (e.g., disease suppressive) microbial taxa for wildlife therapies.},
}
@article {pmid42029232,
year = {2026},
author = {Li, J and Zhang, C and Zhang, H and Xu, W and Protopopov, M and Chang, M and Stoks, R},
title = {The Paradoxical Toxicity of Microplastics under Predation Risk: The Driving Role of Gut Microbiota-Mediated Tolerance.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c01355},
pmid = {42029232},
issn = {1520-5851},
abstract = {Accurate predictions of the ecological risks of microplastics require understanding of their interplay with natural stressors. Here, we revealed that predation risk fundamentally altered the microplastics ecotoxicity on the keystone species Daphnia magna. The microplastics alone were toxic (e.g., reduced growth rate, body size, spine length, and delayed maturity) and became more toxic under predation risk. For instance, the maturation delay at high MP concentrations increased 6.67-fold. Paradoxically, microplastics also enhanced inducible defenses, with fish cues offsetting microplastics that induced reductions in spine length and somatic growth. Contrasting Daphnia genotypes revealed that the fish-adapted clone exhibited superior tolerance to combined exposure to stressors, maintaining robust growth and defensive integrity, unlike the fish-naïve clone. The gut microbiome was identified as a key mechanistic driver. The fish-adapted clone maintained a more stable microbial community structure with functions enriched in carbohydrate metabolism and immune defense. A reciprocal transplantation experiment provided causal evidence: transplanting the adapted microbiota into the predator-naïve clone reduced mortality by 39% and increased intrinsic growth by 22% under combined stress. These findings highlight that microplastics risk assessment may be flawed if they ignore the eco-evolutionary context of natural stressors.},
}
@article {pmid42029478,
year = {2026},
author = {Funk, AM and Brieske, M and Schwarz, FM and Link, T and Jonas, S and Wimberger, P and Freitag, L and Klimova, A and Chavakis, T and Mirtschink, P and Kuhlmann, JD},
title = {A urinary three-metabolite signature enables non-invasive identification of high-risk ovarian cancer patients.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-25-4260},
pmid = {42029478},
issn = {1557-3265},
abstract = {BACKGROUND: Reliable prognostic tools in ovarian cancer are urgently needed to guide risk-adapted treatment decisions, yet the clinical utility of urinary metabolites for non-invasive risk stratification remains largely undefined. Here, we define a clinically relevant urinary metabolite signature that enables non-invasive prognostic risk stratification in ovarian cancer.<br><br>METHODS: Using targeted&#x202f;&#xb9;H NMR spectroscopy, we profiled 149 metabolites involved in energy metabolism, oxidative stress, mitochondrial function, nitrogen metabolism, amino acid degradation, gut microbiome activity and inflammation in pre-operative urine from 199 consecutive patients with newly diagnosed ovarian cancer treated in routine clinical practice between 2013 and 2022.<br><br>RESULTS: Unsupervised clustering revealed biologically heterogeneous subgroups but lacked prognostic resolution and alignment with overt clinical phenotypes. However, single-metabolite analysis identified a condensed three-metabolite prognostic signature comprising glycine, alanine and citrate. A final parsimonious model integrating this metabolite-signature with clinical covariates outperformed established risk factors alone (FIGO-stage, surgical outcome), accurately predicted 60-month overall survival (AUC&#x202f;=&#x202f;0.839) and stratified risk. Patients in the highest-risk quartile (Q4) had markedly shorter progression-free survival (&#x394;median &#x2248;&#x202f;56 months; HR&#x202f;=&#x202f;2.63, 95% CI: 1.54-4.52, p&#x202f;<&#x202f;0.001) and overall survival (&#x394;median &#x2248;&#x202f;86 months; HR&#x202f;=&#x202f;2.49, 95% CI: 1.39-4.46, p&#x202f;=&#x202f;0.009) compared to the lowest-risk group (Q1).<br><br>CONCLUSION: We define a urinary three-metabolite signature that enables non-invasive identification of high-risk ovarian cancer patients beyond established clinical factors and may support molecular stratification and risk-adapted clinical decisions, thereby supporting the clinical scalability of urine as a matrix for metabolic risk profiling in ovarian cancer.},
}
@article {pmid42029644,
year = {2026},
author = {Prince, AM and Zeltiņa, I and Reinis, A and Valciņa, O and Krūmiņa, A},
title = {HBV and the Microbiome-PubMed Database Literature Review.},
journal = {Infectious disease reports},
volume = {18},
number = {3},
pages = {},
pmid = {42029644},
issn = {2036-7430},
abstract = {OBJECTIVE: Hepatitis B virus (HBV) is a globally distributed infectious disease affecting the liver. This literature review aims to summarize all available relevant information on the PubMed database about HBV's connection to the microbiome and to consider possible treatment adjuncts.<br><br>MATERIALS AND METHODS: Database used: PubMed. Keywords used: "HBV", "Hepatitis B", "microbiome". In the PubMed database, 179 research publications were identified using these keywords; 69 studies were excluded as they were irrelevant or retracted. Of the remaining, 110 were analyzed in this literature review, and four additional literature sources were used to supply background information and context. Information was summarized. The analysed studies in total included 14,814 participants (excluding animal studies), of whom 8564 were HBV-infected individuals.<br><br>RESULTS: Results characterizing abundance or decrease in specific bacterial, viral, and fungal species are heterogeneous; multiple studies support that the HBV patient oral and fecal microbiome is different from that in healthy controls (HCs) and varies throughout disease progression. The HBV seems to transform the microbiome negatively, leading to dysbiosis and decreased microbial diversity in most studies. Evidence links HBV microbiome changes with influence on HbeAg seroconversion, HBV-DNA load, metabolic pathways, liver cirrhosis, and hepatocellular carcinoma. The research proposes that members of microbiota could potentially promote or protect against liver injury in HBV. Four studies proposed that the plasma virome in HBV patients was primarily composed of members of the Anelloviridae. One study researched a parasite (Entamoeba gingivalis) in HBV patients. Two studies analyzed HBV patients' fungal profiles.<br><br>CONCLUSIONS: Microbiota research, although promising, at the present moment is heterogeneous. HBV patients' microbiota is distinguishable from HCs, and multiple studies have tried to identify the HBV characteristic microbiome; however, more precise information is needed to draw conclusions. Fecal microbiota transplantation and probiotics have the potential to be therapy adjuncts for HBV patients, but more research is needed.},
}
@article {pmid42029730,
year = {2026},
author = {Restrepo-Benavides, M and Jiménez, P and Figueras, MJ and Restrepo, S and Zambrano, MM and Pujol, I and Guevara-Suarez, M and Fernández-Bravo, A},
title = {Genomic and Functional Diversity of Pseudoalteromonas Associated with the Tropical Bivalve Anadara Tuberculosa.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02753-y},
pmid = {42029730},
issn = {1432-184X},
}
@article {pmid42029786,
year = {2026},
author = {Jotta, VFM and Silva, CA and García, GJY and Marques, AR and Dos Santos Freitas, A and Góes-Neto, A and Badotti, F},
title = {Bacterial diversity in ferruginous duricrust (canga) and the physicochemical variables affecting their prevalence, distribution and predicted metabolic pathways.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {42029786},
issn = {1572-9699},
mesh = {*Bacteria/classification/genetics/metabolism/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Brazil ; *Biodiversity ; *Metabolic Networks and Pathways ; Phylogeny ; *Microbiota ; *Soil Microbiology ; Iron/analysis ; DNA, Bacterial/genetics ; },
abstract = {The ferruginous duricrust (canga) in the Iron Quadrangle (IQ), Minas Gerais, Brazil, occurs within the Campo Rupestre and presents remarkable levels of endemism and species richness. Despite the recognized importance of microorganisms for the maintenance of this ecosystem, current molecular-based studies reveal that both the taxonomic composition and the ecological functions of the canga microbiome are undiscovered. In this study, eighteen samples of canga were collected from the Serra da Piedade State Natural Monument, and their taxonomic diversity was investigated using 16S rRNA metabarcoding. Additionally, the influence of physicochemical variables on microbial diversity and community structure was estimated using statistical tools. Most of the 856,667 reads clustered into ASVs corresponded to Bacteria (99.7%), and the most abundant of the 184 identified genera were Conexibacter, Acidothermus and Bryobacter. Microbial diversity was explained by a combination of physicochemical variables, such as organic matter (OM), iron (Fe), aluminum (Al) and pH, whereas microbial community structure was influenced by the concentrations of Fe, Al and the cation exchange capacity (CEC). Functional prediction analysis based on the main genera identified in the samples indicated that the denitrification pathway may play an important role in the ecosystem. The investigation of the genera and their metabolic pathways based on the literature revealed that they are unexplored and emphasized the biodiversity hotspot yet to be explored in ferruginous duricrust. Therefore, our results reinforce the importance of further studies in this environment, both for future biotechnological applications and for appropriate management and preservation actions.},
}
@article {pmid42030348,
year = {2026},
author = {Larbi, AA and Etsey, M and Brew, O and Koduah, B and Mawuenyega, RE and Amewu, EKA and Essilfie, NK and Wireko, S and Kwarteng, A and Gyan, BA},
title = {Gut microbiome alterations among Ghanaian children with asymptomatic malaria infections.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0348120},
pmid = {42030348},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Ghana/epidemiology ; *Malaria/microbiology/epidemiology/parasitology ; Child, Preschool ; Male ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; Asymptomatic Infections ; Bacteria/genetics/classification ; Infant ; },
abstract = {The human gut microbiome, consisting of bacteria, archaea, fungi, and viruses, influences various physiological processes of the body. The gut microbiome composition is shaped by factors such as diet, geography, and antibiotic use. Malaria has been a global health challenge over the years, especially in low- and middle-income countries. This study investigated how asymptomatic malaria infection altered gut microbial communities in Ghanaian children, offering insights for novel malaria control strategies. Standard aseptic phlebotomy procedures were employed to collect venous blood samples for Plasmodium species detection. The gut microbial community was profiled by sequencing the 16S rRNA V4 region, and sequence data were processed using the DADA2 pipeline in R. Asymptomatic malaria infections were predominantly mixed with P. falciparum and P. malariae. Microbiome analysis revealed that Firmicutes and Bacteroidetes comprised nearly 70% of the total microbial population. Asymptomatic individuals showed a decrease in Firmicutes abundance from 52.5% to 44.0% and an increase in Bacteroidetes from 34.7% to 45.6%. There was also a slight increase in the abundance of Proteobacteria from 3.0% to 4.8%. At the genus level, Prevotella_9 was the most abundant and exhibited the highest variability in the infected groups. The Alloprevotella and Streptococcus genera increased in both infected groups, but Escherichia-Shigella was significantly elevated in only those with mixed infections. Faecalibacterium significantly declined in asymptomatic malaria-infected individuals compared to healthy controls, with variability further reduced in mixed infections. Beta-diversity analysis indicated a significant effect of malaria status on microbial composition (PERMANOVA, p < 0.05), explaining approximately 19.1% of the total variation captured by a 2D Principal Component Analysis (PCA) projection. These findings suggest a potential link between malaria infection and gut microbiota alterations and highlight microbial shifts associated with disease status.},
}
@article {pmid42030942,
year = {2026},
author = {Zaratiana, C and M, Y and Lee, YA and Ong, ABL and Liu, TZY and Low, SMC and Chang, SMS and Tan, S and Mustafa, DNA and Ganesh, A and Chang, X and Koh, XQ and Tay, SH and Lee, WJJ and Yuan, JM and Khor, CC and Koh, WP and Dorajoo, R and Li, YE and Kasahara, K and Wuestefeld, T and Chen, PB},
title = {Gut microbiota modulation of regulatory DNA elements revealed by massively parallel functional characterization.},
journal = {Molecular cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molcel.2026.03.036},
pmid = {42030942},
issn = {1097-4164},
abstract = {Cis-regulatory elements (CREs) are central to dynamic gene regulation in hepatocytes, yet most functional annotations derive from in vitro models that poorly capture physiological regulation. We systematically profiled 109,386 human liver-derived CREs using massively parallel reporter assays in hepatocytes under matched in vitro and in vivo conditions. In vivo-active functional CREs (fCREs) were enriched for H3K27ac and chromatin accessibility and were regulated by diverse transcription factors in the human liver. We further demonstrate that gut microbiota-derived signals modulate fCRE activity and target gene expression in vivo, in part via the KEAP1/NFE2L2 antioxidant pathway. Specific microbial metabolites directly altered the activity of selected fCREs, and genetic variation within fCREs modified their responsiveness to microbial signals. Together, these findings reveal microbiota-dependent regulation of hepatic CREs and highlight condition-specific gene regulatory mechanisms in vivo.},
}
@article {pmid42031118,
year = {2026},
author = {Kim, JY and Colgan, SP and Cartwright, IM},
title = {Neutrophil-Derived Reactive Oxygen Species and Bystander Tissue Damage in Inflammatory Bowel Disease.},
journal = {Free radical biology &amp; medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2026.04.146},
pmid = {42031118},
issn = {1873-4596},
abstract = {Neutrophils (PMNs) are indispensable effectors of innate immunity whose oxidative and proteolytic capabilities permit rapid microbial containment at mucosal surfaces. Nowhere is this more functionally consequential than in the gastrointestinal tract, where PMN recruitment to the intestinal mucosa serves as both a critical antimicrobial safeguard and a primary driver of epithelial injury in inflammatory bowel diseases (IBD). Upon activation, PMNs deploy an intricate oxidative network centered on the phagocyte NADPH oxidase complex-derived superoxide and hydrogen peroxide in conjunction with the halogenating and nitrating chemistries catalyzed by myeloperoxidase (MPO). These pathways generate a rich repertoire of oxidants-including hypochlorous acid (HOCl), hypobromous acid, reactive nitrogen species, and secondary radical products-that interact with proteins, lipids, nucleic acids, and extracellular matrix components with distinct reaction kinetics and spatial preferences. Importantly, the magnitude, composition, and distribution of these oxidants shape tissue outcomes ranging from transient signaling alterations to epithelial barrier dysfunction and mutational injury contributing to dysplasia. Recent advances in redox proteomics, spatial transcriptomics, intravital imaging, and single-cell analyses have expanded our understanding of how PMN oxidative radical pathways operate within specific mucosal microenvironments and how their outputs intersect with epithelial repair pathways, the microbiome, innate immune crosstalk, and disease chronicity. These studies reveal that PMNs do not function as a uniform oxidative manner; rather, distinct subsets specialize in oxidative burst, extracellular trap formation, metabolic adaptation, or reparative functions. Together, these data emphasize that oxidative injury in IBD is not an unavoidable byproduct of inflammation but rather a dynamic, context-dependent process that with significant potential as a therapeutic target. In this review, we synthesize current knowledge of PMN oxidative radical biology with a focus on the gastrointestinal mucosa. We examine the architecture of PMN reactive oxygen species (ROS) systems, delineate mechanisms of oxidative tissue injury, integrate translational and microbiome implications, and evaluate therapeutic strategies aimed at reducing bystander damage while preserving essential host defense. Through this framework, we highlight future directions that may enable the development of selective redox-modulating therapies capable of restoring mucosal integrity without compromising antimicrobial function.},
}
@article {pmid42031176,
year = {2026},
author = {Yechen, W and Wang, F and Xiao, L and Chen, Y and Li, L},
title = {Shared pathogenic mechanisms between systemic lupus erythematosus and autoimmune hepatitis: A unified view of autoimmune convergence.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {},
number = {},
pages = {168274},
doi = {10.1016/j.bbadis.2026.168274},
pmid = {42031176},
issn = {1879-260X},
abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) and autoimmune hepatitis (AIH) are clinically distinct autoimmune disorders characterized by multisystem involvement and liver-restricted inflammation, respectively; nevertheless, they exhibit considerable overlap in their underlying immunopathogenic features.<br><br>AIM: To provide a systematic synthesis of recent advances in genetics, immunology, and microbiome science, and to delineate the convergent pathogenic mechanisms that underpin both SLE and AIH.<br><br>METHODS: A comprehensive literature review was conducted using PubMed and other databases up to 2025, focusing on shared genetic, cellular, and microbial determinants in SLE and AIH. Core topics included genetic susceptibility loci, breakdown of immune tolerance, T-cell dysregulation, innate immune activation, and alterations in gut microbiota composition and function.<br><br>RESULTS: SLE and AIH share several genetic risk variants, including HLA-DRB1*03:01, PTPN22, STAT4, and TNFAIP3. Both diseases are characterized by defective central and peripheral immune tolerance, imbalances in Th17/Treg and Tfh/Tfr compartments, and aberrant B-cell activation. Innate immune pathways-encompassing Toll-like receptor and NLRP3 inflammasome signaling as well as complement dysregulation-further amplify inflammation. Moreover, gut dysbiosis and perturbations in microbial metabolites, such as short-chain fatty acids, bile acids, and tryptophan derivatives, function as key mediators linking intestinal homeostasis to both systemic and hepatic autoimmunity.<br><br>CONCLUSION: SLE and AIH represent overlapping entities along a unified autoimmune spectrum, driven by shared genetic susceptibility, convergent immune dysregulation, and microbial influences. This review advances an integrated immunological framework that bridges systemic and organ-specific autoimmunity, underscores the pivotal role of innate immunity and gut-liver crosstalk, and provides a mechanistic rationale for cross-disease therapeutic strategies targeting these common pathways.},
}
@article {pmid42031199,
year = {2026},
author = {Wang, Z and Song, B and Sun, X and Huang, D and Häggblom, MM and Yu, Z and Kong, T and He, B and He, B and Zhang, H and Sun, W},
title = {Arsenic oxidation by root endophytes mediates arsenic speciation within rice (Oryza sativa).},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128194},
doi = {10.1016/j.envpol.2026.128194},
pmid = {42031199},
issn = {1873-6424},
abstract = {Arsenic (As) uptake through rice consumption is a major exposure pathway that severely threatens the health of over 140 million people. Since flooded cultivation makes rice specifically vulnerable to As contamination, dry rice cultivation has been proposed to reduce As accumulation. While microorganisms play important roles in As biogeochemical cycles, the impact of the root-associated microbiome, especially endophytes, on As uptake and metabolism in rice growing under different water regimes remains elusive. In this study, different water regimes significantly altered As speciation in the rhizosphere but less impacted those in roots, in which As(V) dominated. While the endosphere community was significantly altered, microbial As transformation potentials were less impacted by different water treatments. Within rice roots, As(III) oxidase gene (aioA) abundance was consistently higher than that of the genes for As reduction (As(V) respiratory reductase arrA and As(V) detoxification reductase arsC) under both treatments, indicating that As(III) oxidation might be the major As transformation pathway in planta. Activity measurements of the endosphere microbial community demonstrated that As(III) oxidation was significantly faster compared to reduction processes. The major endosphere microbial communities harboring aioA genes were affiliated with Rhodocyclaceae, Xanthobacteraceae, and Burkholderiaceae under dry conditions, while members of Rhodocyclaceae dominated under flooded conditions. These results suggest that dominant microbial As(III) oxidation in rice roots may contribute to maintaining a higher As(V) proportion in planta and potentially reduce As translocation to edible grains.},
}
@article {pmid42031220,
year = {2026},
author = {Coccurello, R},
title = {The skin microbiome and affective symptoms: neuroimmune, neuroendocrine, and sensory pathways linking inflammatory dermatoses to mood and anxiety burden.},
journal = {Frontiers in neuroendocrinology},
volume = {},
number = {},
pages = {101251},
doi = {10.1016/j.yfrne.2026.101251},
pmid = {42031220},
issn = {1095-6808},
abstract = {The skin functions as a neuro-immuno-endocrine organ with an extensive microbial interface capable of bidirectional signaling with the central nervous system. While the gut-brain axis is well established, the skin-microbiota-brain (SMB) axis remains underexplored, particularly with respect to affective symptom dimensions (depression, anxiety, stress) that commonly co-occur with chronic inflammatory dermatoses. This review synthesizes evidence across clinical, translational, and experimental studies and organizes it by strength (associational findings, mechanistic plausibility, and limited interventional signals). We outline a systems-level model in which cutaneous microbial dysbiosis is associated with brain-relevant pathways via immune, neuropeptide, and metabolic routes. Candidate mediators include cytokines (IL-6, IL-17, TNF-α), neuropeptides (e.g., substance P, CGRP), and microbial-derived metabolites (e.g., SCFA-like compounds and tryptophan catabolites). These signals are hypothesized to influence neuroimmune tone and neurovascular signaling based largely on broader systemic inflammation and stress biology; direct causal evidence specifically attributing affective outcomes to skin microbiome perturbations in humans remains limited. In parallel, top-down neuroendocrine signaling via hypothalamic-pituitary-adrenal (HPA) axis activation, cortisol-related signaling, and sympathetic outflow can alter skin barrier function, antimicrobial peptide expression, and microbial ecology, potentially contributing to symptom-maintaining loops (e.g., itch-sleep disruption-stress). Importantly, we consider counterarguments (psychosocial burden, reverse causality, treatment effects, and the localized nature of lesions) and identify research priorities required to test causality (longitudinal sampling, mechanistic biomarker panels, and preregistered interventional studies with affective endpoints and mediation analyses). By integrating dermatological, microbiological, and neuroimmunological evidence within a symptom-centered framework, the SMB axis is positioned as a biologically plausible but still evolving model that may help explain affective symptom burden in subsets of patients with inflammatory skin disease and guide mechanism-informed translational research.},
}
@article {pmid42031436,
year = {2026},
author = {Greenwood-Van Meerveld, B and Mawe, GM and Beyder, A and Brierley, SM and Clarke, G and Gulbransen, BD and Margolis, KG},
title = {Fundamentals of Neurogastroenterology: Basic Science.},
journal = {Gastroenterology},
volume = {170},
number = {6},
pages = {1099-1113},
doi = {10.1053/j.gastro.2026.01.040},
pmid = {42031436},
issn = {1528-0012},
mesh = {Humans ; *Enteric Nervous System/physiopathology ; *Gastrointestinal Diseases/physiopathology/therapy/microbiology ; *Gastroenterology/trends ; Gastrointestinal Microbiome ; *Brain-Gut Axis/physiology ; Animals ; *Gastrointestinal Tract/innervation/physiopathology ; Neuronal Plasticity ; Neuroimmunomodulation ; *Brain/physiopathology ; Risk Factors ; },
abstract = {This review highlights major advances in neurogastroenterology since Rome IV, offering a condensed summary of a comprehensive document to appear in the forthcoming Rome V book. Prepared by an international team of experts, it emphasizes pivotal studies that have deepened understanding of the physiological and pathophysiological mechanisms underlying disorders of gut-brain interaction (DGBI). These disorders are inherently complex and multifactorial, shaped by interactions among neuronal, epithelial, immune, smooth muscle, interstitial, and microbial populations. The review outlines cutting-edge technologies advancing the field and explores key themes, including brain-gut interactions, neurobiology, and neuroplasticity of the enteric nervous system, neuroimmune function, microbiome influences, and abnormalities of the gut-brain axis in DGBI. Risk factors for DGBI are considered, with serotonergic signaling presented as a conceptual framework for linking symptomatology and pathophysiology. Finally, we discuss how these scientific advances can translate into novel therapeutic strategies to improve patient care.},
}
@article {pmid42031439,
year = {2026},
author = {Wong, RK and Fang, X and Ghoshal, UC and Kashyap, PC and Mulak, A and Lee, YY and Sperber, AD and Holtmann, G},
title = {Sociocultural Aspects of the Pathophysiology, Clinical Presentation, and Management of Disorders of Gut-Brain Interaction.},
journal = {Gastroenterology},
volume = {170},
number = {6},
pages = {1190-1204},
doi = {10.1053/j.gastro.2026.02.006},
pmid = {42031439},
issn = {1528-0012},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Brain-Gut Axis/physiology ; *Gastrointestinal Diseases/physiopathology/therapy/psychology ; Risk Factors ; *Brain/physiopathology ; Social Stigma ; Diet ; },
abstract = {Sociocultural determinants such as cultural norms, diet, and environmental factors, along with their effects on the gastrointestinal microbiome, can modify the risk to develop disorders of gut-brain interaction (DGBI). These factors also shape symptom perception and health care-seeking behaviors, and how society and health care providers respond to patients with DGBI. This document summarizes the knowledge about the role of sociocultural factors in the manifestation of DGBI and the management of these patients. Symptom expression and societal response to DGBI varies across different cultural settings, influencing individual patient outcomes and the overall societal burden of disease. Patients with DGBI are often stigmatized, leading to a bias toward conditions with visible abnormalities and underfunded services for DGBI. Recognizing the role of sociocultural factors for DGBI outcomes presents an opportunity to refine pathophysiologic concepts and improve patient outcomes. This calls for greater awareness and equitable resource allocation for DGBI research and treatment.},
}
@article {pmid42031645,
year = {2027},
author = {Amarnani, A and Rivera, CF and Cornwell, M and Weinstein, T and Azad, Z and Gottesman, SRS and Loomis, C and Lee, A and Ullah, N and Prasad, J and Yi, M and Cooney, L and Barnes, BJ and Gisch, N and Ruggles, KV and Ramkhelawon, B and Silverman, GJ},
title = {A pathogenic gut lipoglycan drives systemic thromboinflammation in lupus nephritis.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ard.2026.03.002},
pmid = {42031645},
issn = {1468-2060},
abstract = {OBJECTIVES: The gut microbiome plays a crucial role in regulating systemic immunity and has been implicated in several chronic inflammatory diseases. Intestinal expansions of Ruminococcus gnavus (RG), a dominant gut commensal, correlate with disease flares in lupus nephritis (LN), but the underlying mechanism remains unknown.<br><br>METHODS: In a Pilot cohort of patients with biopsy-proven LN, subsetted by gut microbiota community, immune status was characterised using bulk-blood RNA sequencing libraries, serum levels of representative host proteins, and levels of immunoglobulin (Ig)G antibodies to the novel lipoglycan (LG) produced by pathogenic RG strains. A Validation LN cohort was evaluated for blood transcriptomic profiles and levels of anti-LG antibodies. In murine models, mechanistic hypotheses were tested after RG gut colonisation or after intraperitoneal injection with an LG preparation, with outcomes determined by transcriptomic analyses, platelet functional readouts, and tissue histology.<br><br>RESULTS: In a Pilot cohort of patients with LN, RG gut expansions were associated with high-level platelet, neutrophil, and monocyte activation. Serum levels of platelet factor 4 and release of neutrophil extracellular traps (NETs) were significantly higher in patients with high serum IgG antibody against the novel RG-specific LG, a marker of in vivo immune exposure. An LN Validation cohort confirmed these correlates and showed that anti-LG antibodies serve as a surrogate for thromboinflammatory profile in this LN-associated endotype. In mice, gut colonisation with LG-producing RG strains or a single LG injection caused megakaryocytosis and platelet activation; RG colonisation with LG-producing strains induced tubulointerstitial injury with NETosis. In vivo responses to LG toxin were Toll-like receptor 2-dependent.<br><br>CONCLUSIONS: Gut expansions of the RG pathobiont may contribute to autoimmune pathogenesis through the LG toxin and cause LN flares through thromboinflammatory mechanisms in this previously unrecognised LN endotype.},
}
@article {pmid42031776,
year = {2026},
author = {Samson, R and Hassard, F and Dharne, M},
title = {Gut virome-microbiome interactions across hosts and environments.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42031776},
issn = {2055-5008},
abstract = {The Gut microbiome-virome dynamics and interactions Collection highlights gut viruses, mainly bacteriophages, as determinants of microbial community structure and host-relevant functions across human, animal, and environmental systems. The Collection welcomes studies that quantify virus-microbe interactions, evidence-based linking viruses to microbial hosts, characterise infection dynamics, and connect them to ecological or clinical outcomes. It prioritises methodological rigour and translational relevance in diagnostics, surveillance, and phage-based interventions.},
}
@article {pmid42032033,
year = {2026},
author = {Ma, C and Chen, C and Shang, X and Wang, Y and Liu, H and Yu, Y and Wang, Q and Wang, X and Jia, L and Liang, S},
title = {Gut microbiome-metabolome profiling reveals divergent growth performance in the spotted knifejaw (Oplegnathus punctatus).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50031-1},
pmid = {42032033},
issn = {2045-2322},
support = {24ZYCGSN00150//Tianjin Science and Technology Plan Project/ ; CARS-47-Z01//Tianjin Comprehensive Experimental Station of the National Marine Fish Industry Technology System/ ; },
}
@article {pmid42032216,
year = {2026},
author = {Choi, Y and Ryu, S and Kang, A and Lee, W and Park, J and Kang, MG and Jang, KB and Kwon, Y and Kwak, MJ and Jeong, KC and Song, M and Kim, Y},
title = {Fecal virome transplantation alleviates weaning stress-induced behavioral alterations and intestinal health by reshaping the gut microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49647-0},
pmid = {42032216},
issn = {2045-2322},
support = {RS-2025-16068814//National Research Foundation of Korea/ ; },
}
@article {pmid42032279,
year = {2026},
author = {Ducarmon, QR and Karcher, N and Giri, S and Tytgat, HLP and Delannoy-Bruno, O and Pekel, S and Springer, F and Wörz, P and Schudoma, C and Typas, A and Zeller, G},
title = {Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42032279},
issn = {2058-5276},
support = {LUMC Fellowship//Leids Universitair Medisch Centrum (Leiden University Medical Center)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KD2102A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; },
abstract = {Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .},
}
@article {pmid42032627,
year = {2026},
author = {Duncan, WD and Sabharwal, A and Diehl, AD and Dutta, N and Diller, M and Joachimiak, MP and Chandrasekharan, GM},
title = {Representing dental caries and dysbiosis within the oral microbiome in the Oral Health and Disease Ontology.},
journal = {Journal of biomedical semantics},
volume = {17},
number = {1},
pages = {},
pmid = {42032627},
issn = {2041-1480},
abstract = {BACKGROUND: Dental caries is an oral health condition in which cariogenic bacteria demineralize and decay teeth. It arises due to interaction between the host, environment, and oral microbiome. Current terminologies and ontologies, however, do not accurately represent the important role that the microbiome has in the formation of carious lesions. Rather, they focus on the anatomical features of carious lesions and often obfuscate the distinctions between dental caries as a disease affecting a tooth, as lesions that are produced because of the disease, and as lesions produced as a result of dysbiosis in the oral microbiome. To capture the current state of evidence and provide flexibility for evolving literature on host-environment-microbiome interactions, there is a need to revise and expand the ontological framework for dental caries.<br><br>RESULTS: Several established terminologies and ontologies were reviewed for terms used to represent dental caries and the oral microbiome. We found that they either did not represent or misrepresented the current scientific understanding of caries and its relation to the microbial dysbiosis. As a result of these deficiencies, we added terms and relations to the Oral Health and Disease Ontology (OHD) that more accurately represent how oral microbial dysbiosis influences the development of dental caries.<br><br>CONCLUSIONS: The Oral Health and Disease Ontology is an advance over existing ontologies for representing the impact of oral microbial dysbiosis on dental caries. It provides a semantic framework that better serves the needs of cariology researchers and can more easily incorporate new oral microbiome findings.},
}
@article {pmid42032888,
year = {2026},
author = {Wu, S and Wang, Y and Li, H and Fang, X and Guo, J and Luo, X and Li, M and Song, F and Tan, Q and Deng, X and Xiao, S and Liu, H and Hu, C and Pan, Z},
title = {Rhizosphere microbiome influences fruit quality in citrus.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71159},
pmid = {42032888},
issn = {1469-8137},
support = {2023YFD2300603//The National Key Research and Development Program of China/ ; 2017YFD0202001//The National Key Research and Development Program of China/ ; 2019YFD1000103//The National Key Research and Development Program of China/ ; },
abstract = {Fruit quality is shaped by both crop genetics and cultivation environments, with soil conditions driving rhizosphere microbiome assembly. While rhizosphere microbes are known to enhance nutrient utilization and plant metabolism, their direct contribution to fruit quality regulation remains poorly understood. In this study, we demonstrate that the Satsuma mandarin (Citrus unshiu Marc.) and Navel orange (Citrus sinensis L. Osbeck) rhizosphere microbiome influence fruit sugar concentration, a key determinant of fruit quality. The rhizosphere core microbiota and soil mineral nutrients were positively correlated with fruit quality indices. Fruit quality-correlated bacterial operational taxonomic units (OTUs) explained an average of 32.6% of the observed variation in quality parameters. Inoculation with three bacterial strains (affiliated with Burkholderia, Pseudomonas, Rhizobium) and two bacterial consortia significantly increased fruit sugar concentrations. Metagenomic analysis linked sugar-associated microbes to iron (Fe) utilization, revealing genomic enrichment of siderophore biosynthesis gene clusters. Consistently, the selected bacterial strains exhibited siderophore secretion capabilities, increased leaf Fe content by 23.3-47.8% in citrus rootstock. Further field application of chelated-Fe fertilizer also increased fruit sugar concentration. Collectively, our results revealed an influence of the rhizosphere microbiome on fruit quality that is related to Fe acquisition optimization and subsequent sugar accumulation in citrus.},
}
@article {pmid42032897,
year = {2026},
author = {Lin, Y and Barandouzi, ZA and Houser, MC and Xiao, C and Alese, OB and Mathebula, S and Bai, J and Gbolahan, O and Bruner, DW},
title = {Gut Microbiome and Psychoneurological Symptoms Among Patients With Colorectal Cancer and Their Caregivers: A Pilot Study.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {10998004261447509},
doi = {10.1177/10998004261447509},
pmid = {42032897},
issn = {1552-4175},
abstract = {Purpose: Survivorship in colorectal cancer (CRC) is often accompanied by co-occurring psychoneurological symptoms (PNS, e.g., fatigue, depression, pain), which negatively affect quality of life. Caregivers of individuals with CRC also experience PNS due to caregiving burdens, amplifying distress across the dyad. PNS may be influenced by the activity of the gut microbes. The purpose of this pilot study was to examine gut microbiome diversity and composition, and their association with PNS in CRC patients and their caregivers. Methods: Baseline data from a technology-based dyadic intervention were included in this analysis. Eleven patients and eight caregivers provided stool samples and completed PROMIS measures of PNS at baseline. Gut microbiome profiles were assessed using 16S rRNA gene sequencing. Alpha and beta diversity metrics and differential abundance analyses were used to characterize the gut microbiome and examine its associations with PNS. Results: Patients exhibited significantly lower microbial alpha diversity than caregivers in the full sample (p = 0.033). Dyadic comparisons identified 92 differentially abundant taxa, with patients showing depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic taxa. Microbiome-symptom models revealed significant interactions by group (patient vs. caregiver) and taxa-level effects, with patients showing stronger positive associations between microbial alterations and higher PNS severity. Conclusions: CRC patients actively on chemotherapy demonstrated reduced diversity and depletion of beneficial taxa that may contribute to heightened PNS. Caregivers, despite healthier profiles, reported substantial symptom burden that were linked to gut microbiome features, highlighting dyadic interdependence and the potential for microbiome-targeted, dyadic interventions in survivorship care.},
}
@article {pmid42033327,
year = {2026},
author = {Williams, CE and Tacoaman, YFL and Fontaine, SS and Logan, ML},
title = {The lizard microbiome: patterns, drivers, and functional implications.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag049},
pmid = {42033327},
issn = {1574-6968},
abstract = {The lizard microbiome is a dynamic community that plays a crucial role in the health and survival of these animals. As global change poses significant threats to lizard populations around the world, understanding the interactions between lizards and their microbial communities is increasingly important. Here, we synthesize a rapidly growing body of research on the composition, diversity, transmission, and functional roles of lizard microbiomes. We discuss the implications of microbiome variation for lizard physiology, as well as the potential for microbiomes to inform conservation strategies for threatened species. Finally, we highlight priorities for future research, which include the need to quantify microbiome diversity and function across additional taxa, as lizards remain underrepresented in the microbiome literature. We also stress the importance of experimental and field research that can reveal the adaptive significance of lizard microbiomes in the face of environmental change. Our synthesis highlights the contributions of lizard microbiome science to the fields of ecology, evolution, and conservation biology and demonstrates how the microbial communities that live in and on lizards enhance our understanding of their biodiversity and inform efforts to protect vulnerable populations.},
}
@article {pmid42033818,
year = {2026},
author = {Póvoa, AA and Amorim Magalhães, E and Dos Santos, KP and Canellas, AL and Soares-Gomes, A and Dos Santos, HF},
title = {Comparative analysis of microbial diversity and pathogenic potential in marine litter reveals timber as a key reservoir in sandy beaches ecosystems.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {141937},
doi = {10.1016/j.jhazmat.2026.141937},
pmid = {42033818},
issn = {1873-3336},
abstract = {Many materials create new habitats for microbial colonization and the persistence of potentially pathogenic bacteria. Despite this, comparative studies addressing the microbial diversity and pathogenic potential across different types of marine litter remain scarce. This study investigated microbial communities associated with plastics, aluminum, and timber collected from the strandline of two types of beaches. Amplicon sequencing of the 16S rRNA gene revealed that bacterial community structure and diversity varied primarily according to substrate type rather than beach environment. Nevertheless, all types of marine litter evaluated hosted rich and diverse bacterial communities, with several taxa recognized as potential pathogens of both marine organisms and humans. Timber supported the richest, most diverse, and most specific microbiome, including a high number of taxa known to contain potential pathogens. Among these, Flavobacterium, Mycobacterium, Pseudoalteromonas, Acinetobacter, and Staphylococcus were particularly notable, as they are recognized pathogens of both marine organisms and humans, representing potential ecological and sanitary risks. These findings highlight that marine litter on sandy beaches functions as a selective substrate influencing biofilm formation, microbial dispersal, and the persistence of pathogens in coastal ecosystems. Timber, in particular, emerges as an underrecognized reservoir for microbial diversity and resistance genes, warranting greater attention in marine pollution and public health monitoring.},
}
@article {pmid42033825,
year = {2026},
author = {Mukhopadhyay, S and Ooi, QE and Mukherjee, A and Bhattacharya, R and Sarkar, P and Tan, ZD and Phang, B and Chey, SL and Lupascu, M and Bandla, A and Swarup, S},
title = {Xenobiotic dynamics in mangroves and peatlands: Microbial mechanisms for nature-based mitigation.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142149},
doi = {10.1016/j.jhazmat.2026.142149},
pmid = {42033825},
issn = {1873-3336},
abstract = {Peatlands and mangroves provide substantial ecosystem services, but are increasingly threatened by xenobiotic contamination, posing escalating ecological risks. Here, we present the first integrative synthesis of the xenobiotic dynamics in these systems, mapping contaminant distributions and identifying emerging research priorities. Over time, research has shifted from oil spills and heavy metal pollution towards persistent organic pollutants, microplastics and climate risks. Peatlands remain substantially understudied compared to mangroves, especially for emerging contaminant classes. Xenobiotics disrupt the environment-biota linkages in these systems by impairing microbiome functionality; yet, subsets of microbial communities persist through adaptation and sharing of genomic traits. These traits enable xenobiotic sequestration, degradation or utilization. We compile a wetland-associated catalogue of microbial mechanisms and cross-environment analogues to guide bioprospecting and nature-based xenobiotic transformations. We recommend coupling wetland restoration with systematic microbiome exploration, positioning wetlands as in-situ buffers and ex-situ reservoirs for scalable, nature-based solutions for xenobiotic mitigation.},
}
@article {pmid42033865,
year = {2026},
author = {Wang, F},
title = {Polyphenols and physical activity stimulate gut microbiota mediated Nrf2 signaling to combat neurodegeneration.},
journal = {Pathology, research and practice},
volume = {283},
number = {},
pages = {156478},
doi = {10.1016/j.prp.2026.156478},
pmid = {42033865},
issn = {1618-0631},
abstract = {Polyphenols and regular physical activity are increasingly recognized as complementary lifestyle interventions that influence the gut-brain axis and contribute to neuroprotection. Emerging evidence highlights the central role of the gut microbiota in mediating these effects by transforming dietary and host-derived substrates into bioactive metabolites. These metabolites can activate the nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway, a key regulator of cellular antioxidant defenses, mitochondrial function, and anti-inflammatory responses processes that are critically impaired in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. This review synthesizes current mechanistic insights into how polyphenol-derived metabolites and exercise-induced alterations in gut microbial composition converge to modulate Nrf2 signaling. We discuss the roles of key microbiota-derived metabolites, including short-chain fatty acids, urolithins, and indole derivatives, in regulating oxidative stress, neuroinflammation, and synaptic function. Furthermore, we examine evidence from preclinical models supporting the synergistic effects of dietary polyphenols and physical activity on gut microbiota-mediated neuroprotection. Finally, we address translational challenges and highlight the potential of integrating dietary and exercise-based strategies to harness microbiota-dependent Nrf2 activation. This integrative framework provides a basis for developing personalized, microbiome-informed interventions aimed at delaying or mitigating neurodegeneration.},
}
@article {pmid42033990,
year = {2026},
author = {Wu, Q and You, J and Li, D and Tang, S and Wu, S and Wang, Q and Teng, W},
title = {Oxygen vacancy-rich nanosystems eradicate stubborn periodontal biofilms by synergistic EPS degradation, metabolic activation and microbiome restoration.},
journal = {Biomaterials},
volume = {333},
number = {},
pages = {124234},
doi = {10.1016/j.biomaterials.2026.124234},
pmid = {42033990},
issn = {1878-5905},
abstract = {Periodontitis-associated biofilms pose a severe public health threat due to a dual defense mechanism. This involves a protective physical matrix barrier and biological interference from persistent bacteria and microbial dysbiosis. Current strategies often fail to penetrate deeply, eradicate dormant persisters and resolve microbial dysbiosis, leading to biofilm resistance and disease recurrence. In this study, we develop a multifunctional nanoplatform combining photothermal, photodynamic therapy and peroxidase-like catalysis to execute a sequential strategy. This system integrates molybdenum oxide nanodots rich in oxygen vacancy (MoO3-x) with the photosensitizer indocyanine green (ICG). It exhibits improved optical and enzymatic performance due to the introduced oxygen vacancies. Upon irradiation, the system produces localized hyperthermia and ROS storms to destabilize the biofilm matrix and promote ultrasmall nanodots penetration. The thermal and oxidative stress increase membrane permeability and reactivate metabolism of dormant persisters. Metagenomic analyses confirms that MoO3-x/ICG-treated biofilms show decreased abundance of key persistence-related genes and great enrichment in metabolic pathways. Additionally, the platform exhibits therapeutic effects and a successful shift towards a healthier oral microbiota in periodontitis model. Overall, MoO3-x/ICG demonstrates excellent biofilm eradication and successfully prevents biofilm regrowth or secondary infection. This work targets the entire biofilm lifecycle and presents a nanoplatform for long-term management of periodontal infections.},
}
@article {pmid42034052,
year = {2026},
author = {Aggarwal, N and Shen, H and Lee, LT and Zhou, L and Zhu, MT and Koh, XQ and Ng, AXY and Li, M and Jumat, NHB and Cheah, WY and Li, S and Saini, M and Lee, JWJ and Foo, JL and Wun, KS and Hwang, IY and Ho, CL and Lee, YS and Dan, YY and Chang, MW},
title = {Engineered commensals for metabolic modulation of the gut-liver-brain axis.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.03.048},
pmid = {42034052},
issn = {1097-4172},
abstract = {The gut-liver-brain axis is central to metabolic and neurological homeostasis and is mediated by host- and microbiota-derived metabolites. Disruptions in this axis contribute to complex disorders, underscoring the need for targeted, multi-metabolite interventions. Here, we engineered commensal Lactobacillus plantarum WCFS1 strains to specifically modulate metabolites dysregulated in hepatic encephalopathy (HE), a disorder driven by hyperammonemia and amino acid imbalance. One strain couples ammonia assimilation with branched-chain amino acid (BCAA) biosynthesis, whereas the other enhances L-glutamine utilization to suppress ammonia generation. In two preclinical HE models, these strains reduced systemic ammonia by up to 10-fold, restored BCAA and L-glutamine balance, and improved anxiety-like and cognitive behaviors. Notably, they outperformed rifaximin, a clinically used HE therapy, while preserving gut microbiota diversity. These findings establish engineered commensals as a modular, responsive platform for multi-metabolite modulation of host-microbiota metabolism, offering a programmable strategy to restore metabolic homeostasis in disorders of the gut-liver-brain axis.},
}
@article {pmid42034241,
year = {2026},
author = {Juritsch, AF and Deehan, EC and Armet, AM and Mannon, PJ and Ramer-Tait, AE},
title = {Eating for Inflammatory Bowel Disease: Assessing the Effect of Dietary Carbohydrates on Gut Microbiota and Implications for Disease Management.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101551},
doi = {10.1016/j.tjnut.2026.101551},
pmid = {42034241},
issn = {1541-6100},
abstract = {Targeting the gut microbiome through diet remains a priority in the treatment and management of inflammatory bowel diseases (IBD) for patients and clinicians alike. However, expert consensus is lacking, and cross-sectional studies indicate that patients with IBD often adopt low-fiber, high-sugar, and high-protein diets in an effort to control gastrointestinal symptoms and inflammation with negative implications for gut microbial functions and gastrointestinal inflammation. Although dietary carbohydrates are key modulators of gut microbial composition and function, substantial disagreement persists regarding how carbohydrate digestibility and structural properties influence IBD outcomes. This narrative review summarizes current knowledge on the role of dietary carbohydrates in IBD risk and progression and critically evaluates recent dietary interventions in which the gut microbiota was included among outcomes to elaborate a potential role of dietary carbohydrates in the clinical management of IBD. We conclude by outlining research priorities needed to affirm a role for dietary carbohydrate modification in the clinical management of IBD and to support the development of practical, evidence-based dietary guidance.},
}
@article {pmid42034408,
year = {2026},
author = {Liu, M and Suo, X and Mai, X and Smagghe, G and Yin, S and Wang, Z and Gai, Y and Niu, Q},
title = {Trichoderma asperellum 152-42 confers resistance to Fusarium root rot in alfalfa through JA-mediated induced systemic resistance and reshaping of the rhizosphere microbiome.},
journal = {Pesticide biochemistry and physiology},
volume = {220},
number = {},
pages = {107087},
doi = {10.1016/j.pestbp.2026.107087},
pmid = {42034408},
issn = {1095-9939},
mesh = {*Medicago sativa/microbiology ; *Fusarium/physiology ; Rhizosphere ; *Oxylipins/metabolism/pharmacology ; *Cyclopentanes/metabolism/pharmacology ; *Plant Diseases/microbiology/prevention &amp; control ; Plant Roots/microbiology ; *Microbiota ; Disease Resistance ; *Hypocreales ; *Trichoderma/physiology ; Soil Microbiology ; Plant Systemic Acquired Resistance ; },
abstract = {Fusarium root rot, caused by Fusarium spp., threatens alfalfa production, and Trichoderma species are emerging as potential biocontrol agents against this soilborne pathogen. However, the mechanisms by which Trichoderma strains trigger plant systemic resistance and remodel the rhizosphere microbiome to suppress pathogen infection remain unclear. Here, we screened five Trichoderma strains through in vitro antagonism, siderophore production, and growth-promoting assays to identify the optimal strain. Integrating pot experiments, physiological and biochemical analyses, transcriptome sequencing, and microbiome amplicon sequencing, we elucidated its mode of action and validated its effects in field trials. Our results demonstrate that Trichoderma asperellum 152-42 exhibited the strongest comprehensive performance, achieving 72% pathogen inhibition in dual culture assays. In pot experiments, pretreatment with this strain reduced the disease index by 25%. Mechanistically, the strain activated the jasmonic acid (JA) signaling pathway, enhanced defense enzyme activities and defense gene expression, and induced coordinated upregulation of genes involved in sucrose metabolism and MAPK signaling. Rhizosphere microbiome analysis revealed that the strain selectively enriched beneficial taxa, including plant growth-promoting bacteria and arbuscular mycorrhizal fungi, suppressed pathogenic Fusarium, and enhanced both bacterial community stability and fungal network complexity. Field trials confirmed that this strain increased crude protein content by 26% and hay yield by 10-13%. Our study reveals the integrated mechanism by which T. asperellum 152-42 controls Fusarium root rot through "direct antagonism-JA/ET immune priming-metabolic reprogramming-microecological regulation," providing both a valuable strain resource and a theoretical foundation for sustainable alfalfa production.},
}
@article {pmid42034417,
year = {2026},
author = {Ding, X and Cao, K and Li, Y and Li, X and Zhong, Q and Chen, Y and An, M and Liu, H and Zhou, R and Wu, Y},
title = {Nano-bioprotectant dsRsGH1@ε-PL@CMCS enhances RNAi efficacy against Rhizoctonia solani via dual mechanisms: Interacting with the vesicle transport protein SEC22 and modulating the tobacco phyllosphere microbiota.},
journal = {Pesticide biochemistry and physiology},
volume = {220},
number = {},
pages = {107104},
doi = {10.1016/j.pestbp.2026.107104},
pmid = {42034417},
issn = {1095-9939},
mesh = {*Nicotiana/microbiology/drug effects/genetics ; *Rhizoctonia/drug effects/genetics ; *Chitosan/analogs &amp; derivatives/chemistry/pharmacology ; *RNA Interference ; *Microbiota/drug effects ; *RNA, Double-Stranded/pharmacology ; Plant Diseases/microbiology/prevention &amp; control ; Plant Proteins/genetics/metabolism ; },
abstract = {Nanocarrier-mediated delivery of double-stranded RNA (dsRNA) is a promising strategy for plant disease control. Our previous study has shown that the self-assembled ε-poly-l-lysine/carboxymethyl chitosan (ε-PL@CMCS) nanocarrier significantly improves the efficiency of RNA interference (RNAi) against Rhizoctonia solani AG3 TB. However, the molecular mechanisms underlying this enhancement and the potential ecological impacts on phyllosphere microbial communities remain unclear. In this study, we confirmed that dsRsGH1@ε-PL@CMCS had no adverse effects on the growth and development of plants. Transcriptome analysis revealed that DEGs were significantly enriched in 'SNARE interactions in vesicular transport' pathway. Among them, dsRsGH1@ε-PL@CMCS specifically upregulate the vesicle transport protein SEC22 in Nicotiana tabacum. Surface plasmon resonance (SPR) assay demonstrated that the dsRsGH1@ε-PL@CMCS binds to SEC22 protein with 7.6-fold higher affinity than that of the naked dsRsGH1. Silencing SEC22 in the dsRsGH1@ε-PL@CMCS treatment reduced the silencing efficiency of RsGH1 from 53.3% to 39%, confirming its essential role. Concurrently, high-throughput sequencing revealed that SIGS treatments did not disrupt bacterial community structure but increased fungal diversity and suppressed the pathogen, while enriching beneficial fungi such as Tulasnella. Our findings elucidate a molecular link between nano-bioprotectant dsRsGH1@ε-PL@CMCS-enhanced RNAi and host vesicle transport, while confirming the biocompatible and microbiome-modulating potential. This provides a dual perspective for developing efficient and sustainable RNAi-based strategies for protecting plants.},
}
@article {pmid42034426,
year = {2026},
author = {Zhou, N and Wei, R and Yang, S and Hu, F and Feng, Y and Zheng, H},
title = {Antibiotic resistance gene profiles in the gut microbiomes of Apis cerana, Apis mellifera, and Bombus terrestris.},
journal = {Pesticide biochemistry and physiology},
volume = {220},
number = {},
pages = {107059},
doi = {10.1016/j.pestbp.2026.107059},
pmid = {42034426},
issn = {1095-9939},
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; China ; },
abstract = {The gut microbiota of honeybees has been increasingly recognized as a reservoir of antibiotic resistance genes (ARGs). However, comprehensive comparisons of ARG profiles between honeybees and bumblebees inhabiting the same environments are limited. Moreover, the diversity of mobile genetic elements (MGEs) in bee gut microbiomes and their potential role in mediating the horizontal transfer of ARGs have not yet been fully elucidated. In this study, metagenomic sequencing of 48 gut samples from farmed Apis mellifera, Apis cerana, and Bombus terrestris across four regions in China revealed 127 ARG subtypes, which collectively conferred resistance to nine major antibiotic classes. We found that A. mellifera, which carried the highest load of ARGs, concurrently harbored the greatest abundance of MGEs among the three species. Although ARG abundance varied significantly by region, no consistent geographical pattern emerged across the bee species. Importantly, strong positive correlations were detected between the abundances of ARGs and MGEs, particularly between the insertion sequence gene Tn3 and plasmid gene IncQ1. Metagenome-assembled genome analyses further confirmed the co-occurrence of ARGs (sul2, aph(3″)-Ib, and aph(6)-Id) with MGEs (Tn3 and IncQ1) across the three bee species, providing direct evidence that horizontal gene transfer mediated by MGEs contributes to the dissemination of ARGs within bee gut microbiomes. Overall, these findings highlight the critical role of the bee microbiome as a reservoir for ARGs and as a bioindicator for environmental pollutants, providing important insights into the mechanisms of ARG dissemination in ecosystems.},
}
@article {pmid42034466,
year = {2026},
author = {Sarkar, A and Raulo, A and Stothart, MR and Ibata, NGO and Harty, S and Metcalf, CJE and Bohannan, BJM and Bennett, GM and Carmody, RN},
title = {The island biology of the host microbiome.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.001},
pmid = {42034466},
issn = {1878-4380},
abstract = {Microbiomes perform critical functions for their hosts, and understanding microbiome variation is important for both basic and applied science. However, host traits alone cannot explain the entirety of microbiome variation, because, alongside host traits, microbiomes are shaped by multiple ecological processes. Researchers have thus turned to theories of island biology, conceptualising animal hosts as islands and animal microbiomes as metacommunities that assemble within and disperse between host islands. To develop realistic models, this host-as-island metaphor must be examined by explicitly comparing geological and host islands. Here, we critically examine the host-as-island metaphor by evaluating how microbiome variation is shaped by the four metacommunity processes that explain biodiversity on geological islands: local interspecies interactions, local selection, dispersal, and stochasticity. Key differences between host islands and geological islands include the complexity of microbiome transmission networks arising from host mobility and sociality and the capacity of hosts to evolve to control their microbiomes. We conclude with discussions of how eco-evolutionary dynamics differ between geological islands and host islands, and the reciprocal relevance of island biology and microbiome science.},
}
@article {pmid42034784,
year = {2026},
author = {Ziółkowska, EA and Nix, P and Olszowy, B and Williams, LL and Eultgen, EM and Nowacka, A and Celorrio, M and Friess, SH and Heuckeroth, RO and Cooper, JD},
title = {Antibiotic treatment reveals the contributions of the gut microbiome to CLN2 disease in the central and enteric nervous system.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49850-z},
pmid = {42034784},
issn = {2045-2322},
support = {R01 DK129691/NH/NIH HHS/United States ; R21 NS116574/NS/NINDS NIH HHS/United States ; },
abstract = {The Neuronal Ceroid Lipofuscinoses (NCLs) are fatal inherited lysosomal storage diseases, with pronounced neuron loss in the central nervous system (CNS). Gastrointestinal issues are frequently reported by people with NCLs, although mechanisms underlying these symptoms are poorly understood. We recently demonstrated degeneration occurs within the enteric nervous system (ENS) in several NCLs. Given that the gut microbiome has been shown to be altered a CLN2 mouse model (Tpp1[R207X/R207X]) and may potentially influence both CNS and ENS pathology, we investigated the long-term impact of modulating the gut microbiome in these mice. This was done by administering a VNAM antibiotic cocktail (vancomycin, neomycin, ampicillin, and metronidazole) for 1-week post-weaning, examining its effects at disease endstage. While VNAM treatment markedly altered the gut microbiome and caused significant loss of enteric neurons in wildtype mice, it did not exacerbate key pathological parameters in either bowel or brain of Tpp1[R207X/R207X] mice. These included histomorphometric changes in the small intestine and neurodegeneration of enteric neurons, or CNS neuropathology. However, we did find evidence for moderate protective effects of VNAM upon enteric neurons in the ileum, and upon CNS microglia, but all other pathologies were unaltered in Tpp1[R207X/R207X] mice. These findings suggest that intestinal and ENS pathology is primarily driven by TPP1-deficiency rather than changes in the gut microbiome. Indeed, these alterations to the gut microbiome may occur secondary to the impact of CLN2 disease upon the bowel.},
}
@article {pmid42034942,
year = {2026},
author = {Milovanova, LY and Nezhdanov, KS and Milovanova, SY and Druzhinin, DS and Zakharov, VV and Kosivtsova, OV and Braga, VI and Volkov, AV and Moiseev, SV},
title = {Chronic kidney disease and cognitive impairment: The role of diet and gut microbiota.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {148},
number = {},
pages = {113135},
doi = {10.1016/j.nut.2026.113135},
pmid = {42034942},
issn = {1873-1244},
abstract = {Several important milestones have been achieved in recent years in the area of slowing the progression of chronic kidney disease (CKD). Consequently, additional facets of reducing quality of life (QoL) in CKD patients have emerged, including progressive cognitive impairment (CI) in up to 50% of patients. Accumulating evidence suggests that gut microbiome dysregulation may promote CI in a paradigm of kidney-brain-gut axis. Systemic inflammation, oxidative stress, uremic toxins and increased intestinal permeability ("leaky gut") are key components of the kidney-brain-gut axis dysfunction. Correcting this cross-stalk through dietary changes may improve brain function and prevent further kidney damage. Beneficial nutritional guidelines include plant-based (Mediterranean style) low-protein diet, substitution of animal protein with soy isolate, ketoanalogues of essential amino acids supplementation, modification of the gut microbiota through prebiotics, probiotics, synbiotics and metabiotics. Although being a subject of debate, there are many worthwhile areas for research in kidney-brain-gut axis dysfunction. In this review, we aimed to address knowledge gaps in studies of CI in CKD patients in the context of the kidney-brain-gut axis.},
}
@article {pmid42034943,
year = {2025},
author = {Chatzinikolaou, R and Rouskas, K and Argiriou, A},
title = {Exploring the links between nutrition, gut microbiome, and neurodevelopmental disorders.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {148},
number = {},
pages = {113030},
doi = {10.1016/j.nut.2025.113030},
pmid = {42034943},
issn = {1873-1244},
abstract = {Neurodevelopmental disorders (NDDs), such as autism spectrum disorder (ASD), emerge during early childhood, affecting cognitive and behavioral health and motor development. While genetic factors contribute to the onset of ASD, recent studies highlight the significant role of environmental factors, particularly nutrition, in influencing the severity and manifestation of symptoms, primarily through the gut microbiome. This review explores how dietary imbalances, such as the consumption of ultra-processed foods, disrupt gastrointestinal health and microbiome composition, which in turn impact neurodevelopmental outcomes. It further explores the gut-brain axis and how early-life exposures, along with dietary and environmental factors, play a significant role in shaping brain development. The review concludes by underscoring the potential of a deeper understanding of these interactions to pave the way for more effective interventions aimed at improving developmental outcomes in children with ASD and other related NDDs. Key findings reveal that specific gut microbiota imbalances, such as a reduction in Bifidobacterium, are commonly associated with ASD. Additionally, dietary patterns like the Mediterranean and ketogenic diets show promise in supporting cognitive function and promoting neurodevelopment. Maternal nutrition, stress, and epigenetic factors during early life are also shown to influence brain development, contributing to gut dysbiosis, neuroinflammation, and the development of NDDs. To enhance our understanding of NDDs, future research should focus on large-scale longitudinal studies, maternal nutrition, and integrative multi-omics approaches.},
}
@article {pmid42034975,
year = {2026},
author = {Wang, H and Chen, Z and Qi, L and Wang, Z and Xu, D and Mao, Y and Shen, Z and Chen, K},
title = {Metagenomic profiling of Poa alpigena rhizosphere and bulk soil microbiomes across differing land-use contexts in the Qinghai lake alpine wetland.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04999-5},
pmid = {42034975},
issn = {1471-2180},
support = {This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T).//This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T)./ ; },
}
@article {pmid42035068,
year = {2026},
author = {Wadan, AS and El-Gemaie, DSA and Bayoumi, AM and Zein, MM and El Sattar Ahmed, MA and El-Khawaga, AM and Nagy, MM},
title = {Organ-on-chip (OoC) and nano-biomaterials: next generation of precision oral and dental healthcare research.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04410-5},
pmid = {42035068},
issn = {1477-3155},
abstract = {Periodontitis and dental caries are the most widespread non-communicable oral disorders worldwide, affecting approximately 3.5 billion people worldwide. Nevertheless, existing in vitro models do not accurately emulate the intricate interactions between the oral microbiome, the host immune response, and the fluctuating physicochemical environment. This lack of physiologically realistic models makes it extremely difficult to understand disease mechanisms and to design effective therapies. While organ-on-a-chip technology has revolutionized biomedical research, its application in oral healthcare and dental precision medicine remains fragmented, often lacking the integration of functional materials necessary for precise monitoring and treatment. Herein, this review offers a comprehensive overview of the oral microenvironment, emphasizing the essential biophysical signals of the tooth surface, gingival crevice, and periodontal contact that must be replicated. We rigorously assess current oral-on-a-chip systems, pinpointing their deficiencies in replicating multi-tissue interactions and real-time monitoring. New oral-on-chip and organ-on-chip systems need to be made as a next-generation platform that combines microfluidics with advanced/ functional nanomaterials that bridge this gap. This suggested system incorporates sustainable, biodegradable, and bio- and nanomaterials with integrated nanosensors for real-time monitoring of pH and cytokines, providing a comprehensive solution for modeling oral illnesses. Our primary objective is to establish a framework for creating high-fidelity, sustained in vitro oral models that can expedite the advancement of precision oral healthcare.},
}
@article {pmid42035169,
year = {2026},
author = {Wu, Y and Li, J and Yu, J and Yang, C and Mao, S},
title = {Temporal dynamics shifts in multi-kingdom rumen microbiota and fermentation profiles of water buffalo under heat stress.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00570-9},
pmid = {42035169},
issn = {2524-4671},
support = {32361143788//National Natural Science Foundation of China/ ; },
}
@article {pmid42035387,
year = {2026},
author = {Sun, J and Tang, S and Yan, J and Wang, J and Bai, R and Wang, X and Han, B and Yu, T},
title = {Biomimetic nanovesicles and nanotechnology for oral and maxillofacial diseases.},
journal = {Discover nano},
volume = {21},
number = {1},
pages = {},
pmid = {42035387},
issn = {2731-9229},
support = {2024YFC2510702//National Key Research and Development Program of China/ ; 2022YFA1206100//National Key Research and Development Program of China/ ; U21A2055//National Natural Science Foundation of China/ ; 52373123//National Natural Science Foundation of China/ ; Z211100002921066//Beijing Municipal Science Technology Commission/ ; F252067//Beijing Natural Science Foundation/ ; BJPSTP-2025-01//Beijing Physician Scientist Training Project/ ; },
abstract = {Oral and maxillofacial diseases, such as dental caries, periodontal disease, and tissue defects, demonstrate limited therapeutic effect due to the oral cavity's complex microecological environment, intractable chronic inflammation, and the challenge of regenerating dental and periodontal tissues. Biomimetic nanovesicles (BNVs), including extracellular vesicles (EVs) and artificial nanovesicles (ANVs), play a beneficial therapeutic role in these diseases. BNVs are capable of delivering a variety of therapeutic agents, including RNAs, proteins, drugs, and nanoparticles, with their efficiency, specificity, and safety enhanced by nanotechnological modification and engineering. This review provides a comprehensive overview of BNV classification and characterization, summarizes their functional advantages in disease treatment, and highlights their applications in oral and maxillofacial disorders, particularly in microbiome modulation, immunoinflammatory regulation, and tissue regeneration. The opportunities and challenges of translating BNVs into clinical practice are also assessed.},
}
@article {pmid42035799,
year = {2026},
author = {Chen, S and Zhu, B and Lu, X and Huang, Y and Wang, S and Wang, W and Chen, G and Wu, X and Zhou, J and Wu, F and Wu, K},
title = {Integrative multi-kingdom gut microbiome analysis uncovers clinical signatures of major depressive disorder.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {121858},
doi = {10.1016/j.jad.2026.121858},
pmid = {42035799},
issn = {1573-2517},
abstract = {BACKGROUND: Accumulating evidence indicates that gut microbiome is significantly altered in major depressive disorder (MDD). However, most studies have focused on bacteria, while the functional and ecological contributions of eukaryotes, archaea, and viruses in MDD remain poorly understood.<br><br>METHODS: Fecal samples were collected from 121 first-episode, drug-na&#xef;ve young adults with MDD and 117 healthy controls (HC) with matched demographic characteristics for shotgun metagenomic sequencing. Clinical data included the Hamilton Depression Scale (HAMD) and the MATRICS Consensus Cognitive Battery (MCCB). We systematically explored the multi-kingdom gut microbiome, functional genes, and metabolic pathways in MDD and their clinical associations, further assessing their diagnostic potential via machine learning.<br><br>RESULTS: MDD patients showed significant alterations in multi-kingdom microbiota diversity, accompanied by coordinated diversity relationships across microbial kingdoms relative to HC. In addition, we further identified 19 bacterial, 16 eukaryotic, 15 archaeal, and 10 viral species, as well as 22 functional genes and 32 metabolic pathways, that differed between groups. Importantly, five bacterial and four viral species were significantly associated with cognitive function, such as a positive correlation between Bifidobacterium pseudocatenulatum and attention/vigilance in MDD. Finally, validation demonstrated that a Random Forest model integrating multi-kingdom microbiota and functional features achieved superior diagnostic performance, significantly outperforming models based solely on bacterial features.<br><br>CONCLUSION: This study revealed extensive multi-kingdom microbial dysbiosis in MDD, providing deeper insight into disease-associated ecological disruption and highlighting the potential of microbial markers for enhancing clinical auxiliary diagnosis.},
}
@article {pmid42036057,
year = {2026},
author = {Stem, AD and Alayyoub, M and Aalizadeh, R and Nikolopoulou, V and Lisgara, A and Shvartsman, A and Anitha, M and Patterson, A and Coble, R and Rushing, B and Sumner, S and Vasiliou, V},
title = {Integrated Multi-Omics Reveals Synergistic Hepatotoxicity of Ethanol and PFOS Co-Exposure.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {112101},
doi = {10.1016/j.cbi.2026.112101},
pmid = {42036057},
issn = {1872-7786},
abstract = {Alcohol-associated liver disease (ALD) and exposure to per- and polyfluoroalkyl substances (PFAS) share key mechanisms of hepatotoxicity, yet their combined effects remain poorly characterized. We evaluated the impact of concurrent ethanol and perfluorooctanesulfonic acid (PFOS) exposure using a murine Lieber-DeCarli model characterized via multi-omic, spatial lipidomic, and metagenomic analyses. Exposure to PFOS resulted in rapid weight loss, while co-exposure led to decreased survival and pronounced hepatomegaly exceeding the effects of either exposure alone despite reduced cumulative ethanol intake. Histological analysis revealed enhanced hepatocellular injury with combined macrovesicular and microvesicular steatosis, consistent with impaired lipid handling and mitochondrial dysfunction. Transcriptomic and metabolomic profiling demonstrated disruption of xenobiotic metabolism, fatty acid β-oxidation, mitochondrial function, and bile acid transport, with PFOS acting as a dominant driver of metabolic stress and ethanol amplifying injury-related responses. Spatial lipidomics revealed hepatocyte-scale remodeling of membrane phospholipids, characterized by increased phosphatidic acid and depletion of phosphatidylinositol and phosphatidylserine under PFOS-containing conditions. Plasma metabolomics indicated systemic metabolic disturbance, including altered amino acid and redox pathways and depletion of microbiome-derived indole metabolites. Metagenomic analysis revealed reduced bacterial load and severe dysbiosis characterized by loss of commensal anaerobes, expansion of opportunistic taxa, and decreased microbial biosynthetic capacity. These findings indicate that PFOS increases susceptibility to alcohol-induced liver injury potentially through coordinated disruption of hepatic metabolism and gut-liver crosstalk, highlighting environmental PFAS exposure as a potential modifier of ALD severity.},
}
@article {pmid42036304,
year = {2026},
author = {Giubilei, I and Turco, S and Cardacino, A and Mahawar, L and Albrectsen, BR and Mazzaglia, A},
title = {Clearing the Noise: Seasonal Dynamics of Endophytic Bacteria in Fagus sylvatica Leaves Revealed by Application of PNA Clamps.},
journal = {Physiologia plantarum},
volume = {178},
number = {3},
pages = {e70897},
doi = {10.1111/ppl.70897},
pmid = {42036304},
issn = {1399-3054},
support = {CN00000022//Agritech National Research Center/ ; },
mesh = {*Plant Leaves/microbiology ; *Fagus/microbiology ; Seasons ; *Endophytes/physiology/genetics ; *Bacteria/genetics/classification ; Microbiota ; },
abstract = {The characterization of the seasonal dynamics of endophytic bacteria in beech leaves can be hindered by co-amplification of chloroplast and mitochondrial plant DNA. This study applies established peptide nucleic acid (PNA) clamps to suppress host-derived amplification while resolving bacterial succession across the vegetative season. Chloroplast- and mitochondrion-specific PNAs inverted the proportion of host to bacterial reads, enabled the recovery of bacterial sequence variants, and increased alpha diversity accordingly. Beta-diversity analyses showed that, once host contamination was removed, samples displayed a clear seasonal trajectory. Early-season leaves contained high abundances of Pseudomonas together with taxa likely introduced through plant-insect-microbe interactions. As leaves matured, the microbiome shifted toward a more stable composition dominated by well-established genera. The transition from early transient taxa to the later enrichment of phyllosphere-adapted and nutrient-cycling genera demonstrates that beech leaves host a temporally structured microbiome shaped by leaf development and seasonal environmental stress.},
}
@article {pmid42036496,
year = {2026},
author = {Tow, WK and Teh, CSJ and Ooi, CW and Lee, RFS and Krishnasamy, M and Palanisamy, UD and Sundralingam, U},
title = {Metagenomic insights into urolithin formation from rambutan rind extract by rat faecal-derived microbiome.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13841-x},
pmid = {42036496},
issn = {1432-0614},
abstract = {Ellagitannins and ellagic acid are microbially converted into urolithins, metabolites associated with antioxidant, anti-inflammatory, and mitochondrial-related activities. Although several human-derived urolithin-producing strains and their associated enzymes have recently been characterised, the diversity of microbial strategies across host systems remains poorly understood. This study investigated urolithin production in the Sprague-Dawley rat faecal-derived microbial communities supplemented with rambutan rind extract, an ellagitannin-rich agricultural by-product containing 35-40% geraniin. Rambutan rind extract supplementation was associated with reduced isobutyric acid levels at study endpoint. Ex vivo anaerobic fermentation of hydrolysed rambutan rind extract (113 µM ellagic acid equivalent) resulted in the formation of urolithin C (9.4 ± 0.6 µM) and Isourolithin A (12.5 ± 0.6 µM) by day 9. Shotgun metagenomics analysis revealed very low relative abundance of Actinobacteria (< 0.009%), despite this phylum encompassing most previously characterised urolithin-producing taxa. Canonical ellagic acid degradation genes and the MetaCyc EA degradation pathway were not detected. Comparative pathway analysis indicated overlap in general metabolic pathways with Ellagibacter isourolithinifaciens DSM 104140[T] reflecting shared metabolic frameworks rather than conserved urolithin biosynthetic pathways, with highly divergent homologues (Eadh1, Eadh2, Eadh3, and Ucdh). Together, these findings demonstrate that rambutan rind extract can support urolithin formation in rat faecal-derived microbial consortia and highlight functional associations consistent with alternative or yet-uncharacterised microbial strategies for ellagitannin biotransformation. These findings support a discovery-driven framework for investigating urolithin biotransformation in non-human gut microbiomes using ellagitannin-rich agricultural substrates. KEY POINTS: • Rambutan rind extract supports urolithin formation in rat-derived gut microbiota. • Substrate concentration influences urolithin production under ex vivo conditions. • Rat gut microbiota shows homologues' divergence in urolithin-associated proteins.},
}
@article {pmid42036511,
year = {2026},
author = {Laue, HE and Fleury, ES and Romano, ME and Hoen, AG and Braun, JM},
title = {Itching to know: the Microbiome, Allergic Disease, and Antimicrobial Chemicals.},
journal = {Current environmental health reports},
volume = {13},
number = {1},
pages = {},
pmid = {42036511},
issn = {2196-5412},
support = {K99/R00 ES034086/ES/NIEHS NIH HHS/United States ; R03 ES035140/ES/NIEHS NIH HHS/United States ; R01 ES032836/ES/NIEHS NIH HHS/United States ; },
}
@article {pmid42036749,
year = {2026},
author = {Yue, Y and Cai, Y and Murayama, R and Ding, X and Wan, X and Liu, G and Hashimoto, H and Anzai, N and Hashimoto, K},
title = {Antibiotic-induced Microbiome Depletion Selectively Reduces Baseline Hypothalamic Oxytocin Signaling without Affecting MDMA-induced Oxytocin Response in Rats.},
journal = {Clinical psychopharmacology and neuroscience : the official scientific journal of the Korean College of Neuropsychopharmacology},
volume = {24},
number = {2},
pages = {402-407},
doi = {10.9758/cpn.25.1381},
pmid = {42036749},
issn = {1738-1088},
abstract = {OBJECTIVE: To determine whether antibiotic-induced microbiome depletion influences baseline or 3,4-methylenedioxymethamphetamine (MDMA)-induced oxytocin signaling in rats.<br><br>METHODS: Male Wistar rats received broad-spectrum antibiotics (ABX) or water for 7 days, followed by a single oral administration of MDMA (30 mg/kg). Plasma oxytocin levels were measured by ELISA, and oxytocin-immunoreactivity in the paraventricular (PVN) and supraoptic (SON) nuclei were quantified by immunofluorescence.<br><br>RESULTS: ABX treatment induced marked cecal enlargement without affecting body weight, confirming microbiome disruption while maintaining systemic stability. Peripheral oxytocin concentrations were unchanged; however, baseline central oxytocin expression in both the PVN and SON was significantly reduced after ABX treatment. MDMA increased central oxytocin expression, and this response was not significantly altered by microbiome depletion. Similarly, MDMA-induced peripheral oxytocin levels did not differ between control and ABX-treated rats.<br><br>CONCLUSION: Antibiotic-induced microbiome depletion selectively attenuates baseline central oxytocin signaling while leaving peripheral oxytocin regulation intact. In contrast, MDMA-induced oxytocin responses in both the brain and circulation are preserved despite microbiome disruption. These findings suggest that gut microbiota contribute to central oxytocin homeostasis under basal conditions but are not essential for acute MDMA-induced oxytocin activation.},
}
@article {pmid42036782,
year = {2026},
author = {Song, B and Zeb, J},
title = {The mosquito midgut harbors stable bacteria that enhance host hemolymph immunity.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70720},
pmid = {42036782},
issn = {1526-4998},
support = {//City University of Hong Kong and the University of Hong Kong./ ; },
abstract = {BACKGROUND: Mosquito symbionts have the potential to control mosquito-borne diseases by reducing vector competence through direct or indirect interactions with pathogens. However, the microbiome of field-collected mosquitoes is often unstable, and it remains unclear whether certain symbiont species can both colonize their hosts stably and modulate host immunity. In this study, we collected second-instar Aedes albopictus and Culex pipiens larvae from field water sources in Hong Kong and reared them to fourth-instar larvae and adults under laboratory conditions. We investigated microbiome changes from water to mosquito midguts and identified stable bacterial species (≥ 0.01% relative abundance) across mosquito stages using 16S rRNA-based bacteriome analysis. We further isolated symbiotic bacteria on culture plates, screened stable species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, and evaluated their functional potential.<br><br>RESULTS: Mosquito microbiomes were influenced by water source, developmental stage, and host species. Taxonomically, Proteobacteria and Bacteroidetes dominated mosquito midguts. Each mosquito species maintained four stable bacterial species (&#x2265;&#x2009;0.01% relative abundance) throughout development. We confirmed culturable Comamonas thiooxydans as a stable symbiont of Culex pipiens and Vibrionimonas magnilacihabitans in Aedes albopictus. Genomic predictions suggested their involvement in antimicrobial peptide synthesis. Functionally, these bacteria enhanced host survival and increased hemolymph antimicrobial activity against Erwinia carotovora subspecies carotovora 15 (ECC15), but not across mosquito species.<br><br>CONCLUSION: Our findings suggest that mosquitoes harbor generally unstable bacterial communities with only a few species-specific stable symbionts, which may contribute to host survival and immune function. &#xa9; 2026 Society of Chemical Industry.},
}
@article {pmid42036837,
year = {2026},
author = {Yancey, CE and Brumfield, KD and Buss, JA and Colwell, RR and Ettwiller, L},
title = {A Bait-and-Switch Strategy Links Phenotypes to Genes Coding for Polymer-Degrading Enzymes in Intact Microbiomes.},
journal = {Microbial biotechnology},
volume = {19},
number = {4},
pages = {e70359},
doi = {10.1111/1751-7915.70359},
pmid = {42036837},
issn = {1751-7915},
support = {//New England Biolabs/ ; OCE1839171//National Science Foundation/ ; CCF1918749//National Science Foundation/ ; CBET1751854//National Science Foundation/ ; R01ES030317A/ES/NIEHS NIH HHS/United States ; 80NSSC20K0814/NASA/NASA/United States ; 80NSSC22K1044/NASA/NASA/United States ; },
mesh = {*Microbiota ; *Chitin/metabolism ; Soil Microbiology ; *Bacteria/enzymology/genetics/classification ; Phenotype ; Chitinases/genetics/metabolism ; Genetic Association Studies ; },
abstract = {Natural microbial communities, with their vast diversity and complexity, are among the richest sources of untapped novel enzymes. Identifying novel enzymes can be challenging because microbiomes often lack clear, measurable phenotypes, unlike laboratory cultures where enzymatic activity can be linked to genetic elements. These constraints have left much of the functional diversity within microbiomes inaccessible to enzyme discovery efforts. Here, we present a genotype/phenotype association framework directly on microbial communities for enzyme discovery. For this, we developed a 'bait-and-switch' treatment strategy that generates measurable dual phenotypes directly within intact microbiomes. Using soil microbiomes as a test system, we applied chitin-rich compost as 'bait' to enrich chitin-degrading organisms, followed by glucose addition to functionally 'switch' the community. This treatment produced a distinct phenotypic signature: prevalence of known chitin degradation genes increases during the bait phase, and their transcripts are rapidly downregulated during the switch phase. By performing hypothesis-free association analysis of protein domains with this dual phenotype, we identified the glycoside hydrolase 18 as the most significantly associated protein domain. Experimental validation confirmed chitinase activity in 63% of tested enzymes, including candidates from unculturable bacteria and those with previously uncharacterized domain architectures. This species-independent, reference-free approach to discover novel enzymes has broad applications in microbiome engineering, biopolymer processing and systems biology, offering a generalizable strategy for functional gene discovery in complex microbial systems.},
}
@article {pmid42036885,
year = {2026},
author = {Kakooza, D and Yu, H and Jeong, J and Shin, JC and Kim, WJ and Moon, SK and Kim, H},
title = {Oral PHGG ameliorates atopic dermatitis-like dermatitis with concurrent modulation of colonic IgA and cecal microbiota: implications for the gut-skin axis.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70676},
pmid = {42036885},
issn = {1097-0010},
support = {RS-2026-25497299//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A6A1A03025159//Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education/ ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is increasingly recognized as a systemic inflammatory disorder linked to intestinal immune and microbiome dysregulation. However, whether dietary galactomannan fibers can mitigate AD through coordinated modulation of the gut-skin axis remains unexplored. This study investigated the anti-atopic potential of orally administered partially hydrolyzed guar gum (PHGG), a low-viscosity, fermentable galactomannan enriched in low-mass oligosaccharides (mannose/galactose ratio of 1.87).<br><br>RESULTS: In TNF-&#x3b1;/IFN-&#x3b3;-stimulated HaCaT keratinocytes, PHGG (100-400&#x2009;&#x3bc;g&#x2009;mL[-1]) suppressed IL-6, IL-8, and MCP-1 secretion and down-regulated AD-relevant mediators, including TARC, MDC, RANTES, and TSLP. In TNF-&#x3b1;-challenged Caco-2 cells, PHGG reduced IL-8 and MCP-1 and partially restored barrier-associated transcripts (TJP1, TJP2, OCLN, CLDN1) and MUC2. In 2,4-dinitrochlorobenzene (DNCB)-induced AD BALB/c mice, oral PHGG (100-400&#x2009;mg&#x2009;kg[-1]&#x2009;d[-1]) attenuated lesion severity, epidermal hyperplasia, collagen loss, and mast cell infiltration without adverse effects on body weight or organ weights. PHGG reduced circulating immunoglobulins and inflammatory cytokines, suppressed skin type 2 helper T-cell (Th2)-associated mediators, and restored colonic immune homeostasis, as evidenced by increased immunoglobulin A (IgA) and decreased interleukin 1 beta (IL-1&#x3b2;) and IL-6. Cecal 16S rRNA profiling revealed that PHGG shifted dysbiotic microbial signatures toward fiber-responsive Bacteroidales lineages (e.g., Muribaculaceae, Alistipes, Rikenellaceae) and partially normalized community structure in beta-diversity analyses.<br><br>CONCLUSION: These findings demonstrate that oligosaccharide-enriched PHGG ameliorates AD-like inflammation through concurrent modulation of cutaneous immune responses, colonic mucosal immunity, and gut microbial community structure, supporting a gut-skin axis mechanism. Future studies quantifying microbial metabolites are warranted to establish causal mediators of gut-to-skin signaling. &#xa9; 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.},
}
@article {pmid42036926,
year = {2026},
author = {Dong, X and Chu, Y and Yi, X and Meng, D and Fu, J and Tong, Z and Sun, M and Duan, J},
title = {Metal-organic frameworks for pesticide remediation: From adsorption and photocatalysis to health-relevant risk reduction.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70856},
pmid = {42036926},
issn = {1526-4998},
support = {32372609//National Natural Science Foundation of China/ ; 32302414//National Natural Science Foundation of China/ ; 2023YFD1400900//National Key Research and Development Program of China/ ; },
abstract = {Conventional remediation strategies implicitly assume that efficient pollutant removal equates to effective health-risk mitigation; however, growing epidemiological and microbiome evidence challenges this assumption, particularly for pesticide exposure. Accumulating studies demonstrate that pesticide residues and their transformation products can disrupt gut microbial homeostasis and metabolic regulation, indicating that removal efficiency alone is insufficient to evaluate remediation success. Against this backdrop, this review advances a risk-oriented paradigm for pesticide remediation by redefining metal-organic frameworks (MOFs) from high-performance adsorbents or photocatalysts into exposure-modulating materials bridging environmental decontamination with human health protection. We summarize recent progress in MOF design for pesticide adsorption and photocatalytic degradation, emphasizing structure-function relationships governing molecular recognition, pore confinement, surface chemistry and degradation-pathway control. Beyond performance metrics, this work examines how MOF-enabled adsorption and photocatalysis shape transformation-product profiles determining biological perturbation potential. Evidence linking pesticide exposure to gut microbiota dysbiosis and metabolic disorders underscores the health relevance of pathway-selective remediation. Finally, we outline future directions toward health-relevant remediation, advocating a shift from pollutant-centric efficiency metrics to risk relevant endpoints considering exposure profiles and biological disruption. By coupling programmable molecular selectivity with pathway-controlled degradation, MOFs emerge as enabling platforms for next-generation remediation strategies advancing environmental sustainability and human health protection. © 2026 Society of Chemical Industry.},
}
@article {pmid42037062,
year = {2026},
author = {Malas, J and Reczek, S and Porter, I and Lenzy, YM and Barbosa, V and Porter, C and Hampton-Marcell, J},
title = {Scalp microbiome differences in subjects with self-reported hair loss: A quantitative approach to microbial dysbiosis.},
journal = {International journal of cosmetic science},
volume = {},
number = {},
pages = {},
doi = {10.1111/ics.70101},
pmid = {42037062},
issn = {1468-2494},
abstract = {OBJECTIVE: Hair loss is a common issue that affects a large proportion of the population, leading to lower self-confidence and quality of life. Microbial dysbiosis of the scalp has been shown to be associated with several different disorders leading to hair loss. Though several 'microbiome friendly cosmetic treatments are currently on the market, there is no agreement on the best technique for assessing dysbiosis, leading to a lack of scientific rigour for quantifying the effective treatments. To help address this, the association between self-perceived hair loss and the scalp microbiome in an African-American cohort (n = 36) was investigated.<br><br>METHODS: Using a self-controlled design, swabs were collected from both 'sparse' and 'normal' scalp sites. The scalp microbiome was characterized via 16S rRNA gene sequencing and a dysbiosis score was calculated based on the proportion of all taxa within the samples. Further, we identified the taxa that contributed most to abnormal or dysbiotic hair sites using a machine learning random forest classifier and a negative binomial mixed-effects model.<br><br>RESULTS: The dysbiosis index is sensitive to participants' self-assessment of hair loss and interindividual variation. We found a core set of operational taxonomic units (OTUs) assigned to 7 genera that significantly contributed to increased scalp dysbiosis.<br><br>CONCLUSION: This study demonstrates that self-perceived hair loss is associated with significant and measurable alterations in the scalp microbiome, making the reported dysbiosis index a practical tool that may be used to assess microbiome changes following cosmetic or medical interventions for hair loss and other microbiome-associated disorders.},
}
@article {pmid42037123,
year = {2026},
author = {Rodríguez-Sojo, MJ and Hidalgo-García, L and Molina-Tijeras, JA and López-Escanez, L and Gbati, L and Vezza, T and Diez-Echave, P and Ruiz-Malagón, AJ and García-García, J and García, F and Baños, A and Gil-Martínez, L and López-Posadas, R and Neurath, MF and Gálvez, J and Rodríguez-Cabezas, ME and Rodríguez-Nogales, A},
title = {The Allium cepa Derived Compound Propyl Propane Thiosulfonate (PTSO) Improves Tumorigenesis Due to Its Immunomodulatory Effect: A Preclinical Study.},
journal = {Phytotherapy research : PTR},
volume = {},
number = {},
pages = {},
doi = {10.1002/ptr.70334},
pmid = {42037123},
issn = {1099-1573},
support = {CULTUREDMEAT-Project-MIG-20201012//Centro para el Desarrollo Tecnol&#xf3;gico Industrial/ ; PI19/01058//Instituto de Salud Carlos III/ ; PI20/01447//Instituto de Salud Carlos III/ ; IFI21/00030//Instituto de Salud Carlos III/ ; CD23/00102//Instituto de Salud Carlos III/ ; CD23/00117//Instituto de Salud Carlos III/ ; CD22/00112//Instituto de Salud Carlos III/ ; CP22/00153//Instituto de Salud Carlos III/ ; },
abstract = {Allium-derived organosulfur compounds offer significant health benefits. Specifically, PTSO, an organosulfur compound extracted from Allium cepa, has demonstrated immunomodulatory and prebiotic properties. However, its effects on tumorigenesis and gut dysbiosis in colitis-associated colorectal cancer (CAC) remain unexplored. This study aimed to investigate the impact of two PTSO formulations, free (FP) and encapsulated (EP), on a murine model of CAC focusing on their impact on the immune system and gut microbiome. The antitumor effect of PTSO was characterized in vitro in HCT116 cells and in a CAC murine model induced by the administration of azoxymethane and dextran sulfate sodium. FP and EP were administered orally throughout the assay and 5-fluorouracil was used as a control. FP and EP were effective in reducing tumor burden, with EP showing a greater positive impact on tumorigenesis by reducing both tumor number and size, likely due to enhanced bioavailability. PTSO induced apoptosis through oxidative stress mechanisms and modulated key pathways like STAT3, PI3K/mTOR, and Wnt/β-catenin. Additionally, PTSO, especially EP, exhibited an immunomodulatory effect on myeloid and lymphoid populations and hindered the release of cytokines that prompted inflammation and cancer progression. PTSO also enhanced gut barrier integrity, increased the abundance of beneficial bacteria, like Akkermansia, Leuconostoc mesenteroides, and Weissella confusa, and the release of short-chain fatty acids (SCFAs). This study highlights the potential of PTSO, particularly in its encapsulated form, as a promising therapeutic agent for CRC by targeting both tumor growth and the underlying inflammatory processes while restoring gut microbiota balance.},
}
@article {pmid42037251,
year = {2026},
author = {Funatsu, O and Ishii, H and Shimatsu, R and Shimokawa, Y and Asahina, A and Dekio, I},
title = {Short-Term Promotion of Beneficial Skin Commensal Staphylococcus Species Growth by PS-B1, a Postbiotic Composed of Lactic Acid Bacteria-Fermented Soy Milk.},
journal = {Microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1348-0421.70057},
pmid = {42037251},
issn = {1348-0421},
abstract = {Postbiotics, defined as non-viable microbial cells, their components, or metabolites, are emerging functional ingredients that can modulate host health, including skin barrier function, immune responses, and microbial balance. The human skin microbiome plays a critical role in maintaining skin health, and the selective stimulation of beneficial commensals is of growing interest for cosmetic applications. PS-B1, a postbiotic derived from lactic acid bacteria during soy fermentation, is already used in beverages and cosmetics, but its direct effects on skin-resident bacteria have not been fully elucidated. In this study, we evaluated the effects of preservative-containing and preservative-free PS-B1 on the growth of twelve Staphylococcus strains and seven Cutibacterium acnes strains in vitro. The preservative-containing PS-B1 showed strong growth inhibition for all strains at higher concentrations. In contrast, the preservative-free PS-B1 significantly promoted the growth of Staphylococcus epidermidis, Staphylococcus hominis, and Staphylococcus lugdunensis, while Staphylococcus warneri was the only strain exhibiting growth inhibition. Other species showed no notable changes. Additionally, all C. acnes strains displayed slight growth enhancement. These results indicate that preservative-free PS-B1 selectively stimulates beneficial skin commensals, particularly S. hominis, revealing a previously unrecognized potential of PS-B1 to support a balanced skin microbiome.},
}
@article {pmid42037351,
year = {2026},
author = {Chakraborty, S and Mukherjee, D and Sar, P},
title = {Genome-resolved insights into arsenic-impacted paddy soil and microcosm-derived microbiomes from West Bengal, India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0005926},
doi = {10.1128/mra.00059-26},
pmid = {42037351},
issn = {2576-098X},
abstract = {This study reports 32 metagenome-assembled genomes (MAGs) reconstructed from arsenic (As)-impacted paddy soils of West Bengal, India, and microcosms from these soil samples. These MAGs, represented by 10 bacterial and 2 archaeal phyla, provided critical insights into the metabolic and biogeochemical potential of microbiomes in a highly As-impacted agroecosystem.},
}
@article {pmid42037384,
year = {2026},
author = {Yang, K and King, S and Marshak, A and D'Mello-Guyett, L and Grignard, L and Knee, J and Wong, G and Zhao, L and Lamaka, NG and Save, D and Gose, M and Myers, A and Trehan, I and Cumming, O and Stobaugh, H and Schwartz, DJ},
title = {Gut microbiome associations with acute malnutrition relapse in South Sudan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0358725},
doi = {10.1128/spectrum.03587-25},
pmid = {42037384},
issn = {2165-0497},
abstract = {Severe acute malnutrition (SAM) is a leading cause of childhood morbidity and mortality that is defined by anthropometric measurements, weight-for-height z score, and mid-upper arm circumference (MUAC) falling significantly below healthy standards. While treatments for SAM and our understanding of this disease have advanced, children experiencing SAM frequently relapse to acute malnutrition (AM) following anthropometric recovery. Little is known about the contribution of the gut microbiome to AM relapse. We hypothesized that features of the gut microbiome, including microbial composition, antimicrobial resistance gene carriage, and predicted microbial functional pathways, of children discharged from treatment for uncomplicated SAM in South Sudan, may be associated with AM relapse at 1-month follow-up. Overall, broad microbiome profiles at discharge were not associated with AM relapse. We evaluated the associations of microbiome features with AM relapse 1-month post-recovery using mixed linear effect models. We identified associations between higher MUAC, which may be a proxy for future health trajectories, and increased Sutterella wadsworthensis and trimethoprim-resistant dihydrofolate reductase antimicrobial resistance genes. These findings suggest that the gut microbiome at discharge of children treated for uncomplicated SAM has limited predictive value as a standalone diagnostic tool for identifying relapse risk at 1 month.IMPORTANCESevere acute malnutrition (SAM) is a devastating illness that impacts the morbidity and mortality of millions of children worldwide. Community-based management of acute malnutrition (CMAM) is the standard of care in South Sudan and many other low-resource settings for children presenting with SAM. Despite this intervention, children treated for SAM under CMAM frequently relapse to acute malnutrition (AM) following treatment. With advancements in our understanding of malnutrition, there has been a strong and growing interest in developing microbiome-based strategies to treat, prevent, and predict relapse to AM following treatment for SAM. Our work characterizes gut microbiome features of children from a geographic area that is traditionally underrepresented in gut microbiome research and shows that in isolation, a child's gut microbiome at discharge likely holds low predictive value for relapse to AM post-CMAM treatment; however, we identified key microbes and microbial features meriting further research.},
}
@article {pmid42037847,
year = {2026},
author = {Avendaño-Pérez, AL and Orozco-Covarrubias, L and Saez-de-Ocariz, M},
title = {The Role of Biotics in Rosacea: A Narrative Review.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e105799},
pmid = {42037847},
issn = {2168-8184},
abstract = {Rosacea is a chronic inflammatory dermatosis affecting the central face of adults, characterized by persistent erythema, flushing, papules, pustules, telangiectasias, and, in some cases, phymatous changes. Its pathogenesis involves a multifactorial interplay of immune dysregulation, neurovascular alterations, genetic predisposition, and disturbances of the skin and gut microbiota. Increasing interest in the gut-skin axis has prompted investigation into microbiota-targeted therapies, including probiotics, prebiotics, postbiotics, and synbiotics. This narrative review evaluates current evidence regarding the role of biotics in rosacea. A literature search was conducted in PubMed/MEDLINE, Scopus, and Web of Science using combinations of the terms "rosacea," "gut-skin axis," "probiotics," "prebiotics," "postbiotics," and "synbiotics." Clinical trials, observational studies, and relevant mechanistic investigations published in English were considered. Available data suggest that certain probiotic strains, administered orally or topically, may improve inflammatory lesions, erythema, and skin barrier function, particularly as adjuncts to standard therapy. However, findings are characterized by significant heterogeneity in strains, dosages, study design, outcome measures, and treatment duration. Evidence supporting the use of prebiotics, postbiotics, and synbiotics in rosacea remains limited and, in many cases, extrapolated from related inflammatory conditions or preclinical models. Although microbiota modulation represents a promising therapeutic avenue, current evidence is insufficient to establish standardized clinical recommendations. Larger, well-designed randomized controlled trials with standardized endpoints and long-term follow-up are required to clarify their efficacy, optimal formulations, and safety.},
}
@article {pmid42038049,
year = {2026},
author = {Campbell, L and Thompson, M and Muir, M and Raubenheimer, D and Holmes, A},
title = {Diet-induced metabolic and faecal microbiome responses in pet dogs fed a minimally processed versus extruded kibble diet.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1734572},
pmid = {42038049},
issn = {2297-1769},
abstract = {INTRODUCTION: The extent to which food is processed influences gut functions, such as digestion, nutrient uptake, and microbiome response, with the potential to impact immuno-metabolic health. Despite known associations between ultra-processed food (UPF) intake and chronic diseases in humans, mechanistic links explaining inferred health risks remain unclear. Health risks associated with chronic disease are also a concern for companion animals such as dogs, where nutritionally complete dry processed foods constitute a major component of contemporary pet dog diets. A challenge is that nutrition is complex and even diets based on nutritionally complete processed foods typically vary in multiple dimensions.<br><br>METHODS: Here, we use a randomised, cross-over design to compare short-term effects of two commercially available nutritionally complete canine diets-an extruded kibble diet (EKD) and a mildly cooked, minimally processed diet (MPD). We assigned 24 healthy dogs to one of two groups: all dogs remained on their at-home diet for 1 week, before transitioning to (1) MPD or (2) EKD for 2 weeks each. One dog was removed from the study due to health complications, and the remaining 23 dogs completed both dietary treatment periods. Glycaemic, hormonal, and gut microbiome responses were captured from pre- and post-prandial blood samples and time series of 12 faecal samples from each dog.<br><br>RESULTS: The experimental diets resulted in distinct physiological and gut microbiome responses. MPD was associated with improved faecal consistency (FCS 2.24 &#xb1; 0.67, p = 0.005), lower pre- and post-prandial gastric inhibitory polypeptide (GIP, p < 0.001) and peptide YY (PYY, p < 0.05), and reduced post-prandial glycaemic response compared to EKD (AUC, p = 0.009). Diet was the strongest predictor of microbial response despite between-dog differences, with higher alpha diversity associated with MPD and greater within-individual community turnover following transition to MPD in both treatment groups (Group 1, p < 0.001; Group 2, p < 0.05).<br><br>CONCLUSION: These data show the feasibility of testing diet formulations in pet dogs and understanding the role of host-microbiome interactions in responses to food. The demonstration of distinct outcomes highlights the need for further studies on long-term feeding to better understand mechanisms and implications for health in community pets.},
}
@article {pmid42038231,
year = {2026},
author = {Simonin, EM and Switkowski, KM and Rifas-Shiman, SL and Nadeau, KC and Oken, E and Lightdale, JR},
title = {Associations of cord blood biomarkers with infant colic and excessive crying.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1767660},
pmid = {42038231},
issn = {2296-2360},
abstract = {INTRODUCTION: There are currently no known biomarkers associated with the diagnosis of infant colic, a common early disorder of gut brain interaction (DGBI) that has been found to predict adverse health outcomes, including atopy, migraines and other DGBIs. Infant colic manifests as unsoothable crying and is perceived to be associated with abdominal pain, differentiating it from other crying behaviors. Prior studies have postulated it may involve microbial dysbiosis as well as immunological and neurological dysregulation. The aim of our study was to investigate the associations of cord blood biomarkers at birth with parent reports of colic and excessive crying behaviors at 6 months of age.<br><br>METHODS: We used available data from Project Viva a pre-birth cohort based in the greater Boston, MA area. All infants were born between 1999 and 2002.<br><br>RESULTS: Among participants with information on infant colic and cord blood biomarkers (n&#x2009;=&#x2009;405), we found higher trans fatty acids and an increased abundance of Gammaproteobacteria signature in cord blood from infants with colic and those with excessive crying without colic, compared to those unaffected by colic. The majority of inflammatory and immune system cord blood biomarkers previously measured, including metabolites and cytokine stimulation, showed no association with either colic or excessive crying.<br><br>DISCUSSION: This exploratory study examined cord blood biomarkers of inflammation or immune dysregulation to support the underlying mechanism of infant colic, and identified trans fatty acid levels and Gammaproteobacteria microbial signatures as possible candidate predictors. On the other hand, we also found a lack of association with most of the cord blood immune and neurological biomarkers that we assessed. In turn, we propose that colic biomarkers may be present closer to its manifestation as a clinical condition of early infancy.},
}
@article {pmid42038244,
year = {2026},
author = {Shi, Z and Zhu, H and Tao, X and Liu, F and Zhao, L and Zhang, J and Zhang, J},
title = {Lactoferrin combined with Bifidobacterium animalis subsp. lactis BB-12 improves respiratory tract infections and modulates Gut microbiome function in children: a randomized, double-blind, placebo-controlled trial.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1778240},
pmid = {42038244},
issn = {2296-2360},
abstract = {OBJECTIVES AND STUDY: To explore the effects and mechanisms of lactoferrin combined with Bifidobacterium animalis subsp. lactis BB-12 on Respiratory tract infections (RTIs) in healthy children through a randomized, double-blind, placebo-controlled trial.<br><br>METHODS: Eligible healthy children aged 0-6 years were randomized into intervention group (IG, n&#x2009;=&#x2009;60, receiving lactoferrin and probiotic for 3 months) and control group (CG, n&#x2009;=&#x2009;34, receiving placebo). The study primarily assessed changes in the incidence and severity of RTIs, and monitored gastrointestinal adverse events. Fecal samples were collected pre- and post-intervention to analyze gut microbiota composition and metabolomic profiles, including short-chain fatty acids (SCFAs).<br><br>RESULTS: After the intervention, the incidence of RTIs showed no significant difference between groups (55% vs. 61.8%, p&#x2009;=&#x2009;0.52), but both the RTI severity score (3.0 vs. 4.0, p&#x2009;<&#x2009;0.05) and mean duration per RTI episode (3.54 d vs. 5.27 d, p&#x2009;<&#x2009;0.05) were significantly lower in the IG. No serious adverse events were reported, and the incidence of indigestion was significantly reduced in the IG compared with the CG (8.3% vs. 23.5%, p&#x2009;=&#x2009;0.04). The intervention significantly altered phylogenetic diversity (PD-whole tree within IG: p&#x2009;=&#x2009;0.0011; baseline between IG and CG: p&#x2009;=&#x2009;0.63; post-intervention between IG and CG: p&#x2009;=&#x2009;0.029) and community structure (weighted UniFrac within IG: 0.012; between IG and CG at 3 months: p&#x2009;=&#x2009;0.036 vs. baseline p&#x2009;=&#x2009;0.01). The gut microbiota in the intervention group exhibited a trend toward greater stability over time. Integrated microbiome-metabolite analysis showed attenuation of fatty acid oxidation-and energy metabolism-related metabolic drivers after intervention, together with no significant changes in fecal SCFA levels.<br><br>CONCLUSIONS: The intervention improved clinical outcomes and induced phylogenetic restructuring of the gut microbiota rather than changes in overall abundance, accompanied by a shift toward greater stability in gut microbial structure and energy metabolic patterns.<br><br>CLINICAL TRIAL REGISTRATION: identifier ChiCTR2500111308.},
}
@article {pmid42038418,
year = {2026},
author = {Vlasovets, O and Schaipp, F and Simpson, L and Bolyen, E and Caporaso, JG and Mueller, CL},
title = {Sparse regression, classification, and microbial network estimation in QIIME2 with q2-classo and q2-gglasso.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {42038418},
issn = {2331-8422},
abstract = {MOTIVATION: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many tools for data pre-processing and analysis, plugins for statistical regression, classification, and microbial network estimation tailored to compositional count data are relatively scarce.<br><br>RESULTS: We present q2-classo and q2-gglasso, two novel QIIME 2 plugins that implement penalized regression, classification, and graphical modeling approaches for microbial compositional data. q2-classo enables the prediction of a continuous or binary outcome of interest using compositional microbiome data as predictors. Both sparse log-contrast regression and classification, as well as tree-aggregated log-contrast models are available. q2-gglasso enables the estimation of taxon-taxon association networks through sparse graphical model estimation, such as, e.g., the SPIEC-EASI framework, as well as adaptive and latent graphical models. The latent model can decompose taxon-taxon associations into a sparse direct interaction matrix and a latent (low-rank) matrix which enables robust principal component embedding of a data set. Within the QIIME 2 ecosystem we demonstrate their application on the Atacama soil microbiome dataset, illustrating robust model selection, classification, and microbial network estimation with covariates and latent factors.<br><br>AVAILABILITY: The software is freely available under the BSD-3-Clause License. Source code is available at https://github.com/bio-datascience/q2-gglasso and https://github.com/bio-datascience/q2-classo-latest, with installation through QIIME 2 and Docker.},
}
@article {pmid42038449,
year = {2026},
author = {Yu, Y and Wang, C and Wang, R and Chen, Y and Wei, Z and Xiao, Y and Elbelt, U and Pietzner, A and Weylandt, KH},
title = {Age-related alterations in fatty acid metabolism: a clinical study of erythrocyte and plasma profiles in a population from Brandenburg, Germany.},
journal = {Frontiers in aging},
volume = {7},
number = {},
pages = {1725187},
pmid = {42038449},
issn = {2673-6217},
abstract = {INTRODUCTION: Aging is accompanied by changes in lipid metabolism that may influence cellular homeostasis and risk for age-related disease. Circulating polyunsaturated fatty acid (PUFA) status is increasingly recognized as an important marker of metabolic health and may shift with age. Product-to-precursor ratios of fatty acids, including PUFA are commonly used as proxy indices of desaturation and elongation but do not directly reflect enzyme activity.<br><br>METHODS: In this cross-sectional study, plasma and erythrocyte fatty acid profiles were measured by gas chromatography-flame ionization detection (GC-FID) in patients (n = 1277) from a metabolic disease clinic in Brandenburg, Germany. Participants were stratified into five age groups (&#x2264; 34, 35-44, 45-54, 55-64, &#x2265; 65 years) and differences between groups were assessed using statistical tests.<br><br>RESULTS: Participants aged &#x2265; 65 years had higher total omega-3 (n-3) and lower total omega-6 (n-6) PUFA levels in both matrices. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) increased with age, whereas linoleic acid (LA) and dihomo-gamma-linolenic acid (DGLA) decreased. Ratio-based indices showed consistent age associations. The delta-5-desaturase index (D5D) and arachidonic acid (AA)/LA ratio were positively associated with age, while elongation of very long chain fatty acids (ELOVL)2 and ELOVL6 were inversely associated.<br><br>DISCUSSION: Overall, blood PUFA profiles and multiple ratio-based indices showed consistent, age-related trends in this clinical cohort. Interpretation is limited by the cross-sectional design and the lack of key determinants of PUFA status (e.g., diet, clinical covariates, genetic information and gut/microbiome factors). Nevertheless, these results underscore age-related shifts in PUFA composition and enzymatic proxy indices, providing new insights into lipid metabolism across the lifespan.},
}
@article {pmid42038454,
year = {2026},
author = {Therdtatha, P and Buakhao, T and Kullawong, N and Jinatham, V and Vichasilp, T and Nakayama, J and Popluechai, S},
title = {Associations among diet, gut microbiota, and hypertension: a cross-sectional study in Thai subjects.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21135},
pmid = {42038454},
issn = {2167-8359},
mesh = {Humans ; *Gastrointestinal Microbiome ; Thailand/epidemiology ; Male ; Cross-Sectional Studies ; *Hypertension/microbiology/epidemiology ; Female ; Middle Aged ; *Diet ; Adult ; Feces/microbiology ; Aged ; Feeding Behavior ; Southeast Asian People ; },
abstract = {Background: Although the link between the gut microbiota and hypertension has been investigated, its specific role in the increasing prevalence of this disease in Thailand, influenced by changing dietary patterns, remains unexplored. This cohort study investigated the association between the gut microbiome and hypertension-related dietary habits in Thai subjects. Methods: The fecal microbiomes of 31 Thai adults, including non-hypertensive (NHT, n = 12) and hypertensive (HT, n = 19) subjects, were grouped and analyzed according to their dietary and medical records. Alpha and beta diversity analyses were performed to determine significant differences (p < 0.05) in microbial diversity between groups. Variations in the microbiome profiles were identified using Linear Discriminant Analysis Effect Size (LEfSe) based on a linear discriminant analysis score > 2.0 (p < 0.05). Multiple Factor Analysis (MFA) was employed to integrate anthropometric data, dietary consumption, and gut microbiome, enabling the visualization of features driving overall variation. Functional profiles of the gut microbiome were predicted using PICRUSt2 based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) categories. Differential abundance and microbial-functional associations were evaluated using ALDEx2 and HAllA, respectively. Results: Our exploratory analysis suggests that hypertension-related differences are strongly associated with host factors (age and clinical profiles) rather than diet or microbial composition. Key taxonomic signatures of the HT group include the expansion of Phascolarctobacterium and depletion of Alistipes, which relates to anthropometric and blood profiles. Functional analysis revealed a profound restructuring of the gut ecosystem in the HT group, characterized by functional dysbiosis where microbial-functional association patterns shift distinct from changes abundance. Conclusions: These findings suggest that the gut microbiota's potential role in hypertension may involve altered interaction dynamics, which may provide a new perspective for targeted interventions in the Thai population.},
}
@article {pmid42038696,
year = {2026},
author = {Cao, Y and Wang, Z and Xue, J and Wang, L and Qin, W and Sun, Q and Chang, J},
title = {Chronic Kidney disease and cognitive frailty in aging: molecular crosstalk and clinical implications.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1778574},
pmid = {42038696},
issn = {1663-4365},
abstract = {BACKGROUND: Chronic kidney disease (CKD) and cognitive frailty frequently co-occur in older adults, compounding adverse health outcomes and placing substantial strain on healthcare systems.<br><br>SUMMARY: This review outlines the molecular pathways that link CKD to cognitive decline, including chronic inflammation, oxidative stress, vascular dysfunction, hormonal dysregulation, and interactions along the gut-kidney-brain axis. Recent advances in neuroimaging offer objective biomarkers of brain atrophy, white matter injury, and disrupted functional connectivity.<br><br>KEY MESSAGES: Multi-omics and single-cell technologies are uncovering cell-type-specific mechanisms and candidate biomarkers, paving the way for precision medicine approaches. Emerging strategies include integrated geriatric-nephrology care models and targeted interventions, such as SGLT2 inhibitors, IL-6 antagonists, microbiome modulation, and structured exercise programs. Bioengineering and artificial intelligence now enable the integration of multimodal data to support risk prediction, disease monitoring, and individualized therapeutic planning. Future priorities should focus on longitudinal cohort studies, interventional trials with cognitive endpoints, and the development of rigorously validated AI-driven predictive models. Effectively addressing CKD-related cognitive frailty will require translating molecular insights into clinical practice to mitigate vulnerability in aging populations.},
}
@article {pmid42038770,
year = {2026},
author = {Abdelouahab, M and Idrissa, D},
title = {Pangenomics-Driven Reverse Vaccinology for the Discovery of New Vaccine Candidates Against Bordetella pertussis.},
journal = {Bioinformatics and biology insights},
volume = {20},
number = {},
pages = {11779322261442522},
pmid = {42038770},
issn = {1177-9322},
abstract = {Despite widespread vaccination, pertussis resurgence persists due to waning immunity and emerging resistant strains in Bordetella pertussis. This study employs a pangenomics-driven reverse vaccinology approach to identify novel vaccine candidates. Analyzing 160 genomes revealed a closed pan-genome, with approximately 60% conserved genes, including 3389 core genes of which 1312 participate in pathogen-specific pathways. Non-homologous proteins were identified by comparison against human and microbiome proteomes, yielding 205 candidates. Essentiality assessment via the Database of Essential Genes (DEG) refined this to 63 non-homologous essential proteins. A multi-criteria selection process evaluated purifiability based on physicochemical properties and transmembrane helices, accessibility (extracellular or secreted localization), and immunogenicity through antigenicity prediction and B-cell epitope mapping. This pipeline culminated in 11 high-potential vaccine targets. The in silico methodology offers rapidity, cost-effectiveness, and reduced side effects compared with conventional vaccinology, though experimental validation is essential for confirmation.},
}
@article {pmid42038981,
year = {2026},
author = {Wu, L and Tu, Y and Xiao, S and Zeng, J and Sun, G and Li, Y},
title = {Recent perspectives on precision-targeting therapy against oral biofilm.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2662093},
pmid = {42038981},
issn = {2000-2297},
abstract = {BACKGROUND: Oral biofilm-derived diseases pose a significant clinical challenge due to their persistent nature and increasing drug resistance, contributing to a substantial global economic burden. Conventional treatments-such as mechanical debridement, antiseptic agents, and laser therapy-though partially effective, often lack specificity, resulting in non-targeted microbial killing and disruption of the ecological balance.<br><br>OBJECTIVE: This review provides an updated overview of the application of precision antimicrobial therapies against oral biofilms, with a particular focus on pH-responsive materials and bacteriophage-based strategies.<br><br>DESIGN: A comprehensive literature search was conducted across PubMed and Google Scholar databases from January 2016 to January 2026. A total of 84 full-text articles were included for qualitative synthesis.<br><br>RESULTS: The collective findings demonstrate that multiple precision-targeting strategies-spanning from bacteriophage therapy to pH-responsive antimicrobial materials-exhibit distinct advantages in combating oral biofilms.<br><br>CONCLUSION: The common core principle underpinning these approaches lies in their 'precision-targeting' capability: the ability to identify and interfere with specific targets or biological processes. This attribute not only significantly enhances therapeutic efficacy but also paves the way for developing personalized, microbiome-preserving strategies for the prevention and management of oral diseases.},
}
@article {pmid42039085,
year = {2026},
author = {Nuccio, DA and Grippo, A and Singh, P},
title = {The prairie vole gut-brain-microbiota-axis: a narrative review.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e4},
pmid = {42039085},
issn = {2632-2897},
abstract = {The microbiota-gut-brain axis (MGBA) has garnered considerable attention for its role in health, disease, and higher psychological processes. One area of particular importance is the relationship between the MGBA and stress. Although numerous animal models are suitable for research on stress, the number suitable for research on the impact of social stressors with translatability to humans is limited. The prairie vole is regarded as an ideal organism for probing the impact of social stress, as these animals not only exhibit social behaviours rare in mammals but also lack many drawbacks that come with using non-human primates. Moreover, the neurophysiological basis of their social behaviours is well characterized, and numerous studies have examined the impact of social stress, particularly social isolation, on these animals. However, only a limited number of studies have examined the prairie vole gastrointestinal system, intestinal microbiome, or MGBA. Consequently, this leaves ample opportunity for future research. In this review article, we summarize basic aspects of prairie vole ecology, behaviour, and neurophysiology, then review the limited but valuable body of research examining the gastrointestinal system and microbiome of prairie voles. Additionally, we note potential challenges and opportunities for future MGBA research utilizing prairie voles.},
}
@article {pmid42039182,
year = {2026},
author = {Lap, CR and van Houten, M and Bogaert, D and Biesbroek, G},
title = {A perfect storm: the immunological and pathophysiological landscape of pediatric post-COVID-19 condition.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1794596},
pmid = {42039182},
issn = {1664-3224},
mesh = {Humans ; *COVID-19/immunology/complications/virology/epidemiology ; *SARS-CoV-2/immunology ; Child ; Gastrointestinal Microbiome/immunology ; Dysbiosis/immunology ; Adolescent ; Immunity, Innate ; Post-Acute COVID-19 Syndrome ; },
abstract = {Pediatric Post-COVID Condition (PPCC) represents a significant and complex long-term sequela of SARS-CoV-2 infection, affecting a subset of children and adolescents even after mild acute disease. While acute COVID-19 is generally milder in children due to a more robust innate immune response, the mechanisms driving the persistence of symptoms in PPCC remain incompletely understood and likely multifactorial. This narrative review synthesizes current epidemiological data and explores the "perfect storm" of immunological and pathophysiological alterations underpinning the condition. We examine critical hypotheses including a dysregulated immune response characterized by altered T-cell subsets, monocyte activation, and autoantibody production. We discuss the potential role of persistent SARS-CoV-2 viral reservoirs in "sanctuary sites" like the gastrointestinal tract and the reactivation of latent viruses such as Epstein-Barr virus (EBV). Furthermore, the review details downstream pathogenic pathways, including vascular endothelial inflammation (thrombo-inflammation), neuroinflammation, and metabolic dysfunctions affecting the mitochondria and tryptophan-kynurenine pathway. Finally, we address the role of microbiome dysbiosis in perpetuating systemic inflammation and the gut-lung axis dysfunction. Given the heterogeneity of clinical presentations, we conclude that PPCC is likely a syndrome of overlapping biological phenotypes. Future research must prioritize identifying these specific biological endotypes to develop targeted diagnostic and therapeutic strategies for the pediatric population.},
}
@article {pmid42039195,
year = {2026},
author = {Liu, Y and Liao, X and Chen, Q and Wang, H and Dai, H},
title = {What is the impact of the virome and mycobiome on female reproductive tract health? A systematic scoping review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1749584},
pmid = {42039195},
issn = {1664-3224},
mesh = {Female ; Humans ; *Virome ; *Mycobiome ; *Vaginosis, Bacterial/microbiology/virology ; *Microbiota ; Papillomavirus Infections/microbiology/virology ; Vagina/microbiology/virology ; *Reproductive Health ; *Genitalia, Female/microbiology/virology ; Bacteriophages ; },
abstract = {BACKGROUND: Traditional research on the female reproductive tract (FRT) microbiome has focused on the dominance of bacteria, particularly Lactobacillus, as a marker of health. This bacteriocentric paradigm, however, cannot fully explain clinical enigmas like the high recurrence of bacterial vaginosis (BV) or the persistence of HPV infection. This review introduces a new pan-microbiome framework that highlights the overlooked roles of the virome and mycobiome as the ecosystem's neglected components.<br><br>METHODS: We conducted a systematic scoping review following the PRISMA-ScR guidelines. We searched PubMed, Embase, and Web of Science databases for studies published up to October 2025. Inclusion criteria focused on original research and metagenomic studies examining the female reproductive tract (FRT) virome, mycobiome, and bacteriome, specifically their interactions and clinical associations with bacterial vaginosis (BV) and HPV persistence. Data were extracted and synthesized to evaluate the pan-microbiome framework.<br><br>RESULTS: The virome and mycobiome, despite their low biomass, are increasingly recognized as potential ecosystem modulators. Bacteriophages, for instance, are proposed to act as community "modulators," either through lytic cycles that maintain bacterial diversity or lysogenic cycles that may contribute to stabilizing pathogenic biofilms in dysbiosis like BV by introducing virulence genes. Similarly, fungi like Candida can transition from harmless commensals to pathogens when the protective bacterial balance is disturbed.<br><br>CONCLUSION: FRT health is an emergent property of the complex interactions among bacteria, viruses, and fungi. A comprehensive understanding requires a pan-microbiome perspective. Future therapeutic strategies should move beyond a "one-bug, one-drug" approach toward "ecosystem restoration," using targeted methods like phage therapy or vaginal microbiota transplantation to attempt to restore the balance of the entire microbial community.},
}
@article {pmid42039264,
year = {2026},
author = {Yu, L and Zhang, H and Shi, C and Zhou, Q and Li, J and Lu, B and Lu, H and Jin, T and Zhu, Y and Zuo, T and Xu, M and Su, M and Zhang, Y and Shubhra, QTH and Hu, X and Deng, H and Cai, X},
title = {Targeted intestinal barrier repair via probiotic-derived engineered outer membrane vesicles: A 3A1M strategy with antioxidant, anti-inflammatory, anti-ferroptotic, and microbiome modulation effects.},
journal = {Acta pharmaceutica Sinica. B},
volume = {16},
number = {4},
pages = {2527-2552},
pmid = {42039264},
issn = {2211-3835},
abstract = {Intestinal barrier disruption, driven by oxidative stress, ferroptosis, immune imbalance, and gut microbiota dysbiosis, plays a crucial role in inflammatory bowel disease (IBD) pathogenesis. Current treatments are often ineffective and cause side effects, emphasizing the need for novel therapies. Here, we have developed an engineered probiotic-derived outer membrane vesicle (OMV), GDO@CM, combining antioxidant gallic acid (GA) and anti-inflammatory H2S for targeted intestinal barrier repair. Constructed from Escherichia coli Nissle 1917 (EcN)-derived OMVs, GA and diallyl trisulfide (DATS) are incorporated into the hydrophilic inner cavity and lipid bilayer, respectively, while mannose-decorated chitosan (CM) is electrostatically attached to the OMVs surface, enhancing stability and enabling targeted delivery to damaged colonic lesions. GDO@CM efficiently enters activated immune cells and epithelial cells, where GA scavenges reactive oxygen species and inhibits ferroptosis, while H2S amplifies anti-inflammatory effects. OMVs further synergize with GA and DATS to suppress pathogenic bacteria. These combined actions facilitate effective barrier repair and alleviate IBD symptoms. Single-cell RNA sequencing reveals that GDO@CM reduces inflammation, increases the proportion of reparative M2 macrophages and intestinal stem cells, and promotes epithelial cell proliferation via the APP/CD74 axis. Our findings establish GDO@CM as a promising multi-target therapeutic for IBD, offering a novel strategy for intestinal barrier restoration.},
}
@article {pmid42039389,
year = {2026},
author = {Li, W and Zarek, CM and Wang, H and Gan, S and Sabaiefard, P and Del Valle, P and Kim, J and Poulides, N and Coughlin, LA and Lichterman, JN and Zhang, C and Chiu, RS and Srinivasan, T and Velasquez, MJ and Raman, I and Maddox, VJ and McDonald, J and Kittler, R and Raj, P and Li, XV and Zhan, X and Liao, C and Xavier, JB and Koh, AY},
title = {A microbiota-derived bile acid overcomes antibiotic-induced hyporesponsiveness to immune checkpoint therapy by enhancing CD8 [+] T cell antitumor immunity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.15.718788},
pmid = {42039389},
issn = {2692-8205},
abstract = {UNLABELLED: Gut microbiota are critical determinants of effective immune checkpoint therapy (ICT), yet the microbial mediators and host mechanisms that enhance antitumor immunity remain poorly understood. Here, we identify the microbiota-derived bile acid taurodeoxycholic acid (TDCA) as a metabolite associated with immune checkpoint therapy (ICT) response. TDCA administration alone is sufficient to overcome antibiotic-induced ICT hyporesponsiveness across multiple murine tumor models. Mechanistically, TDCA directly enhances CD8[+] T cell-mediated antitumor immunity, increasing cytotoxicity. These effects required signaling through the bile acid receptor TGR5. Together, these findings reveal TDCA as a gut microbial metabolite that restores ICT efficacy after antibiotic disruption by directly augmenting CD8[+] T cell anti-tumor activity. This work supports metabolite replacement as a therapeutic strategy to mitigate antibiotic-associated loss of cancer immunotherapy response.<br><br>SIGNIFICANCE: TDCA is a microbiota-derived metabolite that restores immune checkpoint therapy efficacy after antibiotic disruption by directly enhancing CD8&#x207a; T-cell-mediated anti-tumor immunity through bile acid receptor TGR5 signaling. Our findings suggest that supplementation with defined microbial metabolites can mitigate antibiotic-associated loss of immunotherapy response without requiring broader microbiome reconstitution.},
}
@article {pmid42039437,
year = {2026},
author = {Flamholz, ZN and De Los Santos, J and Ireland, K and Keenan, J and Kazmi, JS and Mahant, AM and Correa, A and Frenette, PS and Herold, BC and Manwani, D and Kelly, L},
title = {Distinct prokaryotic gut microbiome and proviral-immune axes of pathophysiology in Sickle Cell Disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.13.718288},
pmid = {42039437},
issn = {2692-8205},
abstract = {Sickle cell disease (SCD) is a chronic, inherited condition rising across the globe. Prior studies revealed a direct link between the gut microbiome and disease micropathology via aged-like (ANs) neutrophils in mouse models. In SCD patients community-level shifts in the gut microbiome included decreases in diversity and the Firmicutes/Bacteroides (F:B) ratio, coupled to a loss of short chain fatty acid producing microbes and a shift to non-canonical butyrate production and aerobic fatty acid oxidation pathways. ANs and the proviral microbiome associate with multiple blood cytokines, while bacterial gut microbiome features largely do not. Prophages depleted of genes related to lysis, transcriptional regulation, and host takeover were enriched in SCD patient guts, pointing to domestication of these elements, and 25% of prophages were shared at high identity between study patients. In sum, we identify a viral-immune axis in SCD pathophysiology and targetable functional alterations to the gut microbiome in a heterogeneous chronic disease both affected by and effecting microbiome composition and function.},
}
@article {pmid42039480,
year = {2026},
author = {Liu, J and De Paolis Kaluza, MC and Bromberg, Y},
title = {16S rRNA k-mer composition encodes microbial functional potential.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.718937},
pmid = {42039480},
issn = {2692-8205},
abstract = {16S rRNA amplicon sequencing is widely used to profile microbiome taxonomic composition and functional potential. Most 16S rRNA-based analysis methods depend on comparing sequenced reads against reference marker genes from previously characterized organisms. Thus, method accuracy declines in environments dominated by uncharacterized microbes. We uncovered a direct link between 16S rRNA and genome-encoded functions. Using fully sequenced bacterial genomes, we show that (i) whole-genome k-mer composition is predictive of functions encoded in the genome and (ii) 16S rRNA k-mer profiles reflect their source genome k-mer compositions. Leveraging these relationships, we developed embeRNA, a neural network-based framework that predicts functions directly from 16S rRNA k-mer embeddings, without taxonomy assignment or phylogenetic placement. Furthermore, by producing per-function probability scores rather than categorical assignments, embeRNA allows users to adapt decision thresholds to match study goals and sample characteristics, e.g. balancing precision vs. recall or accounting for community novelty. We trained embeRNA on a large collection of bacterial function-omes and evaluated it using a stringent "novel microbes" benchmark, where all test 16S rRNA sequences were dissimilar to those seen in training (all <97% identical). On this test set of phylogenetically novel organisms, embeRNA outperformed reference-based methods overall and achieved significantly better performance for the "hard to label" set of functions. In testing on soil metagenomes with paired 16S rRNA amplicon and whole metagenome shotgun (WMS) sequencing data, embeRNA recovered most WMS-inferred functions and yielded abundance profiles strongly correlated with WMS results. Together, our results indicate that 16S rRNA k-mer composition carries substantial functional signal and that 16S amplicon data can be used to complement WMS-based inference to broaden functional characterization of microbiomes, particularly in understudied environments.},
}
@article {pmid42039490,
year = {2026},
author = {Nagai, M and Band, V and Chi, L and Smelkinson, M and Schwarz, B and Brandes, NT and Burns, A and Perez-Chaparro, PJ and McCauley, KE and Corral, D and Bouladoux, N and Link, VM and Zheng, L and Constantinides, MG and Otto, M and Moutsopoulos, NM and Belkaid, Y},
title = {Ketogenic diet synergistic reprogramming of both host and microbiome promotes tissue regeneration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.11.717958},
pmid = {42039490},
issn = {2692-8205},
abstract = {Nutrition influences host physiological processes, yet how diets reshape host physiology, microbial functions, or host-microbe interactions to promote regeneration remains poorly explored. Here, we show that a ketogenic diet (KD), enriched in fats and low in carbohydrates, reprograms both skin microbial and immune functions to promote tissue repair. KD enhances IL-17A activity in γδ T cells and mucosal-associated invariant T (MAIT) cells, accelerating tissue repair, while KD-induced skin lipidomic alterations enhance both the abundance and metabolic output of Staphylococcus epidermidis . Metatranscriptomic and lipidomic analyses revealed increased riboflavin biosynthesis and sphingomyelinase (Sph)-dependent ceramide production in S. epidermidis under KD conditions. Genetic depletion of microbial ribD, a key enzyme for riboflavin biosynthesis, or of sph compromised the ability of the bacteria to promote tissue repair. Thus, host nutritional status drives tissue regeneration by synergistically rewiring host and microbial functions, providing new insights into how diet can be harnessed to regulate host physiology.},
}
@article {pmid42039586,
year = {2026},
author = {Ghosh, S and Koontz, V and Xin, Y and Bammidi, S and Meyer, D and Wang, H and Babu, VS and Dutta, P and Cherukaraveedu, D and Mohanakrishnan, SA and Mondal, AK and Das, J and Nguyen, J and Soundararajan, A and Adekale, IA and Bhaumik, D and Hose, S and Rowan, S and Pattabiraman, PP and Kannan, RM and Handa, JT and Yi, J and Sripathi, SR and Qian, J and Sinha, D},
title = {Gut-derived metabolic reprogramming drives immune aging and tissue degeneration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.14.718497},
pmid = {42039586},
issn = {2692-8205},
abstract = {Aging is characterized by changes in gut microbiome, metabolic imbalance and chronic inflammation, yet how these processes integrate to drive tissue degeneration remains poorly defined. Using age-related macular degeneration (AMD) as a model of tissue aging, we identify a diet-induced metabolic-immune axis that promotes systemic and retinal degeneration. In mice, a high-fat, cholesterol-enriched (HFC) diet induced perturbations in the gut structural integrity and microbiome repertoire, as well as systemic metabolic aging signatures, prominently marked by reduced circulating histidine. Plasma histidine levels were similarly decreased in AMD patients and inversely correlated with body mass index (BMI) in control donors. These diet-induced gut microbiome changes and subsequent metabolic alterations promoted peripheral innate immune reprogramming, with expansion of inflammatory neutrophils and monocytes that infiltrated the outer retina in a mouse model. Mechanistically, the gut-derived IGF1R/AKT2 signaling acts as a central regulator of global epigenetic remodeling and systemic immune aging under high-fat conditions in C. elegans . In a mouse model with an age-dependent dry AMD-like pathology, distinct retinal pigment epithelium (RPE) subpopulations exhibited downregulation of the histidine transporter SLC7A5, linking metabolic stress to activation of MIF/CD74-dependent inflammatory signaling between RPE and infiltrating immune cells. Histidine supplementation or AKT2 phospho-state modulation attenuated systemic immune activation and rescued retinal degeneration. These findings identify histidine-axis dysregulation as a mechanistic bridge between diet-induced microbiome changes, metabolic stress, immune aging, and retinal degeneration.},
}
@article {pmid42039609,
year = {2026},
author = {Maldonado Pereira, L and Mutawi, TMA and Singh, A and Sanderson, B and Rekowski, MJ and Barnaba, C and Medina Meza, IG},
title = {Dietary Oxysterols Reprogram Hepatic Lipid Metabolism and Reshape the Gut Metabolome-Microbiome Interface.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.12.717948},
pmid = {42039609},
issn = {2692-8205},
abstract = {Dietary oxysterols are biologically active cholesterol oxidation products ubiquitous in Western diets, yet their systemic effects on host metabolism and the gut microbiome remain largely unexplored. Here, we employed an integrated multi-omics approach - shotgun metagenomics, quantitative proteomics, untargeted metabolomics, and bulk RNA-seq - to characterize the impact of DOxS exposure on the gut-liver axis in rats fed a Western diet (WD vs. WD-DOxS). Hepatic proteomics revealed near-complete suppression of the mevalonate/cholesterol biosynthesis pathway, particularly in males, while de novo lipogenesis enzymes (Scd1, Fasn, Plin2) were paradoxically upregulated, consistent with dual oxysterol signaling through SREBP inhibition and LXR activation. Bile acid synthesis was concurrently suppressed, confirmed by metabolomics. Strikingly, RNA-seq across liver, heart, and brain detected virtually no differentially expressed genes, establishing that DOxS act predominantly through post-transcriptional mechanisms. In the gut, DOxS increased microbial α-diversity while depleting Limosilactobacillus reuteri, with concomitant loss of the barrier-protective metabolite 3-indoleacrylic acid. Tissue-specific responses were widespread, with liver and colon frequently mounting opposing metabolic and immune responses to the same dietary challenge. Cross-omics integration revealed convergent microbiome-metabolite axes connecting microbial remodeling to both hepatic lipid reprogramming and colonic barrier disruption. These findings reposition dietary oxysterols from food-quality markers to active modulators of the gut-liver axis, with implications for metabolic disease and intestinal barrier integrity.},
}
@article {pmid42039633,
year = {2026},
author = {Basting, CM and Anderson, J and Escandón, K and Wieking, G and Guerrero, C and Reichel, J and Cromarty, R and Swanson, E and Schroeder, T and Creagan, E and Barrett, M and Funderburg, N and Hunt, P and Graham, M and Avila-Rios, S and Salgado, G and Schacker, TW and Klatt, NR},
title = {Multi-omics links microbial dysbiosis, systemic inflammation and metabolomic disruptions to SNAE risk in treated HIV.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.09.717347},
pmid = {42039633},
issn = {2692-8205},
abstract = {Serious non-AIDS events (SNAEs), including non-AIDS malignancies, cardiovascular disease, and hepatic complications, remain major causes of mortality in treated HIV infection. These outcomes are driven by persistent immune activation, systemic inflammation, and metabolic dysfunction despite effective viral suppression with antiretroviral therapy (ART). To investigate mechanisms underlying SNAE pathogenesis, we performed a cross-site multi-omic analysis integrating plasma proteins, plasma metabolites, and mucosal microbiomes (ileum and rectum) in 82 ART-treated people with HIV (PWH) and 10 people without HIV (PWoH) from the United States and Mexico. Geography was the dominant source of variation, particularly across lipid classes. However, individuals at high risk for SNAEs, defined by low CD4 T cell counts and low CD4/CD8 ratios, shared a consistent signature of systemic inflammation, mitochondrial dysfunction, and microbial dysbiosis including elevated plasma IL-6, ω-oxidation products (adipic and suberic acids), and depletion of short-chain fatty acid-producing commensals in the gut mucosa, including Akkermansia muciniphila , Bacteroides uniformis , and Ruminococcus . Notably, A. muciniphila abundance correlated with lower IL-6 levels, fewer HIV RNA-producing cells in lymph nodes, and higher CD4/CD8 ratios. Together, these findings identify a shared inflammatory and metabolic phenotype in PWH and implicate A. muciniphila as a potential microbiome-based target to mitigate immune activation and SNAE risk in treated HIV.},
}
@article {pmid42039744,
year = {2026},
author = {Stavart, C and Gohy, S and Lebeer, S and Van Bambeke, F and Crabbé, A and Pilette, C},
title = {Crosstalk between the microbiome and the mucosal immunoglobulin A system in the lung, in health and disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1796523},
pmid = {42039744},
issn = {2235-2988},
mesh = {Humans ; *Microbiota/immunology ; *Lung/immunology/microbiology ; *Immunoglobulin A/immunology ; Homeostasis ; Animals ; *Immunity, Mucosal ; *Lung Diseases/immunology/microbiology ; *Respiratory Mucosa/immunology/microbiology ; *Immunoglobulin A, Secretory/immunology ; },
abstract = {The lung, and more specifically the airway epithelium, is continuously exposed to a wide range of inhaled environmental agents. Acting as a frontline physical and biochemical barrier, the airway epithelium orchestrates early host defense mechanisms, among which immunoglobulin A (IgA) plays a central role. Long considered sterile, the healthy lung is now recognized as a complex mucosal ecosystem harboring diverse and dynamic microbial communities, including bacteria, fungi, viruses, and archaea. Although the lung microbiome is generally transient and low in biomass, accumulating evidence suggests that it contributes to pulmonary homeostasis by supporting immune system maturation, preserving structural tissue integrity, and limiting pathogen colonization. How immune homeostasis is maintained in this constantly challenged environment remains however a central and largely unanswered question. This review synthesizes current state-of-the-art knowledge on the origin, composition, and functional determinants of the lung microbiome, with a specific focus on its bidirectional interplay with secretory IgA. We discuss microbiota-specific IgA responses, factors influencing IgA-microbiome interactions, and how these processes are disrupted in chronic and inflammatory lung diseases. Finally, we highlight major knowledge gaps and explore emerging therapeutic perspectives targeting IgA-microbiome crosstalk to restore pulmonary immune homeostasis.},
}
@article {pmid42039747,
year = {2026},
author = {Huang, S and Xu, X},
title = {Editorial: Perspectives in extra-intestinal microbiome 2025.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1824939},
doi = {10.3389/fcimb.2026.1824939},
pmid = {42039747},
issn = {2235-2988},
}
@article {pmid42039766,
year = {2026},
author = {Rehman, A and Ali, N and Tariq, MR and Ali, SW and Mushtaq, A and Safdar, W and Yusuf, AM},
title = {The Role of Gut Microbiome in Obesity and Weight Management: A Review of Current Evidence and Future Directions.},
journal = {Food science &amp; nutrition},
volume = {14},
number = {4},
pages = {e71801},
pmid = {42039766},
issn = {2048-7177},
abstract = {Obesity has become an emerging challenge all over the world. In 2022, one in eight people was living with obesity. It is most common in adults and children. It is due to an imbalance between energy consumption and utilization. However, the human gut microbiome regulates energy metabolism, a complex ecosystem of microorganisms residing in the gastrointestinal tract, which stimulates hormone production, produces various metabolites, and interacts with brain responses involved in maintaining energy balance in the body. Dysbiosis, characterized by an imbalance in microbial composition, has been linked to increased energy harvesting, impaired bile acid metabolism, chronic low-grade inflammation, impaired appetite regulation, and excessive intake, ultimately leading to obesity. The primary focus of this review is to discuss the current understanding of the roles of diet, exercise, pharmacological agents, and surgery in shaping gut microbial communities and host physiology. Dietary interventions, such as the use of probiotics, prebiotics, high-fiber diets, ketogenic diets, and intermittent fasting, modulate microbial metabolites like short-chain fatty acids, which play a crucial role in regulating energy balance and inflammation, thereby contributing to the prevention of weight gain. Physical activity induces positive changes in gut microbiota, enhancing metabolic adaptability and supporting immune system regulation. Pharmacological treatments, especially anti-obesity and anti-diabetic drugs, have both direct and microbiota-mediated effects on weight and glucose metabolism. Similarly, surgery leads to significant changes in gut microbiota, which play a role in long-term enhancements in metabolic health. So, this review aims to discuss various weight management approaches targeting the gut microbiome, drawing on current studies. However, these interventions require further investigation for their effectiveness.},
}
@article {pmid42039771,
year = {2026},
author = {Miao, B and Zou, X and Yang, S and Zhou, Z and Geng, Y and Zhang, S and Gong, J and Ran, M},
title = {Alterations in the Hair Follicle Bacteriome and Mycobiome in Androgenetic Alopecia: A Cross-Sectional Study of 72 Patients and 24 Healthy Controls.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {590873},
pmid = {42039771},
issn = {1178-7015},
abstract = {PURPOSE: Androgenetic alopecia (AGA) is characterized by perifollicular micro-inflammation, although its precise trigger remains elusive. Given that the hair follicle harbors a distinct microbiota which may modulate local immune responses, this study aimed to comprehensively profile the bacterial and fungal microbiome within the deep hair follicles of AGA patients versus healthy controls, and to evaluate the influence of disease severity, age, sex, and geographical environment.<br><br>PATIENTS AND METHODS: We recruited 96 subjects (72 AGA patients and 24&#xa0;healthy controls), collecting a total of 192 plucked hair follicle samples from the vertex and occipital scalp. Bacterial 16S rRNA (V3-V4) and fungal ITS regions were sequenced using the Illumina HiSeq platform. Bioinformatics pipelines were employed to analyze &#x3b1;- and &#x3b2;-diversity, as well as taxonomic composition, across multiple stratifications: disease stage, scalp region, age, sex, and geographical location.<br><br>RESULTS: Bacterial community structure showed relative stability between groups. In contrast, fungal communities were markedly dysbiotic in AGA. A key finding was the significant depletion of the commensal yeast Malassezia in AGA follicles compared to controls (p < 0.01). Conversely, opportunistic taxa such as Thermomyces and Bifidobacterium were enriched in advanced disease stages. Notably, microbial &#x3b1;-diversity increased with both disease severity and age, indicating a disruption of the follicular niche ("niche collapse"). Male AGA patients exhibited distinct fungal shifts compared to females, and geographical location significantly shaped the follicular microbiome in patients but not in healthy controls.<br><br>CONCLUSION: Androgenetic alopecia involves fungal dysbiosis with loss of commensal Malassezia and gain of opportunistic microbes. Driven by host and environmental factors, this reframes AGA as an ecological imbalance, opening avenues for microbiome-targeted therapies.},
}
@article {pmid42039799,
year = {2026},
author = {Chigozie, VU and Esimone, CO},
title = {Bacterial secondary metabolites as resistance-modifying adjuvants: microbial origins, molecular mechanisms, and translational relevance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779022},
pmid = {42039799},
issn = {1664-302X},
abstract = {The accelerating crisis of antimicrobial resistance (AMR) necessitates strategies that extend beyond the continual discovery of new conventional antibiotics. Bacterial secondary metabolites, historically valued as sources of antimicrobial scaffolds, are increasingly recognized for their roles as resistance-modifying and anti-virulence agents. This review synthesizes key advances from 2020 to 2025 that reposition bacterial secondary metabolites as integral components of next-phase AMR intervention strategies. We examine their chemical and biosynthetic diversity, ecological functions, and molecular mechanisms of action, including efflux pump inhibition, β-lactamase suppression, interference with ribosomal protection, and disruption of biofilms and quorum-sensing networks. Mechanistic and evolutionary analyses are integrated to explain why many metabolites impose higher barriers to resistance development than single-target antibiotics. We further discuss contemporary discovery and optimization pipelines encompassing genome mining, multi-omics approaches, synthetic biology, and AI-assisted structure-activity modeling. Translational considerations are critically evaluated, with emphasis on pharmacokinetic and pharmacodynamic constraints, rational combination therapy design, preclinical validation, and emerging development pipelines. Regulatory, manufacturing, and commercialization challenges are addressed alongside opportunities enabled by nanocarrier delivery systems, microbiome-informed strategies, and personalized medicine. Overall, this review highlights bacterial secondary metabolites as evolution-resilient anti-resistance modalities capable of restoring and extending the efficacy of existing antibiotics, offering a pragmatic and mechanistically grounded path forward in combating AMR.},
}
@article {pmid41840402,
year = {2026},
author = {Krupa-Kozak, U and Owczarczyk-Saczonek, A and Lange, E and Starowicz, M and Kopcewicz, M and Kęszycka, P and Czerwińska, J and Rybak-d'Obyrn, J and Oczkowski, M and De Biasi, J and Bieglecka, K and Kleniewska, M and Bączek, N and Małkowska, J and Pastuszak, K},
title = {INulin-type β-fructans supplementation to modulate gut microbiota and assessment of its effects on health status and GUT-SKIN axis parameters in patients with psoriasis (INGUTSKIN): the 8-week, randomised, double-blind, placebo-controlled clinical study protocol.},
journal = {Nutrition journal},
volume = {25},
number = {1},
pages = {},
pmid = {41840402},
issn = {1475-2891},
support = {OPUS project No 2022/45/B/NZ9/03004//Narodowe Centrum Nauki/ ; },
abstract = {BACKGROUND: A strong, bidirectional association exists between gastrointestinal health and skin homeostasis in many chronic skin inflammations, including psoriasis (PS). It is postulated that, apart from genetic predisposition, the rise of local and systemic immune response in PS could be a consequence of intestinal dysbiosis associated with increased intestinal permeability. We hypothesised that restoring gut microbiome homeostasis and proper functioning of the intestinal barrier in PS patients would alleviate the inflammatory symptoms and severity of the skin lesions. The study aims to determine the effect of chicory-derived inulin-type β-fructans (ITFs) on health-related parameters in mild PS patients through molecular analysis of gut microbiota characteristics and assessment of a wide spectrum of biomarkers of the gut-skin axis.<br><br>METHODS: The randomised, placebo-controlled clinical trial (RCT) with prebiotic intervention is proposed. Adult mild PS patients (Psoriasis Area and Severity Index; PASI&#x2009;<&#x2009;10) with a body mass index (BMI)&#x2009;<&#x2009;30&#xa0;kg/m[2] following an omnivore diet will be enrolled into the trial and randomized to one of two groups: prebiotic (receiving 15&#xa0;g/per day of ITFs) or placebo (receiving 15&#xa0;g/per day of maltodextrin) for 8 weeks in a double-blind manner. Body composition, clinical parameters, nutritional status, quality of life, immune and inflammatory parameters, intestinal barrier permeability, characteristics of faecal bacteria, and metabolic dysfunction markers will be determined at baseline and after supplementation. Compliance and adverse reactions will be evaluated.<br><br>DISCUSSION: The dysregulation in intestinal microbiota-host interplay is connected with the development of many chronic skin inflammations, including PS. A proper diet is a relatively easy-modifiable factor that may influence the course of PS treatment. Among dietary components, prebiotics have garnered our interest as ingredients with a proven ability to enhance host health by modulating the gut microbiota. With the proposed RCT, we will determine the impact of ITFs on gut microbiota characteristics and evaluate whether this ITFs-induced microbiota modulation is an effective method to alleviate inflammation and reduce the severity of skin lesions in PS. We expect that the RCT results will enable the introduction of personalised dietary therapy with prebiotic ITFs, which, unlike other PS therapies, would not pose a high risk of side effects.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Registration Number: NCT05971992.},
}
@article {pmid41845221,
year = {2026},
author = {Chin, YC and Huang, CC and Hsu, IL and Tsai, WH and Chou, CH and Fang, YT and Su, JJ and Yeh, YT and Tsai, HY and Huang, CH and Huang, SW},
title = {Lactobacillus protects against lead-induced hepatotoxicity by preserving the gut barrier and microbiota remodeling.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41845221},
issn = {1471-2180},
abstract = {UNLABELLED: Lead (Pb) toxicity is a global health concern that primarily affects the liver. This study explored the protective effects of lactobacilli against Pb(II)-induced hepatotoxicity in mice. Three strains of lactobacilli—Lacticaseibacillus paracasei GMNL-32, Limosilactobacillus fermentum GMNL-93, and Lacticaseibacillus casei GMNL-277—were evaluated for Pb adsorption and antioxidant activity. In a chronic Pb(II) exposure mouse model, GMNL-93 and GMNL-277 more effectively mitigated Pb(II)-associated liver damage, and upregulated RNA expression of gut function-associated proteins (e.g., Cldn3, Cldn5, and Muc5). Microbiome and functional pathway analyses suggested strain-specific modes of action: GMNL-93 was associated with shifts in microbial composition and enrichment of pathways linked to redox balance and bile acid metabolism, whereas GMNL-277 was linked to enhanced thiamine-related metabolism; GMNL-32 showed comparatively limited protective. Overall, lactobacilli are promising candidates for reducing lead toxicity through directly interaction and microbiome-dependent host protection.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04956-2.},
}
@article {pmid41845222,
year = {2026},
author = {Wang, B and Liang, X and Huang, Y and Zhou, M and Liu, S and Su, J and Zhang, Y and Lan, G and Xu, Y and Wang, C and Wang, Y},
title = {Multi-omics-based metabolomic kinetics study of corn stover fermented by combined probiotic and enzymatic treatment.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41845222},
issn = {1471-2180},
support = {CARS-39-27//the National Wool Sheep Industry Technology System/ ; jytms20231736//Liaoning Provincial Department of Education General Project/ ; 2024010768-JH3/107, 2024012131-JH4/4800//Liaoning Provincial Natural Science Foundation Project/ ; S202410160014//College Student Innovation Project/ ; },
abstract = {UNLABELLED: This study employed metabolomics to systematically investigate the dynamic changes of metabolites during the Probiotics-enzyme composite fermentation of corn stover. The results showed that the early fermentation stage was primarily driven by indigenous microorganisms. As fermentation progressed, the abundances of Firmicutes and Bacillus gradually increased, becoming the core functional microbiota, and their metabolic activities significantly lowered the feed pH. Additionally, Burkholderiaceae and Rhizobiaceae played pivotal roles in enhancing the crude protein content, while microorganisms such as Desulfobacterota, Erwiniaceae, Monascaceae, and Burkholderiaceae effectively degraded fiber components, thereby improving the feed’s nutritional value. To elucidate the mechanisms underlying metabolic dynamics, metabolomics analysis was conducted on days 7, 14, 21, and 28 of fermentation. The study found that during the early stage (days 7–14), the metabolism of peptides and sugar alcohols was synergistically regulated by various exogenous microorganisms. In contrast, during the mid-to-late stages (days 14–28), Firmicutes and Bacillus gradually dominated the synthesis and transformation of organic acids and secondary metabolites. By integrating prior microbiome data, this study systematically reveals the correlation mechanisms between dynamic metabolite changes and microbial communities, providing a crucial theoretical basis for understanding feed conversion rules during bacteria-enzyme composite fermentation of corn stover.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04958-0.},
}
@article {pmid42023843,
year = {2026},
author = {Olagoke, O and Zheng, X and Chung, S and Mengistie, HD and Asfaha, K and Read, TD and Dean, D},
title = {Phylogenetic diversity, functional pathways, and network interactions of ocular chlamydia-like organisms (CLOs) in trachoma-endemic Ethiopia.},
journal = {mBio},
volume = {},
number = {},
pages = {e0053426},
doi = {10.1128/mbio.00534-26},
pmid = {42023843},
issn = {2150-7511},
abstract = {Trachoma is the leading infectious cause of blindness worldwide and classically attributed to Chlamydia trachomatis (Ct). However, other members of the phylum Chlamydiae, particularly environmental chlamydia-like organisms (CLOs), may modulate ocular ecology and influence disease outcomes. Here, we investigated CLO distribution, phylogeny, and microbiome associations among 1,059 individuals from trachoma-endemic communities in Ethiopia using targeted 16S rRNA sequencing and metagenomic shotgun sequencing. CLOs were detected in 249 (23.3%) participants of all ages and sexes and were significantly less likely to be associated with Ct or trachomatous scarring (TS) and trichiasis (TT). Phylogenetic analyses revealed extensive CLO diversity with six novel phylotypes, the most abundant of which was ancestral to Sorochlamydiaceae-a family linking pathogenic Chlamydiaceae, which includes the genus Chlamydia, and symbionts of protists. CLO-positive microbiomes exhibited significantly greater species richness and evenness with distinct differences in community composition relative to CLO-negative microbiomes. These effects were most pronounced among males and older adults. Functional profiling revealed widespread depletion of biosynthetic and metabolic pathways in CLO-positive microbiomes, particularly in participants with TS/TT, suggesting reduced community biosynthetic capacity and niche modification. Species interaction network analyses demonstrated substantial reorganization of microbial associations in the presence of CLOs with increased connectivity and centrality compared to CLO-negative networks. These findings identify CLOs as prevalent, phylogenetically diverse, and ecologically influential members of the microbiome. Their inverse association with Ct and TS/TT underscores the importance of considering intracellular symbionts beyond Ct in understanding conjunctival microbial ecology, resilience, and trachoma pathogenesis and for designing novel control strategies.IMPORTANCETrachoma caused by Chlamydia trachomatis (Ct) remains the leading infectious cause of blindness globally. While control efforts focus exclusively on Ct, other members of the phylum Chlamydiae, such as chlamydia-like organisms (CLOs), inhabit mucosal surfaces but remain understudied in the eye. Using targeted 16S rRNA and metagenomic shotgun sequencing of conjunctival samples from villagers in trachoma-endemic Ethiopia, CLOs were prevalent (23.3%; 249/1,059), phylogenetically diverse, including novel Chlamydiae phylotypes, and inversely associated with both Ct infection and severe scarring disease. CLO microbiomes had increased microbial diversity, altered community composition, depleted metabolic pathway abundance, and reorganized species interaction networks compared to CLO-negative microbiomes. These findings challenge the singular focus on Ct in trachoma control and research and suggest that CLOs represent ecologically significant members of the conjunctival microbiome. Further research on their interactions with ocular microbial communities could reveal new insights into trachoma pathogenesis and inform more holistic approaches to disease control.},
}
@article {pmid42023881,
year = {2026},
author = {Wang, P and Wang, M and Shen, Y and Yao, Y and Yan, K and Wang, S and Li, Z and Dong, Y and Li, B and Li, J},
title = {Linkage of gut microbiota dysbiosis to chronic kidney disease in patients with graded proteinuria levels.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0329425},
doi = {10.1128/spectrum.03294-25},
pmid = {42023881},
issn = {2165-0497},
abstract = {Chronic kidney disease (CKD) is highly prevalent worldwide, with proteinuria serving as a key diagnostic and prognostic indicator. The concept of the "gut-kidney axis" suggests that gut microbiota dysbiosis may contribute to CKD pathogenesis; however, its relationship with proteinuria severity remains unclear. This study investigated dynamic changes in gut microbiota composition and function among CKD patients with varying levels of proteinuria, enrolling 148 participants: 54 healthy controls (HC), 49 CKD patients with mild proteinuria (PROU_L), and 45 with massive proteinuria (PROU_M). Fecal samples were analyzed using 16S rRNA gene sequencing to characterize microbiota structure, differential taxa, and functional potential, alongside clinical indicators and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Compared with HC, CKD patients exhibited significantly reduced gut microbiota ɑ-diversity (Chao1 and Shannon indices), which increased as proteinuria worsened. β-diversity also differed significantly among groups. The Faecalibacterium-dominated enterotype (beneficial) declined from 50.0% (HC) to 40.82% (PROU_L) and 28.9% (PROU_M), whereas the Prevotella-dominated enterotype (potentially pathogenic) increased from 7.4% (HC) to 20.41% (PROU_L) and 24.4% (PROU_M). With worsening proteinuria, probiotics, such as Akkermansia and Coprococcus, decreased progressively, while potentially pathogenic bacteria, including Enterobacteriaceae, Haemophilus, and Ruminococcus, were enriched. KEGG-based functional analysis indicated that microbiota nitrogen metabolism became increasingly overactivated from HC to PROU_L and PROU_M, whereas unsaturated fatty acid synthesis was inhibited. Enzymes such as fumarate reductase correlated with the degree of proteinuria. This study characterizes gut microbiota dysbiosis in CKD patients with varying proteinuria levels, revealing reduced probiotics, enrichment of pathogens, and metabolic dysfunction, which may contribute to the progression of renal injury.IMPORTANCEChronic kidney disease (CKD) affects nearly one billion people and remains a leading global cause of death; yet the molecular dialog between gut-microbiome imbalance and the severity of proteinuria is poorly defined. We profiled 148 participants-54 healthy controls, 49 CKD patients with mild proteinuria, and 45 with massive proteinuria-and uncovered a graded dysbiosis that intensifies as proteinuria worsens. Faecalibacterium-dominated enterotypes decline, whereas Prevotella-dominated communities expand; beneficial taxa, such as Akkermansia and Coprococcus, are progressively displaced by uremic-toxin producers (Enterobacteriaceae, Haemophilus). Concurrently, nitrogen metabolism pathways become hyperactive while unsaturated fatty acid synthesis is suppressed. These data illuminate the gut-kidney axis as a driver of CKD progression, deliver stage-specific microbial biomarkers for precision risk stratification, and identify tractable microecological targets for early intervention.},
}
@article {pmid42023935,
year = {2026},
author = {Hsu, K-LC and Furstenau, TN and Shaffer, I and Macek, MD and Ernst, RK and Fofanov, VY},
title = {Ethnicity-specific microbiome in early childhood caries: a functional perspective of oral biofilm.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0178725},
doi = {10.1128/msystems.01787-25},
pmid = {42023935},
issn = {2379-5077},
abstract = {UNLABELLED: National surveillance data show persistent racial and ethnic disparities in early childhood caries (ECC), but the underlying causes of these differences have not been determined. This study examined both functional and taxonomic differences in ECC-related microbial activity between two high-risk groups of children: African American (AA) and Latin American Hispanic (LAH). Metatranscriptomic profiling of paired non-caries and caries plaque revealed consistent population-level shifts in gene expression and enabled species-level attribution of metabolically active microbes in caries lesions. A core set of well-established cariogenic organisms was consistently present and highly over-expressed in caries of both groups, including Streptococcus mutans, Veillonella parvula, Propionibacterium acidifaciens, and Lactobacillus rhamnosus. Beyond identifying the core organisms and functions active in lesions, we have also made two significant observations. First, the active communities in the two groups have substantially diverged: 4,900+ genes across 413 Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were consistently (25%+ of samples) over-expressed in AA children, and 6,500+ genes across 382 KOs were consistently (57% of samples) over-expressed in LAH children. This reproducibility across multiple samples indicates robust group-level differences rather than random variation or single-sample effects. Second, although AA and LAH children exhibited similar functional responses to caries (sharing 1,392 KOs), these shifts were expressed by different bacterial species, indicating that distinct taxa may occupy similar metabolic niches in different groups. Taken together, these findings suggest that there is no single universal caries-associated microbiome; instead, a shared cariogenic core is necessary, but differences among the non-core taxa and their functional activity may be key to understanding ECC disparities.<br><br>IMPORTANCE: The disparity in tooth decay among young children has long been demonstrated in national surveillance data. While various factors including family, culture, access to health insurance, and medical infrastructure have been studied, the global transcriptomic perspective remains underexplored. Employing RNA-Seq technology, we examine functional and taxonomic differences in caries-associated microbial activity between two high-risk populations. Besides a core set of well-established cariogenic organisms, we observed significant and consistent differences in the active microbial communities between these two high-risk populations, African American (AA) and Latin American Hispanic (LAH) children. In AA children, Pseudopropionibacterium propionicum and Cardiobacterium hominis consistently showed the highest caries-related gene expression. In contrast, among LAH children, Propionibacterium acidifaciens, Selenomonas sp., Rothia dentocariosa, Atopobium parvulum, and Streptococcus sanguinis were the primary drivers of gene expression in caries lesions. By identifying the unique microbial mechanisms and pathways active in each population, we can better define the core factors required for caries development and uncover how differences in microbial function contribute to persistent disparities.},
}
@article {pmid42024122,
year = {2026},
author = {Liang, KL and Jiang, RS and Chen, YH and Wang, PH and Lin, CF and Chang, CY},
title = {Nasal Microbiota in Immune Disorders: Bacterial and Fungal Colonization Patterns and Aspergillus Detection Methods.},
journal = {American journal of rhinology &amp; allergy},
volume = {},
number = {},
pages = {19458924261436615},
doi = {10.1177/19458924261436615},
pmid = {42024122},
issn = {1945-8932},
abstract = {BackgroundThe human respiratory tract hosts a complex microbial ecosystem. The host immune status plays an important role in regulating the microbial composition at different body sites, including the nasal cavity.ObjectiveThis study investigated the effects of immune disorders on nasal microbial colonization and explored Aspergillus detection methods in immunodeficient hosts.MethodsNasal swabs from healthy volunteers, patients with allergic airway disease, and immunodeficient patients were analyzed using 16S rRNA bacterial and ITS2 fungal microbiome analyses. Aspergillus colonization in immunodeficient individuals was examined using conventional methods (galactomannan testing, quantitative PCR, and fungal culture). The effects of nasal irrigation on fungal colonization were also evaluated.ResultsNo significant differences in the overall microbial composition were found between the healthy, allergic, and immunodeficient groups; however, distinct features were observed within each group. Immunodeficient patients showed higher Aspergillus DNA concentrations and positive culture rates than healthy controls. Nasal irrigation significantly decreased Aspergillus DNA concentration.ConclusionThis study highlights the complex relationship between the immune system and airway microbiota. Although microbiome analysis may not be optimal for analyzing upper respiratory tract microbiology in immunomodulated patients, nasal irrigation could potentially reduce fungal colonization in immunocompromised individuals at risk of developing infections.},
}
@article {pmid42024170,
year = {2026},
author = {Jiang, L and Tang, Y and Xu, L and Wei, Y and Liu, M and Che, X and Xin, R and Zhu, Y},
title = {Microbiome in adult severe caries and cross-kingdom biofilms validation.},
journal = {Clinical oral investigations},
volume = {30},
number = {5},
pages = {},
pmid = {42024170},
issn = {1436-3771},
support = {ZDXX25182//Nanjing Medical Science and Technique Development Foundation/ ; ZKX23053//Nanjing Medical Science and Technique Development Foundation/ ; 0224C010//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; },
mesh = {*Biofilms/growth &amp; development ; Humans ; *Dental Caries/microbiology ; Candida albicans ; Adult ; Saliva/microbiology ; *Microbiota ; Streptococcus mutans ; Male ; Veillonella ; Female ; Microscopy, Electron, Scanning ; Microscopy, Atomic Force ; Microscopy, Confocal ; Metagenomics ; Middle Aged ; },
abstract = {OBJECTIVES: Adult severe caries (ASC) is a form of rampant caries that develops in adulthood, causing severe impairment of oral function and reducing quality of life. However, the pathogenic mechanism of ASC remains unclear. This study aimed to identify the core microbiota in patients with ASC and preliminarily investigate the microbial interactions and pathogenicity of key ASC-associated core microorganisms.<br><br>MATERIALS AND METHODS: Saliva samples were collected from 7 adult patients with severe caries and 6 caries-free volunteers for metagenomic analysis. Based on microbiome profiling results, an in vitro cross-kingdom biofilm model composed of Streptococcus mutans (S. mutans), Candida albicans (C. albicans) and Veillonella parvula (V. parvula) was established to simulate a high caries-risk microenvironment. Scanning electron microscopy (SEM), crystal violet (CV) staining, and live/dead bacterial staining were used to evaluate biofilm formation. Acid production assays, acid stress challenge tests, confocal laser scanning microscopy (CLSM) and qRT-PCR were performed to analyze the acidogenicity and synthesis of extracellular polysaccharides (EPS). Additionally, atomic force microscopy (AFM) was used to assess the surface roughness of demineralized dentin slices.<br><br>RESULTS: Metagenomic analysis revealed significant enrichment of C. albicans and V. parvula in the saliva of patients with high caries susceptibility. The in vitro cultured cross-kingdom biofilms exhibited enhanced growth and EPS synthesis compared with single-species S. mutans biofilms. Moreover, cross-kingdom biofilms significantly increased surface roughness of demineralized samples, with a stronger effect than single- and dual-species biofilms.<br><br>CONCLUSIONS: Colonization by C. albicans and V. parvula increases biofilm biomass, enhances microbial survival under stress, and elevates biofilm virulence, which induces demineralization of dentin slices in vitro.<br><br>CLINICAL RELEVANCE: This study demonstrates that the interspecies interactions among caries-related microorganisms in ASC patients confer enhanced virulence and cariogenicity, providing novel insights for the investigation and prevention of high caries susceptibility.},
}
@article {pmid42024267,
year = {2026},
author = {Geraldi, MV and Lorentzon, M},
title = {Response to the letter to the editor: "multiplicity, microbiome interventions, and measurement biases in bone health".},
journal = {Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA},
volume = {},
number = {},
pages = {},
pmid = {42024267},
issn = {1433-2965},
}
@article {pmid42024296,
year = {2026},
author = {Venkatachalam, SK and Srinivasan, S and Santhoshkumar, M and Duraisamy, N and Vinayagam, R and Senthilkumar, D},
title = {Marine Polysaccharides: A Promising Source for Probiotic Delivery Systems.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42024296},
issn = {1867-1314},
}
@article {pmid42024426,
year = {2026},
author = {Kabir, AH and Thapa, A and Pant, B and Khan, M and Saiful, SA and Talukder, SK},
title = {Trichoderma afroharzianum behaves differently in interaction with pea plants under varying iron availability.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag107},
pmid = {42024426},
issn = {1365-2672},
abstract = {AIMS: Trichoderma afroharzianum T22 is widely recognized for enhancing plant stress resilience, yet its effects in pea plants may vary depending on iron (Fe) availability.<br><br>METHODS AND RESULTS: We assessed the impact of T22 on pea grown under differential Fe status through integrated physiological and omics analyses. We found that the benefits of T22 are highly context dependent, demonstrating improvements in photosynthesis and Fe/N accumulation under Fe deficiency but minimal effects under sufficiency. RNA-seq identified 262 DEGs under Fe deficiency and 555 DEGs under Fe sufficiency following T22 inoculation, with the latter primarily associated with basal metabolic functions, indicating potential colonization costs rather than adaptive responses. Particularly, T22 inoculation upregulated symbiosis-related genes (Nodule-specific GRPs, Major facilitator, sugar transporter-like), Fe transporters (NRAMPs, HMAs), and redox-associated genes (Glutathione S-transferase, Glutathione peroxidase) in the roots under Fe shortage, reflecting a coordinated response to enhance nutrient acquisition and stress tolerance. Microbiome profiling revealed that T22 reshaped the root community by enriching several bacterial taxa such as Comamonadaceae, Pseudomonadaceae and Mitsuaria under Fe deficiency. These enriched bacterial taxa may act as potential 'helpers' to T22 by providing complementary beneficial effects under Fe deficiency. In contrast, under Fe-sufficient conditions, microbial restructuring was largely limited to the enrichment of Rhizobiaceae and Pararhizobium. Fungal taxa showed minimal changes, except for the enrichment of Paecilomyces in response to T22 under Fe-deficient conditions.<br><br>CONCLUSIONS: These findings indicate that T22 acts in a context-dependent manner, with bacterial enrichment varying with Fe availability, while fungal taxa were largely unaffected.},
}
@article {pmid42024499,
year = {2026},
author = {Reasoner, SA and Frainey, BT and Hale, OF and Borden, A and Graham, MK and Turner, E and Brenes, LR and Soderstrom, CBW and Green, H and Schmitz, JE and Laub, MT and Kelly, MS and Clayton, DB and Hadjifrangiskou, M},
title = {Unmasking pathogen traits for chronic colonization in neurogenic bladder.},
journal = {Cell reports},
volume = {45},
number = {5},
pages = {117302},
doi = {10.1016/j.celrep.2026.117302},
pmid = {42024499},
issn = {2211-1247},
abstract = {Individuals with neurogenic bladder are susceptible to chronic bacterial colonization and urinary tract infections. Neurogenic bladder arises from conditions including spinal cord injuries and spina bifida. We established a longitudinal cohort of 77 children and young adults with spina bifida. Using enhanced urine culture, 16S rRNA sequencing, and whole-genome sequencing of bacterial isolates, we characterized the urine microbiota. We also retrieved prior bacterial isolates from Vanderbilt's MicroVU biobank, enabling 5-year evolutionary comparisons within subjects. Urine samples showed high abundance of pathogens, including E. coli and Klebsiella. Across time points, subjects exhibited either rapid cycling of strains, often after antibiotics, or persistence of a single strain. Neither pattern consistently correlated with increased antibiotic resistance. Instead, mutations in cell envelope genes mediated immune evasion and altered phage susceptibility, highlighting fitness trade-offs induced by niche adaptation to the bladder. This cohort enables the identification of bacterial adaptation mechanisms.},
}
@article {pmid42024560,
year = {2026},
author = {Punzi, L and Baggio, C and Galozzi, P and Lorenzin, M and Cozzi, G and Damasco, AC and Sfriso, P and Oliviero, F and Ramonda, R},
title = {Gout: one year in review 2026.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/9xhnbu},
pmid = {42024560},
issn = {0392-856X},
abstract = {The year 2025 marked a significant evolution in the understanding and management of gout, characterised by a growing focus on personalised medicine and multidimensional pathogenetic models.This review provides a comprehensive analysis of the scientific literature published during 2025, highlighting key advancements across several fields. Specifically, we discuss emerging epidemiological trends, such as the rising incidence of early-onset gout, and the integration of artificial intelligence into diagnostic imaging. Groundbreaking genetic studies are explored, identifying early-onset disease as a potentially distinct subset, alongside new insights into the 'gut-kidney axis' and the role of the microbiome in urate homeostasis.Furthermore, this review examines updated pathogenetic mechanisms involving immunometabolic reprogramming and evaluates the latest therapeutic strategies for both gouty arthritis and asymptomatic hyperuricaemia.},
}
@article {pmid42024669,
year = {2026},
author = {Zheng, Y and Zhang, L and Tian, J and Li, N and Li, Q and Li, F and Meng, J and Zhang, Z and Yun, X and Duan, S},
title = {Lung microbiota dysbiosis mediates PM2.5-induced pulmonary inflammation through antibiotic-reversible mechanisms.},
journal = {Journal of immunotoxicology},
volume = {23},
number = {1},
pages = {2660647},
doi = {10.1080/1547691X.2026.2660647},
pmid = {42024669},
issn = {1547-6901},
mesh = {Animals ; *Particulate Matter/toxicity/adverse effects ; *Dysbiosis/drug therapy/immunology ; Mice ; *Lung/microbiology/immunology/drug effects/pathology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Pneumonia/drug therapy/microbiology/immunology/chemically induced ; *Microbiota/drug effects ; Mice, Inbred C57BL ; Humans ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Signal Transduction ; Male ; Inflammasomes/metabolism ; Pyroptosis ; Macrophages/immunology ; },
abstract = {Fine particulate matter (PM2.5) exposure contributes to over 4 million premature deaths annually, yet the mechanistic role of lung microbiota in PM2.5-induced pulmonary inflammation remains poorly understood. In collaboration of 16S rRNA and single-cell RNA multi-omics analysis and in vivo/in vitro experimental validation with antibiotic intervention strategies, the study here examined PM2.5-microbiota interactions in murine PM2.5 exposure models and cellular systems. It was found that PM2.5 exposure induced lung microbiota dysbiosis characterized by Gram-negative bacterial expansion, particularly Proteobacteria dominance, accompanied by reduced microbial diversity. scRNA analysis revealed coordinated activation of TLR4/MyD88/NLRP3 inflammatory signaling pathways and p53/p21/p16-mediated cell cycle arrest. Moreover, PM2.5 exposure activated NLRP3 inflammosome-dependent macrophage pyroptosis as evidenced by increased interleukin (IL)-1β, IL-18, caspase-1, and GSDMD expression. In vitro studies demonstrated that the inflammatory changes induced by PM2.5 exposure were statistically indistinguishable from those of LPS-positive controls, confirming endotoxin-like mechanisms. Critically, antibiotic pretreatment effectively attenuated PM2.5-induced inflammatory responses, cell cycle arrest, and tissue pathology, which established causality between microbiota disruption and pulmonary dysfunction. In conclusion, this study revealed lung microbiota dysbiosis as a critical mediator of PM2.5-induced pulmonary inflammation through Gram-negative bacterial expansion and subsequent endotoxin-like activation of inflammatory cascades, thereby providing novel mechanistic insights and potential microbiome-targeted therapeutic strategies for air pollution-associated respiratory diseases.},
}
@article {pmid42024954,
year = {2026},
author = {Gunsch, CK and Brown, J},
title = {Rethinking Microbiome of the Built Environment (MoBE) Management: From Pathogen-Centric Control to Microbiome-Informed Engineering.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02788},
pmid = {42024954},
issn = {1520-5851},
}
@article {pmid42025004,
year = {2026},
author = {Barros, M and Pietruska, A and Khalid, Z and Gulizia, JP and Hauck, R},
title = {Secondary analysis of the intestinal microbiota of healthy chickens.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106915},
doi = {10.1016/j.psj.2026.106915},
pmid = {42025004},
issn = {1525-3171},
abstract = {The intestinal microbiota plays a key role in poultry health and performance. Its composition is influenced by multiple factors such as diet, age, bird type, and housing. The aim of this secondary analysis was to summarize existing data and outline a baseline reference intestinal microbiota that could serve as a reference for future research and industry applications. For this, the intestinal microbiota of chickens across all intestinal segments and feces under standard conditions, without feed additives or infections were compiled and analyzed. A total of 3,562 samples from 79 BioProjects were retrieved from the National Center for Biotechnology Information database, together with their metadata including intestinal segment, bird type, age, housing system, continent, and sequenced hypervariable region. Across all samples, 2,603 unique bacterial genera in 73 phyla were identified, with Firmicutes being the most abundant phylum in all segments. The number of core genera was highest in the ceca, followed by the duodenum. Alpha diversity was highest in the ceca and lowest in feces, as well as highest in Africa and lowest in North America. For beta diversity, Principal Component Analysis revealed a minor overlap among intestinal segments and a major overlap for the other investigated factors. Metabolic pathway predictions revealed 8,674 unique functional orthologs (FOs), with the relative abundance of about 40 to 60% of the FOs constant across intestinal segments and other investigated factors. In conclusion, while microbial community composition may vary substantially between different flocks or production systems, core metabolic functions are often consistent. These findings provide a baseline framework for evaluating how treatments, infections, or management practices may impact the chicken intestinal microbiota.},
}
@article {pmid42025006,
year = {2026},
author = {Song, H and Wang, J and Hao, Y and Li, X and Yan, S and Han, S and Zhao, J and Han, Y and Sun, S and Chen, X and Purba, MA and Chen, H and Li, C},
title = {Gut microbiota dysbiosis induced by tibial dyschondroplasia in turn accelerates disease pathogenesis through the gut-bone axis in broilers.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106927},
doi = {10.1016/j.psj.2026.106927},
pmid = {42025006},
issn = {1525-3171},
abstract = {Tibial dyschondroplasia (TD) is a common and economically significant skeletal disorder in broilers, characterized by unmineralized, avascular cartilage plugs protruding into the metaphyseal region. Despite some evidence connecting the gut microbiota to skeletal disorders, the specific microbial drivers of TD pathogenesis remain unclear. In this study, we performed fecal microbiota transplantation in both healthy and TD model broilers to assess the influence and contribution of gut microbiota dysbiosis to TD pathogenesis. The broilers were allocated into 4 groups: CON (normal control group broilers), TD (TD model broilers), TDRN (TD model broilers that received FMT from normal broilers) and NRTD (normal broilers that received FMT from TD model broilers). Results demonstrated that FMT successfully transferred the TD phenotype from diseased to healthy broilers (NRTD group), whereas transplantation from healthy donors did not reverse the TD phenotype in TD broilers (TDRN group). This to some extent indicates that gut microbiota as a critical pathogenic driver. Microbiome analysis revealed significant depletion of Lactobacillus and enrichment of Streptococcus and Escherichia-Shigella in all TD-affected groups (TD, TDRN, NRTD) compared to controls (P < 0.05). Metabolomic profiling identified seven stably dysregulated metabolites. Among them, chenodeoxycholic acid showed a strong positive correlation with Lactobacillus abundance and tibial mineral content, while 2-methoxyestradiol (an estrogen metabolite) exhibited inverse associations. Collectively, these findings provide evidence that gut microbiota dysbiosis causally contributes to TD and define the Lactobacillus-chenodeoxycholic acid axis and estrogen metabolism as promising targets for preventive and management strategies against TD in broilers.},
}
@article {pmid42025064,
year = {2026},
author = {Hu, D and Tan, Y and Dai, L and Ma, X and Yang, S and Chen, Z and Chen, Y},
title = {Effects of PLA microplastic particle size and addition level on soil phosphorus cycling and Chinese cabbage growth in a Luvisol from Southwest China: A controlled pot experiment.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142070},
doi = {10.1016/j.jhazmat.2026.142070},
pmid = {42025064},
issn = {1873-3336},
abstract = {Biodegradable microplastics such as polylactic acid (PLA) are increasingly used in agriculture as "eco-friendly" alternatives, but they can persist in soil and may disrupt nutrient cycling in phosphorus-limited subtropical systems. We carried out a pot experiment using P-deficient Luvisol soil. We measured how PLA microplastic particle size (10 μm vs 500 μm) and addition level (0.1% vs 1.0% w/w) affect soil P cycling and Chinese cabbage (Brassica rapa var. pekinensis) growth. We measured plant performance, P uptake, antioxidant enzymes, soil P fractions, rhizosphere microbial community composition, and P-cycling gene abundances. We then used partial least squares path modeling (PLS-PM) to link these factors. Cabbage growth responses depended on both particle size and concentration: at 1.0% (w/w), PLA-particularly the 10 μm particles-significantly reduced cabbage growth (shoot fresh weight decreased by ∼50%) and P uptake, whereas 0.1% (w/w) PLA had little effect. Under 1.0% PLA, SOD and POD activities increased, so oxidative stress increased. PLA also reduced labile P pools (Olsen-P and Resin-P decreased by 28%-38%). At the same time, P shifted from more available forms to less available organic fractions, and this immobilization was stronger with smaller particles. These changes happened together with rhizosphere disruption, including lower microbial diversity, more Proteobacteria, and higher abundances of several P-scavenging genes. PLS-PM showed that PLA limited plant growth mainly in an indirect way, because it changed the rhizosphere microbiome and lowered P availability. Overall, PLA microplastics can still disturb soil P dynamics and reduce crop growth in P-limited soils, so fragmentation and accumulation in agroecosystems should be managed.},
}
@article {pmid42025143,
year = {2026},
author = {Cheng, MC and Lin, HC and Liaw, CC and Lin, YC and Kuo, PH and Chen, CC and Wu, MS and Lee, SS and Chang, CC},
title = {Gut microbial resistance and metabolism of selective serotonin reuptake inhibitors drive multidrug resistance and contribute to antidepressant tachyphylaxis.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {54},
number = {5},
pages = {100273},
doi = {10.1016/j.dmd.2026.100273},
pmid = {42025143},
issn = {1521-009X},
abstract = {Selective serotonin reuptake inhibitors (SSRIs) are among the most widely used antidepressant medications in modern clinical practice. However, the underlying mechanisms of the rapid onset of tolerance to antidepressants (antidepressant tachyphylaxis [ADT]) led by SSRIs are not well-investigated. To clarify the roles of the interaction between gut microbes and SSRIs in the development of ADT and other adverse effects, we isolated 4 sertraline (STR; an SSRI)-resistant microbial strains, one of which was identified as uropathogenic Escherichia coli (E coli G5100a). Through transcriptomic analysis and multidrug efflux pump antagonism assays, resistance-nodulation-division-type and partially ABC-type multidrug efflux pumps were confirmed as the primary mechanisms by which E coli G5100a resists STR toxicity. The upregulation of these genes also led to increased resistance to chloramphenicol, rifampicin, and β-lactam-type antibiotics. Furthermore, Global Natural Product Social Molecular Networking-based metabolite analysis and liquid chromatography-mass spectrometry profiling revealed that E coli G5100a metabolized approximately 25% of STR in the culture medium. Two major STR metabolites were isolated and structurally elucidated as STR ketone (1) and N-acetylsertraline (2) using NMR and mass spectrometry analyses. Using the DeePred-BBB model, we confirmed that none of the putative SSRI-related metabolites were able to pass through the blood-brain barrier. These findings suggest that STR may induce multidrug resistance in gut microbiota, potentially contributing to clinical SSRI-related side effects and ADT. This study provides a novel perspective on the origins of SSRI-induced side effects in clinical settings, offering new insights for the future development of central nervous system-targeted pharmaceuticals. SIGNIFICANCE STATEMENT: Selective serotonin reuptake inhibitors may alter the composition of the intestinal microbiota. Specific gut microbes are likely to express metabolic resistance genes in response to selective serotonin reuptake inhibitor induction. The potential mechanisms in the development of SSRI tolerance from the perspective of the gut microbiome were identified.},
}
@article {pmid42025145,
year = {2026},
author = {Liem, J and Chen, X and Lim, JJ and Mao, Q and Cui, JY and Lin, YS},
title = {Impact of the gut microbiome on hepatic cytochrome P450 3A4 (CYP3A4) in humanized pregnane X receptor-constitutive androstane receptor-CYP3A4/3A7 mice.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {54},
number = {5},
pages = {100284},
doi = {10.1016/j.dmd.2026.100284},
pmid = {42025145},
issn = {1521-009X},
abstract = {The interaction between the gut microbiome and drug metabolism is bidirectional and can influence the pharmacokinetics of certain drugs. In mice, the gut microbiome has been shown to influence Cyp3a11. However, evidence for microbial regulation of human cytochrome P450 3A4 (CYP3A4) is lacking. We aimed to bridge this gap by manipulating the microbiome of a humanized mouse model expressing CYP3A4, CYP3A7, pregnane X receptor and constitutive androstane receptor. Three groups of male and female humanized mice were studied: conventional (CV), germ-free (GF), and germ-free mice conventionalized (GFCV) using sex-matched pooled human fecal samples. The presence of microbiome upregulated CYP3A4 expression by 7.6-fold in male CV mice (P < .001) but downregulated CYP3A4 expression by 1.69-fold in female CV mice (P = .012) compared with GF mice. The human fecal microbiome transplant to sex-matched GF mice resulted in decreased microbial diversity (P < .05 in males and P < .01 in females) and was not effective in restoring CYP3A4 expression, suggesting complex underlying microbe-CYP3A4 interactions. We show that the hepatic CYP3A4 mRNA and protein expression were strongly correlated (R = 0.91; P = 2.6 × 10[-6]). A total of 57 bacterial species from the mouse gut microbiome were identified to be significantly correlated with CYP3A4 protein expression (P < .05). Five bile acids and no short-chain fatty acids were correlated with CYP3A4 protein expression. In summary, alterations in the gut microbiome influenced hepatic CYP3A4 in humanized mice in a sex-dependent manner, with distinct microbes strongly correlating with this regulatory pattern. SIGNIFICANCE STATEMENT: To the best of our knowledge, this study is the first to evaluate the expression of cytochrome P450 3A4 under different microbial conditions in a humanized mouse model, including conventionalization of germ-free mice using pooled sex-matched human feces. Alterations in the gut microbiome influenced hepatic cytochrome P450 3A4 in a sex-dependent manner and were strongly correlated with microbial species.},
}
@article {pmid42025264,
year = {2026},
author = {Ciftcioglu, UGE and Nalbantoglu, OU},
title = {Deeptaxim: Comprehensive classification analysis for taxonomic datasets using image-based deep-learning models.},
journal = {Computational biology and chemistry},
volume = {124},
number = {Pt 1},
pages = {109063},
doi = {10.1016/j.compbiolchem.2026.109063},
pmid = {42025264},
issn = {1476-928X},
abstract = {Advancements in deep learning have opened new possibilities for the classification of microbiome data, offering solutions to the challenges posed by its complexity and variability. This work explores the application of deep learning techniques for accurate and reliable classification of microbiome data, addressing the challenges of high-dimensionality and sparsity. Focusing on diseases known to be closely linked with gut microbiome alterations, we convert microbiome data into image format using the hierarchical structure of the taxonomic tree (cladogram). Our proposed model, Deeptaxim, leverages 2D-CNN-based Autoencoder, U-Net, and GAN architectures to enhance classification performance across two distinct dataset groups. The primary goals are to (1) utilize cladogram-based image data to capture complex microbial relationships, (2) develop optimized deep learning models for microbiome-based disease classification, (3) assess Deeptaxim's transfer learning capabilities for low-sample datasets, and (4) evaluate its robustness when applied to a broader range of diseases. Our findings demonstrate that the use of taxa-ordered images instead of tabular taxonomic data and employing CNN as a classifier led to superior classification performance compared to conventional methods typically used for taxonomic data. Furthermore, it proved that a model trained on a comprehensive dataset can significantly improve the classification performance on data with fewer examples or different disease types through transfer learning. Proposed model thanks to its NN-based framework, not only facilitates working with alternative datasets but also can be integrated into other NN-based methods as a head/neck module of other models. Thus, Deeptaxim can be adapted, extended, and ported to serve as a wellness index.},
}
@article {pmid42025389,
year = {2026},
author = {Wang, X and Zeng, W and Bai, Q and Zhong, K and Luo, Q and Deng, J and Cen, C and Wang, K and Li, R and Li, J and Zhang, J and Ye, T and Fang, N and Chen, X and Wang, T},
title = {Gut microbiota-derived trimethylamine-N-oxide protects pulmonary vascular barrier integrity via Vav guanine nucleotide exchange factor 3 (VAV3)-mediated cytoskeletal remodelling in acute lung injury.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70449},
pmid = {42025389},
issn = {1476-5381},
support = {82241024//National Natural Science Foundation of China/ ; 82270053//National Natural Science Foundation of China/ ; 82470030//National Natural Science Foundation of China/ ; 82570083//National Natural Science Foundation of China/ ; 2021B1515020006//Guangdong Outstanding Young Scientist Funding/ ; SL2023A03J01309//Science and Technology Program of Guangzhou, China/ ; SL2024A04J01572//Science and Technology Program of Guangzhou, China/ ; GZNL2023A02013//R&amp;D Program of Guangzhou National Laboratory/ ; 20221800906372//Dongguan Science and Technology of Social Development Program/ ; },
abstract = {BACKGROUND AND PURPOSE: Acute respiratory distress syndrome (ARDS) and acute lung injury (ALI) are characterised by increased pulmonary capillary permeability, but lack effective pharmacotherapies. Emerging evidence implicates gut-lung axis dysregulation in ARDS pathogenesis through microbiome-host interactions, but the specific role of the microbiota-derived metabolite, trimethylamine-N-oxide (TMAO), remains unclear.<br><br>EXPERIMENTAL APPROACH: Plasma TMAO and hypersensitive C-reactive protein (hs-CRP) levels were measured in ARDS patients and healthy controls. A lipopolysaccharide (LPS)-induced ALI mouse model was employed to evaluate the effects of TMAO administration versus the inhibition of its gut microbiome-derived synthesis. In vitro, the necessity of VAV3 in the mechanism of TMAO was confirmed using gene knockdown techniques to assess endothelial barrier integrity.<br><br>KEY RESULTS: Plasma TMAO levels were significantly elevated in ARDS patients compared with healthy controls, and showed a positive correlation with hs-CRP. In the murine ALI model, TMAO administration reduced lung vascular leakage and neutrophil infiltration, whereas inhibiting its synthesis worsened the injury. Mechanistically, TMAO enhances the integrity of the endothelial barrier by up-regulating VAV3, which in turn drives Rac1-dependent cortical actin reorganisation. Knockdown of VAV3 abolished the protective effects of TMAO on the endothelial barrier integrity.<br><br>CONCLUSION AND IMPLICATIONS: This study identifies TMAO as an adaptive mediator within the gut-lung axis that mitigates pulmonary vascular hyperpermeability. The protective mechanism operates via the VAV3-Rac1-cytoskeletal signalling pathway, highlighting the therapeutic potential of TMAO in ALI/ARDS.},
}
@article {pmid42025417,
year = {2026},
author = {Warren, J and de Vries, C and Hunt, LH and Thorpe, AC and Busi, SB and Kelly, MG and Simons, DL and Taylor, JD and Read, DS and Walsh, K},
title = {Discovery of nitrogen-responsive microbial indicators as metrics of freshwater ecosystem health.},
journal = {Water research},
volume = {300},
number = {},
pages = {125959},
doi = {10.1016/j.watres.2026.125959},
pmid = {42025417},
issn = {1879-2448},
abstract = {Microorganisms represent the most taxonomically and functionally diverse components of freshwater environments. Whilst distinct microbial communities exist across freshwater habitats, such as the water column and sediments, epilithic and epiphytic biofilm communities are critical in performing key roles in biogeochemical cycling and freshwater food webs. Despite their biogeochemical and ecological importance, microorganisms are underrepresented in freshwater monitoring programmes and lack metrics to interpret complex ecological communities and assess ecosystem health. We developed a framework for identifying microbial indicators of ecosystem health by analysing 16S rRNA gene sequences from bacterial communities in 1574 freshwater biofilm samples collected from 694 sites across England's river networks. Tree-based machine learning regression was used to assess taxa importance, and threshold-indicator analysis was applied to identify pollutant concentrations that alter the composition of freshwater biofilm communities, providing a foundation for incorporating microbial data into ecosystem health metrics. We applied this framework to measure the response of bacterial communities within English freshwater biofilms to an oxidised nitrogen gradient. Our results demonstrate that bacterial taxa can predict a large proportion of the variance in oxidised nitrogen concentrations, and we identified specific concentrations at which sensitive and tolerant taxa respond. This study represents a step toward developing a microbial metric of ecosystem health, advancing the potential use of microbial indicators in future monitoring programs. This framework could enable investigation of new and emerging pressures by examining how environmental perturbations affect functional processes, potentially across various trophic levels, providing a more comprehensive view of environmental dynamics in biomonitoring.},
}
@article {pmid42025430,
year = {2026},
author = {Shiba, T and Takamori, M and Katagiri, S and Kobayashi, R and Kawauchi, A and Ohsugi, Y and Lin, P and Ekuni, D and Egusa, M and Iwata, T and Maeda, S},
title = {Effects of Nonsurgical Periodontal Treatment on Bacterial and Clinical Parameters in Down Syndrome Patients Based on 16S rRNA Gene Amplicon Sequencing.},
journal = {Acta medica Okayama},
volume = {80},
number = {2},
pages = {85-97},
doi = {10.18926/AMO/70451},
pmid = {42025430},
issn = {0386-300X},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; *Down Syndrome/complications/microbiology ; Adult ; *Periodontitis/microbiology/therapy ; Young Adult ; Microbiota ; },
abstract = {Individuals with Down syndrome (DS) are more susceptible to periodontal disease; however, microbial changes following treatment remain insufficiently understood. This study evaluated the effects of nonsurgical periodontal therapy on clinical outcomes and oral microbiome dynamics in 6 patients with DS using 16S rRNA gene amplicon sequencing. Bacterial diversity, composition, network structure, and predicted functional pathways were analyzed using dental plaque samples. Bleeding on probing decreased significantly (p=0.047) after treatment, with a trend toward reduction in periodontal inflamed surface area (p=0.05). The abundance of Fusobacteria at the class level decreased significantly after treatment. The abundance of Mogibacterium timidum was higher in the pretreatment group than in the posttreatment group. M. timidum was positively correlated with Treponema denticola and associated with multiple bacterial taxa in the network during pretreatment. Predicted functional pathways related to aromatic compound degradation were more abundant in posttreatment samples than in pretreatment samples. An increase in the abundance of Fusobacterium and the positive correlation between T. denticola and M. timidum, together with their associations with other periodontal pathogens before treatment, may contribute to the development of periodontitis in individuals with DS. Nonsurgical periodontal therapy produces measurable clinical improvement and promotes microbial shifts in patients with DS.},
}
@article {pmid42025461,
year = {2026},
author = {Valentine, CJ and Beseler, L and Langley, KL},
title = {Practical strategies to incorporate maternal nutrition into neonatology practice to impact infant outcomes.},
journal = {Seminars in perinatology},
volume = {},
number = {},
pages = {152233},
doi = {10.1016/j.semperi.2026.152233},
pmid = {42025461},
issn = {1558-075X},
abstract = {BACKGROUND: Maternal diet is an important clinical adjunct to care for optimal infant outcome. Clinicians should have a heightened awareness to the importance of the first 1000 days from conception to 2 years for key critical nutrients. The Registered Dietitian can be a key partner to ensure mothers are assessed nutritionally for food insecurity and dietary adequacy in pregnancy and lactation.<br><br>METHODS: A clinical review of the PubMed literature was done to establish recent guidelines for pregnancy and lactation- highlighting key dietary patterns, calories and nutrients that have been associated with pregnancy, human milk composition, and impacting fetal, neonatal, and lifelong health outcomes.<br><br>RESULTS: Critical nutrients such as calories, Docosahexaenoic acid (DHA), choline, folate, Vitamin B1,B2, B12, D, minerals, trace elements, and fiber were found to play key roles in optimizing pregnancy and lactation and resultant infant growth, development, and the microbiome.<br><br>CONCLUSION: The perinatal provider should incorporate key maternal nutrient recommendations into dietary guidelines to ensure a healthy trajectory for the mother-infant dyad.},
}
@article {pmid42025567,
year = {2026},
author = {Araujo, ASF and de Medeiros, EV and da Costa, DP and Mendes, LW and Cherubin, MR and Beirigo, RM and Lambais, GR and Melo, VMM and Santana, RM and Kavamura, VN and Pereira, APA},
title = {Soil biodiversity first: reframing desertification and restoration governance in Brazil's semiarid region.},
journal = {Trends in ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2026.04.004},
pmid = {42025567},
issn = {1872-8383},
abstract = {Desertification in Brazil's Caatinga is driven by largely overlooked belowground degradation. Integrating whole-soil microbial indicators into policy enables earlier diagnosis, function-based restoration, and climate-resilient dryland management. We discuss how soil biodiversity can be positioned as an early indicator, a restoration target, and a governance tool within the Caatinga Microbiome Initiative.},
}
@article {pmid42025642,
year = {2026},
author = {Airaksinen, V and Pesonen, M and Bernhardsen, GP and Chortatos, A and Keski-Nisula, L and Backman, K and Täubel, M and Kirjavainen, PV and Lehto, SM},
title = {Do prenatal affective symptoms have an impact on the infant oral microbial exposure? Results from the Kuopio Birth Cohort Study.},
journal = {Journal of affective disorders},
volume = {408},
number = {},
pages = {121828},
doi = {10.1016/j.jad.2026.121828},
pmid = {42025642},
issn = {1573-2517},
abstract = {BACKGROUND: Up to one-fifth of pregnant women are affected by depression, which has been associated with disruptions in the maternal microbiome during pregnancy. Stress-related disruptions in the maternal vaginal microbiome can be carried over to the offspring, and lead to adverse developmental outcomes.<br><br>OBJECTIVE: We investigated whether maternal depressive and anxiety symptoms during pregnancy associated with compositional alterations of the oral microbial exposure of infants during vaginal birth.<br><br>METHODS: We conducted a secondary analysis of 324 mother-newborn pairs participating in the Kuopio Birth Cohort Study in Eastern Finland. Depressive symptoms were measured in the first and the third trimesters of pregnancy using the Edinburgh Postnatal Depressive Scale (EPDS). Bacterial exposure was assessed with 16S rRNA gene amplicon sequencing of oral swab samples collected at birth. The studied microbial features included alpha and beta diversity metrics, as well as the relative abundances of individual taxa characterized at the genus and phylum levels. Linear regression models adjusted for covariates (body mass index, gestational diabetes and use of antibiotics at birth) were constructed with depressive symptoms as the exposure variables and microbial exposure measures as the outcome variables.<br><br>RESULTS: No statistically significant associations were observed between maternal depressive or anxiety symptoms during pregnancy and alpha or beta diversity metrics of newborn oral microbial exposure at birth.<br><br>CONCLUSION: Despite existing animal studies and one human study suggesting otherwise, we did not detect any statistically significant associations between maternal depressive symptoms during pregnancy and the composition of newborn oral microbial exposure at birth.},
}
@article {pmid42025708,
year = {2026},
author = {Lee, A and Rao, K and Singh, P and Fehlman, J and Gao, J and Takakura, W and Lynett, A and Haller, E and Ball, S and Marand, A and Liu, A and Shah, E and Menees, S and Punglia, R and Nojkov, B and Eswaran, S and Baker, J and Chey, WD and Owyang, C and Young, V and Hasler, WL},
title = {A Randomized Trial of Rifaximin vs Low FODMAP Diet for Symptom Outcomes and Microbiome Changes in Irritable Bowel Syndrome.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2026.04.014},
pmid = {42025708},
issn = {1542-7714},
abstract = {BACKGROUND AND AIMS: The low FODMAP diet (LFD) and rifaximin are effective in <50% individuals with irritable bowel syndrome (IBS), highlighting the need to identify predictors of treatment response. We therefore conducted a randomized controlled trial comparing LFD and rifaximin to identify microbial predictors of response.<br><br>METHODS: Sixty-five adults with IBS-D were randomized to LFD or rifaximin for 5 weeks. Primary endpoints were changes in mean daily abdominal pain and bloating at week 5 versus baseline. Secondary endpoints included changes in IBS Symptom Severity Score (IBS-SSS) and Bristol Stool Form Scale (BSFS) at week 5 versus baseline. Exploratory endpoints included responders defined as &#x2265;30% reduction in abdominal pain or bloating. Stool samples collected at weeks 0, 2, 4, and 5 underwent 16S rRNA sequencing, and glucose breath testing (BT) was performed at weeks 0 and 5.<br><br>RESULTS: Both LFD and rifaximin significantly improved abdominal pain (-0.29 with LFD vs. -0.24 points/week with rifaximin); bloating (-0.29 vs. -0.19 per week); and IBS-SSS (-14.2 vs. -13.3 per week) at week 5 (all P<.0001), with no significant change in BSFS. BT results were inconsistent predictors of response, with positive baseline hydrogen BT associated with lower odds of rifaximin response, and methane conversion at week 5 showed discordant associations with rifaximin response. In contrast, distinct baseline taxa were associated with treatment response. LFD responders had lower abundance of putative saccharolytic taxa (Butyricimonas, Bacteroides, Intestinibacter), whereas rifaximin responders were enriched in taxa with putative short-chain fatty acid-producing and bile acid-modifying potential (Ruminococcus, Coprococcus, Odoribacter). Non-responders exhibited enrichment of putative proteolytic taxa (Bilophila, Alistipes, Prevotella).<br><br>CONCLUSIONS: LFD and rifaximin are equally effective for IBS-D, with distinct microbial predictors of response. However, these findings require validation before informing personalized treatment approaches.},
}
@article {pmid42023670,
year = {2026},
author = {Santillan, E and Neshat, SA and Wuertz, S},
title = {Predicting microbial community responses to disturbance using genome-resolved trait-based life-history strategies.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag099},
pmid = {42023670},
issn = {1751-7370},
abstract = {Understanding how microbial communities respond to disturbance remains a fundamental question in ecology, with broad implications for biodiversity, ecosystem function, and biotechnology. Trait-based approaches offer general rules to predict community responses by linking ecological strategies to measurable traits. Whereas life-history strategy frameworks such as the competitor-ruderal-stress-tolerant (CSR) model are well established in plant and animal ecology, their application to microbial communities has been limited. Here, we experimentally tested how microbial communities shift across a gradient of disturbance frequency in replicated bioreactors treating synthetic wastewater. We applied six conditions by doubling the organic loading rate at different frequencies, from undisturbed to press disturbance, and monitored changes over 42 days using genome-resolved metagenomics, 16S rRNA gene sequencing, biomass quantification, and effluent chemistry. By integrating ordination, network analysis, and machine learning, we identified emergent community-level life-history strategies, with competitor-dominated communities under undisturbed conditions, ruderal-associated strategies at intermediate disturbance frequencies, and stress-tolerant strategies under sustained high-frequency (press) disturbance. These strategies were reflected in functional trade-offs, shifts in community composition, and genomic trait distributions. A simulation-based approach was used to generate a CSR classification of metagenome-assembled genomes, which was consistent with patterns observed in other microbial ecosystems. Our results demonstrate that life-history frameworks can capture predictable microbial dynamics across disturbance regimes. This approach provides a unifying tool for linking microbial structure, function, and traits across scales, helping to reconcile ecological theory with microbial resource management in natural and engineered ecosystems.},
}
@article {pmid42023825,
year = {2026},
author = {Ma, Z and Zhang, Y and Yang, H and Zheng, G and Li, L and Zhang, R and Ji, X and Ji, C and Xia, Y and Zhao, Y},
title = {The dietary index for gut microbiota, genetically predicted gut microbiome, and the risk of chronic kidney disease: a cohort study.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00453a},
pmid = {42023825},
issn = {2042-650X},
abstract = {Background: the dietary index for gut microbiota (DI-GM) is a recently proposed index that reflects the diversity of the gut microbiota from the perspective of dietary intake. However, its association with chronic kidney disease (CKD) has not been widely studied. Methods: this prospective cohort study included 166 865 participants free of CKD at baseline. The DI-GM was assessed through a 24 h dietary recall questionnaire. Incident CKD was ascertained using hospital inpatient records, death registry data, and primary care data. A genetic risk score for gut microbial abundance was constructed based on 19 variants. The Cox proportional hazards model was used to estimate the hazard ratio (HR) and 95% confidence interval (CI) for CKD incidence. Results: during a median follow-up of 9.44 years, 3977 participants developed CKD. In the fully adjusted model, compared with the lowest group for the DI-GM (0-3 points), participants in higher DI-GM groups (4, 5, and ≥6 points) had a significantly lower risk of CKD. The adjusted HRs (95% CIs) for these groups were 0.81 (0.74, 0.88), 0.79 (0.72, 0.86), and 0.73 (0.67, 0.80), respectively (P for trend <0.0001). Significant multiplicative interactions were observed between genetically predicted gut microbial abundance and adherence to the DI-GM (P for interaction = 0.004). Conclusion: adherence to the DI-GM was strongly linked to a reduced risk of incident CKD, particularly in individuals with high gut microbial abundance.},
}
@article {pmid41857116,
year = {2026},
author = {Frater, J and Nicourt, M and Landi, F and Maxwell, B and Thiodet, J and Mestrallet, E and Warr, SJ and Pizarro, M and Fa, JE and Lemoine, S},
title = {Geophagy in Gibraltar Barbary macaques is a primate tradition anthropogenically induced.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41857116},
issn = {2045-2322},
support = {101034349-6//Marie Sk&#x142;odowska-Curie Action COFUND - R2STAIR/ ; SRG2223\231596//British Academy Leverhulme Small Research Grant/ ; },
abstract = {UNLABELLED: We report, for the first time, geophagy – the deliberate consumption of earth – in the Barbary macaque (Macaca sylvanus) population living at the human-primate interface in Gibraltar. We evaluate potential adaptive functions of this behavior in an anthropogenic context, drawing on predictions from the protection and supplementation hypotheses. Geophagy occurred at exceptionally high rates compared to other macaque species and locations, and it was more common in summer when tourist numbers peak. It was also more likely when macaques consumed greater amounts of tourist-derived food, supporting a protective function. Local ecological factors contributed as well, with the distribution of red soil (terra rossa) influencing geophagy frequency. Although the behavior was not linked to female reproductive status, supplementation cannot be fully dismissed given the very limited insectivory in this population. We propose that tourist-derived foods may disrupt gut microbiome composition, producing discomfort that individuals mitigate through soil ingestion. Geophagy is likely socially learned, as groups showed consistent preferences for specific soil types, and its practice in presence of conspecifics offered opportunities for social learning. Reports from other sites indicate that geophagy is not unique to Gibraltar, but in this population it appears to be anthropogenically induced and socially transmitted, forming a locally maintained tradition.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-44607-0.},
}
@article {pmid42019623,
year = {2026},
author = {Sant'ana, AB and Tomich, T and Rotta, PP and Carvalho, D and Silva, LHR and Vieira, JVF and Junqueira, RVB and Zambon, RM and Silva, AL},
title = {Dietary tannins and compounds from fermentation of saccharomyces cerevisiae effects on intake, productive performance, enteric methane emission, and rumen microbial diversity of lactating dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27817},
pmid = {42019623},
issn = {1525-3198},
abstract = {The reduction of enteric methane emissions from ruminants is a central topic in research on sustainable livestock research. Feed additives targeting the rumen microbiome are among the strategies being explored to reduce methane emissions and improve nutrient efficiency. In this context, the aim of this study was to investigate the effects of an additive composed by condensed tannins and Saccharomyces cerevisiae yeast compounds on intake, productive performance, nitrogen metabolism, methane emission, and rumen microbial biodiversity of lactating Holstein and Holstein × Gyr dairy cows. Sixteen dairy cows (8 Holstein and 8 Holstein × Gyr) were allocated to 2 treatments following a randomized block design according to milk yield and DIM: a control treatment (CON; without additive) and an additive treatment (ADT), in which the diet contained 2.7 g/kg DM of a commercial feed additive composed of condensed tannins from Acacia mearnsii and yeast compounds derived from Saccharomyces cerevisiae (Muucare Nature®). The trial lasted 84 d, including a 24-d adaptation period. The animals were housed in tie stalls and kept under identical conditions. Between d 17-19 and 47-49, samples of orts and feeds offered to the animals were collected. On d 18 and 19, as well as 48 and 49, spot collections of feces and urine were performed. Rumen fluid was collected via an esophagus on d 22 and 52, and the microbial composition was later analyzed by 16S rRNA sequencing. The VFA concentrations and rumen ammonia nitrogen were also quantified. Methane emission was measured using the sulfur hexafluoride tracer technique. The additive increased the apparent digestibility of DM and OM by about 6% without affecting feed intake, milk yield, and feed efficiency. Methane emission per ECM (g/kg) was reduced by almost 30%, and methane emission per milk yield (g/kg) showed a similar trend. The ADT cows showed higher propionate production and a lower acetate-to-propionate ratio. The microbial diversity in the rumen was altered, with a reduced α diversity and a different community composition, including an increased abundance of Prevotella ruminicola. The total amount of methanogens was unchanged, although one species, Methanobrevibacter smithii, tended to be less abundant. The additive reduced methane emission and improved nutrient digestibility, rumen fermentation, and nitrogen efficiency. These results indicate that the additive based on Acacia tannins and Saccharomyces cerevisiae yeast is a sustainable tool to reduce methane emissions in dairy production systems without compromising milk production.},
}
@article {pmid42019697,
year = {2026},
author = {Gao, Y and Liu, Y and Hussain, I and Wang, L and Cheng, F and Zheng, Z and Cai, Y and Wang, X},
title = {Integrated microbiome-metabolomics profiling reveals substrate-dependent variation in agricultural Jiaosu from fruit waste.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134668},
doi = {10.1016/j.biortech.2026.134668},
pmid = {42019697},
issn = {1873-2976},
abstract = {Agricultural Jiaosu (AJ), a novel biotechnology, is used to stably obtain beneficial microbiome and metabolites from organic waste. It is widely applied in agriculture and environmental remediation and is particularly suitable for the efficient treatment of fruit waste. However, the characteristics and differences in the microbiome and metabolome of AJ prepared from different substrates remain unclear. Herein, the substrate-dependent variations in microbial consortia and metabolomic profiles across six types of AJ prepared from different substrates were revealed through integrated microbiome and metabolomics analyses. Metabolomics analysis identified a total of 3,159 metabolites, and random forest machine learning analysis of differentially expressed metabolites indicated that 50% of the top 20 marker metabolites across the six AJ samples belonged to organoheterocyclic compounds, organic acids and derivatives, shikimates and phenylpropanoids. Microbial analysis revealed that Lactobacillus and Lentilactobacillus constituted the core microbiome in all six AJ, and that mixed fruit waste AJ exhibited the highest microbial diversity. Carbohydrate metabolism genes (19.57% of total metabolic genes) were predominant. Notably, genes encoding enzymes involved in pyruvate, propanoate, and butanoate metabolic pathways exhibited high expression in the mixed fruit waste AJ. Correlation and co-occurrence network analyses revealed robust interconnections among physicochemical properties, differential metabolites, and significant microorganisms within the AJ system. This study demonstrates how substrate selection shapes the functional microbiome and metabolic landscape of AJ through integrated multi-omics analysis, offering mechanistic insights for the engineered production of AJ.},
}
@article {pmid42019703,
year = {2026},
author = {Burch, K and Sahyoun, AM and Abutineh, S and Munkhsaikhan, U and Alipour, M and Zahran, G and Ait-Aissa, K and Wang, Q and Samy, S and Kassan, A and Ishrat, T and Abidi, AH and Kassan, M},
title = {From mouth to mind: Investigating oral microbial contributions to autism spectrum disorder.},
journal = {Neuroscience and biobehavioral reviews},
volume = {186},
number = {},
pages = {106702},
doi = {10.1016/j.neubiorev.2026.106702},
pmid = {42019703},
issn = {1873-7528},
abstract = {Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition characterized by persistent social communication challenges and restricted, repetitive patterns of behavior. ASD arises from both genetic and environmental influences. Growing evidence also points to microbial dysbiosis, especially in the gut and mouth, as a potential contributor to neurodevelopment and symptom patterns. While gut microbiome alterations have been well documented in ASD, the oral microbiota has received comparatively less attention, despite its established roles in systemic inflammation, immune regulation, and even neurological function. Understanding these microbial shifts may help identify early biomarkers and guide oral health interventions to improve outcomes in ASD populations. This narrative review synthesizes current knowledge on the relationship between oral microbiota dysbiosis and ASD, with three primary objectives: (1) to characterize oral microbiome alterations observed in individuals with ASD compared to neurotypical controls; (2) to explore potential mechanisms linking oral dysbiosis to core and comorbid ASD symptoms; and (3) to evaluate therapeutic strategies targeting the oral microbiome as potential interventions for ASD.},
}
@article {pmid42019706,
year = {2026},
author = {Li, G and Wu, M and Yang, X and Song, Y and Zhao, T and Zeng, Z},
title = {Disruption of the core intestinal microbiota contributes to fluoride-induced neurotoxicity in the host organisms.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {},
number = {},
pages = {110547},
doi = {10.1016/j.cbpc.2026.110547},
pmid = {42019706},
issn = {1532-0456},
abstract = {Fluoride is a potential environmental toxic substance associated with dental fluorosis, skeletal fluorosis, and neurotoxic effects. However, the underlying mechanisms remain poorly understood, especially concerning the potential role of fluoride-induced intestinal microbiota dysbiosis in modulating the nervous system via the gut-neuraxis. In this study, an interspecies insect model of fluoride-induced neuronal damage was established to investigate the underlying mechanisms. The results showed markedly elevated malondialdehyde levels, along with reduced glutathione content and decreased catalase and acetylcholinesterase activity in the hemolymph, while histopathological analysis further confirmed the extent of oxidative damage in the nervous tissues caused by fluoride exposure. Using 16S rRNA amplicon sequencing, we found that fluoride decreased the relative abundance of core intestinal microbiota such as Enterococcus, Staphylococcus, and Delftia, while increasing the abundance of unclassified norank_o_Chloroplast and norank_f_Mitochondria taxa. Additionally, the intestinal microbiome exhibited significant heterogeneity, a reduced gut microbiome health index, and an elevated microbial dysbiosis index under fluoride exposure. Metabolomics results indicated that metabolic pathways such as D-amino acid metabolism, aminoacyl-tRNA biosynthesis, ABC transporters, and purine metabolism were enriched following fluoride treatment. Fluoride exposure also significantly altered the levels of several neurotransmitter-related metabolites, including L-glutamate, L-glutamic acid, N-acetyl-L-glutamic acid, L-glycine, spermidine, and serotonin (P < 0.05). Pearson's correlation analysis revealed a relationship between intestinal microbiota dysbiosis and disruptions in neurotransmitter metabolites. These findings provide new insights into the mechanisms of fluoride-induced neurotoxicity, improving the understanding of neurological pathology in fluorosis-endemic areas.},
}
@article {pmid42019707,
year = {2026},
author = {Guo, W and Jin, B and Pang, L and Liu, Y and Liu, D and Dong, Z and Chen, G},
title = {Unraveling olanzapine toxicity in planarian: Multi-omics reveals mechanisms of behavioral and regenerative deficits.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {306},
number = {},
pages = {110548},
doi = {10.1016/j.cbpc.2026.110548},
pmid = {42019707},
issn = {1532-0456},
abstract = {The pervasive release of antipsychotic pharmaceuticals into aquatic environments poses significant ecotoxicological risks. An integrated multi-omics framework was employed to comprehensively elucidate the toxicological effects and underlying mechanisms of olanzapine (OLA) on the freshwater planarian Dugesia constrictiva. Exposure to environmentally relevant (0.5 μg L[-1]) and elevated (5 μg L[-1]) concentrations of OLA induced significant morphological alterations and behavioral deficits. Pronounced neurotoxicity was evidenced by severe damage to the central nervous system, culminating in the complete loss of neural structures at higher concentrations. OLA exposure significantly impaired planarian regeneration, accompanied by alterations in stem cell proliferation and differentiation. Transcriptomic analysis revealed that OLA exposure dysregulated key cellular pathways, enhancing autophagy while suppressing neurodevelopment, immune function, and apoptosis. Metabolomic profiling further confirmed profound disruptions in energy metabolism and biosynthetic pathways, including the downregulation of steroid hormone biosynthesis and diverse amino acid metabolism. Moreover, OLA exposure induced significant shifts in the planarian microbiome, characterized by reduced alpha diversity, the emergence of opportunistic pathogens (Legionella), and a marked depletion of dominant taxa (Rhodoferax), indicating OLA-induced microbial dysbiosis. Collectively, our results provide novel mechanistic insights into the complex, cascading ecotoxicological effects of OLA on a representative aquatic invertebrate and underscore the significant environmental hazards posed by pharmaceutical contaminants in aquatic ecosystems.},
}
@article {pmid42019863,
year = {2026},
author = {Kim, T and Nguyen, I and Thomas, N and Picker, M and Clemente, JC and Agrawal, M and , },
title = {Intestinal inflammation impacts gestational weight gain in women with inflammatory bowel disease and growth in offspring.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2026.04.013},
pmid = {42019863},
issn = {1542-7714},
}
@article {pmid42020064,
year = {2026},
author = {Peters, BA},
title = {Evidence grows for the gut-kidney axis, but questions still remain.},
journal = {Kidney international},
volume = {109},
number = {5},
pages = {832-834},
doi = {10.1016/j.kint.2026.02.015},
pmid = {42020064},
issn = {1523-1755},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Kidney/microbiology/metabolism ; Metabolomics ; Cross-Sectional Studies ; Metagenomics ; },
abstract = {Lin et al. presented the largest cross-sectional study to date on the gut microbiome and kidney health. Their use of a vast sample size, discovery and validation approach, shotgun metagenomics, and integration with serum metabolomics represents a significant advance. In this commentary, we place these new findings into context with prior research and highlight the need for studies with a prospective design to identify true temporal relationships of the gut microbiome with kidney health.},
}
@article {pmid42020126,
year = {2026},
author = {Ticlla, MR and Dumbaugh, M and Condori-Catachura, S and Kenfack, J and Hattendorf, J and Van Der Donck, L and Arista, KM and Arora, N and Gebert, S and Ackermann, L and Ahannach, S and Riveros, M and Blas, MM and Kenmoe, S and Barrière, FY and Shea, AA and Pinedo-Cancino, V and Rivas-Ruiz, R and Di Cecco, V and Esemu, L and Ochoa, TJ and Lebeer, S and Martin Hilber, A and Merten, S},
title = {Improving menstrual and vaginal health for all (IMVAHA): protocol for a randomised cross-over trial assessing the impact of menstrual products on the vaginal microbiome of women aged 18-35 years in Cameroon, Peru and Switzerland.},
journal = {BMJ open},
volume = {16},
number = {4},
pages = {e108568},
doi = {10.1136/bmjopen-2025-108568},
pmid = {42020126},
issn = {2044-6055},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Menstrual Hygiene Products ; Adult ; *Microbiota ; Young Adult ; Adolescent ; Cross-Over Studies ; Cameroon ; *Menstruation ; Switzerland ; Peru ; Randomized Controlled Trials as Topic ; Cross-Sectional Studies ; Health Surveys ; },
abstract = {INTRODUCTION: Menstrual health is critical to achieving gender equity and reaching the 2030 Sustainable Development Goals, yet evidence on the health impacts of menstrual products-particularly on the vaginal microbiota-is limited. The Improving Menstrual and Vaginal Health for All (IMVAHA) project aims to address this knowledge gap through qualitative exploration, a health survey and clinical trial embedded in three sister projects: Laura (Peru), Leke (Cameroon) and Marie (Switzerland). This paper outlines the protocol for the IMVAHA health survey and clinical trial studies, which aim to (1) assess menstrual hygiene practices, product preferences and vaginal health; and (2) evaluate longitudinal changes in vaginal microbiota associated with the use of pads, tampons and menstrual cups.<br><br>METHODS AND ANALYSIS: The IMVAHA project will take place in urban Cameroon, urban Peru, and in Switzerland. The baseline survey will explore vaginal and menstrual health behaviours and preferences, including vaginal complaints, menstrual products and menstrual stigma. Descriptive statistics will be calculated for a cross-sectional profile of vaginal and menstrual health within and between contexts, and mixed effects linear regression models will be run to identify associations between contextual factors and key vaginal and menstrual outcomes. From survey participants, 300 eligible, consenting women (100 per country) will be enrolled in a 7-month crossover clinical trial. As a self-controlled trial, a dedicated control group is not necessary. Each participant will use pads, tampons and menstrual cups for two menstrual cycles per product, providing vaginal swabs at baseline and post-menstruation. Swabs will undergo 16S rRNA sequencing, pH testing and screening for toxic shock syndrome-related bacteria. A short survey on health behaviours and symptoms, menstrual hygiene practices and participant experiences with different menstrual products will be administered during each menstrual period. The primary outcome of the clinical trial is the log ratio of Dialister to Lactobacillus crispatus abundance measured after the use of different menstrual products. Mixed-effects linear regression will assess differences in the primary outcome across product types. Secondary analyses will include per-protocol comparisons and ORs with 95% CIs.<br><br>ETHICS AND DISSEMINATION: The study complies with the Declaration of Helsinki, Council for the International Organizations of Medical Sciences guidelines and local regulations. Ethical approval has been obtained in all three countries (National Ethics Committee for Human Health Research in Cameroon (CE N&#xb0; 2024/03/1649/CE/CNERSH/SP); the Institutional Review Board of the Universidad Peruana Cayetano Heredia and Universidad Nacional de la Amazon&#xed;a Peruana in Peru (217572) and the Ethics Commission of Northwest and Central Switzerland (2024-02135)). Informed consent will be obtained from all participants after detailed explanation of study procedures and risks. Data will be securely stored, with participant anonymity maintained. A political economy analysis will explore regulatory environments for menstrual products, and findings will be disseminated through policy briefs, stakeholder networks, academic publications and conferences.<br><br>TRIAL REGISTRATION NUMBER: NCT06646185.},
}
@article {pmid42020220,
year = {2026},
author = {Zhang, W and Xu, JH and Yu, T and Chen, QK},
title = {Retraction notice to "Effects of berberine and metformin on intestinal inflammation and gut microbiome composition in db/db mice" [Biomedicine &amp; Pharmacotherapy 118 (2019) 109131].},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {},
number = {},
pages = {119408},
doi = {10.1016/j.biopha.2026.119408},
pmid = {42020220},
issn = {1950-6007},
}
@article {pmid42020299,
year = {2026},
author = {Gao, J and Lau, HC and Fuhler, GM and Yu, J},
title = {Gastric microbiota-mediated immune remodelling in gastric cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338505},
pmid = {42020299},
issn = {1468-3288},
abstract = {Increasing evidence indicates that the gastric microbiota plays crucial roles in regulating the tumour microenvironment (TME), influencing gastric tumourigenesis and progression. Several bacteria, including Streptococcus, Lactobacillus and Bacteroides, have shown robust immunomodulatory effects on TME. In this review, we summarise current understanding of the crosstalk between the gastric microbiota and TME in gastric cancer (GC). Functional alterations of the gastric microbiota from healthy mucosa to malignancy are delineated, with emphasis on the impacts of bacteria on different immune cell populations in gastric tumours, such as CD8[+] T cells, macrophages, dendritic cells and regulatory T cells. The immunomodulatory roles of microbial metabolites and pathogen-associated molecular patterns in shaping immune cell infiltration, cytokine profiles and checkpoint molecule expression are also explored. While immune checkpoint blockade (ICB) has emerged as a promising treatment of various cancers, its efficacy in GC remains unsatisfactory due to the immunosuppressive gastric TME. We therefore evaluate the intricate interplays between the gastric microbiota and immunotherapy, and suggest potential microbiota-targeting strategies (eg, microbiota modulation, probiotics supplementation and combination therapies) to enhance antitumour immune response and boost ICB efficacy. We conclude by highlighting current challenges and providing future directions for microbiota research in GC. Overall, a deeper understanding of host-microbe interactions can provide promising avenues for precision medicine and the development of microbiota-targeting interventions against GC.},
}
@article {pmid42020421,
year = {2026},
author = {Shahzadi, I and Xue, W and Ubaid Ullah, H and Maddamsetti, R and You, L and Wang, T},
title = {Integrating theory and machine learning to reveal determinants of plasmid copy number.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72303-0},
pmid = {42020421},
issn = {2041-1723},
support = {12401660//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470701//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Plasmids are extrachromosomal mobile genetic elements whose copy numbers (PCNs) critically influence microbial evolution, antibiotic resistance and pathogenicity. Despite their importance and immense diversity, the ecological, evolutionary and molecular factors determining PCN remain poorly understood. Here, we present a theoretical model to explain the empirical power-law relationship between plasmid size and copy number, one of the fundamental quantitative principles governing PCN control. However, this relationship alone has limited predictive power. To improve PCN prediction, we introduce a data-driven approach incorporating diverse features. Trained and tested on 11,051 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct a large-scale analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, revealing putative niche specific taxonomic PCN hotspots and hypothesis-generating ecological trends. These results provide valuable insights into plasmid ecology, antibiotic resistance genes (ARGs) surveillance and shed lights on the gut plasmidome, a "dark matter" in human microbiome.},
}
@article {pmid42020446,
year = {2026},
author = {Goswami, S and Ansari, A and Saraf, C and O'Toole, PW and Shanahan, F and Ahuja, V and Ghosh, TS},
title = {Gut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patterns.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72289-9},
pmid = {42020446},
issn = {2041-1723},
support = {BT/RLF/Re-entry/55/2021//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; DST/INSPIRE/Fellowship/2023/IF230228//Department of Science and Technology, Ministry of Science and Technology (DST)/ ; },
abstract = {Bifidobacteria are key health-associated members of the human gut microbiome and are widely used as probiotics, but their colonization success varies substantially between individuals, partly due to baseline microbiome composition. We analyzed 51,244 gut microbiomes from 149 cohorts (45 countries) to identify non-Bifidobacterial taxa associated with the Bifidobacterial features. We observed several consistent and age-/life-style-specific association patterns of different non-Bifidobacterial taxa with the different Bifidobacteria. Multiple Bifidobacteria showed positive associations with butyrate-producing Firmicutes and Collinsella; negative associations involved pathobiont-Firmicutes and specific Bacteroidota taxa. B. adolescentis and B. breve showed the strongest positive and negative associations, respectively, with health-associated adult gut microbiome members. We quantified these relationships as Association-Scores, stratified by age/life-style/sequencing-strategy/disease, which were significantly reproducible after adjusting for multiple microbiome-linked, host life-style/clinical covariates, and predictable using species-specific genomic functions. We used these Association-Scores to derive microbiome-level Receptive-Scores that quantify how permissive a baseline microbiome is to increases or persistence of a given Bifidobacterium. In an external dataset of eight Bifidobacterium interventions (n = 1633 gut microbiomes), Receptive-Scores combined with baseline abundance of the administered Bifidobacteria significantly predicted post-treatment persistence/increase in 69.23% of trial-probiotic pairs. Together, this work identifies microbiome features governing Bifidobacterial colonization and provides tools to predict personalized probiotic responses.},
}
@article {pmid42020464,
year = {2026},
author = {Bergo, NM and Peres, FV and Vieira, DC and Modolon, F and Moreira, JCF and Lizárraga, RGM and Romano, RG and Bendia, AG and Lemos, LN and de Moura Emilio, A and Amendola, AM and Castano, DCD and Chuqui, MG and Paula, FS and Brandão, WSG and Fonseca, G and Vasconcelos, ATR and Jonck, CR and Moreira, DL and Brandini, FP and Pellizari, VH},
title = {Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37419-9},
pmid = {42020464},
issn = {2045-2322},
support = {5850.0109317.18.9 and 21167-2//Petr&#xf3;leo Brasileiro S.A. (PETROBRAS)/ ; E-26/201.046/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {The pelagic environment represents a mosaic of biogeographical domains shaped by regional oceanographic processes. Here, a coastal-to-open ocean microbiome investigation was conducted from 64 water samples of the Santos Basin (SB), located in the subtropical South Atlantic Ocean. We combined shotgun metagenomics with a hybrid machine learning workflow to investigate the taxonomic diversity, community structure, and ecosystem functions of pelagic microbiomes. The workflow integrated self-organizing maps (unsupervised) for pattern discovery and Random Forest (supervised) for predictive modeling. Unsupervised machine learning revealed a clear spatial and vertical (light-driven) distribution, with indicator taxa reflecting biogeochemical patterns consistent with global surveys. Supervised learning identified phosphate, salinity, and nitrate, influenced by local upwelling and La Plata River plume, as the primary environmental drivers of microbial community structure. In terms of functionality, the SB microbiome displayed depth- and region-specific patterns: photoautotrophs and nitrogen fixers dominated photic waters (with differences between coastal and oceanic stations), whereas chemolithoautotrophs and mixotrophs prevailed in the aphotic zone. Notably, nitrification signatures were more frequent in northern mesopelagic communities, while sulfur-oxidation pathways were enriched toward the south. Genes for CO bio-oxidation and dimethylsulfoniopropionate (DMSP) degradation were present across all depths. Furthermore, potential non-cyanobacterial diazotrophs were detected in the deep waters, underscoring previous underappreciated to nitrogen cycling. Our findings indicated that the Santos Basin hosts a functionally diverse microbiome including putative novel lineages. The taxonomic and functional patterns observed in the SB might provide insights into potential ecological responses to shifts in nutrient dynamics and physical processes. This investigation provides an ecogenomic baseline for understanding the microbial ecosystem services in subtropical oceans and reveals the potential of machine learning to uncover ecological patterns in underexplored marine regions.},
}
@article {pmid42020632,
year = {2026},
author = {Kalra, A and Dominoni, D and Boonekamp, J},
title = {The impact of microplastics on the mice gut microbiome: a meta-analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49190-y},
pmid = {42020632},
issn = {2045-2322},
}
@article {pmid42020638,
year = {2026},
author = {Ahmadi, S and Sedaghat, FR and Asl, YM and Khabbaz, A and Hosseinzadeh, N and Poortahmasbe, V and Hasani, R and Hosseini, S and Yazdchi, M and Mehdizadehfar, E and Salehi-Pourmehr, H and Naseri, A and Hasani, A},
title = {Faecalibacterium prausnitzii and Akkermansia muciniphila: driving the multiple sclerosis-a systematic review.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {42020638},
issn = {1572-9699},
support = {70699//Research Center for Infectious Diseases and Tropical Medicine, Tabriz University of Medical Sciences/ ; },
mesh = {Humans ; *Multiple Sclerosis/microbiology ; *Gastrointestinal Microbiome ; *Faecalibacterium prausnitzii/physiology ; Dysbiosis/microbiology ; Akkermansia ; },
abstract = {The gut microbiota (GM) is a complex microbial ecosystem, and its alteration contributes to the development of several diseases including multiple sclerosis (MS). Progressive research concerning neurodegenerative diseases and GM reveals that GM dysbiosis has been linked to fostering the development and progression of MS. Among existing bacteria, F.prausnitzii and A.muciniphila are key species implicated in this disease. Thus, the present study systematically reviewed and synthesized the research on the involvement of F. prausnitzii and A. muciniphila in MS patients versus healthy individuals. We systematically searched PubMed, MEDLINE, EMBASE, and Web of Science databases for relevant published articles from January 2010 till January 2023. Out of 400 articles, 16 met the required criteria. The included research investigations originated from the US, Germany, Norway, Egypt, Iran, Brazil, China, the UK, and Romania. Most publications reported decreased levels of F. prausnitzii and increased levels of A. muciniphila in MS patients compared to controls. This review underscored the importance of the F. prausnitzii and A. muciniphila in MS, which could explain the chronic inflammation that characterizes this disease and not only help in understanding its etiology and progression but also open new avenues for the treatment strategies focusing on gut health. Moreover, understanding the role of F. prausnitzii and A. muciniphila could lead to novel biomarkers for early detection and progression monitoring MS.},
}
@article {pmid42020750,
year = {2026},
author = {Grieshop, MP and Behr, AA and Bowden, S and Lin, JD and Molari, M and Reynolds, GZ and Brooks, EF and Doyle, B and Moore, AA and Rodriguez-Nava, G and Salinas, JL and Banaei, N and Bhatt, AS},
title = {Transposable elements are driving rapid adaptation of Enterococcus faecium.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42020750},
issn = {1476-4687},
abstract = {Bacterial pathogens adapt rapidly to clinical and within-host selective pressures[1]. Insertion sequences (IS) are transposable elements that can contribute to pathogenic adaptation[2], but their activity and consequences in contemporary clinical populations are not well characterized. Here, combining large-scale genomic surveys with long-read sequencing of clinical isolates and longitudinal gut metagenomes, we quantify pathogen IS dynamics from global patterns to within-host evolution. Across 19,485 publicly available high-contiguity ESKAPEE pathogen genomes, Enterococcus faecium genomes are the most IS dense, dominated by replicative ISL3 family elements, which have proliferated in clinical lineages over the past 30 years. We find extensive chromosomal structural variation, largely involving ISL3, within a new single-hospital collection of bloodstream isolates. Long-read metagenomic sequencing of 28 longitudinal stool samples from 12 haematopoietic cell transplantation (HCT) recipients demonstrates within-host IS dynamics and their regulatory consequences. In one patient, an ISL3 insertion upstream of a folate transporter formed a strong promoter, increasing transcription and improving relative fitness under folate limitation. Enhanced folate scavenging may enable E. faecium to thrive in the setting of microbiome collapse, which is common in HCT and other critically ill patients[3]. Together, these results show that a recent ISL3 expansion is driving rapid evolution in healthcare-associated E. faecium, with consequences for its metabolic fitness that may help explain its increasing clinical burden. Several other pathogens also show elevated IS loads in our survey, which suggests that IS expansion-mediated evolution might be more broadly relevant.},
}
@article {pmid42020819,
year = {2026},
author = {Eberly, JO and Berríos-Ortiz, L and Hurd, A and Shergill, L and Dyer, AT and Menalled, FD},
title = {Wheat Rhizosphere Bacterial Community Response to Bromus tectorum (L.) and Fusarium pseudograminearum Crown Rot.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02778-3},
pmid = {42020819},
issn = {1432-184X},
support = {2020-70006-32978//National Institute of Food and Agriculture/ ; },
abstract = {Annual crop yield losses due to plant diseases and weeds can be substantial. In the northern Great Plains, Bromus tectorum (L.) (also known as cheatgrass or downy brome) and Fusarium pseudograminearum (causing crown rot) form a multi-trophic pest complex threatening wheat production sustainability. This study assessed the impact of these pests on the wheat rhizosphere bacterial community. Field trials were conducted over four site-years in plots inoculated with F. pseudograminearum using a randomized split-plot design with two seeding and nitrogen fertilizer rates and B. tectorum presence/absence. A seed fungicide treatment was also used to evaluate its effect on F. pseudograminearum abundance. Rhizosphere bacterial communities were analyzed using full-length 16 S rRNA sequencing on the Oxford Nanopore platform, followed by diversity analysis, structural equation modeling (SEM), and co-occurrence network analysis. Alpha and beta diversity were significantly different between location-years. The SEM results showed a negative relationship (β = -0.180, p = 0.002) between F. pseudograminearum presence and rhizosphere bacterial community alpha and beta diversity. Effects of B. tectorum presence, seeding rate, nitrogen fertilizer, and fungicide treatment were not significant. Correlation analysis identified specific bacterial taxa responsive to F. pseudograminearum presence, including putatively beneficial species belonging to the genera Massilia, Bacillus, and Neobacillus, which were positively correlated with pathogen presence, suggesting a stress response mechanism. Network analysis revealed that F. pseudograminearum presence reduced network cohesion, and connectivity measures compared to treatments with lower pathogen load. These findings demonstrate that fungal pathogen presence can impact rhizosphere bacterial networks even when overall diversity metrics show minimal changes, highlighting the importance of network-based approaches in understanding plant-microbe-pathogen interactions in agricultural systems.},
}
@article {pmid42021054,
year = {2026},
author = {Kennedy, MS and Chang, EB},
title = {From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2649448},
doi = {10.1080/19490976.2026.2649448},
pmid = {42021054},
issn = {1949-0984},
mesh = {Humans ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Animals ; Anti-Bacterial Agents ; },
abstract = {Predicting and promoting gut microbiome recovery following perturbations such as antibiotic treatment, dietary shifts, or inflammation remain major challenges in microbiome science and clinical practice. In this review, we explore recent advances in microbiome restitution by framing recovery as a dynamic ecological process shaped by complex interactions between microbial taxa, host physiology and environmental conditions. We review current evidence addressing four key questions that outline the salient ecology of perturbation and recovery: which microbial taxa are present in the microbiota and which taxonomic or functional qualities might increase susceptibility to perturbation; what is the nature of the perturbation, including the type and probable targets of the perturbation, as well as the indirect ecological and environmental consequences of that perturbation; what is the time course of perturbation and recovery, exploring prehabilitation strategies and successional trajectories as a staged recovery framework; and where does perturbation and recovery unfold in the gut, with attention to both regional and microscale spatial patterns. Highlighting recent advances from multi-omics approaches and longitudinal studies, we demonstrate how each of these factors and their interactions critically shape both robustness to disturbance and the trajectory of recovery. We advocate for multimodal, context-specific interventions that harness ecological principles to drive regrowth and community assembly, including diet, targeted microbial transplantation and modulation of the abiotic gut environment. Ultimately, resolving the challenge of microbiome restitution will require personalized strategies informed by ecological understanding and longitudinal functional monitoring. This paradigm provides a foundation for future translational advances to promote eubiosis and improve patient outcomes in microbiome-related diseases.},
}
@article {pmid42021149,
year = {2026},
author = {Sun, RZ and Liu, XQ and Yang, ZL and Liu, XG and Wang, HW and Deng, X},
title = {Compartment-specific assembly and genotype-associated differentiation of root microbiomes in saline-alkali-sensitive and -tolerant maize inbred lines.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08813-2},
pmid = {42021149},
issn = {1471-2229},
support = {XDA 26030201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 063GJHZ2025027GC//International Partnership Program of the Chinese Academy of Sciences for Grand Challenges/ ; },
}
@article {pmid42021382,
year = {2026},
author = {Mazumder, M and Pavagadhi, S and Bhattacharya, R and Mukherjee, A and Majedi, SM and Hin, ITC and Swarup, S},
title = {Live-exudation assisted phytobiome culturomics system (LEAP-CS): a high-throughput culturomics system for studying plant-microbiome interactions through diffusible metabolites.},
journal = {Plant methods},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13007-026-01539-0},
pmid = {42021382},
issn = {1746-4811},
}
@article {pmid42021415,
year = {2026},
author = {Faticov, M and Tack, AJM and Ortner, D and Berg, G and Abdelfattah, A},
title = {Multiple origins of the apple seed microbiome: disentangling sexual and asexual transmission pathways.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00901-y},
pmid = {42021415},
issn = {2524-6372},
support = {Grant Number: 844114, awarded to AA//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; },
abstract = {BACKGROUND: The seed microbiome plays a key role in the assembly of the plant microbiome, which has major impacts on plant health. Nonetheless, little is known about the origin of the seed microbiome. We investigated the relative contributions of two potential transmission routes: sexual inheritance (via reproductive organs) and asexual inheritance (via the plant vascular system). To do that, we sampled flower ovaries and pollen sacs, fruiting spurs both before bloom and at seed maturity stages and mature seeds from five field-grown apple trees (Malus domestica BORKH. cv 'Gala Galaxy Selecta').<br><br>RESULTS: We showed that bacterial alpha diversity differed among tissues: spurs sampled before bloom had significantly higher richness and Shannon diversity than all other compartments, whereas ovary, pollen, spurs at seed maturity, and seeds did not differ in either richness or Shannon diversity. In addition, bacterial community composition differed significantly across all tissue types (ovary, pollen, spurs before bloom, spurs at seed maturity, and seeds). Source tracking revealed that both sexual (30.3%) and asexual (23.8%) pathways contributed to seed microbiome assembly, with spurs at seed maturity being the dominant source. Notably, a large proportion (45.9%) of the seed microbiome originated from unknown sources.<br><br>CONCLUSIONS: Overall, such insights into seed microbiome origin offer new opportunities to enhance seed health and crop productivity through microbiome-assisted breeding.},
}
@article {pmid42021487,
year = {2026},
author = {Sokol, H and Elkrief, A and Routy, B},
title = {A "healthy gut state" as the key determinant of immune checkpoint inhibitor efficacy.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2026.04.034},
pmid = {42021487},
issn = {1525-0024},
abstract = {The gut ecosystem emerges as a key determinant of immune checkpoint inhibitor (ICI) efficacy. Rather than individual "beneficial" bacteria, a broader framework of gut health better explains inter-individual variability in ICI response: a non-inflamed gastrointestinal tract with preserved epithelial barrier and functionally eubiotic microbiome promotes responsiveness, while gut inflammation and barrier disruption predict poor outcomes. Integrating human and mechanistic mouse data, we propose shifting research focus toward clinically actionable gut-health axes to optimize cancer immunotherapy.},
}
@article {pmid42021627,
year = {2026},
author = {Aiube, YRA and Moreira, APB and Caires, TA and Tenório, MMB and de Moura, RL and Salomon, PS},
title = {Revealing novelty from the southwestern Atlantic, Yemanjia gen. nov. and Olokunococcus gen. nov. from the coral cyanobiome of the Abrolhos Bank.},
journal = {Journal of phycology},
volume = {62},
number = {2},
pages = {533-555},
pmid = {42021627},
issn = {1529-8817},
support = {001/2018//Funda&#xe7;&#xe3;o Esp&#xed;rito Santense de Tecnologia - FEST-RENOVA/ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {*Cyanobacteria/classification/genetics/physiology ; Animals ; *Anthozoa/microbiology ; Phylogeny ; Atlantic Ocean ; RNA, Ribosomal, 16S/analysis/genetics ; Symbiosis ; Coral Reefs ; },
abstract = {Cyanobacteria comprise over 6000 species and inhabit diverse environments, including marine invertebrates such as sponges and corals. High-throughput sequencing has indicated an abundance of Cyanobacteria communities in these hosts, yet taxonomic resolution has remained low below the phylum level. Most cultured Cyanobacteria from corals have been isolated from black band disease lesions. However, many other associated taxa remain unidentified, such as the Cyanobacteria detected with microscopy and isotopic studies near coral symbiosomes. Recently, a polyphasic approach revealed six new genera from sponges. Following a similar strategy-integrating molecular phylogeny, morphology, ecology, and chemotaxonomy-we describe two novel genera and three new species of Cyanobacteria from reef-building corals of the Abrolhos Banks (southwestern Atlantic). Two filamentous strains were assigned to the new genus Yemanjia (Cymatolegaceae), closely related to the genus Rhodoploca. A third coccoid strain was assigned to the new genus Olokunococcus (Aegeococcaceae), phylogenetically related to Aegeococcus. All isolates presented phycoerythrins. The closest formally described relatives of these new taxa are all sponge-associated, suggesting an evolutionary and ecological link between host and Cyanobacterial lineage. By providing formal taxonomic anchors for coral-associated Cyanobacteria, our results expand the current knowledge of the coral cyanobiome and facilitate the interpretation of existing and future coral microbiome datasets.},
}
@article {pmid42021774,
year = {2026},
author = {Nagybanyai-Nagy, B and Tengölics, R and Sajben, C and Olasz, D and Schwarcz, A and Molnar, T and Csecsei, P},
title = {Serum microbiome-related metabolites-including short-chain fatty acids and indole derivatives-predict outcome and delayed cerebral ischemia after aneurysmal subarachnoid hemorrhage: a two-timepoint LC-MS study.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1768108},
pmid = {42021774},
issn = {1664-2295},
abstract = {BACKGROUND: Delayed cerebral ischemia (DCI) remains a major determinant of poor outcome after aneurysmal subarachnoid hemorrhage (aSAH). Growing evidence suggests that gut microbiota-derived metabolites, including short-chain fatty acids (SCFAs) and tryptophan-related indole compounds, modulate neuroinflammation and cerebrovascular vulnerability. However, their temporal dynamics and clinical relevance after aSAH are insufficiently characterized.<br><br>METHODS: In this prospective observational study, 80 consecutive patients with aSAH were enrolled at a tertiary neurocritical care center. Serum concentrations of SCFAs (propionic, butyric, isobutyric, valeric, isovaleric, caproic acids) and tryptophan-derived metabolites (tryptophan, indole-3-propionic acid [IPA], indole-3-acetic acid, indole-3-lactic acid) were quantified using LC-MS on Day 1 and Day 9 after hemorrhage. Functional outcome at 3&#x202f;months was assessed using the modified Rankin Scale (mRS), and DCI was diagnosed according to consensus criteria. Associations were analyzed using non-parametric statistics, ROC analyses, and multivariable logistic regression adjusted for established clinical confounders.<br><br>RESULTS: Patients with unfavorable 3-month outcomes (mRS 4-6) showed significantly lower Day 1 levels of propionic, isobutyric, and isovaleric acids, persistently reduced tryptophan at both time points, and markedly lower IPA concentrations on Day 9. DCI was associated with reduced tryptophan and propionic acid levels on both days and a pronounced decrease in IPA on Day 9. Tryptophan and propionic acid demonstrated excellent discriminative performance for outcome and DCI (AUCs up to 0.99). In multivariable models, low Day 1 propionic acid and low Day 9 IPA independently predicted unfavorable outcome, while Day 9 tryptophan, IPA, and propionic acid independently predicted DCI.<br><br>CONCLUSION: Distinct temporal alterations in gut microbiota-derived metabolites after aSAH are strongly associated with functional outcome and DCI. SCFAs and tryptophan-related metabolites-particularly propionic acid, tryptophan, and IPA-emerge as promising biomarkers and potential mechanistic mediators in secondary brain injury after aSAH.},
}
@article {pmid42022011,
year = {2026},
author = {Talavera-Marcos, S and Aguirre de Cárcer, D},
title = {Ecological drift simulations reveal key factors influencing minimal microbiome engineering and community assembly.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag067},
pmid = {42022011},
issn = {2730-6151},
abstract = {In this work, we describe an engineering approach that leverages ecological drift to generate minimal microbiomes; microbial consortia that are relatively simple, cohesive, and functionally complete. This process can be applied to any microbial ecosystem, provided that the target microbiome can be experimentally mimicked. Empirical support for this approach has emerged from multiple independent studies. We use simulations across diverse scenarios, significantly varying niche structures and biotic interactions, to explore the experimental conditions and source microbiome characteristics that favor successful outcomes, within a computational framework that also enables the study of microbial community assembly. Our results indicate that the effectiveness of this approach is constrained by several factors, and that perfect outcomes should not be routinely expected. Nevertheless, despite its drawbacks, this strategy remains a powerful tool for simplifying microbiomes and isolating key co-adapted populations, enabling the construction of low-diversity consortia that retain community function and present ecological cohesion.},
}
@article {pmid42022109,
year = {2026},
author = {Xie, W and Han, D and Tan, J and Zhao, D and Dong, J and Wu, J and Yang, X and Xie, S},
title = {Porphyromonas gingivalis drives trimethylamine-N-oxide accumulation via modulation of gut microbial trimethylamine lyase in mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786725},
pmid = {42022109},
issn = {1664-302X},
abstract = {INTRODUCTION: Trimethylamine N-oxide (TMAO), a gut microbiota-derived metabolite, is linked to cardiovascular, neurodegenerative, and metabolic diseases. Emerging evidence indicates a bidirectional interaction between the periodontal pathogen Porphyromonas gingivalis (Pg) and gut microbiota, potentially influencing host TMAO metabolism. However, whether Pg modulates the choline-trimethylamine (TMA) axis remains unclear.<br><br>METHODS: Wild-type male C57BL/6J mice received oral Pg under chow or a high-choline diet. Plasma and cecal concentrations of TMA and TMAO were quantified, intestinal barrier function was evaluated via histological analysis, and the determination of ZO-1 and occludin expression was performed. Cecal microbiota composition was profiled by 16S rRNA gene sequencing, and microbial choline-TMA lyase markers (cutC/cutD) were measured.<br><br>RESULTS: Pg elevated plasma TMAO under chow, accompanied by reduced &#x3b1;-diversity, altered &#x3b2;-diversity, and decreased expression of intestinal barrier proteins. Under high-choline conditions, the diet itself increased plasma and intestinal levels of TMAO and TMA. Pg co-exposure further amplified these effects, raising plasma TMAO, cecal TMA, and cutC/cutD levels. Microbiome analysis revealed elevated abundances of Lachnoclostridium, Odoribacter, and Colidextribacter, and reduced levels of taxa (Prevotellaceae NK3B31, Anaerostipes, and Ruminococcus) negatively correlated with TMAO-related parameters. Moreover, cutC/cutD levels were positively correlated with Colidextribacter and Lachnoclostridium, but negatively correlated with Anaerostipes and Prevotellaceae NK3B31, consistent with the modulation of TMA/TMAO metabolism by these taxa.<br><br>CONCLUSION: This study demonstrates that oral administration of Pg facilitates systemic TMAO elevation by reshaping gut microbial communities and enhancing choline-TMA lyase function, and compromising intestinal barrier integrity. These findings establish an oral-gut metabolic axis connecting periodontitis to host TMAO metabolism, and highlight promising periodontal and microbiota-targeted strategies for alleviating TMAO-associated systemic disorders.},
}
@article {pmid42022112,
year = {2026},
author = {Phulpoto, IA and Qazi, MA and Yang, J and Wang, H},
title = {Editorial: Forest soil microbiome and their interactions with the plants.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1819757},
pmid = {42022112},
issn = {1664-302X},
}
@article {pmid42022122,
year = {2026},
author = {Horseman, TS and Fong, KSK and Dombach, JL and Kamau, E and Gehrich, AP},
title = {Vaginal microbiome dysbiosis and a rectal reservoir of uropathogens characterize postmenopausal women with recurrent urinary tract infections: a cross-sectional study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1812000},
pmid = {42022122},
issn = {1664-302X},
abstract = {INTRODUCTION: Recurrent urinary tract infections (rUTIs) in postmenopausal (PM) women pose a significant clinical challenge, complicated by rising antibiotic resistance among uropathogens. The vaginal microbiota in this population remains underexplored. We aim to characterize vaginal flora of PM women with and without a history of rUTIs, and to evaluate relationships to demographic variables, clinical characteristics, and rectal pathogen colonization.<br><br>METHODS: We conducted a cross-sectional study of 62 PM women (n&#x202f;=&#x202f;31 rUTI, (n&#x202f;=&#x202f;31 control). Vaginal swabs were analyzed using 16S rRNA and a next-generation sequencing tool designed to identify UTI pathogens and antibiotic resistance (AMR) markers. Rectal swabs were cultured to identify uropathogens and their phenotypic resistance. These were integrated with subject demographic and historical clinical data.<br><br>RESULTS: Compared to controls, rUTI vaginal microbiota exhibited a marked depletion in Lactobacillus crispatus and L. iners, species commonly associated with vaginal health, alongside an enrichment of L. gasseri and L. jensenii. The rUTI cohort also had a greater burden of AMR markers (p&#x202f;=&#x202f;0.0003). Notably, Gram-negative uropathogens in the rUTI group frequently carried multidrug resistance genes, at rates nearly three times higher than controls. The rUTI cohort was further characterized by enrichment of Gram-negative uropathogens in the vagina. These alterations were more pronounced with increasing years in menopause.<br><br>DISCUSSION: The rectum emerged as a key reservoir, with notable concordance of organisms across rectal and urogenital sites. Our findings indicate that rUTIs in postmenopausal women are associated with a dysbiotic vaginal microbiome that is closely linked to a rectal reservoir of multidrug-resistant uropathogens.},
}
@article {pmid42022125,
year = {2026},
author = {Wang, S and Xie, L and Yan, Z and Ma, J and Zhao, R},
title = {Hybrid expert system for robust detection of rare sequence signals: a computational proof-of-concept in host-dominated backgrounds.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821073},
pmid = {42022125},
issn = {1664-302X},
abstract = {Deciphering microbial symbiosis in robust environmental and host-associated systems increasingly depends on the reliable recovery of weak biological signals from sequencing data dominated by non-target background. In practice, low-abundance symbiont-derived signatures are often obscured by background DNA, recurrent technical artifacts, and context-dependent false-positive calls, limiting the accuracy of downstream ecological and functional inference. Here, we present SymbioFilter, a hybrid expert system designed to improve the specificity and stability of rare-signal detection in host-associated microbiome sequencing data with substantial background noise. (i.e., overwhelming host-derived DNA, recurrent alignment errors, and sequencing artifacts). Specifically, this framework is intended for specialized usage cases where standard host-depletion strategies fail, such as capturing minor microbe-induced host somatic mutations or rare microbial homologs, which reflect subtle and intimate interactions between microbes and the host. SymbioFilter integrates three coordinated layers: (i)ensemble-based candidate detection, (ii)machine-learned background/noise discrimination using an XGBoost classifier, and (iii) rule-guided suppression of artifact-prone genomic regions using curated repetitive and blacklist annotations. Rather than relying on a single decision rule, the framework combines probabilistic classification with expert-defined constraints to preserve weak true signals while reducing recurrent false positives. This design specifically targets analytical failure modes common to host-dominated and low-input datasets, where precision is frequently compromised by rare-event noise. As a stringent proof-of-concept benchmark, we evaluated SymbioFilter in synthetic gradient spike-in datasets. Crucially, to ensure rigorous computational evaluation with an absolute ground truth-a standard that is currently unattainable in complex, real-world microbiome samples at ultra-low abundances-we utilized plasma cfDNA-like low-frequency conditions as a highly controlled, demanding proxy. Across gradient abundance levels, the framework consistently reduced false-positive inflation, improved agreement with the known ground truth, and maintained stable classification performance. Compared with a baseline pipeline and a widely used variant-calling workflow, SymbioFilter achieved lower mean squared error, stronger true-positive/true-negative balance, and consistently high precision-recall behavior, particularly under the most challenging low-abundance settings. Although validated here in a proxy benchmark environment, the computational principles of SymbioFilter address a broader class of sequencing problems central to microbial symbiosis research: identifying rare, functionally relevant biological signals in complex, noise-prone backgrounds. By providing a transferable, modular, and open computational strategy for robust signal recovery, SymbioFilter offers a useful methodological foundation for future studies of host-microbe interactions, resilient community assembly, and symbiosis-associated ecosystem stability. The code is freely available for academic use at https://github.com/hello-json/SymbioFilter.},
}
@article {pmid42022328,
year = {2026},
author = {Wu, Y and Chen, Y and Mao, J and Li, K and He, Q and Zhou, Z},
title = {Mechanistic insights into the role of oral microbiome in the malignant transformation of oral lichen planus to oral squamous cell carcinoma.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1694005},
pmid = {42022328},
issn = {2234-943X},
abstract = {Oral Lichen Planus (OLP) is a common oral potentially malignant disorder, and its transformation into Oral Squamous Cell Carcinoma (OSCC) has become a research focus. In recent years, increasing attention has been paid to the role of the oral microbiome in tumor initiation and progression. Studies have shown that dysbiosis of the oral microbiome may contribute to and accelerate the malignant transformation of OLP to OSCC through multiple mechanisms, including the induction of inflammatory responses, disruption of immune regulation, promotion of oxidative stress, and epithelial-mesenchymal transition (EMT). This review summarizes recent advances in research on the characteristic changes in the oral microbiome and associated molecular mechanisms during the malignant transformation of OLP, aiming to provide a theoretical basis and scientific support for early warning and microecological-targeted interventions in OLP malignancy.},
}
@article {pmid42022578,
year = {2026},
author = {Zeng, Y and Pan, S and Zhang, A and Wang, J and Huang, F and Yu, J and Luo, Q and Ren, B and Tahri, W},
title = {Biogas production and microbial profile estimation in bioreactor landfills.},
journal = {Frontiers in chemistry},
volume = {14},
number = {},
pages = {1742729},
pmid = {42022578},
issn = {2296-2646},
abstract = {INTRODUCTION: This study investigated the municipal solid waste (MSW) biodegradation process, simulating landfill conditions using a bioreactor. A core objective was to identify key markers in leachate that could forecast the methane (CH4) generation process during anaerobic digestion (AD). To further understand the causes of CH4 production inhibition and to propose strategies for enhancing AD system performance, we aimed to compare the microbial community structures in leachate from different reaction periods and in solid MSW samples.<br><br>METHODS: A bioreactor was utilized to replicate the landfill's MSW biodegradation process. Research workers analyzed the relationship between the methanogenic process and the properties of leachate from anaerobic digestion. To investigate the underlying causes of inhibition, we compared the features and differences in the microbial community structure of leachate samples from different reaction periods and solid samples (end-state MSW and cover layer).<br><br>RESULTS: The biogas production potential was found to be 74.36 L kg[-1], and the rate constant for MSW digestion gas production was 0.0359 days[-1]. A correlation was observed between the leachate's pH, TOC/TN ratio, and the CH4 generation process, though the correlation between pH variation and methanogenesis showed a clear lag, indicating pH alone is not a sufficient predictive signal. The system became unstable due to ammonia buildup, with a TOC/TN value below 13 coinciding with minimal gas output. Microbial analysis showed that the genetic similarity between leachate and MSW samples was inversely related to the length of the reaction period. A key observation was the absence of Nitrospirain leachate, which likely interrupts the nitrogen conversion cycle. The nitrification process was found to primarily occur in the cover layer. Decreased CH4 generation was mostly caused by ammonia inhibition, which reduced the activity of acetate-utilizing methanogenic archaea. The intermediate cover layer acted as a biochemical reaction zone with greater microbial diversity.<br><br>DISCUSSION: The findings indicate that due to ammonia buildup, the fermentation system became unstable when the TOC/TN value fell below 13. The absence of Nitrospirain leachate is identified as a critical factor disrupting the nitrogen cycle. Therefore, inoculation with Nitrospira-containing agents is proposed as crucial for maintaining system stability and enhancing treatment efficiency. The intermediate cover layer, harboring greater microbial diversity, contributed to enhanced anaerobic digestion and supported increased system stability, functioning as a vital biochemical reaction zone. These insights provide recommendations for enhancing the AD system's CH4 production capacity.},
}
@article {pmid42022800,
year = {2026},
author = {Liu, Z and Li, H and Xiang, Y and Ren, S and Pan, W and Ling, Z and Dong, J and Liang, Z and Quan, J and Fan, L and Lin, L and Wu, L and Yu, X},
title = {Longitudinal multi-omics evidence reveals lung injury and concurrent disruption of intestinal flora and serum metabolism by cigarette smoke and influenza virus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1731390},
pmid = {42022800},
issn = {2235-2988},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Orthomyxoviridae Infections/pathology/complications/virology ; Influenza A virus ; Biomarkers/blood ; Lung/pathology ; Disease Models, Animal ; *Lung Injury/pathology/metabolism/etiology ; RNA, Ribosomal, 16S/genetics ; Metabolome ; Pulmonary Disease, Chronic Obstructive/etiology ; *Smoke/adverse effects ; Metabolomics ; Mice, Inbred C57BL ; Female ; Feces/microbiology/chemistry ; Male ; Multiomics ; },
abstract = {BACKGROUND: Cigarette smoke (CS) exposure is the primary risk factor for chronic obstructive pulmonary disease (COPD), and respiratory viral infections, particularly influenza A virus (IAV), are major triggers of acute exacerbations of COPD (AECOPD). However, the dynamic interactions among pulmonary pathology, gut microbiota, and host metabolism during these episodes remains unclear. This study aimed to delineate the longitudinal characteristics of virus-induced AECOPD and identify potential biomarkers.<br><br>METHODS: Mice were exposed to cigarette smoke for eight weeks, followed by intranasal inoculation with IAV. A longitudinal assessment was conducted from day 1 to day 15 post-infection, integrating analyses of lung pathology, lung function, gut microbiome, and both serum and fecal metabolomes. Additionally, random forest modeling was employed to identify specific metabolic biomarkers associated with the acute exacerbation stage.<br><br>RESULTS: Mice exposed to cigarette smoke and IAV exhibited significant pulmonary immune cell recruitment, impaired lung function, and emphysematous changes, peaking at day 5 post-infection. By day 15, acute airway inflammation had subsided; however, interstitial immune cell infiltration, collagen deposition, and emphysema persisted. 16S rRNA sequencing revealed dynamic shifts in gut microbiota composition, with the abundance of Intestinimonas positively correlating with pulmonary inflammatory markers. Untargeted metabolomics demonstrated sustained downregulation of serum unsaturated fatty acid biosynthesis pathways from day 3 to day 15, and these metabolites were negatively correlated with lung inflammation. Random forest analysis identified 1-Methylnicotinamide (1-MNA) as a promising biomarker for distinguishing virus-triggered AECOPD, achieving an area under the curve (AUC) of 1.0.<br><br>CONCLUSION: This study demonstrates that cigarette smoke combined with influenza infection induces persistent lung injury alongside concurrent disruption of intestinal flora and serum metabolism. The findings show that gut microbiota and metabolites are potential biomarkers and supplementation with unsaturated fatty acids may represent a novel therapeutic strategy for virus-induced AECOPD.},
}
@article {pmid42022809,
year = {2026},
author = {Tian, YP and Li, QH and Li, YM and Zhao, JY and Wei, XX and Wang, JY and Zhou, YL and Yang, SB and Li, W and Guo, P and Wang, LX and Dai, TT and Hu, SF and Zhong, ZQ and Xie, YM and Lv, ZH},
title = {Gut microbiota and metabolome signatures in preterm infants with high versus low risk for neurodevelopmental impairment: a prospective, matched, longitudinal multi-omics study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799859},
pmid = {42022809},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Infant, Premature ; Prospective Studies ; *Metabolome ; Longitudinal Studies ; Female ; Male ; Infant, Newborn ; Feces/microbiology ; *Neurodevelopmental Disorders/microbiology ; Metagenomics ; Infant ; Metabolomics ; Bacteria/classification/genetics/isolation &amp; purification ; Biomarkers ; Dysbiosis/microbiology ; Multiomics ; },
abstract = {Preterm birth is a leading global cause of neurodevelopmental impairment (NDI), yet early predictive biomarkers remain elusive. The gut microbiome, developing in parallel with the brain and communicating via the microbiota-gut-brain axis, holds potential as a source of such biomarkers. However, specific longitudinal multi-omics signatures predictive of NDI risk in preterm infants are poorly defined. We conducted a prospective, matched, longitudinal study of 60 preterm infants, classified at 3 months corrected age (CA) into high-risk (HR, n=30) or low-risk (LR, n=30) groups for NDI based on combined motor (TIMP) and neurological (GMs) assessments. Fecal samples from birth (meconium) and 3 months CA underwent shotgun metagenomic sequencing and untargeted metabolomics. Groups were rigorously matched for gestational age, birth weight, sex, and clinical exposures. While α- and β-diversity did not differ between groups, profound taxonomic and functional divergence emerged. At 3 months CA, the LR gut was enriched with Akkermansia muciniphila, whereas the HR gut was dominated by Klebsiella variicola. Functional metagenomics revealed a dysbiotic HR trajectory, enriching pathways for bacterial virulence, stress response, and-notably-multiple pathways annotated for human neurodegenerative diseases, contrasting with LR expansion of core biosynthesis. Metabolomics confirmed a dysfunctional HR state, showing impaired amino acid metabolism and aberrant neuroactive pathway enrichment. Critically, meconium features correlated with 3-month neurobehavioral scores, demonstrating ultra-early predictive potential. Integrated networks at 3 months directly linked Akkermansia muciniphila and co-varying glycerophospholipids to superior neurodevelopmental scores, forming a beneficial "Akkermansia-lipid" axis, while Klebsiella variicola and triterpenoids formed a dysbiotic hub. Our study defines a high-risk gut ecosystem trajectory in preterm infants, characterized by early commensal depletion, pathobiont expansion, and a functional shift towards inflammation and neuroinflammation. These signatures offer novel targets for early risk prediction and microbiome-targeted interventions.},
}
@article {pmid42022943,
year = {2026},
author = {Fu, F and Zhang, C and Xu, Z and Ji, P and Zhang, Z},
title = {Gastric Microbiome Alterations in Sepsis-Related Gastrointestinal Bleeding: Two Case Reports and Literature Review.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {10},
number = {3},
pages = {e70318},
pmid = {42022943},
issn = {2397-9070},
abstract = {Sepsis, characterized by life-threatening organ dysfunction resulting from an uncontrolled response to infection, can impact various systems of the body, including the digestive system. Prior research has identified sepsis as a significant risk factor for gastrointestinal bleeding. However, there is limited reporting on the gastric microecology of individuals with sepsis complicated by gastrointestinal bleeding. This paper presents the cases of two patients, shedding light on this issue. The first case was a 29-year-old female who developed sepsis during perioperative liver transplantation, while the second case features a 34-year-old female with acute pancreatitis complicated by septic shock. Both patients underwent gastroscopy following gastrointestinal bleeding, revealing evident gastric mucosal injuries. Notably, the second patient exhibited suppurative gastritis. Metagenomic Next-Generation Sequencing (NGS) of gastric juice from these two patients unveiled microecological alterations in the stomach. The sequencing results indicated a substantial presence of pathogenic sequences, underscoring the role of direct gastric mucosal injury due to infection as a significant contributor to gastrointestinal bleeding. This study not only introduces a novel approach to pinpointing the causes of gastrointestinal bleeding in sepsis but also provides valuable insights for clinical diagnosis and treatment.},
}
@article {pmid42022944,
year = {2026},
author = {Zhao, Z and Ling, J and Chen, J},
title = {Oral Microbiome and Constipation: A Causal Link Revealed by Mendelian Randomization.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {10},
number = {3},
pages = {e70390},
pmid = {42022944},
issn = {2397-9070},
abstract = {BACKGROUND: Constipation affects approximately 15.3% of the global population. While the gut microbiome's role in constipation has been studied, the causal relationship between the oral microbiome and constipation remains unexplored.<br><br>METHODS: We utilized Mendelian randomization (MR) and large-scale GWAS data to investigate the causal relationship between the oral microbiome and constipation. Oral microbiome data were sourced from a metagenome-wide association study (mgGWAS) on 2984 individuals, while constipation GWAS data came from 176&#x2009;629 samples in the Japan Biobank. Statistical methods included inverse variance-weighted (IVW) analysis, weighted median, and MR-Egger regression.<br><br>RESULTS: The MR analysis revealed significant associations between specific oral microbiome and constipation. Treponema denticola, found in saliva, was positively associated with an increased risk of constipation (OR&#x2009;=&#x2009;3.961, 95% CI&#x2009;=&#x2009;1.085-14.453, p&#x2009;=&#x2009;0.037). Conversely, certain bacteria like Pauljensenia sp000308055 showed protective effects (OR&#x2009;=&#x2009;0.409, 95% CI&#x2009;=&#x2009;0.167-0.999, p&#x2009;=&#x2009;0.0496). In the tongue coating, Neisseria sicca exhibited a significant positive association with constipation (OR&#x2009;=&#x2009;4.864, 95% CI&#x2009;=&#x2009;1.293-18.302, p&#x2009;=&#x2009;0.019), while Aggregatibacter segnis demonstrated a protective effect (OR&#x2009;=&#x2009;0.400, 95% CI&#x2009;=&#x2009;0.188-0.854, p&#x2009;=&#x2009;0.018).<br><br>CONCLUSION: This study is the first to explore the potential causal relationship between oral microbiome and constipation. The findings suggest that specific oral bacteria may influence the risk of constipation, highlighting the need for further research to validate these relationships and understand the mechanisms involved. Moreover, the study underscores the importance of considering both oral and gut microbiome in the context of gastrointestinal health and disease management.},
}
@article {pmid42023035,
year = {2026},
author = {Shi, Z and Zhang, Y and Chen, Y and Wu, S and Zhou, Z and Chen, Z},
title = {Investigating oral microbiome profiles of children with cleft lip and palate in different states of caries.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2660486},
pmid = {42023035},
issn = {2000-2297},
abstract = {OBJECTIVE: To investigate the characteristics of oral salivary microbiota in children with cleft lip and palate (CLP) under different states of caries.<br><br>METHODS: Based on the presence or absence of CLP and the total number of decayed, missing and filled surfaces, 105 participants were divided into four groups: children with CLP and high caries (CLP-HC), children with CLP and low caries (CLP-LC), children without CLP but with high caries (NCLP-HC) and children without CLP but with low caries (NCLP-LC). Saliva samples from them were analyzed using 16S rRNA gene sequencing.<br><br>RESULTS: Alpha diversity differed significantly among the four groups with Ace and Chao indices, but not with Shannon and Simpson. Principal coordinate analysis based on the Weighted-UniFrac distance matrix showed no significant differences among the four groups, while results from the Unweighted-UniFrac distance matrix revealed significant differences. CLP-HC and CLP-LC had significantly higher Microbial Dysbiosis Index than NCLP-LC. LEfSe analysis was performed for pairwise comparisons, identifying differentially enriched bacterial genera among groups. Network analysis based on Spearman correlation revealed the interaction characteristics of microbial communities in different groups.<br><br>CONCLUSIONS: Differences in microbial features were observed among the four groups, which could provide new insights for personalized oral health management for CLP patients.},
}
@article {pmid42023165,
year = {2026},
author = {Xu, Z and Zhang, L and Guo, J and Xia, Q and Ge, Z and Wang, Z and Mu, R and Dong, J and Qin, Z and Chen, J and Wang, Y},
title = {Controlled release of berberine modulates the wound microbiome to accelerate wound healing.},
journal = {Asian journal of pharmaceutical sciences},
volume = {21},
number = {2},
pages = {101148},
pmid = {42023165},
issn = {2221-285X},
abstract = {The wound microbiome has been shown to play a significant role in influencing the wound healing process. Coptis chinensis, a traditional Chinese medicine (TCM) known for its heat-clearing properties, contains berberine (BER) as major active ingredient, which exhibits notable antibacterial activity. In this study, we investigated the effect of BER on wound healing and wound microbiome through three distinct delivery strategies, including solution form, burst-release scaffolds (PCL/BER), and sustained-release scaffolds (PCL/PLGA/BER), compared with an untreated negative control (NC) group. Drug release studies confirmed that PCL/BER caused a pronounced burst release, while the incorporation of PLGA enabled sustained release of BER for up to 120 h. Further in vivo studies showed that the sustained BER release from the PCL/PLGA/BER resulted in the most effective improvement in wound healing. Microbiome analysis using 16S rRNA sequencing identified Staphylococcus xylosus (S. xylosus) as the key species influencing wound healing outcomes in response to BER delivery. S. xylosus overabundance in the NC group and its depletion in the BER solution and burst BER release groups impaired wound healing. In contrast, sustained BER delivery maintained an optimal S. xylosus abundance that promoted a favorable immune microenvironment by modulating CXCL10 and (IFN-α) expression. Our findings emphasize the importance of coordinating drug release kinetics with microbiome dynamics for optimal wound healing outcomes and provide valuable insights for developing future delivery systems for heat-clearing TCMs, with a focus on microbiome-modulation therapeutic strategies.},
}
@article {pmid42023268,
year = {2026},
author = {Wu, Q and Yu, Z and Cao, J and Li, H and Zhang, S},
title = {Oral microbiome dysbiosis mediates the link between emotional disorders and systemic inflammation in heart failure.},
journal = {Brain, behavior, &amp; immunity - health},
volume = {54},
number = {},
pages = {101240},
pmid = {42023268},
issn = {2666-3546},
abstract = {Emotional disorders (EDs) are prevalent in heart failure (HF) and predict poor outcomes, yet their interplay with oral health and systemic inflammation remains unclear. This integrated cross-sectional analysis of NHANES data and a prospective oral microbiome cohort revealed that EDs were significantly associated with poorer cardiovascular health (Life's Essential 8 score), an effect partially mediated by tooth loss and self-rated oral health. Furthermore, HF patients with EDs exhibited distinct oral dysbiosis, marked by depletion of beneficial bacteria (e.g., Cardiobacterium) and enrichment of pro-inflammatory taxa (e.g., Megasphaera), which correlated with systemic inflammation. Our findings posit that EDs may impact cardiovascular health by disrupting the oral microbiome and promoting inflammation, highlighting a potential psychoneuroimmunological pathway in HF progression.},
}
@article {pmid42023434,
year = {2026},
author = {Han, A and Pattaroni, C},
title = {"Scratching the surface" of cutaneous immunity where the microbiome sets the tone and itch turns the volume up.},
journal = {Immunology and cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imcb.70118},
pmid = {42023434},
issn = {1440-1711},
abstract = {Commensal-driven humoral immunity and itch-scratch neuroimmune responses cooperate to shape microbial homeostasis and host defense in the skin.},
}
@article {pmid42023455,
year = {2026},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {The Gut Microbiome in Sleep Disorders: A Review of Recent Evidence.},
journal = {Actas espanolas de psiquiatria},
volume = {54},
number = {2},
pages = {586-601},
doi = {10.62641/aep.v54i2.2123},
pmid = {42023455},
issn = {1578-2735},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sleep Wake Disorders/microbiology/therapy/physiopathology ; Dysbiosis/complications/microbiology ; Fecal Microbiota Transplantation ; },
abstract = {Alterations in the gut microbiome have been shown to influence sleep through gut-brain interactions. However, the interplay between the gut microbiome and sleep disorders remains insufficiently understood. This narrative review provides an overview of recent evidence on the role of the gut microbiome in sleep disorders, examining host-microbial regulation of the sleep cycle, the relationship between gut microbiome dysbiosis and sleep disorders, the influence of the gut microbiome on sleep-related breathing disorders, sleep deprivation, and sleep fragmentation, as well as microbial therapeutic approaches to sleep disorders. Through its effects on bacterial metabolites, immune responses, and neuronal signaling, the gut microbiome might be potentially involved in the regulation of sleep-wake cycles. Disturbances in sleep have been associated with shifts in gut microbiome composition, but this relationship remains incompletely understood and it suggests a bidirectional nature. Evidence indicates that interventions targeting the gut microbiome, such as the use of psychobiotics and fecal microbiota transplantation, may have potential for improving sleep outcomes, but further research is needed to determine their actual effectiveness. Understanding the full range of factors influencing the gut microbiome and their interactions with other variables will be essential for elucidating the mechanisms behind gut-sleep interactions. Thus, future studies should focus on clarifying causality, identifying key biomarkers, and developing microbial-based interventions to establish effective therapeutic strategies.},
}
@article {pmid41832248,
year = {2026},
author = {El-Tanani, M and Satyam, SM and Rabbani, SA and Rangraze, IR and Matalka, IIA and Muhana, F and El-Tanani, Y and Aljabali, AAA and Khan, MA and Parvez, S and Porntaveetus, T},
title = {Next generation approaches in cancer immunotherapy targeting mechanisms beyond PD1 and PDL1.},
journal = {Discover oncology},
volume = {17},
number = {1},
pages = {},
pmid = {41832248},
issn = {2730-6011},
abstract = {UNLABELLED: Cancer immunotherapy has revolutionized oncology by leveraging the immune system’s ability to recognize and eliminate tumor cells. Among the most impactful advances are immune checkpoint inhibitors that target the programmed death-1 (PD-1) receptor and its ligand PD-L1, which can restore T cell activity and generate durable responses across several cancer types. However, their effectiveness is limited by both primary and acquired resistance, restricting long-term benefit to a subset of patients. This review highlights current progress in cancer immunotherapy and explores emerging strategies beyond PD-1/PD-L1 blockade. Novel inhibitory and co-stimulatory immune checkpoints such as lymphocyte activation gene-3 (LAG-3), T cell immunoglobulin mucin-3 (TIM-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), OX40, CD137 (4-1BB), and CD40 are examined for their potential to enhance anti-tumor immunity. The rationale for combining immunotherapy with chemotherapy, radiotherapy, targeted therapies, oncolytic viruses, and neoantigen vaccines is discussed in the context of overcoming resistance. Additional emphasis is placed on modifying the tumor microenvironment, targeting tumor metabolism, and overcoming stromal barriers. Advanced delivery systems such as chimeric antigen receptor (CAR) T cells, bispecific antibodies, and nanoparticle-based platforms offer improved specificity and reduced toxicity. Biomarker-guided precision immuno-oncology using tumor mutational burden, microsatellite instability, and immune gene signatures is advancing clinical decision-making. Gut microbiota modulation and artificial intelligence-based tools are also emerging as critical components in optimizing therapeutic outcomes. Collectively, this review proposes a multidimensional and personalized immunotherapy paradigm aimed at broadening clinical efficacy and overcoming resistance beyond conventional PD-1/PD-L1 inhibition.<br><br>GRAPHICAL ABSTRACT: [Image: see text]},
}
@article {pmid42013859,
year = {2026},
author = {Estrem, CE and Dua, M and Fees, CP and Hoeprich, GJ and Au, M and Goode, BL and Deng, LL and Flavell, SW},
title = {Identification of bacterial signals that modulate enteric sensory neurons to influence behavior in C. elegans.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.03.070},
pmid = {42013859},
issn = {1879-0445},
abstract = {The bacterial microbiome influences many aspects of animal health and disease. Bacteria can have beneficial functions, for example providing nutrients, whereas others can act as pathogens. Bacteria are sensed by host cells to induce adaptive changes in physiology and behavior. While immune and intestinal cells detect bacterial signals through well-characterized mechanisms, recent studies indicate that neurons can also directly sense bacteria. However, the bacterial sensory mechanisms in neurons are less well understood. In Caenorhabditis elegans, the enteric sensory neuron NSM innervates the pharyngeal lumen and is directly activated by bacterial ingestion; in turn, NSM releases serotonin to induce feeding-related behaviors. However, the molecular identities of the bacterial signals that activate NSM are unknown. To identify them, we probed bacterial macromolecules from nutritive bacteria using biochemical approaches. We find that polysaccharides from bacteria are sufficient to activate NSM. We further identify peptidoglycans from Gram-positive bacteria as specific components capable of activating NSM. NSM responses to polysaccharides require the acid-sensing ion channels DEL-3 and DEL-7, which localize to NSM's sensory dendrite in the pharyngeal lumen. Ingestion of bacterial polysaccharides enhances feeding and reduces locomotion, matching the known effects of NSM on behavior. We also examine signals produced by pathogenic bacteria. This approach identifies prodigiosin, from pathogenic Serratia marcescens, as a metabolite that prevents NSM activation by nutritive bacterial signals. This study identifies molecular signals that underlie neuronal recognition of nutritive bacteria in the alimentary canal and competing signals from a pathogenic bacterial strain that can mask this form of recognition.},
}
@article {pmid42014006,
year = {2026},
author = {Liu, H and Luo, J and Yang, Y and Yang, R and Li, W},
title = {Spleen metabolomics coupled with gut microbiome analysis to elucidate the immunomodulatory mechanisms of longan polysaccharides against cyclophosphamide-induced immunosuppression in mice.},
journal = {International journal of biological macromolecules},
volume = {362},
number = {},
pages = {152109},
doi = {10.1016/j.ijbiomac.2026.152109},
pmid = {42014006},
issn = {1879-0003},
abstract = {Longan polysaccharide (LP) has exhibited excellent immunomodulatory activities by modifying gut microbiota but the specific regulatory mechanism remains unclear. Therefore, spleen metabolomics and metagenomic sequencing of gut microbiota were combined to investigate the immunomodulatory mechanism of LP in cyclophosphamide (CPA)-induced immunosuppressed mice with an intact and antibiotic-depleted microbiota. The results indicated that LP significantly restored thymic and splenic indices, increased lymphocyte proliferation, and mitigated damage to immune organs. LP up-regulated the ratio of CD4[+]/CD8[+] in the mouse spleen to modulated cytokine secretion, thereby increasing serum concentrations of IFN-γ, TNF-α, IL-12, and IL-6. The metabolomic analysis indicated that LP alleviated CPA-induced splenic disturbance by coordinately improving amino acid metabolism, unsaturated fatty acid metabolism, and pyrimidine metabolism. Furthermore, LP significantly reshaped the CPA-induced gut microbiota imbalance, particularly by increasing the relative abundance of unclassified_f__Muribaculaceae and Bacteroides. However, antibiotic intervention almost offset the LP-mediated alleviation of immunosuppression. Our findings provide novel insights into the mechanisms underlying the immunosuppression-alleviating effects of natural polysaccharides.},
}
@article {pmid42014077,
year = {2026},
author = {McCracken, AR and Rodger, A and Saratkar, C and Mariani Sularz, S and Brusch, S and Nunez, JCB and Pespeni, MH},
title = {Precursors of sea star wasting: immune and microbial disruption during initial disease outbreak in southeast Alaska.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2069},
pages = {},
doi = {10.1098/rspb.2025.2947},
pmid = {42014077},
issn = {1471-2954},
support = {//National Science Foundation/ ; },
mesh = {*Starfish/microbiology/immunology ; Animals ; Alaska ; *Vibrio/physiology ; Disease Outbreaks/veterinary ; Transcriptome ; },
abstract = {Sea star wasting (SSW) disease has devastated sea star populations along the North American Pacific coast with some recovery since 2013. Though Vibrio pectenicida has recently been implicated as a causative agent, the dynamics of disease progression and host response in natural environments remain understudied. Here, we integrate transcriptomic and microbial data from wild Pycnopodia helianthoides sampled across sites affected and unaffected by SSW in southeast Alaska during the initial outbreak recorded in the region in 2016. Individuals exposed to SSW but lacking visible signs of disease showed elevated expression of complement system components, pathogen recognition and immune regulatory pathways relative to naive individuals. Differential expression of extracellular matrix and tissue remodelling genes suggests disruption of tissue homeostasis preceding visible signs of disease. Furthermore, network analyses revealed certain microbial abundances, including Vibrio spp., correlated with immune response and tissue integrity gene expression. Although V. pectenicida was detected in some samples, its rarity prevented detailed analysis. Nevertheless, higher prevalence in exposed samples is consistent with growing evidence implicating Vibrio infection as an agent of SSW. Together, our findings offer insight into early host-pathogen dynamics in wild populations, underscoring links between immune activation and microbial shifts with the onset of SSW disease.},
}
@article {pmid42014181,
year = {2026},
author = {Seo, JI and Kim, SM and Yoo, HH},
title = {Phytochemicals in MASLD: A Focused Review of Gut Microbiome-Linked Mechanisms.},
journal = {Phytotherapy research : PTR},
volume = {},
number = {},
pages = {},
doi = {10.1002/ptr.70352},
pmid = {42014181},
issn = {1099-1573},
support = {RS-2023-00217123//National Research Foundation of Korea/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) has emerged as a major global health burden, yet effective pharmacological options remain limited. Recent advances highlight the gut microbiome as a key modulator of liver metabolism, inflammation, and fibrosis, making it a promising therapeutic target. Among various non-pharmacologic strategies, phytochemicals have drawn growing attention for their ability to influence the gut-liver axis through natural, multitarget mechanisms. This mini-review summarizes preclinical and clinical evidence on phytochemicals that demonstrate metabolic benefits in MASLD, with a focus on their microbiome-mediated effects. To this end, we classify these mechanistic pathways into three major continuums: restoration of gut microbial composition (causation), modulation of signaling mediators, i.e., gut microbial metabolites (mediation), and the resulting functional outcomes derived from these causal links (outcome). While early pre-clinical data are encouraging, translation is challenged by issues such as mechanistic complexity, microbiome-dependent heterogeneity, and regulatory ambiguity. Future studies incorporating multi-omics analysis, mechanism-linked trial designs, and stratified patient populations will be critical to advancing phytochemicals as safe, effective, and personalized interventions for MASLD.},
}
@article {pmid42014206,
year = {2026},
author = {George, SM and Chatterjee, P and Chaudhry, R and Bamola, VD and Khan, MA and Purohit, A and Suroliya, V and Muley, R and Chakrawarty, A},
title = {Gut Microbiota Signatures of Sarcopenia: A Comparative 16S rRNA Sequencing Study in Older Indian Adults.},
journal = {Geriatrics &amp; gerontology international},
volume = {26},
number = {4},
pages = {e70500},
doi = {10.1111/ggi.70500},
pmid = {42014206},
issn = {1447-0594},
support = {//National Programme for Health Care of the Elderly, Government of India (NPHCE)/ ; },
mesh = {Humans ; *Sarcopenia/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Aged ; Female ; Cross-Sectional Studies ; India ; *RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Middle Aged ; Feces/microbiology ; Aged, 80 and over ; },
abstract = {AIM: Emerging evidence suggests that alterations in gut microbiota composition may contribute to the onset and progression of sarcopenia through mechanisms involving systemic inflammation, metabolic dysregulation, and reduced production of short-chain fatty acids (SCFAs). However, data from Indian older adults-who exhibit diverse diets and microbiota profiles-are lacking.<br><br>METHODS: This hospital-based cross-sectional pilot study enrolled 30 older adults aged &#x2265;&#x2009;60&#x2009;years, including 15 with sarcopenic and 15 age- and sex-matched nonsarcopenic. Sarcopenia was classified according to the Asian Working Group for Sarcopenia (AWGS-2019) criteria. Stool samples were analyzed using 16S ribosomal RNA (rRNA) sequencing (V3-V4 region, Illumina MiSeq). Taxonomic classification and diversity indices (Chao1, Shannon, UniFrac) were compared between groups.<br><br>RESULTS: The mean age (S.D.) of study participants was 73.27&#x2009;&#xb1;&#x2009;5.96&#x2009;years. A total of 251&#x2009;315 high-quality sequences were generated from 30 fresh human fecal samples. The dominant phylum in the nonsarcopenic group was Firmicutes (41.2%), followed by Bacteroidetes (36.0%), whereas in the sarcopenic group, Bacteroidetes (39.2%) was most common, followed by Firmicutes (37.8%). A decrease in Operational Taxonomic Units (OTUs) of genus Bifidobacterium (2.21% vs. 3.71%), Bacteroides (8.50% vs. 11.11%) was observed in the sarcopenic group. An increase in OTUs of genus Faecalibacterium (10.64% vs. 8.23%) in the sarcopenic group was observed. The alpha-diversity index Chao1, Shannon was reduced in sarcopenic population.<br><br>CONCLUSIONS: Exploratory differences in microbial diversity and relative abundance were observed between sarcopenic and nonsarcopenic older adults. These findings are descriptive and hypothesis-generating and warrant confirmation in larger, adequately powered studies.},
}
@article {pmid42014368,
year = {2026},
author = {Li, Y and Niu, S and Wang, H and Li, J},
title = {Microbiome Modulation with Lactobacillus rhamnosus GG Potentiates Curcumin's Efficacy in Reversing Gemcitabine Resistance of Gallbladder Cancer through Gut Microbiota-PI3K/AKT Axis.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2601007},
doi = {10.4014/jmb.2601.01007},
pmid = {42014368},
issn = {1738-8872},
mesh = {*Lacticaseibacillus rhamnosus/physiology ; *Curcumin/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects ; Gemcitabine ; Phosphatidylinositol 3-Kinases/metabolism ; *Gallbladder Neoplasms/drug therapy/microbiology/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; *Deoxycytidine/analogs &amp; derivatives/pharmacology ; *Drug Resistance, Neoplasm/drug effects ; Animals ; Cell Proliferation/drug effects ; Probiotics/pharmacology ; Cell Line, Tumor ; Signal Transduction/drug effects ; Mice ; Apoptosis/drug effects ; Xenograft Model Antitumor Assays ; },
abstract = {Gemcitabine (GEM) resistance remains a major challenge in the treatment of gallbladder cancer (GBC). This study investigated the synergistic effect of curcumin (CUR) combined with the probiotic Lactobacillus rhamnosus GG (LGG) in reversing chemoresistance through modulation of the gut microbiota. In GEM-resistant GBC-SD cells, the CUR-LGG combination significantly inhibited cell proliferation, suppressed migration and invasion, and induced apoptosis, as demonstrated by CCK-8, wound healing, Transwell, and flow cytometry assays. Western blot analysis revealed corresponding regulation of proliferation markers (Ki67, PCNA), apoptosis-related proteins (Bcl-2, Bax, cleaved Caspase-3), and epithelial-mesenchymal transition markers. In xenograft models, the combined treatment markedly suppressed tumor growth and altered gut microbial composition, increasing beneficial bacteria (Lactobacillus, Bifidobacterium) while reducing pathogenic taxa. LC-MS analysis further demonstrated restoration of bile acid homeostasis, characterized by elevated primary bile acids (GCA, CDCA) and decreased secondary bile acids (DCA, LCA). Mechanistically, the intervention significantly inhibited PI3K/AKT signaling, as confirmed by Western blot and immunohistochemistry. Bioinformatic analysis further identified PI3K/AKT as a central regulatory pathway. These findings indicate that probiotic-assisted CUR therapy reverses GEM resistance by remodeling the gut microbiota and its metabolic outputs, thereby suppressing oncogenic signaling pathways. This strategy provides a promising microbiota-based approach for improving therapeutic outcomes in GBC.},
}
@article {pmid42014402,
year = {2026},
author = {Boscaini, S and Bastiaanssen, TFS and Moloney, GM and Bergamo, F and Zeraik, L and O'Leary, C and Ferri, A and Irfan, M and van der Rhee, M and Lindemann, TIF and Schneider, E and Meyyappan, AC and Harold, KB and Long-Smith, CM and Carbia, C and O'Riordan, KJ and de Alvarenga, JFR and Tosi, N and Del Rio, D and Rosi, A and Bresciani, L and Mena, P and Clarke, G and Cryan, JF},
title = {Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42014402},
issn = {2041-1723},
support = {950050//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Coffee/metabolism ; *Cognition/drug effects/physiology ; Male ; Adult ; Feces/microbiology ; Female ; Caffeine/pharmacology/metabolism ; Young Adult ; Brain/physiology ; Metabolome ; },
abstract = {Coffee influences multiple physiological processes, including gut function, stress, cognition, and the microbiome. However, the mechanisms underlying these effects remain poorly understood. In this study, we examined coffee's impact on the microbiota-gut-brain axis-a bidirectional communication pathway between the gut microbiome and the brain-and assessed whether these effects occur independently of caffeine in healthy participants. Our primary outcome was microbiota composition and function, whereas the secondary outcome was gut microbial metabolites and coffee-related metabolites (NCT05927038 and NCT05927103). Significant group differences emerged in faecal microbiome composition, with coffee drinkers showing increased relative abundance of Cryptobacterium and Eggerthella species, alongside reduced levels of the metabolite's indole-3-propionic acid, indole-3-carboxyaldehyde, and the neurotransmitter γ-aminobutyric acid. Behaviourally, coffee drinkers exhibited greater impulsivity and emotional reactivity, whereas non-coffee drinkers demonstrated better memory performance. Some alterations in the faecal metabolome were reversible following coffee abstinence, and reintroduction triggered acute microbiome changes independent of caffeine. An integrated model identified nine key metabolites-including theophylline, caffeine, and selected phenolic acids-strongly linked to microbial species and cognitive measures. These findings reveal previously unrecognised effects of coffee on the microbiota-gut-brain axis, suggesting that microbiome profiles could potentially predict coffee consumption patterns and highlighting a close association between coffee intake and gut microbial composition.},
}
@article {pmid42014413,
year = {2026},
author = {Zhang, L and Soleimani Samarkhazan, H and Almajidi, Y and Gafarov, R},
title = {The microbial metabolome: remodeling the therapeutic landscape in hematologic malignancies.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00972-2},
pmid = {42014413},
issn = {2055-5008},
abstract = {The gut microbiome's metabolome critically shapes drug efficacy and toxicity in hematologic malignancies. This review explores how microbial metabolites influence chemotherapy, immunotherapy, and transplant outcomes, and how they can be harnessed as biomarkers and therapeutic targets. Moving from association to intervention, we outline a pathway toward metabolome-informed precision oncology, transforming the "second genome" into a actionable ally for improved cancer therapy.},
}
@article {pmid42014454,
year = {2026},
author = {Muller, E and Bamberger, T and Borenstein, E},
title = {Navigating multi-omic integration methods for human microbiome research.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42014454},
issn = {2058-5276},
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)/ ; 2266/25//Israel Science Foundation (ISF)/ ; },
abstract = {Multi-omic studies in human microbiome research hold great potential for advancing our understanding of host-microbiome interactions. However, despite the growing availability of multi-omic datasets, analysing such data remains a major conceptual, analytical and computational challenge. Introduction of new multi-omic integration methods to address these challenges further complicates researchers' efforts to navigate this expanding field. In this Review, we outline the landscape of multi-omic integration methods in the context of human microbiome research. In contrast to previous reviews, we specifically emphasize the different biological questions addressed by various integration approaches, including questions related to interactions between different molecular layers, molecular shifts that occur in disease, subgrouping of patients based on molecular profiles, and identification of biological mechanisms that underlie such associations. Our aim is to provide a timely, convenient and comprehensive resource for the microbiome research community, allowing researchers to identify the multi-omic integration approach that is best suited to their data and objectives.},
}
@article {pmid42014606,
year = {2026},
author = {Singh, S and Shahadab, M and Sachin, K and Pandey, RK and Trivedi, P and Mishra, AK and Jha, HC},
title = {Genomic-microbial coevolution in human development: chromosome 2 fusion, and human accelerated regions.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {37},
number = {1},
pages = {},
pmid = {42014606},
issn = {1432-1777},
}
@article {pmid42014676,
year = {2026},
author = {Al, KF and Wammes, M and Warren, M and Lee, JE and Walton, DM and O'Connor, C and Cameron, L and Burton, JP and Osuch, EA},
title = {A case-series of oral acetate supplementation for gut microbiota alteration and metabolic improvement in patients with affective disorders on psychotropics.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04046-x},
pmid = {42014676},
issn = {2158-3188},
support = {NA//London Community Foundation (LCF)/ ; },
abstract = {Mental illnesses affect one in five Canadians and often require psychotropic medications. While effective, many psychotropic medications can cause weight gain and metabolic side effects. The gut microbiota, influenced by short-chain fatty acids like acetate, plays a role in mental health via the gut-brain axis and may be disrupted as a result of medication use. This case-series explored the feasibility of acetate supplementation contained in delayed-release capsules as an intervention to alter the gut microbiota and reduce metabolic side effects in people taking psychotropic medication for mood and anxiety disorders. Eleven participants aged 22-32 with medication-related weight gain were evaluated at baseline, across three months of delayed-release acetate supplementation, and at one-month follow-up. Adherence was high, with no serious adverse events. Six participants showed signs of metabolic improvements, including clinically-meaningful changes in cholesterol and weight. Mood and anxiety symptoms meaningfully improved in two participants. 16S rRNA gene sequencing revealed alterations in the gut microbiota at both the individual and group levels following the intervention, including increased relative abundance of butyrate-producing bacteria and functional changes potentially influencing cholesterol metabolism. Microbiota differences were also noted between participants with and without metabolic improvements, both pre- and post-intervention, suggesting a potential "responder" phenotype. These findings support further exploration of the effectiveness of delayed-release acetate as a safe adjunctive therapy to offset metabolic concerns and gut microbiome changes in people on psychotropic medication. Larger studies with longer follow-up are needed to confirm these effects and validate responder subgroups.},
}
@article {pmid42014741,
year = {2026},
author = {Toner-Bartelds, C and Mimpen, IL and Parra-Martinez, M and Burgering, BMT and Voest, EE},
title = {Microbiota-derived metabolites as modulators of cancer immunotherapy response.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72178-1},
pmid = {42014741},
issn = {2041-1723},
abstract = {The microbiome is a key regulator of host homeostasis and immune activity, in part through the production of metabolites. These microbiota-derived metabolites can modulate both the innate and adaptive immune system, as well as directly target tumour cells, thereby regulating anti-tumour immunity and response to immunotherapy. Here, we describe the current mechanistic knowledge on how these metabolites exert their effects and outline the methodologies used to detect and assess these metabolites. Finally, we summarize microbiota-targeted therapies capable of improving microbial functionality to ultimately enhance immunotherapy responses and improve patient survival.},
}
@article {pmid42014792,
year = {2026},
author = {Głowska-Patyniak, E and Ostrowska, K and Olechnowicz, J and Hubert, J and Konecka, E and Sharma, AK and Som, A and Dabert, M and Trzebny, A},
title = {A Wolbachia lineage likely representing a new supergroup (Y) dominates the microbiome of the quill mite Syringophilus bipectinatus Heller, 1880 (Acariformes: Syringophilidae).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48644-7},
pmid = {42014792},
issn = {2045-2322},
support = {UMO-2021/03/Y/NZ8/00060//The National Science Centre of Poland/ ; },
abstract = {The microbiome plays a key role in animal biology, including host reproduction. Quill mites (Acariformes: Syringophilidae) are understudied ectoparasites of birds, with many species exhibiting strongly female-biased sex ratios. Previous studies have identified unique strains of Wolbachia and Spiroplasma in quill mites, both known to manipulate host reproduction in other arthropods. To further investigate this association, we analyzed the microbiome of Syringophilus bipectinatus Heller, 1880, a relatively early-diverging quill mite species parasitizing the Red Junglefowl (domestic type) (Galliformes: Phasianidae), using 16S rRNA gene profiling. We categorized mite specimens by sex and developmental stage to test for potential associations between microbiome composition and sex ratios. We report the first detection of Wolbachia in S. bipectinatus with a single amplicon sequence variant (ASV) consistently detected across all analyzed samples, accounting for 56-99% of total bacterial sequence reads. Phylogenetic analysis based on 16S rRNA gene and four protein-coding genes (fbpA, ftsZ, gatB, hcpA) recovered this strain as a deeply divergent Wolbachia lineage that does not cluster with any previously described supergroup. This lineage is therefore interpreted as likely representing a novel Wolbachia supergroup (Y), although its formal status requires further validation using genome-scale data. Its consistent presence across both sexes and all developmental stages suggests a stable and potentially obligate association, although its functional role remains to be determined. In addition, we identified bacterial taxa also reported from avian hosts, including potentially pathogenic genera such as Arcobacter, highlighting the complex microbial ecology of quill mites.},
}
@article {pmid42014833,
year = {2026},
author = {Bokszczanin, K&#x141; and Chojnacka, A and Suchocka, M and Kalaji, HM and Malinowski, R and Kubus, M},
title = {Soil management strategies shape bacterial and eukaryotic community structure in organic and inorganic systems of Malus × domestica production.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49450-x},
pmid = {42014833},
issn = {2045-2322},
abstract = {Understanding the temporal dynamics of soil microbial communities is crucial for assessing the stability of orchard soils. We analyzed bacterial and eukaryotic communities in the rhizosphere of apple trees under seven mulching treatments across two growing seasons (2020 and 2023). To account for potential batch effects between separate sequencing runs, results from each year were juxtaposed to identify recurring microbial patterns. High-throughput 16S and ITS sequencing revealed that management-specific signatures persisted over time despite inter-run variability. Bacterial alpha diversity varied significantly among individual treatments, while beta diversity consistently distinguished management regimes across both years. Fungal alpha diversity remained largely unaffected, but beta diversity revealed significant compositional shifts between organic and inorganic groups. Organic mulching (shredded Miscanthus straw and spent mushroom compost) consistently enriched bacterial families linked to organic matter turnover (Sphingomonadaceae, Flavobacteriaceae, Moraxellaceae), whereas inorganic systems favored Comamonadaceae and Nitrosomonadaceae. Organic soils were also enriched in saprotrophic fungi (Lasiosphaeriaceae) and broader eukaryotes (Ciliophora), while inorganic - Mortierellaceae. Network analyses identified a cohesive bacterial core, whereas fungal/eukaryotic communities were more modular and responsive to mulching type. These findings demonstrate that sustained organic mulching promotes stable microbial configurations associated with soil functioning, highlighting the consistency of management-associated microbial signatures under long-term agricultural practices.},
}
@article {pmid42014845,
year = {2026},
author = {Yu, P and Zhou, W and Li, C and Sun, Q and Yang, Y},
title = {Construction of an engineered Escherichia coli strain with enhanced intestinal colonization and anti-inflammatory efficacy in colitis.},
journal = {Cellular &amp; molecular immunology},
volume = {},
number = {},
pages = {},
pmid = {42014845},
issn = {2042-0226},
abstract = {Engineered probiotics are considered effective and safe therapeutic strategies for the treatment of various diseases. Escherichia coli Nissle 1917 (EcN) has been widely used as a chassis strain because of its safety and well-established genetic manipulation system. However, the limited intestinal colonization ability of EcN limits its potential as a chassis for the construction of synthetic probiotics. Here, an engineered EcN strain (EcN-CPM) with enhanced gastric acid and bile salt tolerance and improved intestinal adhesion was constructed. Oral administration of EcN-CPM to mice with colitis alleviated disease severity and reshaped the disordered gut microbiome by decreasing the abundance of Escherichia-Shigella while increasing the abundance of norank_f_Muribaculaceae. Mechanistically, the EcN-CPM supernatant directly promoted the proliferation of norank_f_Muribaculaceae, a short-chain fatty acid (SCFA)-producing genus. Targeted metabolomics revealed that EcN-CPM restored the DSS-induced depletion of SCFAs, which were negatively correlated with the abundance of Escherichia-Shigella and positively correlated with the abundance of norank_f_Muribaculaceae. Consistent with these findings, EcN-CPM treatment upregulated the expression of Treg-associated markers (Foxp3, Ctla4, and Cd25) and downregulated the expression of Th17-related genes (IL-17A and Roryt) in colonic tissues, restoring the IL-17A/Foxp3 ratio to homeostasis. Untargeted metabolomics further demonstrated that EcN-CPM uniquely restored the levels of seven anti-inflammatory metabolites depleted by DSS treatment. Collectively, these findings demonstrate that EcN-CPM alleviates intestinal inflammation by remodeling the gut microbiota to increase the production of SCFAs and anti-inflammatory metabolites, thereby driving a shift in Th17- and Treg-associated transcriptional signatures. This study establishes a platform for precision-designed synthetic probiotics with enhanced probiotic properties.},
}
@article {pmid42014976,
year = {2026},
author = {Lardinois, LL and Hinojosa, NA and Quintero-Arrieta, H and Sellers, AJ and Leray, M and Barrett, RDH},
title = {Host matters: coral reef fish species show distinct skin microbiome responses to upwelling-driven environmental changes.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05036-1},
pmid = {42014976},
issn = {1471-2180},
support = {doi: 10.69777/330691//Fonds de recherche du Qu&#xe9;bec/ ; 2019-04549//Natural Sciences and Engineering Research Council of Canada/ ; },
}
@article {pmid42014993,
year = {2026},
author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C},
title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05043-2},
pmid = {42014993},
issn = {1471-2180},
}
@article {pmid42015254,
year = {2026},
author = {Dillen, J and Eilers, T and Dricot, CEMK and Van Hee, M and Vandenheuvel, D and Masschelein, J and Lebeer, S},
title = {Modular biosynthesis of microbiome-derived polyketides and nonribosomal peptides: insights and opportunities for Lactobacillaceae.},
journal = {Microbial cell factories},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12934-026-03008-8},
pmid = {42015254},
issn = {1475-2859},
support = {1S28622N//Fonds Wetenschappelijk Onderzoek/ ; 1158725N//Fonds Wetenschappelijk Onderzoek/ ; G049022N//Fonds Wetenschappelijk Onderzoek/ ; 852600//HORIZON EUROPE European Research Council/ ; },
}
@article {pmid42015325,
year = {2026},
author = {Fauszt, P and Szilagyi, E and Mikolas, M and Szilagyi-Tolnai, E and David, P and Kovacs-Forgacs, IN and Csernus, B and Gal, F and Stundl, L and Biro, S and Szabo, C and Remenyik, J and Babinszky, L and Paholcsek, M},
title = {Alleviation of heat stress-induced microbial dysbiosis in pigs through dietary supplementation with vitamins and trace elements.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00575-4},
pmid = {42015325},
issn = {2524-4671},
abstract = {BACKGROUND: Chronic heat stress (HS) is known to impair animal health and productivity, in part by altering gut microbiota. This study investigated how HS affects the pig gut microbiome and whether dietary supplementation with antioxidants and trace elements (vitamins E, C, selenium, and zinc) at moderate (D1) or high (D2) doses can mitigate these effects.<br><br>RESULTS: During the adaptation phase, feed efficiency was similar across groups, but as the experiment progressed, the thermoneutral control improved while the heat-stressed control deteriorated. Supplemented diets (D1/D2) partially alleviated this efficiency loss. Microbiome analysis revealed that HS progressively reduced diversity, reaching the lowest Shannon index during exposure. High-dose supplementation markedly increased richness, exceeding control levels. Total microbial abundance declined under HS, with opportunistic pathogens enriched particularly during early exposure. Guild-level indices further indicated a shift under HS. Aerotolerance indices decreased (ATi: TC&#x2009;>&#x2009;D1&#x2009;>&#x2009;D2&#x2009;>&#x2009;HSC), reflecting hypoxia-prone conditions favoring obligate anaerobes and SCFA producers. Among supplemented groups, D1 most closely stabilized aerotolerance toward control levels, while D2 maintained an SCFA-dominant community and enhanced butyrate capacity. Genus-level correlations with qPCR-based host gene-expression markers were assessed across all groups. HSP70 was the dominant correlate, and the most extreme associations were confined to a few taxa, indicating marked group specificity.<br><br>CONCLUSION: Chronic HS in pigs induced microbial dysbiosis characterized by reduced diversity, loss of beneficial SCFA producers, and expansion of opportunistic pathogens. Dietary supplementation counteracted these adverse changes in a dose-dependent manner. While moderate supplementation provided partial stabilization, high-dose supplementation more effectively restored microbial diversity and enriched beneficial taxa, making it the more effective strategy for mitigating HS-induced microbiome disruption.},
}
@article {pmid42015346,
year = {2026},
author = {Li, Z and Samui, S and Liu, J and Yang, Y and Liu, X and Chen, Q and Li, J and Gopinath, D and Luo, P and Shan, D},
title = {Gut microbiome and metabolic health: mechanisms and precision interventions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644677},
doi = {10.1080/19490976.2026.2644677},
pmid = {42015346},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Fecal Microbiota Transplantation ; Probiotics ; Precision Medicine ; *Metabolic Diseases/microbiology/metabolism/therapy ; Prebiotics/administration &amp; dosage ; Obesity/microbiology/metabolism ; Diabetes Mellitus, Type 2/microbiology/metabolism ; Metabolic Syndrome/microbiology/metabolism ; },
abstract = {The gut microbiome is increasingly recognized as a fundamental regulator of metabolic health, shaping energy balance, insulin sensitivity, inflammatory tone, and inter-organ communication through a broad spectrum of microbial metabolites that engage host signaling pathways. In this review, we synthesize current mechanistic insights into how gut microbial communities shape metabolic function, with particular emphasis on short-chain fatty acids, secondary bile acid signaling, gut barrier integrity, immune modulation, and the microbiota-gut-brain-pancreas axis. We further summarize disease-associated alterations in microbial composition and function across obesity, type 2 diabetes, metabolic dysfunction-associated steatotic liver disease, and metabolic syndrome, highlighting key microbial and metabolic features that contribute to metabolic dysfunction. Evidence from germ-free models, fecal microbiota transplantation studies, and strain-level interventions suggests that shifts in microbial ecology may causally shape metabolic outcomes. We also critically evaluate emerging microbiome-centered therapeutic strategies, including targeted probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation, while addressing factors that underlie inter-individual variability in treatment responses. In addition, we discuss the growing influence of multi-omics technologies, microbial metabolic modeling, and machine learning approaches in advancing precision microbiome medicine. To integrate these advances within a coherent framework, we outline a precision microbiome intervention pipeline linking multidimensional profiling to functional stratification and targeted therapeutic design. We also introduce a conceptual Precision Microbiome Intervention Triangle to mechanistically explain heterogeneity in responses to microbiome-targeted therapies. Collectively, these insights establish and position the gut microbiome as both a mechanistic driver and a modifiable therapeutic target in metabolic disease, and highlight key challenges and future directions for the development of personalized microbiome-based metabolic interventions.},
}
@article {pmid42015619,
year = {2026},
author = {Ganamurali, N and Sabarathinam, S},
title = {Statin-induced gut dysbiosis and sleep disturbances: Mechanistic insights into microbiota-brain-circadian interactions and chronotherapeutic implications.},
journal = {Chronobiology international},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/07420528.2026.2660826},
pmid = {42015619},
issn = {1525-6073},
abstract = {Statins are widely prescribed lipid-lowering agents with well-established efficacy in reducing cardiovascular morbidity and mortality. However, accumulating clinical and experimental evidence suggests that statin therapy may be associated with sleep disturbances, including insomnia, altered sleep architecture, vivid dreams, and reduced sleep quality. Emerging insights implicate the gut microbiota as a key regulator of host circadian rhythms and sleep homeostasis through interconnected pathways involving the tryptophan-serotonin-melatonin axis, short-chain fatty acid (SCFA) production, bile acid signaling, and immune-mediated neuroinflammation. Statins have been shown to modulate gut microbial composition, often reducing SCFA producing taxa and altering bile acid pools, which in turn may disrupt neurochemical signaling and circadian regulation. These microbiota-driven perturbations may contribute to central nervous system effects that underlie sleep-related adverse outcomes. This review integrates current mechanistic and clinical evidence linking statin-induced gut dysbiosis with sleep disturbances, highlighting the role of microbiome-host interactions in mediating off-target drug effects. It further examines implications for vulnerable populations, including shift workers, and discusses the potential of chronotherapy in optimizing statin administration. Finally, microbiota targeted interventions, such as probiotics, prebiotics, and dietary modulation, are proposed as promising strategies to mitigate these adverse effects. A deeper understanding of these interactions may enable personalized therapeutic approaches to enhance both cardiovascular outcomes and sleep health.},
}
@article {pmid42015788,
year = {2026},
author = {Kexin, LI and Jinzu, Y and Kunlin, X and Shaojie, D and Kunmin, X},
title = {Tongue-coating microbiome as a predictor of solid tumors: an updated scoping review of clinical studies.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {46},
number = {2},
pages = {501-508},
pmid = {42015788},
issn = {2589-451X},
mesh = {Humans ; *Microbiota ; *Neoplasms/microbiology/diagnosis ; *Tongue/microbiology ; Medicine, Chinese Traditional ; },
abstract = {This study explores the potential of tongue coating microbiota as a non-invasive biomarker for cancer and precancerous lesions by integrating insights from multi-omics technologies and Traditional Chinese Medicine (TCM) tongue diagnosis. By bridging modern molecular research with TCM diagnostic principles, this study systematically reviewed the relationship between tongue microbiota and oncological conditions, identifying 18 eligible studies through searches in PubMed, Embase, and Web of Science. The analysis reveals significant differences in microbial diversity, abundance, metabolic pathways, and functional characteristics, which enable the partial differentiation of cancer patients from healthy individuals. However, existing research remains constrained by limited sample sizes, inconsistent analytical approaches, and a lack of integrated multi-dimensional datasets. This review highlights the promising diagnostic potential of the tongue coating microbiota in cancer detection, while suggesting that future studies should focus on standardizing methodologies and employing integrated multi-omics approaches to elucidate underlying mechanisms and advance clinical applications.},
}
@article {pmid42015892,
year = {2026},
author = {Satgunaseelan, L and Strbenac, D and Palme, C and Low, TH and Wykes, J and Manzie, T and Clark, JR and Yang, JYH and Gupta, R},
title = {The microbiome landscape of oral cancer in young patients.},
journal = {JNCI cancer spectrum},
volume = {},
number = {},
pages = {},
doi = {10.1093/jncics/pkag022},
pmid = {42015892},
issn = {2515-5091},
abstract = {BACKGROUND: The incidence of oral squamous cell carcinoma (OSCC) is rising in patients under the age of 50, without smoking or alcohol abuse. Viruses are not a causative factor of OSCC in younger patients. The oral microbiome has not been evaluated in this unique patient cohort for a potential bacterial aetiology.<br><br>METHODS: We report the bacterial diversity and composition of the largest cohort of OSCC patients with whole genome sequencing (WGS) (n&#x2009;=&#x2009;72) and compare it with oral mucosa from healthy controls (n&#x2009;=&#x2009;10) using the Strengthening the Organization and Reporting of Microbiome Studies guidelines.<br><br>RESULTS: The microbial diversity between tumour, normal mucosa from cancer patients and healthy control mucosa is significantly different, with specific species (Streptococcus mitis, Haemophilus haemolyticus and Cutibacterium acnes) reduced in normal mucosa of cancer patients as compared to healthy controls (adjusted p&#x2009;<&#x2009;0.05). The microbial diversity is significantly higher in younger patients as compared to older patients (p&#x2009;<&#x2009;0.001), with a reduced abundance of anaerobes in older patients (Aggregatibacter segnis, Gemella morbillorum, Peptostreptococcus stomatis, Filifactor alocis and Porphyromonas endodontalis; adjusted p&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: The OSCC tissue of younger patients is significantly more polymicrobial, and their OSCC microbiomes harbour more anaerobic bacteria as compared to older patients. This compositional difference builds the hypothesis that the oral microbiome of younger OSCC patients may have a more hypoxic, immunosuppressive tumour microenvironment with its associated implications for treatment resistance and a potential link to baseline poor dentition.},
}
@article {pmid42015905,
year = {2026},
author = {Gibson, GR},
title = {Faecal Attraction: 40 Years of Research in Gut Microbiology.},
journal = {Nutrition bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1111/nbu.70052},
pmid = {42015905},
issn = {1467-3010},
abstract = {This article summarises the 2025 British Nutrition Foundation Annual Lecture given on 25/11/25. It overviews aspects of research in anaerobic microbiology, principally involving the human gut. Until October 2025, Gibson was Professor of Food Microbiology at the University of Reading. His research investigated gut microbiome interactions and dietary intervention. The latter included human studies in healthy persons, patients with gut-related disorders, at-risk populations and specialist groups like sportspersons and those in the military. Initial principles such as the type of intervention, dose, duration and outcomes were tested using in vitro models of the human gut.},
}
@article {pmid42016247,
year = {2026},
author = {Xu, D and Qiu, B and Dong, X and Tan, J and Xie, Y and Wan, Y and Chu, C and Miao, C and Ali, A and Chen, M and He, J and Wu, L and Xie, J},
title = {Multi-Target Mechanisms of Whey Protein Against NAFLD: Integrating Bile Acid Metabolism, Gut Microbiota and Hepatic Inflammation.},
journal = {Food science &amp; nutrition},
volume = {14},
number = {3},
pages = {e71655},
pmid = {42016247},
issn = {2048-7177},
abstract = {This study elucidates the protective mechanisms of whey protein (WP) in treating high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD) in mice, emphasizing its role in bile acid regulation, intestinal flora homeostasis, and inflammatory suppression. ICR mice were subjected to a 12-week HFD to establish NAFLD, followed by WP intervention (200 g/kg). Comprehensive analyses included histopathological assessment (HE staining), serum biomarkers, hepatic gene expression (qPCR), gut microbial profiling (16S rRNA sequencing), quantitative bile acid and short-chain fatty acid (SCFA) analysis, and serum metabolomics. Core targets were predicted via network pharmacology and validated through molecular docking. WP administration markedly alleviated NAFLD progression by targeting multiple pathways: (1) It suppressed hepatic lipid deposition and inflammatory injury, downregulating NLRP3, NF-κB, and TNF-α (p < 0.05) while enhancing Nrf2/HO-1-mediated antioxidant defenses; (2) Network pharmacology prioritized IL-1β, STAT3, and MMP9 as pivotal targets, with β-lactoglobulin exhibiting high binding potentials (STAT3: -1.42 kcal/mol); (3) WP restored gut microbial balance, enriching beneficial taxa (e.g., Lactobacillus) and fecal SCFAs; (4) It reprogrammed bile acid metabolism, elevating cholesterol-cleaving enzymes (CYP7A1/CYP27A1) but inhibiting FXR/SHP (p < 0.05), alongside increased hepatoprotective bile acids (TDCA/TUDCA). Metabolomics identified WP-induced anti-inflammatory mediators (e.g., eicosapentaenoic acid) and perturbations in arginine and unsaturated fatty acid pathways, synergistically attenuating steatosis and fibrosis. WP counters NAFLD via a tripartite mechanism: gut microbiome-directed SCFA synthesis, bile acid-driven cholesterol disposal, and dual modulation of inflammation (NLRP3/NF-κB) and oxidative stress (Nrf2/HO-1). These insights position WP as a promising dietary strategy targeting the gut-liver axis.},
}
@article {pmid42016370,
year = {2026},
author = {Fan, Y and Ren, Y and An, J and Wang, X},
title = {Targeted Next-Generation Sequencing Analysis of BALF Microbiota and Clinical Characteristics in Severe versus Non-Severe Community-Acquired Pneumonia.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {588781},
pmid = {42016370},
issn = {1178-6973},
abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) is associated with high mortality. However, data on the bronchoalveolar lavage fluid (BALF) microbiota in Chinese SCAP patients remain limited. This study aimed to characterize the clinical features and BALF microbiome composition in patients with SCAP compared to non-severe CAP using targeted next-generation sequencing (tNGS).<br><br>METHODS: We conducted a retrospective study involving 224 CAP and 97 SCAP patients from two hospitals in Shanxi, China (January 2023-January 2025). Clinical characteristics and inflammatory cytokines were compared between groups. BALF samples were analyzed via tNGS to evaluate microbial alpha and beta diversity. Differentially abundant taxa were identified using Linear Discriminant Analysis Effect Size (LEfSe).<br><br>RESULTS: Compared to the CAP group, SCAP patients were significantly older, had a higher prevalence of comorbidities (hypertension, coronary heart disease, diabetes), and exhibited elevated inflammatory indices (CRP, IL-6, PCT, ESR). SCAP patients also demonstrated a higher likelihood of mixed infections, and the number of detected pathogens showed a positive correlation with the length of hospital stay. tNGS analysis revealed significant differences in alpha diversity and distinct beta diversity clustering between the two groups. LEfSe analysis identified Pseudomonas as a potential biomarker enriched in SCAP, whereas Streptococcus was predominant in CAP.<br><br>CONCLUSION: In patients with SCAP, the BALF microbiota showed a significant increase in alpha diversity, which appears to be closely associated with inflammatory cytokine production and correlates with disease severity. There were pronounced differences between SCAP and CAP in both clinical characteristics and microbiome profiles, highlighting the necessity of integrated diagnostic approaches in pneumonia care. Future research should prioritize delineating the dynamic shifts of microbial communities and their influence on pneumonia severity, with the goal of refining and optimizing treatment strategies.},
}
@article {pmid42016555,
year = {2024},
author = {Gwon, Y and Yu, F and Payne, JB and Mikuls, TR},
title = {Bayesian Modeling on Microbiome Data Analysis: Application to Subgingival Microbiome Study.},
journal = {Statistics in biosciences},
volume = {16},
number = {3},
pages = {556-577},
pmid = {42016555},
issn = {1867-1764},
support = {I01 CX000896/CX/CSRD VA/United States ; U54 GM115458/GM/NIGMS NIH HHS/United States ; },
abstract = {The study of microbiome data has been widely used to investigate associations between the abundance of microbial taxa and human diseases. Identifying and understanding these relationships precisely gives the microbiome a key role in human health, disease status, and the development of new diagnostics and targeted therapeutics. Due to its unique features such as compositional data, excessive zero counts, overdispersion, and complexed structure between taxa, undertaking effective microbiome data analytics presents numerous obstacles. To quantify covariate-taxa effects on the subgingival microbiome study, we proposed a refined Bayesian zero-inflated negative binomial (ZINB) regression model with random subject effects. This proposed approach not only accommodates inflated zero counts and overdispersion similar to the existing ZINB model developed by Jiang et al. (Biostatistics 22(3):522-540, 2021), but also accounts for subject-level heterogeneity through the inclusion of random subject effects. In addition, an efficient Markov chain Monte Carlo (MCMC) sampling algorithm was developed for Bayesian computation. Overall effects of pre-selected group variables on predicted taxa abundance were estimated and tested under the proposed model. We conduct simulation studies and demonstrate that the proposed model outperforms the competing models in achieving a better power with controlling the type I error. The usefulness of the proposed model is applied to a real subgingival microbiome study.},
}
@article {pmid42016568,
year = {2026},
author = {Liu, L and Xu, C and Liu, Y and Yang, J and Ye, Y and Yao, Z and Lin, D and Qiu, H and Ruan, D and Qiu, Y and Wang, S and Lin, M and Zhang, Z and Huang, S and Meng, F and Zheng, E and Cai, G and Wu, Z and Wu, JJ},
title = {Restoring low-fiber diets-induced Lachnospiraceae bacterium loss partially recovers fiber digestion and immune function in mammals.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101401},
pmid = {42016568},
issn = {2665-9271},
abstract = {Mammals rely on their gut microbiota to degrade cellulose, the major component of dietary fiber. Westernized populations harbor a depleted microbiome with reduced fiber-digesting capacity and impaired immune regulation due to prolonged consumption of low-fiber diets. Comparable patterns are evident in other mammals, including Western commercial pigs raised on high-energy, low-fiber diets, exhibiting reduced diversity and abundance of fiber-degrading bacteria. In contrast, semi-free-ranging Chinese indigenous pigs consuming fiber-rich diets retain a more diverse and functionally resilient microbiota, reflecting divergent trajectories of host-microbiota co-evolution. However, the specific cellulose-degrading species lost and strategies to restore these functions remain unclear in mammals. By analyzing 473 human stool metagenomes spanning non-westernized and westernized diets, together with 251 fecal 16S rRNA datasets and 95 metagenomes from Western commercial pigs, Chinese indigenous pigs, and their crossbred progeny, we identified the Lachnospiraceae bacterium as a key symbiont enriched in non-westernized guts. This bacterium possesses an extensive Carbohydrate-Active Enzymes repertoire conferring strong fiber-degrading capacity. Notably, low-fiber diets leave a genetic signature on this keystone gut symbiont, which cannot be reversed by short-term dietary interventions alone. Reintroduction of Lachnospiraceae bacterium to germ-free mice improved feed efficiency and increased acetic acid production. Intestinal transcriptomics and peripheral blood flow cytometry revealed that it activates a broad adaptive immune response, promoting CD4[+] T cell accumulation, B cell activation, and anti-inflammatory cytokine induction. Reintroduction of this bacterium also alleviated dextran sodium sulfate-induced colitis. These findings highlight the preclinical functional potential of this Lachnospiraceae bacterium in mitigating low-fiber diets-induced dysfunction in mammals.},
}
@article {pmid42016597,
year = {2026},
author = {Srinivas, M and O'Sullivan, O and Cotter, PD and van Sinderen, D and Kenny, JG},
title = {Investigating the role of bacterial raw milk community members in chlorate reduction.},
journal = {Access microbiology},
volume = {8},
number = {4},
pages = {},
pmid = {42016597},
issn = {2516-8290},
abstract = {Chlorine-based detergents, used in the dairy industry for cleaning, often degrade into chlorate, contaminating milk and dairy products. Consumption of chlorate has been linked to thyroid dysfunction in adults and impaired neurological development in infants. Despite the ban on chlorine-based detergents in Ireland since 2021, chlorate contamination remains a problem in the dairy supply chain. A recent study identified chlorate-reducing bacteria naturally present in raw milk, highlighting their potential for mitigating chlorate. In this study, shotgun metagenomic sequencing was applied to determine the effects of chlorate concentration and incubation conditions on the raw milk microbiome, specifically focusing on chlorate-reducing bacteria within the community. Chlorate-spiked milk samples from different farms showed reductions in chlorate levels over time, from day 10 onwards when stored at 4 °C and after 24 h when incubated at 25 °C. Pseudomonas and Lactococcus were observed as the most dominant taxa in raw milk samples stored at 4 °C and 25 °C, respectively. High abundances of ydeP and narG genes were observed for 4 °C samples and were attributed to Pseudomonas and various low-abundance genera, respectively. High abundances of the napA gene were noted in 25 °C samples and were attributed to the Lactococcus genus. Overall, this study highlights the presence of naturally occurring chlorate-reducing bacteria as part of the raw milk microbiome and identifies multiple genes linked to various pathways potentially involved in chlorate reduction. Furthermore, incomplete pathways potentially involved in chlorate reduction were found, suggesting metabolic cross-feeding and underscoring the community roles bacteria play in chlorate reduction in raw milk. Additionally, a few previously uncharacterized genes, such as ydeP, belonging to the DMSO reductase gene family were identified at high abundances in samples that showed chlorate reduction, emphasizing the need for further biochemical characterization of these genes to better understand the pathways involved in chlorate reduction in milk.},
}
@article {pmid42016708,
year = {2026},
author = {Diao, J and Li, H and Zheng, S and Niu, J and Yuan, C},
title = {Nonsurgical periodontal therapy remodels oral microbiome-metabolome networks and associates with glycemic and inflammatory improvements in type 2 diabetes mellitus with periodontitis: a 6-month longitudinal study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2660482},
pmid = {42016708},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis and type 2 diabetes mellitus (T2DM) have a bidirectional relationship, yet how nonsurgical periodontal therapy (NSPT) affects oral microbiome-metabolome interactions in this comorbidity remains unclear.<br><br>OBJECTIVE: To longitudinally characterize oral microbiome and metabolome shifts following NSPT in patients with T2DM and periodontitis, and to relate these shifts to periodontal and systemic outcomes.<br><br>DESIGN: A total of 42 participants completed the 6-month follow-up. At baseline, they were randomly assigned to NSPT (supragingival scaling plus scaling and root planning, n&#x2009;=&#x2009;24) or supragingival scaling alone (n&#x2009;=&#x2009;18). Periodontal parameters, glycated hemoglobin (HbA1c), C-reactive protein (CRP), and glucose/lipid markers were measured at baseline, at 3 and 6 months. Oral samples were collected at each visit for microbiome profiling and metabolomics. Microbe-metabolite-clinical features and associations were explored using correlation analyses and pathway annotation.<br><br>RESULTS: NSPT improved periodontal inflammation and was accompanied by favorable changes in systemic inflammation and glucose/lipid indices; HbA1c reduction was more pronounced in those with poorer baseline glycemic control. Both groups showed temporal variability in microbiome and metabolome profiles, but the taxa/metabolites that changed differed between groups. Changes in bleeding index correlated positively with 13-eicosenoic acid, xylose, Rothia aeria, and Alloprevotella tannerae, whereas changes in CRP correlated positively with sorbitol, galactitol, Prevotella nigrescens, and Treponema denticola. Selected microbe-metabolite pairs mapped to glutathione and purine metabolism.<br><br>CONCLUSION: NSPT reshapes oral microbe-metabolite networks in T2DM with periodontitis, implicating redox-related pathways that may link periodontal therapy to systemic inflammation and glycemic control.},
}
@article {pmid42016721,
year = {2026},
author = {Ikuta, K and Kunisawa, A and Dekio, I and Ito, A and Wang, Q and Kawamura, K and Yamada, M and Nakamura, S and Hayakawa, Y and Higurashi, T and Iida, J and Fukusaki, E and Suzuki, T and Matsumoto, M},
title = {Development of a multi-targeted metabolomics platform for semi-quantification of faecal metabolites: a proof-of-concept analysis in human faeces.},
journal = {Microbiome research reports},
volume = {5},
number = {1},
pages = {7},
pmid = {42016721},
issn = {2771-5965},
abstract = {Objectives: Targeted metabolomic analysis of faecal samples has been limited by narrow chemical coverage. Here, we established a multiplexed, triple quadrupole mass spectrometry (TQMS)-based targeted metabolomics workflow. This workflow allows accurate detection and semi-quantification of diverse faecal metabolites and provides a methodological platform for studying host-microbiome metabolic interactions. Methods: Faecal metabolomes from germ-free (GF) mice, ex-germ-free (Ex-GF) mice, and human participants were analysed using TQMS-based targeted metabolomics. The analysis comprised multiple methods targeting amino acids and their derivatives, carbohydrates, short-chain fatty acids, bile acids, lipid mediators, and phospholipids. Results: In total, 607 low-molecular-weight metabolites in 44 chemical categories were detected and semi-quantified. Faecal metabolomes of GF and Ex-GF mice were analysed, uncovering 341 intestinal microbiome-dependent metabolites. A proof-of-concept analysis using faecal samples from five patients with colorectal cancer demonstrated the successful application of this platform to human clinical material, highlighting its strong potential for future disease-oriented metabolomic investigations. Conclusion: We developed a multi-targeted faecal metabolomics platform that substantially expands the chemical space accessible to targeted analysis. This workflow provides a methodological foundation for future large-scale and translational studies.},
}
@article {pmid42016722,
year = {2026},
author = {Hansen, SH and Bhattacharjee, N and Hu, C and Maseng, MG and Grannö, O and Bang, C and Olbjørn, C and Perminow, G and Valeur, J and Bengtson, MB and Frigstad, SO and Andersen, S and Aabrekk, TB and Detlie, TE and Franke, A and Kristensen, VA and Halfvarson, J and Høivik, ML and Iyer, RK and Hov, J},
title = {Bacterial clusters are associated with the risk of severe disease progression in inflammatory bowel disease irrespective of conventional disease categories.},
journal = {Microbiome research reports},
volume = {5},
number = {1},
pages = {4},
pmid = {42016722},
issn = {2771-5965},
abstract = {Background: Inflammatory bowel diseases (IBDs) are complex conditions marked by chronic inflammation in the gastrointestinal tract. Traditional classification separates IBD into Crohn's disease and ulcerative colitis, but this division may not fully capture disease heterogeneity. Here, we examine whether microbiome-driven subtyping can describe novel clinical IBD phenotypes. To achieve this, we applied unsupervised clustering to fecal microbiota profiles from the population-based Inflammatory Bowel Disease in South-Eastern Norway III (IBSEN III) cohort. Methods: A Gaussian Mixture Model (GMM) was used to cluster participants with IBD based on microbiome composition and examine associations between clusters and clinical outcomes, including inflammatory markers and disease severity during the first year after inclusion. Results: Three microbiome-based clusters were identified: CLO (dominated by Clostridia UCG-014), ALF (Agathobacter, Lachnoclostridium, and Faecalibacterium), and RUM (Ruminococcus gnavus). Participants in the RUM cluster had a higher risk of future severe disease than those in the CLO cluster, even among participants with remission-to-mild disease at inclusion (21% vs. 6%, P < 0.00001). This association could not be explained by antibiotic use or baseline disease severity. Cluster membership alone performed comparably to fecal calprotectin in distinguishing severe disease, and a combined model significantly improved accuracy (P < 0.0001). Conclusion: Our findings demonstrate a connection between microbiome composition and the risk of severe disease development, which is partly independent of inflammation levels at the time of sampling. Microbiome-informed subgrouping could lead to more personalized treatment strategies. Further validation is needed to determine the clinical utility of these clusters.},
}
@article {pmid42016780,
year = {2026},
author = {Jabeen, T and Karimi, F and Zomorrodi, AR and Khalilpour, K},
title = {Multi-modal machine learning and gut microbiome pathway analysis for Alzheimer's risk prediction.},
journal = {Alzheimer's &amp; dementia (Amsterdam, Netherlands)},
volume = {18},
number = {},
pages = {e70340},
pmid = {42016780},
issn = {2352-8729},
abstract = {INTRODUCTION: Early Alzheimer's disease (AD) risk assessment requires accessible alternatives to invasive biomarkers. We developed a multi-modal machine learning framework using questionnaire metadata from participants with concurrent microbiome sequencing data.<br><br>METHODS: We analyzed 9832 participants with 120 metadata features across five categories (demographic, dietary, lifestyle, nutritional, medical). Features were selected via Pearson correlation and chi-squared tests. Four algorithms were trained using 10-fold cross-validation with synthetic minority oversampling technique (SMOTE), validated on 1967 samples. The 16S rRNA sequencing data from the same cohort with 2000 samples enabled microbiome composition analysis.<br><br>RESULTS: Medical history (area under the curve [AUC]&#xa0;=&#xa0;0.871) and dietary patterns (AUC&#xa0;=&#xa0;0.874) achieved best performance, outperforming demographic (0.795), lifestyle (0.660), and nutritional (0.569) domains (p&#xa0;<&#xa0;0.001). Microbiome analysis revealed dysbiosis markers (Prevotella/Bacteroides ratio: 1.921) linking dietary factors to potential neuroinflammatory pathways.<br><br>DISCUSSION: These findings support non-invasive, multi-modal screening combining medical and dietary evaluation for AD risk stratification, with preliminary microbiome evidence suggesting gut-brain axis dysbiosis as a mechanistic pathway warranting validation in larger cohorts.},
}
@article {pmid42016853,
year = {2026},
author = {Acharya, AP and Borrelli, MA and Jurczak, MJ and Krakoff, J and Little, SR},
title = {Lipid stress evolved, microbiome-based probiotics reduce lipid uptake in mice.},
journal = {Bioengineering &amp; translational medicine},
volume = {11},
number = {2},
pages = {e70122},
pmid = {42016853},
issn = {2380-6761},
abstract = {Controlling the molecular transport of nutrients through the gut is an attractive strategy to modulate host metabolism. Herein, a technique of stress-based evolution of an individual's own microbiota to enhance lipid metabolism is presented, which is based on sequential culture of these bacteria in higher concentrations of lipids. Using this technique, a probiotic formulation of bacterial colonies that exhibit increased lipid metabolism was generated from oral microbiota samples from mice, canine, and human sources. Mice fed a high-fat diet (HFD) and administered lipid stress evolved (LSE) probiotics excreted increased lipids in stool and reduced triglyceride transport into the blood by three-fold till 3 h post-oral gavage of soybean oil, as compared to controls. In addition, these enhanced probiotics prevented weight gain in mice fed a HFD five-fold better than controls and induced weight loss in mice with diet change three-fold faster than diet change alone. In these mice, there was a marked change in appearance with a more healthy, less oily coat. Controlled metabolic cage experiments demonstrated that the total movement, food intake, and water intake were not significantly different between mice receiving LSE probiotic versus a control probiotic formulation, suggesting that important health measures are unchanged with LSE probiotic administration. Overall, this facile stress-based culture technique can be utilized to modulate bacterial metabolism and applied to different industrial processes of probiotic generation and to affect different disease outcomes such as obesity.},
}
@article {pmid42016931,
year = {2026},
author = {Sun, M and Tu, L and Zhou, Z and Ma, Y and Zhang, H and Jiang, X and Tu, H and Lu, J and Niu, Y and Yue, Y and Yang, R and Chen, M and Fang, H and Si, Z and Chen, P},
title = {Embryonic sheep placenta alleviates muscle-fat wasting symptoms and improves gut microbiome dysbiosis in cachexia mice.},
journal = {Biochemistry and biophysics reports},
volume = {46},
number = {},
pages = {102590},
pmid = {42016931},
issn = {2405-5808},
abstract = {Cachexia is a multifactorial wasting syndrome characterized by muscle-fat depletion, accompanied by significant gut microbiome disturbances. Embryonic sheep placenta (ESP), a functional food known to modulate immunity and gut microbiome, represents a potential intervention substance. By in vitro and in vivo experiments combined with multi-omics analysis, this study provides experimental evidence for the effect of ESP on cachexia. These studies have found that ESP and its extract alleviate cachexia by increasing 91.80% (P < 0.0001) muscle tube diameter, 19.56% (P < 0.01) muscle cross-sectional area and 37.56% (P < 0.05) fat mass. Western blot shows that ESP downregulates the expression of TRIM63 and inhibits the expression of the HSL protein in the AMPK signaling pathway. Integrated multi-omics analysis suggests that ESP reshapes the gut microbiota structure of cachexia mice, restores their gut homeostasis and improves energy metabolism pathways. In conclusion, ESP plays a protective role in cachexia mice by alleviating the symptoms of muscle-fat atrophy, maintaining gut homeostasis and improving energy metabolism pathway.},
}
@article {pmid42017169,
year = {2025},
author = {Lee, JS and Fleming, D and Vulimiri, SV and Powers, M and Davis, JA and Gift, JS and Druwe, IL and Jones, R and Keshava, C and Toledo, M and Cote, I and Persad, AS},
title = {Inorganic arsenic exposure and modifying factors: a systematic evidence map.},
journal = {Human and ecological risk assessment : HERA},
volume = {31},
number = {9-10},
pages = {1525-1542},
pmid = {42017169},
issn = {1080-7039},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {Evidence maps employing systematic review screening tools have been used for identifying and categorizing chemical-specific literature that may be potentially relevant to scientific assessment. Inorganic arsenic (iAs), naturally distributed throughout the Earth's crust, is found in water, food, soil, and air. The epidemiologic evidence shows that iAs is associated with cancer and noncancer human health outcomes. Increased susceptibility to iAs-related disease is associated both with intrinsic and extrinsic factors. Our objective was to explore the use and feasibility of the systematic evidence map (SEM) approach to provide a clearer picture of the available literature on modifying factors that may alter the relationship between iAs exposure and health effects. A literature search (2014-2022) was conducted using PubMed, Web of Science, and Toxnet to identify studies with modifying factors of iAs health effects defined in Populations, Exposures, Comparators, Outcomes (PECO) criteria. Where applicable, health effects were also categorized. The literature search identified 584 studies with modifying factors that met the PECO criteria. Studies on the following modifying factors were identified: alcohol consumption (n= 8), chemical co-exposure (n= 104), genetic polymorphisms (n= 172), lifestages (n=228), microbiome (n=6), nutritional deficiencies (n=150), pre-existing conditions (n= 9), sex (n=65), smoking (n= 45), and other (e.g., arsenic metabolism, epigenetics, UV/sun exposure, DNA damage/repair, coffee consumption) (n=227). The SEM method was effectively utilized to identify studies on modifying factors for inorganic arsenic.},
}
@article {pmid42017455,
year = {2026},
author = {Zocateli, PI and de Olímpio, GV and de Almeida, FA and da Rocha, LO and de Sena Martins, DV and Sangi, S and Olivares, FL and de Matos, EM and Siqueira, J and Viccini, LF and da Paschoa, RP and Silveira, V and Grativol, C},
title = {DNA Methylation Shapes Seed-Borne Microbiome and Proteome Responses During Early Maize-Beneficial Bacteria Interactions.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70552},
pmid = {42017455},
issn = {1365-3040},
support = {//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; PAPIC-2024//Universidade Estadual do Norte Fluminense Darcy Ribeiro/ ; },
abstract = {Microorganism and plant interactions are crucial for development and environmental adaptation. Plant growth promoting bacteria enhance agricultural productivity in a sustainable manner, while epigenetic modifications such as DNA methylation regulate gene expression and adaptive responses. The objective of this study is to determine how DNA hypomethylation influences early interactions between maize (Zea mays) and the endophytic diazotrophic bacterium Herbaspirillum seropedicae, particularly regarding plant growth, metabolism, and the root microbiome. Treatment with the hypomethylating agent 5-azacytidine (5-azaC) altered maize root morphology without affecting bacterial growth. Inoculation with H. seropedicae promoted plant growth and bacterial colonisation in root mucilage, with higher accumulation in 5-azaC treated roots. Global methylation analysis showed that bacterial inoculation modulates cytosine methylation in a manner similar to 5-azaC, suggesting a role in epigenetic regulation. Gene expression analysis of DNA methylation machinery confirmed that hypomethylation drives plant-microbe interactions. Root microbiome profiling revealed that 5-azaC disrupted microbial composition, which was partially restored by bacterial inoculation. Proteomic analysis identified 1,818 proteins and highlighted significant changes in metabolic pathways, especially carbon metabolism and the citric acid cycle. These findings demonstrate that DNA hypomethylation combined with bacterial interaction profoundly affects cellular and metabolic processes and provide insights for sustainable agricultural practices through epigenetic and microbial modulation.},
}
@article {pmid42017663,
year = {2026},
author = {Ma, C and Su, C and Li, J and Wang, J and Liao, J and Cheng, L and Qu, J and Zhang, G and Jiang, J and Shuai, S},
title = {Systematic evaluation of TCGA tumor microbiota reveals context-dependent reliability.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0018026},
doi = {10.1128/msystems.00180-26},
pmid = {42017663},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial profiles from The Cancer Genome Atlas (TCGA) are widely used to study the tumor microbiota, a key component of the cancer ecosystem, yet their reliability remains unclear. Here, we systematically benchmarked two leading TCGA microbial profiles (TMPs) to define their consistency, accuracy, and reliability in host-microbe association studies across 24 cancer types, with a primary focus on the bacterial component. We found that while the TMPs showed substantial agreement in microbial composition, their accuracy in detecting known oncomicrobes was variable, ranging from excellent for human papillomavirus (HPV) to poor for Helicobacter pylori. The concordance of downstream host-microbe associations was moderate for gene expression but nearly absent for methylation and protein data. Our permutation-based framework revealed that while most individual associations were statistically reliable, those involving cell type composition and patient survival were statistically spurious. To empower future research with these insights, we introduced Multi-Omics and Microbiome Associations in Cancer 2 (MOMAC2), an interactive web portal that stratifies all associations by confidence level. We demonstrated its utility by using high-confidence associations to confirm HPV-driven methylation-gene expression axes and guide a novel experimental investigation. Co-culture with Streptococcus anginosus not only validated its predicted gene expression changes in oral cancer cells but also revealed a significant promotion of cancer cell proliferation and migration. Our study provides a rigorous framework for interpreting TCGA's tumor microbiome and highlights that these data require careful, multi-layered validation to yield robust biological insights.<br><br>IMPORTANCE: Bacteria living inside tumors can influence how cancer grows and responds to treatment, but the field has been hampered by controversy over the reliability of the data. Our study provides a much-needed road map for researchers. We rigorously tested the massive Cancer Genome Atlas data set and developed a statistical framework to separate true biological signals from random noise. We discovered that many widely reported links are statistically unreliable and likely false leads. Importantly, our framework successfully pinpoints trustworthy signals. We used it to identify a specific bacterium, Streptococcus anginosus, and proved in the lab that it makes oral cancer cells grow faster and spread. Our publicly available Multi-Omics and Microbiome Associations in Cancer 2 (MOMAC2) web portal now allows scientists to use these reliability-graded findings to accelerate robust cancer microbiome research.},
}
@article {pmid42017723,
year = {2026},
author = {Fatima, M and Omer, H and Nadeem, N and Imtiaz, S},
title = {Cosmetics and their role in modulating skin microbiome health. A narrative review.},
journal = {JPMA. The Journal of the Pakistan Medical Association},
volume = {76},
number = {3},
pages = {417-423},
doi = {10.47391/JPMA.30352},
pmid = {42017723},
issn = {0030-9982},
mesh = {Humans ; *Cosmetics/pharmacology/adverse effects ; *Microbiota/drug effects ; *Skin/microbiology/drug effects ; Probiotics ; Prebiotics ; Dysbiosis ; Skin Microbiome ; },
abstract = {The skin microbiome plays a vital role in immune regulation, barrier function, and protection against pathogens. Cosmetics, traditionally used for aesthetic purposes, also influence skin microbiomes. Depending on their formulation, they can support microbial balance through probiotics, prebiotics and postbiotics, or disrupt it, leading to dysbiosis and conditions such as eczema and acne. Advances in nanotechnology have further altered cosmetic efficacy and microbial interactions. The current narrative review was planned to highlight the dual role of cosmetics in modulating skin microbiome health, to emphasise the need for regulatory oversight, and to explore strategies for developing safe, microbiome friendly skincare products.},
}
@article {pmid42017751,
year = {2026},
author = {Massironi, S and Fanizzi, F and Invernizzi, F and Furfaro, F and Ciocca, L and Arcari, I and Allocca, M and Peyrin-Biroulet, L and Danese, S},
title = {Inflammatory bowel disease and Primary sclerosing cholangitis: immunological links and clinical outlook.},
journal = {Expert review of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1080/1744666X.2026.2664055},
pmid = {42017751},
issn = {1744-8409},
abstract = {INTRODUCTION: Primary sclerosing cholangitis (PSC) represents a progressive fibroinflammatory cholangiopathy intricately linked to inflammatory bowel disease (IBD), forming a distinctive overlap syndrome driven by immune dysregulation and gut - liver axis disruption and characterized by a markedly increased risk of colorectal and hepatobiliary cancers.<br><br>AREAS COVERED: This review summarizes current understanding of the immunopathogenesis and clinical spectrum of PSC - IBD. Key mechanisms include aberrant lymphocyte homing through the &#x3b1;4&#x3b2;7/MAdCAM-1 axis, shared genetic susceptibility loci, alterations in bile acid metabolism, and gut microbial dysbiosis. The clinical course and malignancy risk of PSC - IBD are contrasted with those of isolated PSC and IBD, and surveillance strategies are discussed. Therapeutic approaches under investigation, such as advanced therapies and microbiome-targeted interventions including oral vancomycin, are critically appraised based on recent translational and clinical studies.<br><br>EXPERT OPINION: PSC - IBD demands multidisciplinary, risk-stratified management and intensive cancer surveillance. Although no medical therapy currently halts disease progression, novel agents modulating immune and microbial pathways represent promising avenues. In the future, integration of hepatology, gastroenterology, and immunology within a precision-medicine framework is expected to reshape disease stratification and therapeutic decision-making for this complex overlap syndrome.},
}
@article {pmid42017823,
year = {2026},
author = {Wilkie, I and Von Possel, N and Sauma-Sánchez, T and Reintjes, G and Orellana, LH},
title = {Conserved glycan-utilization strategies shape Akkermansiaceae success across aquatic and gut ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag096},
pmid = {42017823},
issn = {1751-7370},
abstract = {Elucidating interaction mechanisms and substrate specialization is central to understanding bacterial adaptation across ecological niches. Specialized mucin-degrading bacteria of the genus Akkermansia are widely recognized for their beneficial roles in the human gut, yet it remains unclear whether this specialization is unique to the gut or reflects a conserved ecological strategy across different hosts and environments. Here, we show that members of the family Akkermansiaceae share a deeply conserved genetic and mechanistic framework enabling colonization across gut and aquatic ecosystems. Comparative genomics of Akkermansiaceae representatives revealed niche-specific gene repertoires tightly adapted to substrate source and availability. Marine representatives encode distinct combinations of CAZymes and comparatively expanded sulfatase repertoires that enable the degradation of sulfated polysaccharides such as fucoidan, a recalcitrant substrate linked to carbon sequestration. Structural predictions and comparisons identified a conserved molecular system centered on a type IV-like pilus that mediates attachment to complex, fucose-rich glycans. The genes underlying this system are syntenic with the recently described mucin utilization locus in Akkermansia muciniphila, revealing an evolutionary continuity between aquatic and gut lineages. Seawater incubations with fluorescently labeled substrates confirmed fucoidan uptake and degradation by marine Akkermansiaceae. Together, these results reveal a unified glycan-utilization strategy spanning the environmental breadth of Akkermansiaceae and provide a mechanistic framework linking ecological success in marine environments to traits associated with probiotic functions in the human gut.},
}
@article {pmid42017830,
year = {2026},
author = {Vergara-Florez, DC and Duda, TF},
title = {Taxonomy, tissue, and habitat influence mollusc microbial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag092},
pmid = {42017830},
issn = {1751-7370},
abstract = {Microbes play a crucial role in the health, development, and resilience of molluscs, yet the ecological and evolutionary factors shaping their microbial communities remain poorly understood. To uncover the drivers of microbial community composition of molluscs, we conducted a systematic review of 85 studies, including 45 on bivalves from marine and freshwater habitats; 33 on gastropods from marine, freshwater, and terrestrial habitats; and seven on cephalopods. Our synthesis reveals that both intrinsic (e.g., host phylogeny, tissue type) and extrinsic (e.g., environment, geography, and seasonality) factors influence microbial community structure, but the effects are highly taxon- and context-dependent. Although studies of bivalves often emphasize environmental drivers, those of cephalopods more frequently highlight intrinsic host features. Despite growing interest in molluscan microbiomes, we identified significant taxonomic and methodological biases, including a predominant focus on economically important species and gut tissues. We advocate for a broader, integrative approach that includes underrepresented molluscan groups, diverse tissue types, and testing of both intrinsic and extrinsic variables across spatial and temporal gradients. This review highlights the need for standardized, multi-factorial research to better understand and predict microbial community responses to environmental change of one of the most diverse and ecologically important invertebrate phyla.},
}
@article {pmid42018226,
year = {2026},
author = {Yang, Y and Lan, C and Jiang, Z},
title = {Impact of Probiotic-Adjunctive Vonoprazan-Amoxicillin Dual Therapy on Gut Microbiota and Clinical Symptoms in Helicobacter pylori Eradication.},
journal = {Tissue engineering and regenerative medicine},
volume = {},
number = {},
pages = {},
pmid = {42018226},
issn = {2212-5469},
abstract = {BACKGROUND: This study evaluates the impact of Bacillus subtilis dual-strain enteric-coated capsules combined with vonoprazan-amoxicillin (VA) therapy on Helicobacter pylori (Hp) eradication rates, gastrointestinal symptoms, adverse events (AEs), and gut microbiota.<br><br>METHODS: 60 Hp-positive adults were enrolled, allocated to probiotic (n&#x2009;=&#x2009;30) or placebo (n&#x2009;=&#x2009;30) groups. Both groups received a 14-day VA dual therapy, with the probiotic group additionally receiving a 28-day Bacillus subtilis dual-strain capsule regimen and the placebo group receiving matched placebos. Outcomes included Hp eradication rates (intention-to-treat [ITT]/per-protocol [PP] analyses), Gastrointestinal Symptom Rating Scale (GSRS) scores, AEs, antibiotic susceptibility, and gut microbiota changes (16S rRNA sequencing).<br><br>RESULTS: ITT analysis showed identical eradication rates (93.33%) in both groups; PP analysis revealed 96.67% (probiotic) versus 93.33% (placebo). The probiotic group exhibited significantly lower GSRS scores at weeks 4 (T2) and 8 (T3), particularly for diarrhea and acid reflux, with milder AEs (severity score: 5). Probiotic supplementation reduced Hp resistance to metronidazole (26.67% vs. 60.00%) without affecting other antibiotics. Microbiota analysis demonstrated post-eradication reductions in gastric pathogens (e.g., Helicobacter) and increased beneficial bacteria (e.g., Lactobacillus). The probiotic group showed faster restoration of gut &#x3b1;-diversity (higher at T2), enriched butyrate producers (e.g., Blautia, Anaerobutyricum), and decreased opportunistic pathogens (e.g., Klebsiella).<br><br>CONCLUSIONS: Although Bacillus subtilis supplementation did not enhance Hp eradication rates, it significantly improved gastrointestinal symptoms, reduced AEs, increased Hp susceptibility to metronidazole, and accelerated microbiota recovery, supporting its role in microbiome modulation during Hp eradication therapy.},
}
@article {pmid42018414,
year = {2026},
author = {Boumasmoud, M and León-Sampedro, R and Beusch, V and Benz, F and Arnoldini, M and Hall, AR},
title = {Interspecies interaction controls Escherichia coli growth in human gut microbiome samples.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {17},
pages = {e2527793123},
doi = {10.1073/pnas.2527793123},
pmid = {42018414},
issn = {1091-6490},
support = {310030_192428//Swiss NSF/ ; },
mesh = {Humans ; *Escherichia coli/growth &amp; development ; *Gastrointestinal Microbiome/physiology ; Feces/microbiology ; },
abstract = {Gut microbial community composition varies from one person to another. Potentially, this means the ecological interactions experienced by individual strains or species also vary among microbiomes of different people. However, testing this directly in human microbiomes and identifying ecological drivers involved are challenging. Here, we use replicated anaerobic microcosms to quantify variability of population growth for a key commensal species among microbiome samples from different individuals and to identify underlying intra- and interspecific interactions. In a reciprocal transplant experiment, both absolute and relative growth performance of different Escherichia coli strains varied among gut microbiome samples from healthy individuals. This was partly explained by intraspecific competition: growth performance of individual E. coli strains was associated with displacement of resident conspecifics. However, the determinants of E. coli growth varied among samples. In one microbiome sample with a distinctive taxonomic composition, culture acidification by resident microbes impaired growth of all E. coli strains. We identified a strain of Clostridium butyricum contributing to this effect and showed that transferring it into other microbiomes predictably altered pH, fermentation product profiles (butyrate accumulation and acetate/lactate depletion), and population growth of other species including E. coli, thereby reshaping overall taxonomic composition. Our results suggest natural interindividual gut microbiome variation translates to variable ecological interactions with incoming bacteria, but these dynamics can be manipulated by a generalizable interspecies interaction.},
}
@article {pmid42018438,
year = {2026},
author = {Sun, X and Jiang, X and Zhang, L and Li, M},
title = {Extensive individual and microorganism-specific circadian oscillations of the upper respiratory tract microbiome.},
journal = {Cell reports},
volume = {45},
number = {5},
pages = {117284},
doi = {10.1016/j.celrep.2026.117284},
pmid = {42018438},
issn = {2211-1247},
abstract = {The upper respiratory tract microbiome (URM) influences host susceptibility and respiratory disease outcomes, but its normal temporal dynamics remain poorly understood. We conducted temporal metagenomic profiling of the URM by collecting oropharyngeal swabs from 22 healthy adults at 4-h intervals over 48 h. We identify significant 24-h cyclic variations in microbial composition and biomass, with two predominant oscillation patterns: "evening-peak" and "morning-peak" patterns. Temporal variation introduces substantial shifts in microbial profiles, leading to false positives in differential analyses. Microbial rhythmicity is linked to phenotypic traits such as oxygen and nutrient requirements. Nonetheless, rhythmic patterns differ across individuals, and regression analysis reveals that host identity contributes more substantially to microbial rhythmicity than species identity. Functional pathway analysis based on metagenomic sequencing data shows similar circadian fluctuations. Additionally, although anatomically adjacent, the oral cavity and oropharynx exhibit divergent rhythmic behaviors, highlighting local environmental influences on microbial rhythmicity. These findings reveal previously unrecognized temporal dynamics of the URM and provide a temporal framework for more accurate biomarker discovery.},
}
@article {pmid42018480,
year = {2025},
author = {Dormans, T and Kroon, J and Rampanelli, E and Nieuwdorp, M and van Es, N},
title = {Bacterial tryptophan metabolites in cancer and atherosclerosis: insights for a role in immune checkpoint inhibition.},
journal = {Essays in biochemistry},
volume = {69},
number = {6},
pages = {},
doi = {10.1042/EBC20253060},
pmid = {42018480},
issn = {1744-1358},
mesh = {Humans ; *Tryptophan/metabolism ; *Atherosclerosis/metabolism/immunology/microbiology ; *Neoplasms/metabolism/drug therapy/immunology/microbiology ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology ; *Gastrointestinal Microbiome ; Indoles/metabolism ; Animals ; *Bacteria/metabolism ; },
abstract = {The gut microbiota plays a pivotal role in human health, partly through the production of bioactive metabolites from dietary tryptophan. These indole derivatives have emerged as key modulators of immune function, inflammation, and metabolic health and have been linked to various diseases. In the context of cancer, indole derivatives are increasingly being studied as promising modulators of immune checkpoint inhibitor (ICI) therapy, with accumulating evidence indicating potential for various derivatives to enhance therapeutic efficacy. ICI therapy is associated with various immune-related adverse events, including accelerated progression of atherosclerotic cardiovascular disease. Given their immunomodulatory properties, there is a growing interest in the usage of indole metabolites to mitigate these cardiovascular complications. This mini-review summarizes current knowledge on the roles of microbiota-derived indoles in cancer, ICI therapy, and atherosclerosis. Though direct evidence linking bacterial tryptophan-derived metabolites to ICI-associated atherosclerosis is currently lacking, accumulating evidence indicates that indole derivatives regulate pathways involved in both anti-tumor immunity and atherosclerosis. Advancing our understanding of how the microbiome and its metabolites influence both cancer and cardiovascular disease will be crucial for developing personalized, metabolite-based strategies to improve outcomes in patients undergoing ICI therapy.},
}
@article {pmid42018486,
year = {2026},
author = {Jung, A and Bartnick, R and Thomas, DC and Lehndorff, E and Lueders, T},
title = {Conventional and biodegradable microplastics elicit contrasting taxon-level responses in rhizosphere microbiomes of maize and strawberry.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag040},
pmid = {42018486},
issn = {1574-6941},
abstract = {Microplastics (MP) are relevant contaminants in agroecosystems, influencing soil nutrient dynamics and soil-plant-microbial interactions. As agriculture shifts from conventional to biodegradable plastics, their impacts on different crop rhizosphere microbiomes considering both total (DNA-derived) and active (rRNA-derived) communities have not been clearly elaborated. We hypothesized that microbiome impacts would be distinct across different plants and polymer types. Maize and strawberry plants were cultivated with 1% MP by soil weight, including two conventional polymers (LDPE, PET) and one biodegradable polymer (PBAT). Strawberry plants increased biomass across all MP treatments, accompanied by greater soil nitrate depletion. MP-induced impacts on soil prokaryotic communities were mostly additive to plant effects, as determined by 16S rRNA amplicon sequence profiling. PBAT stimulated Cupriavidus spp. and members of Saccharimonadales, suggesting a selection of potential polymer-degraders and microbial interactions, independent of plant species and root proximity. In contrast, conventional MPs induced a less selective response with compositional shifts across a greater number of taxa. MP-induced changes were more apparent in rRNA- than DNA-derived profiles, suggesting a profound response of putative active taxa. Together, we demonstrate that plant species and MP type jointly modulate rhizosphere microbial community response to MP pollution, with direct implications for soil biogeochemistry, rhizosphere functioning, and crop performance.},
}
@article {pmid42018976,
year = {2026},
author = {Feles, EA and Mattner, F},
title = {Perioperative Antibiotic Prophylaxis in Cesarean Section and the Maternal Gut Microbiome: Protocol for a Remote Observational Cohort Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e84909},
pmid = {42018976},
issn = {1929-0748},
mesh = {Humans ; Female ; *Antibiotic Prophylaxis/methods ; *Cesarean Section/methods/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Pregnancy ; Prospective Studies ; *Anti-Bacterial Agents/administration &amp; dosage/therapeutic use ; Adult ; *Surgical Wound Infection/prevention &amp; control ; Cohort Studies ; Observational Studies as Topic ; Perioperative Care/methods ; },
abstract = {BACKGROUND: Cesarean section (CS) requires perioperative antibiotic prophylaxis (PAP) for the prevention of surgical site infections. However, systemic antibiotics during the peripartum period may induce compositional perturbations of the maternal gut microbiome, a system already characterized by reduced resilience. Data on maternal gut microbiome dynamics after CS with PAP are scarce, largely due to logistical and feasibility barriers that limit the participation of pregnant women and new mothers in conventional clinical studies.<br><br>OBJECTIVE: This protocol primarily aims to evaluate the feasibility of a fully decentralized, remote study design for longitudinal gut microbiome research in the peripartum period. Secondary exploratory objectives include the comparative analyses of microbiome composition between CS with PAP and vaginal delivery (VD) without antibiotic exposure to inform future adequately powered studies.<br><br>METHODS: The MAMA (Microbiome Changes Due to Antibiotic Prophylaxis in Mothers at Birth) study is a prospective, 2-arm observational cohort study conducted entirely off-site. Women in the third trimester of pregnancy were recruited at 2 German level-1 perinatal centers and affiliated outpatient facilities. Participants underwent either CS with PAP (single dose cefuroxime 1.5 g intravenously) or VD without antibiotics. Stool samples were self-collected at home and returned by mail at 3 predefined time points: late pregnancy (T0), 2 to 3 days post partum (T1), and 90&#xb1;10 days post partum (T2). Primary outcomes are feasibility indicators, including recruitment rate, sample and questionnaire return rates at each time point, adherence to sampling windows, and participant retention across follow-up. Secondary outcomes are exploratory microbiome measures based on 16S rRNA gene sequencing (V3-V4), including alpha diversity indices, beta diversity metrics, and relative taxonomic abundances. Microbiome analyses are explicitly compositional and hypothesis-generating. Group comparisons and longitudinal within-individual changes will be assessed using nonparametric diversity metrics and multivariate distance-based methods. No confirmatory hypothesis testing is planned.<br><br>RESULTS: Recruitment occurred between May 2022 and October 2023, with 37 women enrolled (25 CSs and 12 VDs). Follow-up was completed with receipt of the final stool sample in March 2024. DNA extraction and sequencing were completed in a single batch in October 2024. Bioinformatic processing and statistical analyses were initiated in June 2025 and are ongoing as of December 2025. Results from the exploratory microbiome analyses are expected to be published in 2026.<br><br>CONCLUSIONS: This protocol demonstrates the feasibility of conducting fully decentralized, longitudinal microbiome research in a peripartum population without requiring on-site visits. By integrating study procedures into maternal realities, the remote design reduces participation barriers and addresses a clinically relevant research gap that has remained largely unexamined despite routine use of PAP. While microbiome-related outcomes are exploratory, the methodological framework established here provides a scalable model for future maternal and postpartum research, supporting ethically grounded, participant-centered study designs and evidence-informed care strategies.},
}
@article {pmid42019076,
year = {2026},
author = {Baig, AM and Iqbal, H and Shi, R and Zeb, A and Khan, S and Tariq, H and Li, X and Irshad, F and Miao, X and Hussain, S and Liu, W},
title = {6PPD-Quinone Triggers Oxidative Stress, Metabolic Reprogramming, and Rhizosphere Microbiota Shifts in Wheat.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01118},
pmid = {42019076},
issn = {1520-5118},
abstract = {The highly toxic tire-derived compound N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) poses emerging environmental risks, yet its fate within the soil-plant system remains unclear. This study reveals that 6PPD-Q induces significant oxidative stress in wheat (Triticum aestivum L.), increasing reactive oxygen species (ROS) by 259% in shoots and 217% in roots and malondialdehyde (MDA) by 57 and 59%, respectively, at a concentration of 200 ng/g compared to the control. This oxidative stress disrupted key antioxidant enzymes (SOD and POD) and reduced the uptake of essential nutrients (Fe, Cu, Mg, Mn, and P). Metabolomic analysis showed perturbation in central carbon metabolism, fatty acid turnover, and amino acid biosynthesis. 16S rRNA sequencing indicated reduced rhizosphere bacterial diversity and shifts in key phyla, linked to nutrient cycling. This work provides mechanistic insights into tire-derived contaminant toxicity in soil-plant systems and highlights the need for further ecological risk assessment.},
}
@article {pmid42019202,
year = {2026},
author = {Chai, S and Zhang, Y and Guo, Y and Cao, D and Wang, J and Yan, Y and Shi, Y and Yuan, Z and Wang, X and Tong, T and Zhen, Z and Huo, Y and Zhang, K and Wang, F and Liu, GR and Li, W and Xu, X and Ban, T and Liu, SL and Liu, H},
title = {Enterolactone mitigates atherosclerosis by facilitating resolution of ferroptosis-associated intimal inflammation via the Keap1/Nrf2/GPX4 pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158178},
doi = {10.1016/j.phymed.2026.158178},
pmid = {42019202},
issn = {1618-095X},
abstract = {BACKGROUND: Atherosclerosis is the inflammatory consequence of lipid accumulation with plaque formation in the vascular intima and is a common condition to develop into various cardiovascular diseases. Current therapies do not always lead to satisfactory treatment outcomes. Enterolactone, a mammalian lignan produced by bacterial transformation from plant lignans, has a preventive effect against cardiovascular disease. However, its effect on atherosclerosis and the underlying mechanism of action remain unclear.<br><br>PURPOSE: To explore the therapeutic effect of ENL on atherosclerosis and elucidate the underlying mechanism.<br><br>METHODS: We established a model of atherosclerosis on ApoE-/- C57BL/6 mice by high fat diet. The aortic root was collected and sectioned to assess arterial plaque area, collagen fibrillar proliferation, and lipid content. RT-qPCR was used to determine the inflammatory response in the artery of mice. The serum from mice was isolated to measure lipid levels, and the fecal microbiota was analyzed by 16S rDNA. H2O2 was used to induce HUVEC injury and ferroptosis to mimic endothelial cell dysfunction in atherosclerosis, and the inhibitory effect of ENL on HUVEC ferroptosis was appraised by monitoring ferroptosis indexes and levels of iron-related proteins.<br><br>RESULTS: In the animals, enterolactone significantly improved lipid metabolism, attenuated ferroptosis occurring in the intima, facilitated the antioxidant mechanisms, and promoted healing of the endothelial lesions, by interacting with Nrf2. Of great importance, enterolactone massively altered the gut microbiota toward a curative outcome by elevating the abundance of beneficial bacteria, such as the SCFA-producing taxa. Additionally, ENL suppresses lipid peroxidation and inflammatory activation in HUVECs by regulating the Keap1/Nrf2/GPX4 pathway, and knocking down Nrf2 attenuates the treatment effect of ENL.<br><br>CONCLUSION: Enterolactone effectively resolves intimal inflammation and redresses atherosclerosis by ameliorating the gut microbiome and modulating lipid metabolism via the Keap1/Nrf2/GPX4 pathway.},
}
@article {pmid42019335,
year = {2026},
author = {Sabatino, R and Pulina, S and Sbaffi, T and Kamburska, L and Titocci, J and Cherchi, M and Pittalis, C and Piscia, R and Vaccarelli, I and Rosati, I and Padedda, BM and Allemanno, F and Casiddu, P and Di Cesare, A},
title = {Lakes and lagoons used for drinking water supply and fisheries as sources of potentially pathogenic bacteria and antimicrobial resistance.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129718},
doi = {10.1016/j.jenvman.2026.129718},
pmid = {42019335},
issn = {1095-8630},
abstract = {Drinking water supplies and water basins used for fisheries represent two essential water sources for humans. Despite the growing accessibility of metagenomic approaches, their routine use for water quality monitoring is still limited. Many key water resources have yet to be fully characterized in terms of microbiome, pathobiome, and antimicrobial resistome. In this study, surface water samples were collected over one year from the artificial Lake Bidighinzu (drinking water supply) and the coastal lagoon Cabras (fisheries) located in the western Mediterranean area. Samples were analyzed for physical and chemical properties, and 16S rRNA gene amplicon and shotgun sequencing were used to characterize bacterial communities, pathobiomes, and antimicrobial resistomes. Physical and chemical properties were generally similar between sites, except for higher salinity in Cabras Lagoon. In Cabras Lagoon, richness of the bacterial community and pathobiome was generally higher in the largest trophic fraction (>20 μm), while in both sites the abundance of potentially pathogenic bacteria (PPB) increased at this fraction. PPB, including ESKAPE pathogens, were more abundant in Lake Bidighinzu. The overall antimicrobial resistome was similar across sites, with high-risk antimicrobial resistance genes (ARGs) such as emrB prevalent. Lake Bidighinzu also had more contigs where ARGs co-occurred with mobile genetic elements. This study highlights microbiological risks in two aquatic systems, particularly Lake Bidighinzu, and underscores the need to integrate metagenomic approaches, possibly with cultivation-based methods, to monitor water quality and assess health risks in drinking water supplies and fisheries.},
}
@article {pmid42019337,
year = {2026},
author = {Yu, B and Jiang, C and Yang, K and Zhang, Y and Gao, Y and Chen, Z and Qian, X and Ouyang, S},
title = {Correlation analysis of heavy metal, antibiotics accumulation, and antibiotic resistance genes induced by long-term biogas slurry application.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129745},
doi = {10.1016/j.jenvman.2026.129745},
pmid = {42019337},
issn = {1095-8630},
abstract = {Biogas slurry (BS), as product of animal manure fermentation, is often used as a fertilizer in farmland. However, the long-term application impact on the soil remains not fully understood. Studies have shown that although long-term application of BS does not lead to excessive antibiotic residues in the soil, it increases the abundance of antibiotic resistance genes (ARGs) and promotes their transfer among potential hosts. The complex co-occurrence of bacteria and ARGs implies enhanced horizontal gene transfer, and the increased abundance of the intl1 gene supports this change. Moreover, the distribution of antibiotic-resistant bacteria and ARGs is closely related to the duration of application. Meanwhile, tetracyclines and fluoroquinolones antibiotics, as well as ARGs, are significantly enriched in soils irrigated with BS, and various potentially pathogenic bacterial genera are present. In addition, the application of BS can increase the soil organic carbon stock and alter the soil bacterial and fungal communities. Long-term application of BS results in the accumulation of tetracyclines and the enrichment of ARGs in the soil. It also has an impact on the diversity of soil microbial functional genes. These findings provide a basis for the formulation of relevant policies and sustainable soil management.},
}
@article {pmid42019448,
year = {2026},
author = {Miao, Z and Huang, Z and Wang, J and Li, Z and Shi, J},
title = {Unveiling the enhancement mechanisms of bio-carriers in anoxic treatment of composite phenolic wastewater: A multi-dimensional comparison from macro-performance to microbiome.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142163},
doi = {10.1016/j.jhazmat.2026.142163},
pmid = {42019448},
issn = {1873-3336},
abstract = {This study conducted a comparative investigation into the enhancement of anoxic biodegradation of composite phenols in simulated coal chemical wastewater using four distinct bio-carriers: activated carbon, ceramsite, iron-carbon, and polyurethane (PU). Five parallel anoxic reactors (R1: blank, R2: activated carbon, R3: ceramsite, R4: iron-carbon, R5: PU) were operated under progressively increasing phenol loads (10-350 mg/L). Results demonstrated that all carriers improved treatment performance compared to the blank reactor (R1). The iron-carbon carrier (R4) exhibited exceptional resilience, maintaining complete phenol degradation up to 300 mg/L, attributed to micro-electrolysis pre-treatment that enhanced biodegradability. The PU carrier (R5) achieved the highest and most stable removal efficiencies for both phenol and COD at the highest loadings, coupled with the most diverse bacterial community and a uniquely enriched fungal genus, Cutaneotrichosporon (76.3%), identified as a key degrader. Microbial community analysis revealed that carrier type significantly shaped the microbial structure. The PU and ceramsite carriers fostered higher biodiversity, while the iron-carbon environment selected for specific functional genera. The findings provide critical insights into the mechanisms-adsorption-biofilm synergy, micro-electrolysis, and targeted microbial enrichment-by which different carriers enhance anoxic treatment, offering a scientific basis for selecting optimal carriers in treating high-strength phenolic wastewater.},
}
@article {pmid42019450,
year = {2026},
author = {Guo, Z and Wang, Z and Liu, Y and Wang, M and Ma, H and Wang, Z and Zhang, S and Chang, Y and Ge, H and Li, C and Yang, H and Miao, H and Zhang, X and Cui, P},
title = {Early-life and lifelong exposure to environmentally relevant enrofloxacin reorganizes a proteobacteria-centered gut-lipid-resistome steady state in marine medaka.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142146},
doi = {10.1016/j.jhazmat.2026.142146},
pmid = {42019450},
issn = {1873-3336},
abstract = {Environmental fluoroquinolone residues such as enrofloxacin (ENR) are increasingly detected in coastal waters, yet the persistence of low-dose effects on gut ecosystem organization remains unclear. We compared an early-life window exposure (5 μg/L ENR, 20-35 days post-hatch; depurated to 150 dph) with a lifelong exposure (5 μg/L ENR from fertilization to 150 dph) in marine medaka (Oryzias melastigma), using an environmentally realistic upper-bound concentration reflecting aquaculture-impacted conditions. We integrated intestinal histology and ultrastructure, inflammatory and lipid-metabolic transcriptional programs, intestinal fatty-acid profiles, 16S rRNA and 2bRAD-M characterization of the gut microbiota and antibiotic-resistance genes. Both regimens increased intestinal hypertrophy or densification and rewired communities into more positively connected, Proteobacteria-centered networks. Lifelong exposure produced a pronounced shift in intestinal lipid programming, marked by enhanced lipogenesis and reduced fatty-acid catabolism, together with selective changes in fatty-acid composition and desaturation balance. Early-life window exposure left persistent, albeit weaker, adult signatures in intestinal morphology, microbial network topology, and lipid-related transcription after prolonged withdrawal. Across cohorts, Proteobacteria indicator taxa covaried with inflammatory and lipid gene modules and with coordinated resistance-gene modules, consistent with a Proteobacteria-rich gut-lipid-resistome steady state. These findings indicate that ENR at an environmentally realistic upper-bound concentration reflecting aquaculture-impacted and hotspot contamination scenarios can durably reorganize host-microbe-resistome linkages, supporting re-evaluation of "no-effect" thresholds for antibiotic pollution from a One Health perspective.},
}
@article {pmid42019469,
year = {2026},
author = {Peng, F and Zeng, YY and Chang, L and Huang, YX and Deng, JT and Liu, YX and He, X and Song, ZH},
title = {Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106914},
doi = {10.1016/j.psj.2026.106914},
pmid = {42019469},
issn = {1525-3171},
abstract = {It is well-established that the gut microbiota plays a crucial role in skeletal muscle development and homeostasis. However, the contribution of the gut microbiome to the distinct meat quality phenotypes observed between fast-growing commercial broilers and slow-growing local chicken breeds remains poorly understood. Therefore, this study aims to elucidate how the gut microbiota modulates pectoral muscle development by comparing muscle growth phenotypes and gut microbiome dynamics across these breeds. Using the fast-growing commercial Arbor Acres (AA) broiler and the slow-growing local breed Taoyuan (TY) chicken as models, we investigated how breed-specific gut microbiota modulate pectoral muscle fiber composition. AA broilers exhibited faster muscle growth but lower oxidative type I fiber proportion than TY chickens. While small intestinal microbiota succession was similar, cecal communities diverged markedly between breeds. Integrated metagenomic sequencing and metabolomics revealed that cecal Phocaeicola dorei abundance was strongly correlated with serum taurolithocholic acid (TLCA) levels and type I fiber content, especially in TY chickens, which prompted the selection of TLCA for functional validation. Reciprocal intestinal microbiota transplantation (IMT) shifted recipient muscle fiber phenotypes toward those of donors, confirming a causal role of the cecal microbiota. Furthermore, in vitro assays using AA-derived myoblasts demonstrated that TLCA promotes mitochondrial biogenesis and type I fiber formation by enhancing p38 MAPK phosphorylation and PGC-1α activation; this effect was abolished by the p38 inhibitor SB203580. Our study demonstrated that gut microbiota-derived TLCA modulates muscle fiber type transformation via the p38 MAPK/PGC-1α signaling pathway. This finding reveals an intricate mechanism whereby the gut microbiota regulates host muscle development through a metabolite-signaling axis, providing critical insights into the gut microbe-myofiber relationship.},
}
@article {pmid42019500,
year = {2026},
author = {Chen, J and Ren, Y and Zhou, Y and Wang, Z and Mao, K and Yu, Z and Li, J and Guo, X and Xu, H and Wang, Y and Wang, Y and Pang, B and Liu, H and Tang, H and Han, JJ},
title = {A generative AI framework unifies human multi-omics to model aging, metabolic health, and intervention response.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2026.03.014},
pmid = {42019500},
issn = {1932-7420},
abstract = {Understanding aging and complex diseases requires diverse data, ranging from molecular profiles to imaging and routine clinical tests. However, most multi-omic datasets measure only a subset of modalities and are confounded by batch effects. Here, we present AURORA (AI unification and reconstruction of omics reassembly atlas), a generative deep-learning platform that integrates seven modalities (including transcriptomics, metabolomics, microbiome, 3D and thermal facial imaging, and clinical laboratory tests) across 581,763 samples from 425,258 individuals. AURORA harmonizes batch effects and reconstructs missing data across modalities, enabling highly accurate multimodal aging clocks and disease risk predictors. It also supports personalized in silico perturbation analyses to predict intervention and drug responses, validated using longitudinal cohorts. As a proof of concept, we provide a prototype AI agent that converts single-input modalities into a multimodal report for users and researchers. Together, AURORA links non-invasive inputs to comprehensive aging biomarkers and therapeutic discovery.},
}
@article {pmid42019590,
year = {2026},
author = {Martínez-López, N and Figueras, A and Novoa, B and Pereiro, P},
title = {Dissecting the host transcriptome and microbiota responses to Viral Hemorrhagic Septicemia Virus (VHSV) in the turbot (Scophthalmus maximus) intestine: insights from moribund and asymptomatic phenotypes.},
journal = {Fish &amp; shellfish immunology},
volume = {},
number = {},
pages = {111370},
doi = {10.1016/j.fsi.2026.111370},
pmid = {42019590},
issn = {1095-9947},
abstract = {Viral infections profoundly influence host physiology, not only by triggering complex immune responses but also by reshaping the associated microbiota. Conversely, the microbiota can modulate antiviral defenses and disease outcomes through its interactions with the host immune system. This dynamic triad -virus, microbiota, and host immunity- has emerged as a central determinant of infection severity and recovery. Yet, despite growing evidence from mammalian models, its functional implications in fish remain poorly understood. Here, we investigated the effects of viral hemorrhagic septicemia virus (VHSV) infection on the intestinal transcriptomic and microbiota profiles of turbot (Scophthalmus maximus), an aquaculture species highly susceptible to this pathogen. Comparative analyses were conducted among asymptomatic and moribund fish at 10 days post-infection, and uninfected controls. Transcriptomic data revealed that moribund individuals exhibited a dysregulated immune response characterized by a strong induction of complement- and coagulation-related genes and other inflammatory pathways, whereas asymptomatic fish displayed expression patterns more closely resembling those of uninfected controls, indicating a more controlled or resolved immune activation. Microbiota analyses showed that VHSV infection induced widespread, severity-dependent changes in the intestinal microbiota, with progressive shifts in the relative abundance of most bacterial taxa from controls to asymptomatic and moribund fish. Interestingly, a subset of bacterial genera deviated from this general trend, displaying an opposite pattern to that observed in both uninfected and moribund individuals, suggesting their potential involvement in resistance mechanisms. Integrative analyses further revealed significant correlations between specific bacterial genera and host genes differentially expressed between asymptomatic and moribund fish, highlighting functional links between microbial composition and immune regulation. Together, these findings reveal complex interactions between VHSV infection, host immunity, and microbiota composition in turbot, providing novel insights into host-microbe-virus relationships that may inform disease management and selective breeding strategies in aquaculture.},
}
@article {pmid41803210,
year = {2026},
author = {Kim, MG and Seo, E and Eor, JY and Kang, A and Kim, TR and Sohn, M and Kim, Y},
title = {Hypnotic and sleep-promoting effects of Limosilactobacillus reuteri LM1063 on pentobarbital-induced sleep and electroencephalogram analysis in mice.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41803210},
issn = {2045-2322},
support = {RS-2025-16068814//National Research Foundation of Korea/ ; },
abstract = {UNLABELLED: Sleep disturbances are an increasing health concern, and limitations associated with long-term use of conventional hypnotics have prompted interest in alternative approaches that support sleep health. Growing evidence suggests that the gut–brain axis contributes to sleep regulation; however, the effects of probiotics on objective sleep parameters and their underlying mechanisms remain incompletely understood and may vary across probiotic strains. The present study investigated the sleep–modulating effects of a selected probiotic strain, Limosilactobacillus reuteri LM1063 (LM1063), using murine models. Sleep latency and duration were assessed using a pentobarbital-induced sleep test, and sleep architecture was evaluated by electroencephalogram (EEG) recordings, including rapid eye movement (REM) and non-rapid eye movement (NREM) sleep. To explore potential mechanisms, neurochemical analyses focusing on key neurotransmitters, including gamma-aminobutyric acid (GABA) and serotonin, were conducted. Administration of LM1063 significantly shortened sleep latency and prolonged sleep duration in mice. EEG analysis revealed shifts in overall sleep architecture toward a sleep-favorable state without disruption of normal sleep organization. These sleep-related changes were accompanied by modulation of GABAergic and serotonergic neurochemical pathways. In conclusion, LM1063 exerts strain-specific sleep-modulating effects through neurochemical mechanisms associated with the gut–brain axis. By integrating behavioral sleep assessment, electrophysiological analysis, and neurochemical profiling, this study provides mechanistic insight supporting the potential translational application of microbiome-targeted approaches for promoting sleep health.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42833-0.},
}
@article {pmid41807505,
year = {2026},
author = {Śmiga, M and Roszkiewicz, E and Wojtal, N and Olczak, T},
title = {Porphyromonas gingivalis produces a functional HemH ferrochelatase important for its survival in a heme-limited environment.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41807505},
issn = {2045-2322},
support = {2023/51/D/NZ6/00324//Narodowe Centrum Nauki/ ; },
abstract = {UNLABELLED: Porphyromonas gingivalis, the keystone pathogen responsible for dysbiosis in the oral microbiome, the development of periodontal diseases, and the contribution to systemic comorbidities, is a heme auxotroph. It encodes only four enzymes in the heme biosynthesis pathway (HemD, HemN, HemG, and HemH). Comparative genomic analyses demonstrated that, while many Bacteroidota members have lost most of the canonical heme biosynthetic enzymes, Porphyromonas species uniquely retained a ferrochelatase (HemH) homolog. This study aimed to functionally characterize the P. gingivalis HemH protein to prove its hypothesized role in heme formation. HemH can bind heme and PPIX and insert iron or manganese ions into the PPIX ring. The deletion of the hemH gene triggers a heme-starvation response characterized by transcriptional activation of heme uptake systems and virulence-associated genes, coupled with repression of transport and surface proteins preferentially expressed in heme-rich conditions. Therefore, it is proposed that HemH may play a role in maintaining proper heme homeostasis. In a heme-limited environment, P. gingivalis may use intracellular iron and PPIX reserves to synthesize heme by HemH, thereby contributing to heme supply.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41999-x.},
}
@article {pmid41820827,
year = {2026},
author = {Ban, Y and Zhang, H and Xu, Y and Chen, F and Wei, Q and Wen, X and Yin, L and Dong, Z and Zhou, Q and Ge, W},
title = {Akkermansia muciniphila confers renal protection in chronic kidney disease: a multi-omics mechanistic investigation.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41820827},
issn = {1471-2180},
support = {202303//Lianyungang Health Science and Technology Project-202303 in Lianyungang City/ ; JOUMIRF010//Research Fund Project, College of Marine Pharmaceutical Industry, Jiangsu Ocean University/ ; },
abstract = {BACKGROUND: Akkermansia muciniphila (A. muciniphila) improved serum metabolism and renal fibrosis in the mouse model of chronic kidney disease (CKD) via the gut-kidney axis, slowing renal function decline. However, the biological components and underlying metabolic pathways remain unclear. Using a CKD mouse model, we aimed to identify the biological constituents of A. muciniphila that drive its regulatory effects in renal injury. Integrated microbiome and metabolomics analyses further elucidated the metabolic mechanisms of renoprotection, providing a theoretical foundation for the development of evidence-based clinical interventions.<br><br>METHODS: A CKD mouse model was established using 5/6 nephrectomy, with sham-operated mice (n&#x2009;=&#x2009;7) serving as controls. Twenty-eight CKD mice were randomly assigned to four groups and treated with PBS, A. muciniphila, pasteurised A. muciniphila, or A. muciniphila combined with vancomycin by gavage. Serum and kidney tissues were collected to assess renal function, and histopathology was performed to identify the key biological components of A. muciniphila. Faecal samples were subjected to integrated microbiome and metabolomic analyses to identify the metabolic pathways involved in renoprotection. Behavioural experiments were performed to observe the effect of A. muciniphila on the behaviour of CKD mice. Single-factor analysis of variance and post-hoc tests were used for intergroup comparisons.<br><br>RESULTS: Serum analysis showed that the levels of serum creatinine, urea nitrogen and cystatin C in mice treated with A. muciniphila combined with vancomycin were significantly decreased. Reverse-transcription polymerase chain reaction showed that the renal injury marker Kim-1 was significantly decreased after A. muciniphila intervention. The levels of the renal injury (Ngal) and fibrosis (Col1a1, TIMP-1 and Fibronectin) markers showed a downward trend. 16&#xa0;S rRNA analysis revealed that, following A. muciniphila intervention, the health index of the intestinal flora in CKD mice was significantly increased; however, the abundances of Turicibacter, Dubosiella and norank_f_UCG-010 were decreased. Metabolomic analysis revealed a strong correlation between A. muciniphila and the tryptophan metabolic pathway. Behavioural experiments showed that the exercise activity and anxiety-like behaviour of CKD mice were significantly improved after intervention with A. muciniphila, and the effect of A. muciniphila combined with vancomycin was better than that of A. muciniphila or pasteurised A. muciniphila alone.<br><br>CONCLUSION: Our findings demonstrate that A. muciniphila combined with vancomycin intervention ameliorates kidney injury, body dysfunction, and anxiety-like behaviour, while delaying disease progression in CKD mice. These effects suggest that bioactive substances secreted by A. muciniphila play a key regulatory role and are closely related to tryptophan metabolism in the intestine. In addition, our results indicate that dysbiosis of the gut microbiota in CKD mice suppresses the regulatory potential of A. muciniphila. This study lays an experimental foundation for future biological mechanism research.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04868-1.},
}
@article {pmid41827016,
year = {2026},
author = {Alonso-Allende, J and Riezu-Boj, JI and Hualde, AR and Milagro, FI and Aranaz, P},
title = {A novel obesity index reveals obesity-associated microbiota changes after weight loss intervention in a Spanish population.},
journal = {Nutrition journal},
volume = {25},
number = {1},
pages = {},
pmid = {41827016},
issn = {1475-2891},
support = {CB12/03/30002//Centro de Investigaci&#xf3;n Biom&#xe9;dica en Red-Fisiopatolog&#xed;a de la Obesidad y Nutrici&#xf3;n/ ; 0011-1383-2022-000000//Gobierno de Navarra/ ; PID2022-141766OB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
abstract = {BACKGROUND &amp; OBJECTIVES: Gut microbiota specific taxa influencing a higher or lower risk for developing obesity and related metabolic parameters remain unclear. Here, we aimed to identify gut microbiome fingerprints associated with obesity using an integrated obesity index (OBIndex), and to evaluate how these profiles change after a hypocaloric nutritional intervention with two different diets.<br><br>SUBJECTS &amp; METHODS: 295 Spanish adult volunteers participating in the Obekit study were classified into LOW or HIGH degree of obesity according to a novel obesity index (OBIndex), based on the combination of three parameters: body mass index (BMI), fat mass (%), and waist circumference (WC). Differential abundant taxa between the two groups were investigated, at baseline together with the changes in their abundance after a weight-loss intervention with two different hypocaloric diets (Moderately high protein (MHP) and low fat (LF)).<br><br>RESULTS: The classification of participants using the OBIndex effectively differentiated obesity status, overcoming the inherent limitations of BMI, WC, and fat mass when considered individually. MHP diet was associated with an improvement in obesity status in women, while LF diet showed better outcomes in men. In relation to these improvements, changes in gut microbiota were observed. We found that Mediterraneibacter levels decreased only in men who experienced a significant improvement in their obesity status. Additionally, Agathobacter levels in participants who improved their physiological condition were reduced to match those of individuals who already exhibited a healthier status at baseline. Alongside these findings, we identified two poorly studied genera, Pseudobutyricicoccus and Intestinimonas, which were associated with a healthier profile at baseline and increased in abundance following the nutritional intervention.<br><br>CONCLUSIONS: Our OBIndex helped to achieve a more accurate separation of our volunteers regarding their obesity status and, thus, identifying four obesity strong related bacteria. Particularly, Mediterraneibacter and Agathobacter were related to a worse obesity status whereas Pseudobutyricicoccus and Intestinimonas showed a negative association with obesity status suggesting a potential protective or anti-obesity role.<br><br>TRIAL REGISTRATION: The study protocol was approved by the ethical committee at the University of Navarra (Registration No. IR.MUI.RESEARCH.REC.1401.370) and registered online at clinicaltrials.gov (identifier NCT02737267).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12937-026-01313-x.},
}
@article {pmid42006347,
year = {2026},
author = {Chen, S and Shanmuganathan, D and Imlach, WL},
title = {Microbiome-derived metabolites alleviate chronic pain in a reserpine-induced model of fibromyalgia.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115406},
pmid = {42006347},
issn = {2589-0042},
abstract = {Fibromyalgia is a chronic pain disorder driven by central sensitization and neuroinflammation, increasingly linked to gut-brain axis dysfunction. Here, we delineate a gut-to-CNS axis for pain modulation, demonstrating that an acetate-producing diet alleviates reserpine-induced-fibromyalgia in a rodent model. We show that diet rich in acetylated high-amylose maize starch shifts the gut microbiome to favor acetate-producing bacteria, increasing systemic acetate levels and reducing pain hypersensitivity. This is associated with reduced spinal microglia activation and anti-inflammatory cytokine gene expression, with elevated IL-10 mRNA in the DRG and IL-10, IL-2, and IL-6 in the spinal cord. Electrophysiologically, we observe reduced hyperexcitability in the dorsal horn and increased inhibitory activity. The mechanism driving this change involves reduced prostaglandin-E2 (PGE2)-mediated suppression of glycinergic inhibition, a direct consequence of maintaining microglia in quiescent state. These findings link dietary metabolites to reduced fibromyalgia-like pathology and identify targeted nutrition as a potential disease-modifying therapy for chronic pain.},
}
@article {pmid42006367,
year = {2026},
author = {Damm, GK and Zhang, F and Koentgen, S and Jayawardana, T and Houshyar, Y and Read, S and Condous, G and El-Assaad, F and Hold, GL},
title = {Gut microbial signatures and stability are associated with a co-diagnosis of endometriosis and inflammatory bowel disease.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115437},
pmid = {42006367},
issn = {2589-0042},
abstract = {Emerging evidence suggests that the gut microbiota plays a crucial role in endometriosis (Endo) and inflammatory bowel disease (IBD). This study aimed to explore gut microbial signatures in women with either or both conditions, compared to healthy controls. Fecal samples underwent 16S rRNA sequencing to profile the gut microbiome. Endo-IBD patients had the most profound alterations including reduced microbial richness and evenness as well as bacterial signature changes. Specific bacteria taxa, including Akkermansia and Alistipes, were notably depleted in Endo-IBD patients, suggesting a compromised gut barrier and heightened inflammatory potential. Conversely, Blautia was enriched in Endo-IBD patients. Longitudinal microbiome assessment indicated a persistent dysbiotic signature in Endo-IBD and IBD groups, with microbial instability correlating with disease severity. The findings highlight an intensified impact of having a diagnosis of both conditions and further highlights the potential for microbiome-based diagnostics and the design of personalized interventions to restore microbial balance.},
}
@article {pmid42006445,
year = {2026},
author = {Donato, GG and Nebbia, P and Stella, MC and Gionechetti, F and Ala, U and Cristofoli, D and Robino, P and Pallavicini, A and Nervo, T},
title = {The Uterine Microbiota in Mares With Endometritis: Impacts of Antibiotic Treatment.},
journal = {Veterinary medicine international},
volume = {2026},
number = {},
pages = {5270993},
pmid = {42006445},
issn = {2090-8113},
abstract = {Despite growing interest in the role of the reproductive microbiota, the uterine microbiota of mares has been only scarcely investigated using sequencing approaches. The aims of this study were to describe the uterine microbiota of mares with endometritis and the effects of antibiotic treatment using both 16S rRNA sequencing and culture. Five mares with clinical signs of endometritis and a positive bacteriological culture were enrolled. During the follicular phase (T0), uterine samples were collected using a double-guarded cytobrush and swab for microbiome and bacteriological analysis, respectively. Following the antimicrobial susceptibility test, they were treated with intrauterine infusions of ceftiofur sodium, and samplings were repeated during the subsequent follicular phase (T1). According to bacterial culture, at T0, Streptococcus equi zooepidemicus was identified in 4 mares and Escherichia coli in one. At T1, 3 mares resulted negative, one was positive for Staphylococcus xylosus, and one continued to test positive for E. coli. According to NGS, the most represented genera at T0 were Streptococcus, Escherichia-Shigella, Corynebacterium, Arcanobacterium, Porphyromonas, and Staphylococcus. The first 3 genera dominated the microbiome of 4 mares with a relative abundance ranging from 44% to 99%. At T1, these genera's relative abundance dropped, and the most abundant were Acinetobacter, Staphylococcus, and Pseudomonas. Furthermore, after intrauterine infusion of ceftiofur, the microbiome was more diverse, according to Shannon and Simpson indexes (p < 0.05).},
}
@article {pmid42006709,
year = {2026},
author = {Yang, L and Ye, Q and Peng, X and Yu, J and Xiao, X and Wang, L and Yang, YY and Yuan, P and Tian, GB and Ding, X},
title = {Plant-bacteria hybrid nanovesicles for targeted sonodynamic therapy: A microbiome-friendly precision strike against H. pylori infections.},
journal = {Materials today. Bio},
volume = {38},
number = {},
pages = {103085},
pmid = {42006709},
issn = {2590-0064},
abstract = {Rising antibiotic resistance and adverse effects on commensal gut microbiota severely compromise conventional antibiotic therapies for Helicobacter pylori infection. Sonodynamic therapy (SDT), which employs low-intensity ultrasound to activate sonosensitizers for localized generation of cytotoxic reactive oxygen species (ROS), presents a promising non-antibiotic alternative with minimal resistance development risk. However, the efficacy of SDT is inherently constrained by the short diffusion radius and lifetime of ROS. Herein, we developed a homologous-targeting biomimetic sonosensitizer platform to overcome this limitation: hybrid membrane nanovesicles (TNVs-DMVs) engineered from turmeric plant-derived exosome-like nanovesicles (TNVs) and H. pylori-derived double membrane vesicles (DMVs). TNVs contain sonosensitizer curcumin and improve its solubility, yet SDT efficacy against H. pylori is limited. The DMVs endow TNVs-DMVs with intrinsic homologous targeting capability towards H. pylori, significantly enhancing the intracellular delivery of curcumin and subsequent ROS generation within bacterial cells. As a result, TNVs-DMVs achieved potent eradication of H. pylori in both acidic and neutral conditions without inducing detectable resistance. Moreover, TNVs-DMVs exhibited superior mucus penetration compared to TNVs alone, enabling effective elimination of H. pylori and its biofilms residing within the protective gastric mucus layer. In an H. pylori-infected mouse model, TNVs-DMVs mediated SDT demonstrated efficacy surpassing free TNVs and comparable to standard triple antibiotic therapy. Importantly, unlike triple therapy which depletes commensal flora, TNVs-DMVs treatment not only preserves intestinal microbiota homeostasis but also significantly increases populations of beneficial bacteria. This rationally designed TNVs-DMVs platform represents a transformative therapeutic modality, offering resistance-free eradication of H. pylori while maintaining microbiome health, distinct from conventional antibiotics.},
}
@article {pmid42006721,
year = {2026},
author = {Xie, Q and Xu, H and Yang, X and Chen, Y and Xu, ZZ},
title = {Natural carrier-free self-assembled binary polyphenol nanoparticles remodel the gut microenvironment for inflammatory bowel disease prevention.},
journal = {Materials today. Bio},
volume = {38},
number = {},
pages = {103063},
pmid = {42006721},
issn = {2590-0064},
abstract = {Developing biocompatible, multi-target therapeutics remains a critical challenge in the management of inflammatory bowel disease (IBD). Herein, we engineered a carrier-free nanoplatform (Cur-Ant NPs) via the facile self-assembly of two natural polyphenols: curcumin (Cur) and anthocyanin (Ant). Spectroscopic analysis and molecular dynamics simulations confirmed that the assembly is stabilized by robust π-π stacking and hydrogen bonding networks, yielding uniform, spherical nanostructures with integrated functionality. In a dextran sulfate sodium (DSS)-induced colitis model, orally administered Cur-Ant NPs demonstrated superior therapeutic efficacy compared to both free polyphenols and the clinical standard, sulfasalazine (SASP). The nanoparticles' potent anti-inflammatory activity was initially validated in a zebrafish model, where they effectively inhibited neutrophil infiltration and scavenged reactive oxygen species (ROS). These protective effects were further substantiated in a murine model, where multi-omics analysis revealed a tripartite mechanism of action: reinforcing the intestinal epithelial barrier, mitigating pro-inflammatory cytokine responses, and remodeling the dysbiotic gut microbiome. Our findings establish Cur-Ant NPs as a potent, safe candidate for IBD prevention and highlight a scalable, green engineering strategy for designing next-generation nanomedicines based on the supramolecular co-assembly of natural bioactive agents.},
}
@article {pmid42006870,
year = {2026},
author = {Lv, Y and Li, D and Ding, N and Kuang, H},
title = {The role of gut microbiota mediated ferroptosis in PCOS and the therapeutic potential of Chinese herbal medicine.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1730795},
pmid = {42006870},
issn = {2296-858X},
abstract = {Polycystic ovary syndrome (PCOS) is a complex reproductive endocrine metabolic disorder whose pathogenesis remains incompletely understood. In recent years, the role of ferroptosis-a novel form of iron-dependent programmed cell death-in the pathogenesis of PCOS has gradually drawn attention. This review proposes an innovative perspective: gut microbiota dysbiosis may be a potential upstream trigger of ferroptosis in PCOS ovarian granulosa cells. Microbiome dysbiosis disrupts iron homeostasis and reduces the production of antioxidant metabolites such as short-chain fatty acids (SCFAs) and bile acids (BAs), thereby exacerbating systemic and local ovarian oxidative stress. This induces ferroptosis, leading to impaired follicular development and insulin resistance. Traditional Chinese Medicine (TCM) demonstrates significant potential in regulating gut microbiota and inhibiting ferroptosis. Based on this, this study explores the role of the gut microbiota-ferroptosis axis in PCOS, focusing on the scientific rationale and application prospects of treating PCOS by intervening in this axis using TCM monomers and compounds such as berberine and quercetin. With its multi-target regulatory effects and favorable safety profile, TCM may offer benefits as an adjunct or alternative to conventional therapies. This research aims to provide theoretical references for developing novel therapeutic strategies.},
}
@article {pmid42006912,
year = {2026},
author = {Allaband, C and Ganz, HH and Rojas, CA and Knight, R},
title = {Cats on dry kibble diet have significantly different microbiome than those on canned wet food.},
journal = {npj veterinary sciences},
volume = {1},
number = {1},
pages = {1},
pmid = {42006912},
issn = {3059-328X},
abstract = {Domestic cats (Felis catus) are understudied regarding how commercial diets impact their gut microbiomes. Here, we reanalyzed the 16S rRNA gene (V4) amplicon sequencing Kittybiome dataset, using new tools and techniques. Results demonstrated significant microbial composition differences between cats eating commercial dry kibble diets and those eating canned wet food. Kibble-fed cats showed enriched Prevotella, Bifidobacterium, and Megamonas amplicon sequencing variants (ASVs), linked to carbohydrate metabolism and metabolic disease.},
}
@article {pmid42007333,
year = {2025},
author = {Weng, S and Lin, J and Chai, D},
title = {Olanzapine and peripheral metabolic dysregulation: organ-resolved mechanisms, risk, and MASLD-aligned care pathways.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1729264},
pmid = {42007333},
issn = {1663-9812},
abstract = {This review examines how olanzapine drives metabolic injury beyond the brain and why an organ-resolved perspective is needed. We synthesize clinical signals of early weight gain, insulin resistance, dyslipidemia, and steatotic liver disease, and integrate translational evidence across liver, adipose tissue, skeletal muscle, pancreatic β-cells, and the gut-liver axis. Mechanistic strands include disordered hepatic lipid handling, suppression of brown-fat thermogenesis, β-cell endoplasmic-reticulum stress with impaired secretion, and skeletal-muscle insulin-signaling defects with altered epigenetic programs that blunt glucose disposal. We summarize modifiers of risk across life stage, treatment exposure, genetic variation, smoking status, and pregnancy, and distill a pragmatic pathway that prioritizes early reassessment, MASLD-aligned liver evaluation, targeted lifestyle treatment, metformin for early deterioration, and GLP-1 receptor agonists when required. We advance the view that weight-independent extra-cerebral mechanisms are central to olanzapine's metabolic liability and that psychiatric practice should adopt metabolic frameworks used in hepatology and endocrinology. We propose an agenda for organ-specific human phenotyping and exposure-aware designs that integrate therapeutic drug monitoring with microbiome, metabolomics, and bile-acid profiling, alongside comparative trials that test stepped algorithms within psychiatric care. This perspective outlines a path to preserve antipsychotic efficacy while reducing preventable systemic metabolic harm.},
}
@article {pmid42007373,
year = {2026},
author = {Poznyak, AV and Vatlin, AA and Pavshintsev, VV and Mitkin, NA and Maltseva, ON and Utkina, AS and Orekhov, AN},
title = {An overview of the role of the gut microbiota in rheumatoid arthritis.},
journal = {Microbiome research reports},
volume = {5},
number = {1},
pages = {3},
pmid = {42007373},
issn = {2771-5965},
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease preceded by a prolonged preclinical phase marked by the emergence of autoantibodies and mucosal immune dysregulation. Evidence from human studies and animal models consistently demonstrates that gut microbiota dysbiosis contributes to this transition, particularly through impaired intestinal barrier function, activation of pro-inflammatory pathways, and molecular mimicry. Specific taxa - including Prevotella copri, Collinsella aerofaciens, and reductions in butyrate-producing bacteria - have been linked to heightened systemic inflammation, increased T helper 17 responses, and the generation of RA-associated autoantibodies. Current research also indicates that anti-rheumatic medications such as methotrexate, sulfasalazine, and minocycline produce measurable shifts in gut microbial composition, suggesting that microbiota-drug interactions may influence treatment response. Therapeutic approaches aimed at modifying gut ecology - including dietary interventions, prebiotics, probiotics, and fecal microbiota transplantation - show early potential in restoring microbial balance, improving intestinal barrier integrity, and reducing inflammatory markers, although evidence in the preclinical RA stage remains limited. Additionally, emerging data highlight the importance of intestinal autophagy and microRNA networks in regulating epithelial integrity and systemic immune activation. Taken together, the literature supports a mechanistic link between gut dysbiosis and the onset of RA. It points to microbiota-targeted strategies as promising avenues for delaying or preventing disease progression. Future studies should prioritize longitudinal analyses and interventional trials focusing specifically on individuals at risk for RA.},
}
@article {pmid42007374,
year = {2026},
author = {Jeong, UJ and Ali, M and Park, YJ and You, JS and Yoon, SS},
title = {A responder-informed gut microbial consortium enhances anti-PD-1 efficacy in a mouse cancer model.},
journal = {Microbiome research reports},
volume = {5},
number = {1},
pages = {2},
pmid = {42007374},
issn = {2771-5965},
abstract = {Aim: Immune checkpoint inhibitors (ICIs), particularly anti-programmed cell death protein 1 (PD-1) therapy, have improved cancer treatment outcomes, yet durable benefit is achieved in only a subset of patients. Growing evidence implicates the gut microbiome as a modulator of ICI responsiveness, but defined and experimentally validated microbial strategies remain limited. This study aimed to identify responder-associated gut microbes and to evaluate a defined bacterial consortium for enhancing PD-1 blockade efficacy. Methods: Publicly available shotgun metagenomic datasets from anti-PD-1-treated cancer patients were re-analyzed to compare gut microbiome profiles between responders and non-responders. Bacterial taxa reproducibly enriched in responders were selected based on consistency across analytical criteria and cultivability and assembled into a four-strain consortium (UJ-04). The immune-adjuvant potential of UJ-04, alone or combined with anti-PD-1 therapy, was evaluated in a B16-F10 melanoma mouse model, with tumor growth and immune responses assessed by flow cytometry. Results: Metagenomic re-analysis identified four commensal bacterial taxa consistently enriched in responder patients, forming the defined UJ-04 consortium. While UJ-04 alone showed minimal antitumor activity, combination treatment with anti-PD-1 significantly enhanced tumor growth inhibition compared with anti-PD-1 monotherapy. This effect was accompanied by increased intratumoral CD8[+] T cells and natural killer cells, with concordant immune trends in peripheral compartments. Conclusion: A responder-informed, defined microbial consortium functionally translates clinical microbiome associations into in vivo validation and enhances PD-1 blockade efficacy by modulating host antitumor immunity. These findings support defined bacterial consortia as microbiome-based immunomodulatory adjuncts for immunotherapy.},
}
@article {pmid42007545,
year = {2026},
author = {Meza, LA and Fitzjerrells, RL and Shemirani, F and Titcomb, TJ and Rubenstein, LM and Eyck, PT and Snetselaar, LG and Shahi, SK and Wahls, TL and Mangalam, AK},
title = {Predicting Dietary Impact on Multiple Sclerosis-Related Symptoms With the Gut Microbiome: A Pilot Study Using Unsupervised Machine Learning.},
journal = {Brain and behavior},
volume = {16},
number = {4},
pages = {e71394},
pmid = {42007545},
issn = {2162-3279},
support = {1RO1AI137075//NIAID/NIH/ ; 1I01CX002212//US Department of Veteran Affairs/ ; 1F31DE033564-01//NIDCR/NIH/ ; NIEHS/NIH P30 ES005605//University of Iowa Environmental Health Sciences Research Center/ ; UM1TR004403//National Center for Advancing Translational Sciences of the NIH/ ; 1506-04312//National Multiple Sclerosis Society/ ; //P. Heppelmann and M. Wacek Fund/ ; //the Carver Trust Pilot Grant/ ; //Center for Biocatalysis and Bioprocessing/ ; //University of Iowa institutional funds/ ; //Carter Chapman Shreve Family Foundation/ ; //Carter Chapman Shreve Fellowship Fund/ ; //Helen Harris Fund/ ; //University of Iowa College of Public Health Preventive Intervention Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Pilot Projects ; Male ; *Multiple Sclerosis/diet therapy/microbiology ; Female ; Adult ; Middle Aged ; *Unsupervised Machine Learning ; Feces/microbiology ; Quality of Life ; *Diet, Paleolithic ; *Diet ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Multiple sclerosis (MS) is a neurodegenerative disease where dietary intervention has emerged as a potential adjunct treatment. Recently, the modified Paleolithic elimination (MPE) diet, also known as the Wahls diet, and the low-saturated fat (LSF) diet, also known as the Swank diet, were linked to reduced fatigue and improved quality of life (QoL) in the WAVES study (NCT02914964). However, how diet impacts these outcomes remains unclear. As diet impacts gut microbiota, we investigated whether the baseline gut microbiota can predict response to diet in people with MS (pwMS).<br><br>METHODS: We performed fecal 16s rRNA sequencing to profile the microbiome changes associated with pwMS receiving the MPE (n = 11) and LSF diet (n = 12). Next, we utilized topic modeling, a machine learning technique, to determine whether baseline microbiome features predicted diet response in the combined MPE + LSF dietary cohort (n = 23).<br><br>RESULTS: Specific genera significantly differed over time on both diets. On the MPE diet, Hungateiclostridiaceae, Ruminiclostridium, and Shuttleworthia decreased, while Coriobacteriaceae Collinsella decreased on LSF. Predictive machine-learning analysis associated a baseline microbiome enriched with Akkermansia, Bacteroides, and Barnesiella with fatigue response in the combined MPE + LSF cohort. For a non-response in Mental QoL improvement in the combined MPE + LSF cohort, our analysis associated an enrichment of Faecalibacterium and Alistipes at the start of the diet.<br><br>DISCUSSION: Utilizing topic modeling, this pilot study identified baseline microbiota communities linked to improvements in fatigue and Mental QoL in pwMS on dietary intervention. These findings highlight the microbiota's role in dietary response and the potential for personalized nutrition. Given the small cohort and exploratory design, the results are hypothesis-generating and require validation in larger mechanistic studies.},
}
@article {pmid42007585,
year = {2026},
author = {De Santiago, A and Barnes, S and Pereira, TJ and Marcellino-Barros, M and Durden, L and Han, MK and Thrash, JC and Bik, HM},
title = {Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag091},
pmid = {42007585},
issn = {1751-7370},
abstract = {Despite growing insights into the composition of marine invertebrate microbiomes, our understanding of their ecological and evolutionary patterns remains poor, owing to limited sampling depth and low-resolution datasets. Previous studies have provided conflicting results that both confirm and deny the existence of phylosymbiosis between marine invertebrates and marine bacteria. Here, we investigated potential animal-microbe symbioses in Pseudoalteromonas, a bacterial genus consistently identified as a core microbiome taxon in diverse invertebrates. Using a pangenomic analysis of 236 free-living and invertebrate-associated bacterial strains (including two new nematode-associated isolates generated in this study), we confirm that Pseudoalteromonas is a symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (e.g., Nematoda, Mollusca, and Cnidaria). Patterns of symbiosis were consistent irrespective of geography (including in Antarctica), with FISH images from nematodes indicating that bacterial symbionts form biofilms in the mouth and esophagus and are sometimes present in female nematode ovaries exhibiting stunted development. The evolutionary history of Pseudoalteromonas is marked by substantial host-switching and lifestyle transitions, and host-associated genomes suggest that these bacteria are facultative symbionts involved in nutritional symbioses. In marine environments, we hypothesize that horizontally acquired symbionts may have co-evolved with invertebrates, using host mucus as a physical niche and food source, while providing their animal hosts with Vitamin B, amino acids, and bioavailable carbon compounds in return.},
}
@article {pmid42007648,
year = {2026},
author = {Xu, S and Cao, Z and Ma, K and Song, J and Miao, Y and Li, Q and Song, D and Fu, J and Yang, P},
title = {A Synthetic Community from Campeiostachys nutans Rhizosphere in the Qinghai-Tibet Plateau Endow Alfalfa with the Ability to Resist Drought and Cold.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14225},
pmid = {42007648},
issn = {1520-5118},
abstract = {Campeiostachys nutans, widely distributed in the Qinghai-Tibet Plateau, possesses notable stress tolerance, yet the exploration of its functional rhizosphere microbes remains limited. In this study, we characterized bacterial variations across rhizosphere surrounding soil, rhizosphere, and endosphere compartments from five grassland types, isolated core strains, and established a synthetic community (SynCom). Results revealed that under PEG-induced drought, SynCom significantly altered alfalfa responses by scavenging reactive oxygen species (ROS), modulating immune gene expression, and synthesizing glutamate metabolites. Additionally, SynCom inoculation conferred cold resistance to alfalfa by enhancing photosynthetic activity, boosting antioxidant enzymes, and producing osmotic adjustment compounds like trehalose. This investigation underscores the capacity of core rhizosphere taxa to enhance stress tolerance, offering novel perspectives for developing microbial inoculants to improve crop productivity under drought and cold stress.},
}
@article {pmid42007708,
year = {2026},
author = {Wang, X and Ma, Y and Yang, Y and Dong, Q},
title = {Mapping the Research Landscape and Evolutionary Trends of the Oral Microbiome in Periodontitis.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {134},
number = {4},
pages = {e70209},
doi = {10.1111/apm.70209},
pmid = {42007708},
issn = {1600-0463},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; *Mouth/microbiology ; Dysbiosis/microbiology ; Bibliometrics ; },
abstract = {The conceptual transition from the "Red Complex" paradigm to the "Ecological Plaque Hypothesis" has fundamentally reshaped the understanding of periodontitis, but a quantitative mapping of this intellectual evolution and its emerging research frontiers remains limited. This study systematically characterized the global research landscape and evolutionary trends of the oral microbiome in periodontitis from 2000 to 2025. English-language articles published between 2000 and 17 November 2025 were retrieved from the Web of Science Core Collection and Scopus databases. After deduplication, bibliometric analyses were performed on 2827 unique publications to evaluate spatiotemporal distributions, collaboration patterns, thematic evolution, and citation bursts. The results revealed exponential growth in publications, particularly after 2020, with the United States and China leading global contributions. Thematic evolution analyses demonstrated a clear shift from single-pathogen-focused research, exemplified by Porphyromonas gingivalis, toward ecological frameworks emphasizing dysbiosis and microbial community structure. Recent citation bursts highlighted growing attention to broader microbial taxa, inflammatory mediators, clinically relevant periodontal indicators, microbiome-based therapeutic strategies, and methodological standardization. Overall, research on the oral microbiome in periodontitis has evolved toward a host-microbiome systems biology framework, with future studies likely to emphasize functional multi-omics integration, AI-assisted diagnostics, and precision interventions targeting oral-systemic health links.},
}
@article {pmid42007760,
year = {2026},
author = {Brignoli, D and Colla, D and Frickel-Critto, E and Castells, CB and Pérez-Giménez, J and Lodeiro, AR},
title = {A synthetic microbial community for soybean biofertilization designed via chlorophyll-based iterative selection.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0254825},
doi = {10.1128/aem.02548-25},
pmid = {42007760},
issn = {1098-5336},
abstract = {Improving the effectiveness of microbial inoculants for soybean is essential to enhance biological nitrogen fixation and reduce fertilizer dependence; however, inoculated Bradyrhizobium strains frequently display inconsistent field performance. Inoculation is usually carried out with single-strain formulations, overlooking the possible influence of the native soil microbiota on nodulation success. This limitation may be addressed by formulating inoculants with consortia that include selected members of the soil microbiota. To this end, a synthetic microbial community (SynCom) was developed through a host-mediated microbiome engineering approach guided by leaf chlorophyll content as a rapid, non-destructive plant trait. The experiment was initiated by inoculating soybean plants with a consortium of 9 Bradyrhizobium spp. and 14 non-rhizobial soil isolates. Across eight consecutive selection rounds under gnotobiotic conditions, rhizosphere communities associated with superior plant performance were pooled and propagated. Recurrent selection induced significant shifts in community composition, consistently favoring Bradyrhizobium diazoefficiens as the dominant nodulating member and enriching taxa from Pseudomonadales, Burkholderiales, and Sphingomonadales. Sequencing-based profiling and network analysis suggested the emergence of a cohesive and functionally enriched community, with increased potential for nitrogen transformations and organic matter turnover. When evaluated in non-sterile soil, the SynCom derived from the sixth selection round increased nodule number and biomass relative to an uninoculated control and a commercial inoculant strain. These results suggest that plant-guided selection can steer rhizosphere community assembly toward beneficial configurations and support the development of improved soybean bioinoculants.IMPORTANCESoybean [Glycine max (L.) Merr.] is a major global crop characterized by high seed protein content, which demands elevated nitrogen assimilation. To meet this demand, the crop can utilize atmospheric nitrogen through the process of biological nitrogen fixation in symbiosis with Bradyrhizobium bacteria, thus mitigating soil nitrogen depletion. Although Bradyrhizobium-based inoculants are applied at sowing, their interplay with other members of the rhizosphere microbiota remains poorly understood. It is well documented that plants and rhizosphere microbiota interact to shape plant growth and soil productivity. Therefore, this work evaluated the inoculation of soybean with a synthetic microbial consortium as a strategy to develop new-generation inoculants. These bioinputs are designed to harness plant-soil-microbe interactions to improve soybean productivity while preserving soil properties.},
}
@article {pmid42008183,
year = {2026},
author = {Hwang, JK and Lim, SM and Kwak, MJ and Kim, SH and Kang, Y and Mustafa, G and Tanpure, RS and Jeon, BH and Hoh, JK and Park, HK},
title = {Distinct early-life gut microbiota patterns across SGA, AGA, and LGA infants.},
journal = {European journal of pediatrics},
volume = {185},
number = {5},
pages = {},
pmid = {42008183},
issn = {1432-1076},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant, Newborn ; Prospective Studies ; Female ; Male ; *Infant, Small for Gestational Age/growth &amp; development ; Infant ; *Birth Weight ; Feces/microbiology ; Gestational Age ; RNA, Ribosomal, 16S ; Infant, Large for Gestational Age ; },
abstract = {UNLABELLED: Birthweight-for-gestational-age influences neonatal physiology and health, yet its role in shaping early gut microbiome development remains insufficiently defined. Small-for-gestational-age (SGA), appropriate-for-gestational-age (AGA), and large-for-gestational-age (LGA) infants may exhibit distinct microbial maturation patterns that could influence later metabolic and developmental outcomes. We conducted a prospective cohort study and enrolled 50 late-preterm and term infants and classified them into SGA (n=18), AGA (n=20), and LGA (n=12). Serial fecal samples were collected at four postnatal time windows (0-14 and 15-80 days). 16S rRNA gene sequencing using Oxford Nanopore MinION characterized microbial composition, diversity, and community networks. Bioinformatic analyses included alpha- and beta-diversity metrics, co-occurrence network analysis, and functional pathway inference using PICRUSt2 mapped to the MetaCyc database. Clinical variables, including feeding pattern and antibiotic exposure, were assessed. Gut microbiome development differed according to birthweight categories. Microbial diversity increased with postnatal age, with SGA infants showing distinct community structures over time. Firmicutes predominated across all groups, while specific taxa exhibited group-specific patterns, including enrichment of Streptococcus spp. in LGA infants and Klebsiella spp. in SGA infants. Co-occurrence network analysis revealed a stable gut microbiota in LGA infants.<br><br>CONCLUSION: Birthweight-for-gestational-age status was associated with distinct trajectories of early gut microbial maturation. SGA infants exhibited delayed microbial stabilization and fragmented interaction networks, whereas LGA infants demonstrated relatively early establishment of stable, Streptococcus-enriched communities. These growth-specific microbial patterns may reflect differences in early metabolic programming and highlight the potential importance of tailored microbiome-targeted strategies to optimize neonatal development.<br><br>WHAT IS KNOWN: &#x2022; Abnormal fetal growth is associated with increased neonatal morbidity and long-term metabolic risk. &#x2022; Early-life gut microbiota play an important role in immune and metabolic development.<br><br>WHAT IS NEW: &#x2022; This longitudinal study demonstrates growth-specific trajectories of early gut microbial maturation among SGA, AGA, and LGA infants born at &#x2265;35-week gestation. &#x2022; SGA infants exhibit delayed microbial stabilization and fragmented microbial interaction networks, whereas LGA infants show relatively earlier establishment of stable microbial communities.},
}
@article {pmid42008215,
year = {2026},
author = {Zhang, J and Yang, X and Xie, L and Liu, Q and Zhang, X},
title = {Sympathetic denervation alters pulmonary microbiota diversity and composition in mice.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42008215},
issn = {1618-1905},
support = {SBGJ202103001//Health Commission of Henan Province/ ; },
}
@article {pmid42008253,
year = {2026},
author = {Narang, H and Talukdar, D and Kumar, B and Mathur, P and Ningombam, A and Singh, M and Bajaj, A and Markandey, M and Kalaivani, M and Verma, M and Kaur, M and Bakshi, S and Jana, P and Jamdhade, M and Bhardwaj, N and Puraswani, M and Ashita, and Ahmed, N and Goyal, MK and Mubbunu, M and Thomas, DM and Mundhra, S and Prasad, S and Garg, R and Gupta, A and Shalimar, and Gunjan, D and Mahapatra, SJ and Agarwal, S and Saraya, A and Garg, P and Makharia, G and Kedia, S and Das, B and Ahuja, V},
title = {Fecal Microbiota Transplant and Multidrug-Resistant Organism Decolonization in Gastrointestinal Disease: A Randomized Clinical Trial.},
journal = {JAMA internal medicine},
volume = {},
number = {},
pages = {},
pmid = {42008253},
issn = {2168-6114},
abstract = {IMPORTANCE: Gut colonization by multidrug-resistant organisms (MDROs) is a risk factor for infection with these pathogens. There are no approved therapeutic interventions to combat it.<br><br>OBJECTIVE: To assess the efficacy of fecal microbiota transplant (FMT) in causing MDRO decolonization and decreasing antimicrobial resistance (AMR) genes and its impact on gut microbiome, virome, and mycobiome composition in patients with gastrointestinal (GI) diseases.<br><br>This randomized, double-blind, sham-controlled clinical trial was conducted in a gastroenterology ward and intensive care unit at a tertiary care center in India. Participants were patients with GI diseases with persistent MDRO colonization. Patient recruitment occurred from July 2022 to June 2024, with follow-up completed in July 2024. Data were analyzed from October 1, 2024, to April 25, 2025.<br><br>INTERVENTION: FMT via colonoscopy or sham intervention (sigmoidoscopy with saline injection).<br><br>MAIN OUTCOMES AND MEASURES: Co-primary outcomes were MDRO decolonization rate and decrease in antimicrobial resistance genes (AMR) at 4 weeks after the intervention. Secondary outcomes included changes in stool microbiome (16S ribosomal RNA amplicon sequencing), virome (viruslike particles shotgun sequencing), and mycobiome (ITS2 sequencing); incidence of MDRO infections; and adverse events within 4 weeks.<br><br>RESULTS: Of 114 randomized patients (mean [SD] age, 40.6 [12.5] years; 80 [70.2%] male; 52 patients [45.6%] with pancreatitis; 43 patients [37.7%] with cirrhosis; 19 patients [16.7%] with other GI disorders), 58 received FMT and 56 received the sham intervention. Most patients were colonized with carbapenem-resistant Enterobacteriaceae or extended-spectrum &#x3b2;-lactamase-producing Enterobacteriaceae at baseline (55 patients [94.8%] in the FMT group and 56 patients [100%] in the sham group). Five patients (2 in the FMT group, 3 in the sham group) were lost to follow-up. Intention-to-treat analysis showed no significant differences in MDRO decolonization (18 patients [31.0%] in the FMT group vs 17 patients [30.4%] in the sham group; absolute difference, 0.6% [95% CI, -16.2% to 17.6%]; P&#x2009;=&#x2009;.94) or AMR genes (median [IQR], 2.5 [1.2 to 3.0] genes in the FMT group vs 2.0 [1.0 to 3.0] genes in the sham group; P&#x2009;=&#x2009;.68), with comparable adverse events. Among 71 patients who underwent 16S ribosomal RNA gene sequencing at 4 to 6 weeks after the intervention, enrichment of bacteria capable of producing short-chain fatty acids was observed in the FMT group. These microbial alterations were not observed in the sham group. However, viral diversity remained unchanged after FMT. Mycobiome analysis revealed that FMT induced only modest, transient alterations in the gut mycobiome.<br><br>CONCLUSIONS AND RELEVANCE: This randomized clinical trial found that while a single session of FMT did not significantly enhance MDRO decolonization or decrease AMR genes in patients with GI diseases, it modulated gut microbiome diversity and composition.<br><br>TRIAL REGISTRATION: Clinical Trials Registry-India Registration No. 2022/07/043847.},
}
@article {pmid42008544,
year = {2026},
author = {McKenney, EA and De Jesus, E and Hatfield, T and Hayes, D and Holder, K and Ivarsson, C and Morais, N and Payne, H and Simpson, K and Staal, AM and Thompson, H and Hildreth, R and Olfenbuttel, C and Lafferty, DJR},
title = {Gut site and sex-specific enrichment of bacterial taxa and predicted metabolic pathways in wild American black bear (Ursus americanus).},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0345317},
pmid = {42008544},
issn = {1932-6203},
mesh = {Animals ; *Ursidae/microbiology/metabolism ; *Gastrointestinal Microbiome ; Female ; Male ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Metabolic Networks and Pathways ; Sex Factors ; Animals, Wild/microbiology ; },
abstract = {American black bears' (Ursus americanus) omnivorous feeding strategy, simple gut morphology, and rapid transit time prevent regulation of the gut microbiome (GMB). We analyzed stable isotopes and 16S rRNA sequences from 48 wild bears to assess the impacts of diet, age, gut site, and sex on GMB composition and PICRUSt2-predicted functional pathways. While alpha and beta diversity did not differ, we identified bacterial taxa and predicted pathways enriched based on gut site and sex. Enterococcus, Incertae, Papillibacter, and Shuttleworthia were enriched in jejunum samples (linear discriminant analysis effect size ≥ 3.5, p = 0.0374); and 6 genera drove colonic Bray-Curtis distances (SIMPER): Weisella (p = 0.0099), Anaeroplasma (p = 0.0495), Megamonas (p = 0.0099), Cellulosilyticum (p = 0.0495), Escherichia-Shigella (p = 0.0396) and Ochrobactrum (p = 0.0297). EdgeR identified isoflavonoid biosynthesis (p-adj = 0.001) and isoterpenoid biosynthesis (p-adj = 0.006) enriched in the colon, and SNARE interaction in vesicular transport (p-adj = 0.000) and secondary bile acid synthesis (p-adj = 0.005) enriched in females. Our findings provide nuanced insights to specific taxa and putative metabolic pathways that reflect sex and gut site differences in black bears, with important implications for understanding bear physiology and informing wildlife management.},
}
@article {pmid42008653,
year = {2026},
author = {Wu, M and Chen, Y and Su, M and Wu, H and Luo, L and Ao, X and Zhao, C and Shui, J and Wen, S and Lin, J and Pu, J and Zeng, J and Jiang, Y and Ng, H and Zhang, Z and Hu, M and Huang, B and Xu, L and Chen, C and Shen, C},
title = {Domestic travel as a driver for the dissemination of mcr-1 in healthy travelers in China: a prospective, genomic epidemiological and gut microbiome study.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0174625},
doi = {10.1128/aac.01746-25},
pmid = {42008653},
issn = {1098-6596},
abstract = {The global spread of plasmid-mediated colistin resistance gene mcr-1 poses a significant threat to public health. Although international travel is a known driver of antimicrobial resistance, the role of domestic travel in high-prevalence settings remains unclear. We conducted a prospective cohort study of 81 healthy volunteers traveling in China (June-September 2022). Fecal samples collected before and after travel were screened for mcr-1-positive Escherichia coli (MCRPEC). Antimicrobial resistance genes (ARGs), virulence factors (VFs), plasmid replicons, and gut microbial dynamics were investigated using whole-genome sequencing and 16S rRNA sequencing. Risk factors were analyzed using logistic regression analysis. Of the 81 participants who were negative for mcr-1 at baseline, 12 (14.8%) acquired mcr-1 after travel. Acquisition was associated with residence near poultry farms (odds ratio [OR] = 5.9, P = 0.04) and diarrhea during travel (OR = 11.22, P = 0.027). MCRPEC exhibited marked genetic diversity comprising 10 sequence types and the carriage of additional 23 ARGs and nine adherence-associated VFs. mcr-1 was located on IncI2, IncX4, IncHI2, or IncP plasmids, with 91.7% (n = 11) transferable in conjugation assays. Gut microbiome analysis showed increased α-diversity, but a stable community structure, indicating colonization without major disruption. Our study demonstrated that domestic travel in China substantially contributes to the dissemination of mcr-1. Poultry exposure and gastrointestinal disturbances are key risk factors. Genetic diversity, plasmid transferability, and co-carriage of resistance and virulence determinants highlight the risk of onward spread. Antimicrobial resistance surveillance should extend beyond international travel and incorporate domestic mobility within a "One Health" framework.},
}
@article {pmid42008677,
year = {2026},
author = {Medina, D and Martins, RA and Prist, PR and Buttimer, S and Neely, WJ and Schuck, LK and Greenspan, SE and Lyra, ML and Kearns, PJ and Woodhams, DC and Bletz, MC and São-Pedro, VA and Haddad, CFB and Becker, CG},
title = {Connecting habitats, boosting disease resistance: Spatial connectivity enhances amphibian microbiome defenses against fungal pathogen.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {17},
pages = {e2520745123},
doi = {10.1073/pnas.2520745123},
pmid = {42008677},
issn = {1091-6490},
support = {IOS-1947681 DEB-2227340 DEB-2413542 BII-2120084//NSF (NSF)/ ; 2021/10639-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; IOS-1845634 and BII 2120084//NSF (NSF)/ ; },
mesh = {Animals ; *Batrachochytrium/pathogenicity ; *Microbiota ; *Ecosystem ; *Amphibians/microbiology ; *Disease Resistance ; *Mycoses/microbiology/veterinary ; Host-Pathogen Interactions ; Chytridiomycota ; },
abstract = {Disruption of habitat connectivity alters host movement patterns and pathogen exposure in wildlife. Changes in exposure dynamics have led to increased research interest in host-associated microbial communities (i.e., microbiomes), particularly in how repeated encounters with pathogens may drive microbial filtering processes that favor the assembly of pathogen-inhibiting microbiomes, a concept known as the adaptive microbiome principle. Understanding how habitat connectivity and pathogen exposure shape adaptive microbiomes remains a key frontier in disease ecology. For widely distributed waterborne pathogens such as the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), sustained host exposure in contiguous terrestrial-aquatic habitats may promote selection of microbiomes with enhanced antifungal properties. In contrast, under conditions of high habitat split, where key habitats such as forests and water bodies are spatially disconnected, limited exposure to Bd during the pre-tbreeding and overwintering seasons may hinder the selection of Bd-inhibitory microbiomes that are critical for host protection during the subsequent breeding season, when pathogen exposure in water bodies is at its peak. Our results demonstrate that habitat split may limit recruitment of putative Bd-inhibitory skin bacteria, while Bd loads increase with habitat split for certain amphibian species. Results from Joint Species Distribution Models also indicate that habitat split is a key driver of reduced skin bacterial diversity, even after accounting for biotic and abiotic metrics. Our study provides evidence that spatial connectivity among natural habitats is essential for maintaining multiple levels of biodiversity, from host species to their associated functional microbiomes, highlighting a critical link between environmental disturbance, microbial defenses, and disease dynamics.},
}
@article {pmid42008732,
year = {2026},
author = {Herceg, Z and Ghantous, A and Gheit, T and Rahman Talukdar, F and Matar, C and Chung, F and Korenjak, M and Zavadil, J and Ribeiro Pinto, LF and Fry, RC and Khoueiry, R},
title = {Cancer epigenetics: unraveling etiology and mechanisms to advance prevention.},
journal = {Journal of the National Cancer Institute. Monographs},
volume = {2026},
number = {72},
pages = {44-58},
doi = {10.1093/jncimonographs/lgaf044},
pmid = {42008732},
issn = {1745-6614},
mesh = {Humans ; *Neoplasms/prevention &amp; control/genetics/etiology/epidemiology ; *Epigenesis, Genetic ; *Epigenomics/methods ; Animals ; Biomarkers, Tumor/genetics ; },
abstract = {The increased understanding of epigenetics has significantly advanced our understanding of cancer development, especially regarding environmental, occupational, and lifestyle exposures. Unlike genetic mutations, epigenetic changes may be reversible, making them critical mediators and promising targets for cancer prevention and control. This review synthesizes two decades of transformative research by the International Agency for Research on Cancer (IARC), which positioned the epigenome as a central focus in cancer epidemiology and mechanistic research among the 10 Key Characteristics (KCs) of carcinogens by the IARC Monographs program. From foundational in vitro and animal studies to large-scale population-based research, IARC researchers contributed to unraveling epigenetic mechanisms of carcinogenesis and identifying epigenetic biomarkers of exposures and cancer risk. We highlight progress in epigenetic biomarker development, mechanistic epigenomics, toxico-epigenomics, and the interplay between diet, microbiome, and epigenome. As IARC marks its 60th anniversary, this review underscores the growing role of epigenetics in guiding global cancer prevention efforts and public health strategies.},
}
@article {pmid42008798,
year = {2026},
author = {Contreras Vidal, C and Carvajal Cabrera, J},
title = {Intrahepatic cholestasis of pregnancy in Chile: Analysis of epidemiological change and a microbiological hypothesis.},
journal = {Medwave},
volume = {26},
number = {3},
pages = {e3161},
doi = {10.5867/medwave.2026.03.3161},
pmid = {42008798},
issn = {0717-6384},
mesh = {Humans ; Pregnancy ; Chile/epidemiology ; *Cholestasis, Intrahepatic/epidemiology/microbiology ; Female ; *Pregnancy Complications/epidemiology/microbiology ; Incidence ; Typhoid Fever/epidemiology ; Pregnancy Complications, Infectious/epidemiology/microbiology ; },
abstract = {Intrahepatic cholestasis of pregnancy is a gestational pathology with an unusual epidemiological and pathophysiological behavior that remains partially unexplained. Its current global incidence ranges from 0.1% to 2%. However, in Chile, the incidence reached up to 15% in the 1970s, with a marked decrease over subsequent decades, being nowadays about 1 to 2%. The reasons for this historical change are not fully understood. A literature-based analysis was conducted, focusing on clinical, microbiological, and epidemiological studies on intrahepatic cholestasis and other hepatobiliary diseases. The aim of this was to explore existing evidence and to propose a microbiological hypothesis that could help explain the epidemiological transition observed in Chile. Notably, the temporal reduction in incidence paralleled a nationwide decline in biliary disease and typhoid fever. We hypothesize that the eradication or significant reduction of certain pathogens, such as Typhi, may have contributed to the normalization of intrahepatic cholestasis of pregnancy rates in Chile.},
}
@article {pmid42008879,
year = {2026},
author = {Murthy, D and Seyhan, AA and den Hollander, P and Lu, S and Kuburich, NA and Gould, C and Karam, AA and Sun, K and Schupp, PG and Safran, H and Kurzrock, R and El-Deiry, W and Mani, SA},
title = {Advancing precision medicine in pancreatic cancer using novel biomarkers and clinical targets.},
journal = {Molecular aspects of medicine},
volume = {109},
number = {},
pages = {101476},
doi = {10.1016/j.mam.2026.101476},
pmid = {42008879},
issn = {1872-9452},
abstract = {Precision-guided therapy is imperative in the battle against pancreatic ductal adenocarcinoma (PDAC), one of the most lethal solid malignancies with limited improvements in survival despite advances in molecular profiling and systemic therapy. While oncogenic drivers such as KRAS, TP53, CDKN2A, and SMAD4 are nearly ubiquitous, their translation into effective targeted therapies has been constrained by profound tumor heterogeneity, a therapy-resistant tumor microenvironment (TME), and a paucity of predictive biomarkers. In parallel, clinical outcomes are increasingly shaped by extrinsic modifiers, including metabolic disease, chronic inflammation, and microbiome dysregulation, which remain under-integrated into current treatment paradigms. Recent progress in precision oncology has enabled regulatory approval of biomarker-defined therapies for select PDAC subsets, including immune checkpoint inhibitors for mismatch repair-deficient tumors, PARP inhibitors for BRCA1/2-mutant disease, and combination cytotoxic regimens such as NALIRIFOX in the metastatic setting. However, these advances benefit only a minority of patients, underscoring the urgent need for improved patient stratification and rational combination strategies. Emerging clinical and translational studies highlight the promise of integrating multi-omic profiling, liquid biopsies, functional precision models (organoids and patient-derived xenografts), and artificial intelligence-driven analytics to uncover actionable vulnerabilities, monitor response, and guide adaptive trial design. In this review, we critically evaluate the clinical relevance of molecular, metabolic, and microenvironmental determinants of PDAC progression and therapeutic resistance. We focus on translational bottlenecks that have limited clinical success to date and highlight biomarker-driven strategies, ongoing clinical trials, and emerging technologies poised to shift treatment from uniform algorithms toward biologically informed, patient-specific therapeutic approaches in pancreatic cancer.},
}
@article {pmid42009106,
year = {2026},
author = {Yoshino, Y and Kimura, Y and Ito, F},
title = {Chronic Inflammation in Virus-suppressed People Living with Human Immunodeficiency Virus Infection: A Microbiology-oriented Perspective on Gut Barrier Failure, Microbial Translocation, and Immune Activation.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {102972},
doi = {10.1016/j.jiac.2026.102972},
pmid = {42009106},
issn = {1437-7780},
abstract = {Potent antiretroviral therapy (ART) has transformed human immunodeficiency virus (HIV) infection into a chronic manageable condition; however, many people living with HIV (PLWH) exhibit persistent immune activation and inflammation despite long-term virological suppression. Residual inflammation is strongly associated with an increased risk of cardiovascular disease, chronic kidney disease, metabolic dysfunction-associated steatotic liver disease, cancer, and neurocognitive impairment. This review summarizes the current evidence on the microbiology-oriented mechanisms that sustain this state. We first outline a multifactorial network in which incomplete repair of intestinal mucosal damage, dysbiosis, reduced short-chain fatty acid production, and disturbed bile acid metabolism generate a patchy "leaky gut." Continuous translocation of bacterial lipopolysaccharide, fungal β-D-glucan, and other microbial products activates monocyte-macrophage and portal-liver inflammatory circuits. These inputs interact with intermittent HIV antigen expression from latent reservoirs, inflammatory cell death, chronic coinfections, lymphoid tissue fibrosis, mitochondrial dysfunction, and traditional lifestyle-related risk factors. Together, they establish a self-reinforcing gut-liver-immune axis that maintains low-grade inflammation and a procoagulant milieu under viral suppression. We then link these mechanisms to organ-specific complications and review the intervention data, focusing on early ART initiation, statin therapy, and cotrimoxazole prophylaxis as a proof-of-concept that modifying inflammatory and mucosal pressures can improve outcomes. Finally, we highlight research priorities and argue that the effective prevention of long-term complications in virally suppressed PLWH requires combination strategies targeting multiple nodes of this network, with particular attention to gut barrier repair and microbiome modulation.},
}
@article {pmid42009160,
year = {2026},
author = {Qannita, RA and Zenati, RA and Abuhelwa, AY and Alqudah, MAY and Aleidi, SM and El-Huneidi, W and Abu-Gharbieh, E and AlShareef, ZM and Alzoubi, KH and Bustanji, Y and Semreen, MH},
title = {Emerging biomarkers for early detection of colorectal cancer.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121013},
doi = {10.1016/j.cca.2026.121013},
pmid = {42009160},
issn = {1873-3492},
abstract = {The worldwide impact of colorectal cancer (CRC) as a primary cause of cancer-related morbidity and mortality demonstrates the urgent need for better early detection methods and personalized treatment approaches. While colonoscopy and fecal tests have contributed to reduced mortality rates from CRC, they encounter important limitations stemming from their invasive procedures and insufficient sensitivity plus patient adherence issues. Consequently, the latest progress in molecular biology and omics technologies has enabled researchers to identify new biomarkers which present effective solutions for early detection and risk assessment while monitoring treatment efficacy. Therefore, this review explores new developments in CRC biomarker research through the lens of emerging liquid biopsy methods like circulating tumor DNA (ctDNA) and microRNAs (miRNAs) as well as genomic, epigenomic, gut microbiome, metabolomic, and proteomic markers. The usage of biomarker-based methods demonstrates transformative potential for CRC treatment by boosting survival rates and lessening global impact through precision medicine development in oncology.},
}
@article {pmid42009250,
year = {2026},
author = {Ramond, P and de Groot, T and Niemann, H and Engelmann, JC},
title = {Community Turnover and Connectivity at Two Study Sites in the North and Wadden Seas: Dynamics From Hours to Seasons.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70310},
doi = {10.1111/1462-2920.70310},
pmid = {42009250},
issn = {1462-2920},
support = {ERC-CoG-772923/ERC_/European Research Council/International ; //Wise NWO/ ; },
mesh = {Seasons ; *Microbiota ; *Seawater/microbiology ; *Geologic Sediments/microbiology ; North Sea ; Ecosystem ; *Bacteria/classification/genetics/isolation &amp; purification ; Temperature ; Salinity ; Oceans and Seas ; },
abstract = {Microbial communities underpin ecosystem processes and biogeochemical cycles in marine ecosystems, yet their spatial and temporal dynamics at hourly scales remain poorly understood. We surveyed two stations from the North Sea (NS) and Wadden Sea (WS), generating six high-frequency time-series datasets across depths and seasons, complemented by sediment cores. Across seasons, the sites in the NS and the WS harbored distinct microbial communities shaped by contrasts in salinity, temperature, and potentially the quantity and lability of organic matter. Connectivity between communities was limited but favoured by known seasonal hydrographic exchanges. Despite taxonomic contrasts between sites, functional turnover remained low, with communities harbouring similar metabolic potential but being adapted to local conditions, suggesting potential functional redundancy. At hourly scales, community turnover was weaker and largely driven by vertical and horizontal mixing between water masses, occasional resuspension from sediments, or a summer bloom from a copiotroph. These shifts were transient and did not disrupt the coupling between taxonomic and functional composition. However, their immediate effects on ecosystem processes, such as organic matter remineralisation and nutrient recycling remain unclear. Continued high-resolution microbiome monitoring, paired with biogeochemical flux measurements, is needed to better predict climate-driven changes in coastal ecosystem functioning.},
}
@article {pmid42009295,
year = {2026},
author = {Zhang, H and Zheng, X and Wang, Q and Zhou, X and Cai, L and Zhan, L and Huang, D and Shi, T},
title = {Post-Heatwave Coral Health Coincides With Host-Specific Symbiodiniaceae-Bacteria Consortia.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70306},
doi = {10.1111/1462-2920.70306},
pmid = {42009295},
issn = {1462-2920},
support = {2022YFC3102003//National Key Research and Development Program of China/ ; 2020YFA0607602//National Key Research and Development Program of China/ ; 2020017//Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 2019017//Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 42376110//National Natural Science Foundation of China/ ; 41876119//National Natural Science Foundation of China/ ; //global Ocean Negative Carbon Emission (ONCE) program/ ; 2023J06043//Science Fund for Distinguished Young Scholars of Fujian Province/ ; },
mesh = {Animals ; *Anthozoa/microbiology/physiology ; Symbiosis ; Coral Reefs ; *Hot Temperature ; *Bacteria/classification/genetics/isolation &amp; purification ; *Dinoflagellida/physiology ; *Microbial Consortia ; Microbiota ; },
abstract = {Coral reefs are facing unprecedented damage due to climate-driven marine heatwaves (MHWs). While coral response to elevated temperatures is inextricably linked to coral-associated microalgae (Symbiodiniaceae) and bacteria, the role of algal-bacterial interactions in affecting coral resilience to thermal stress remains obscure. Here we show coral health indicated by distinct compositions of Symbiodiniaceae-bacteria consortia in two coral species, the massive Porites lutea and the laminar Duncanopsammia peltata, upon exposure to an unusual MHW. P. lutea exhibited thermal resilience by maintaining an obligate partnership with the heat-tolerant Cladocopium C15 under both healthy and bleached states, alongside conservative bacterial community changes between the two states driven primarily by deterministic processes; whereas D. peltata associated with the heat-sensitive Cladocopium C1 in bleached state but the heat-tolerant Durusdinium D1/D4 in healthy state, with stochastically driven, more liberal bacterial community changes between the two states. This distinction between P. lutea and D. peltata in their Symbiodiniaceae-bacteria consortia reflects a specialist/generalist strategy in partner selection given the status of coral health, underscoring an evolutionary trade-off between high-fidelity symbioses for persistence under chronic stress and rapid microbiome turnover for transient bleaching resilience. Broadly, the host-specific, coordinated Symbiodiniaceae-bacteria community differentiation following MHWs, may inform future coral conservation and restoration practises in an era of escalating climate change.},
}
@article {pmid42009386,
year = {2026},
author = {Couturier, J and Kenner, E and Nicula, M and Chowdhury, F and Surette, M and Pai, N},
title = {Protocol for a pilot feasibility randomised controlled trial of fecal microbiota transplantation for adolescent anorexia nervosa.},
journal = {BMJ open},
volume = {16},
number = {4},
pages = {e109115},
doi = {10.1136/bmjopen-2025-109115},
pmid = {42009386},
issn = {2044-6055},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Adolescent ; *Anorexia Nervosa/therapy/psychology ; Pilot Projects ; Feasibility Studies ; Child ; Female ; Male ; Randomized Controlled Trials as Topic ; Gastrointestinal Microbiome ; },
abstract = {INTRODUCTION: Despite its serious impact, anorexia nervosa (AN) remains one of the least understood mental illnesses, with significant gaps in effective treatment options. No medications have been deemed effective and only 50% of individuals respond to conventional psychotherapies. Gastrointestinal (GI) bacteria have been found to be altered in individuals with AN. While, Fecal microbiota transplantation (FMT) has shown potential for alleviating anxiety and depression, its effects remain understudied for individuals with AN. This study aims to determine whether oral capsular FMT is acceptable to adolescents with AN and results in clinical improvement in weight and/or psychological symptoms.<br><br>METHODS: This study will randomise 20 adolescents with AN, ages 12-17 years, to receive either FMT or placebo capsules. These 20 youth, as well as an additional 10 youth who decline trial enrolment, will participate in qualitative interviews. We will track recruitment rates and collect psychological and biological measures (blood, stool, urine and saliva) at multiple timepoints to assess how gut microbiota and their metabolites may influence the symptoms of AN. Interviews with participants and caregivers will explore their experiences and views on FMT as a treatment approach.<br><br>ETHICS AND DISSEMINATION: This study has received ethics approval by the Hamilton Integrated Research Ethics Board (#17493) and investigational drug approval by Health Canada (Dossier ID: c292423). Informed consent will be obtained by research staff from all participants. Findings will be disseminated through academic conferences, clinical forums and partnerships with advocacy organisations to reach clinicians, researchers and individuals with lived experience.<br><br>TRIAL REGISTRATION NUMBER: NCT06593366.},
}
@article {pmid42009997,
year = {2026},
author = {Swain, MP and Mehta, CH and Padya, BS and Sharma, S and Velagacherla, V and Mitra, A and Mohanty, S and Mukherjee, T},
title = {Microbiome modulating remedies for chronic diseases: a review of current interventions and future directions.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {42009997},
issn = {1568-5608},
}
@article {pmid42010118,
year = {2026},
author = {Menozzi, E and Ren, Y and Geiger, M and Macnaughtan, J and Avenali, M and Toffoli, M and Gilles, M and Calabrese, R and Mitrotti, P and Gallo, L and Famechon, A and Del Pozo, SL and Mezabrovschi, R and Koletsi, S and Loefflad, N and Yalkic, S and Limbachiya, N and Clasen, F and Yildirim, S and Shoaie, S and Blottière, H and Morabito, C and David, A and Quinquis, B and Pons, N and Le Chatelier, E and Valzania, F and Cavallieri, F and Fioravanti, V and Toschi, G and Blandini, F and Almeida, M and Ehrlich, SD and Meslier, V and Schapira, AHV},
title = {Microbiome signature of Parkinson's disease in healthy and genetically at-risk individuals.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {42010118},
issn = {1546-170X},
support = {MR/T046007/1//EU Joint Programme - Neurodegenerative Disease Research (Programi i P&#xeb;rbashk&#xeb;t i BE-s&#xeb; p&#xeb;r K&#xeb;rkimet mbi S&#xeb;mundjet Neuro-degjeneruese)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; },
abstract = {Parkinson's disease (PD) is a major cause of disability. GBA1 variants are the most common genetic risk factor for PD and increase the risk up to 30-fold. Why only approximately 20% of GBA1 variant carriers develop PD remains unknown. Here, by combining clinical and fecal metagenomics data from 271 patients with PD, from 43 carriers of GBA1 variants not manifesting PD symptoms (GBA-NMC) and from 150 healthy controls, and using an innovative microbiome analysis, combining differential abundance of species and coherence of differential abundance variation between the groups as assessed by Cliff's delta (δ), we show that the composition of a large component of the gut microbiome (approximately 25%) in GBA-NMC is intermediate between healthy controls and patients with PD. This component is strongly correlated with disease progression in patients and prodromal symptoms suggestive of future development of PD in both GBA-NMC and healthy individuals. We found microbiome alterations similar to those described here in three independent cohorts from the United States, Korea and Turkey, totaling 638 patients with PD and 319 healthy controls, and we conclude that gut microbiome alterations can identify both genetically and non-genetically at-risk individuals in the general population who may be progressing toward PD, thus serving as an early marker of disease development in the premanifest phase.},
}
@article {pmid42010351,
year = {2026},
author = {Ahannach, S and Condori-Catachura, S and Dillen, J and Dricot, C and Gehrmann, T and Wittouck, S and Kenfack, JM and Van Beeck, W and De Boeck, I and Eilers, T and Ticlla, M and Santullo Latorre, A and Smets, W and Temmermans, J and Arconada Nuin, E and , and Van Puyvelde, S and Spacova, I and Verhoeven, V and Lebeer, S},
title = {Considerations for the design of impactful citizen-science projects in microbiome research.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {42010351},
issn = {1750-2799},
abstract = {Citizen science offers a transformative approach to microbiome research. It allows the collection of rich, context-specific data from diverse sources, such as varying human populations and environments. Here, we describe guidelines that cover the design and implementation of community-engaged citizen-science projects focused on microbiome research. We outline essential research steps, beginning with defining the objectives and forming a transdisciplinary team, and continuing with community interaction, standardized self-sampling protocols, strategies for data processing, analysis and communication of results to community members and policymakers, as well as the implementation of robust data management practices that uphold participant privacy and data sovereignty. The guidelines highlight culturally-sensitive outreach strategies and capacity building in research teams and communities, emphasizing ethical considerations and tailored recruitment strategies. Community engagement may help reduce sampling bias but does not automatically ensure participant diversity: intentional inclusion strategies are essential. They cover culturally sensitive outreach, ethical considerations and tailored recruitment approaches that support inclusive participation and meaningful collaboration. These recommendations draw inspiration from a range of health and environment-related citizen-science projects in Belgium, Peru and Cameroon, and collaborative projects across the world. Specific examples highlight the importance of adapting methodologies to diverse cultural contexts and logistical constraints. While wet-laboratory sample processing and downstream analyses are detailed elsewhere, this Perspective focuses on the unique considerations and best practices needed for designing impactful cocreative citizen-science projects that combine scientific discovery with community, environmental health and well-being. It can serve as a blueprint for future citizen-science initiatives that aim to expand access to microbiome research, foster global collaboration and promote long-term research equity and environmental sustainability.},
}
@article {pmid42010400,
year = {2026},
author = {Li, X and Wei, W and Wei, S and Xu, W and Mo, L and Wang, J and Zhu, H and Liu, Z and Jin, F},
title = {Altered microbial cargo in fecal microbiome-derived outer membrane vesicles as novel biomarkers for vascular dementia.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05040-5},
pmid = {42010400},
issn = {1471-2180},
support = {2022A21//the Doctoral Research Startup Project of Central People's Hospital of Zhanjiang/ ; 2022A10//the Doctoral Research Startup Project of Central People's Hospital of Zhanjiang/ ; 2022A14//the Doctoral Research Startup Project of Central People's Hospital of Zhanjiang/ ; 2022A22//the Doctoral Research Startup Project of Central People's Hospital of Zhanjiang/ ; 2021X091662//Weifang Municipal Health Commission Scientific Research Project/ ; 2022A1515010749//the Natural Science Foundation of Guangdong Province/ ; 2024B01238//Zhanjiang City Science and Technology Plan Project/ ; },
}
@article {pmid42010457,
year = {2026},
author = {Guo, J and Liang, C and Cairang, L and Si, L and Yan, J and Liu, D},
title = {Metagenomics reveals gut microbial differences and ecological adaptation in plateau zokor (Eospalax baileyi) populations.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05069-6},
pmid = {42010457},
issn = {1471-2180},
support = {LHZX-2023-02//Sanjiangyuan National Park Joint Grant from the Chinese Academy of Sciences and the People's Government of Qinghai Province/ ; },
}
@article {pmid42010642,
year = {2026},
author = {Min, K and Kim, SI and Lee, M and Kim, Y and Jeong, C and Kim, S and Kim, SJ and Kim, H and Cho, B and Joo, Y and Park, H and Lee, M},
title = {Trimethylamine-producing microbe Bacillus megaterium KCTC 3007 promotes antitumor immunity in endometrial cancer via type I interferon response pathways.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02373-1},
pmid = {42010642},
issn = {2049-2618},
support = {grant of the MD-PhD/Medical Scientist Training Program//Korea Health Industry Development Institute/Republic of Korea ; KGCR-2022-01//Korean Gynecologic Cancer Research/ ; 2022R1A2C2008976 and RS-2023-00228315//Ministry of Science and ICT, Korean Government/ ; },
abstract = {BACKGROUND: Endometrial cancer (ECa) is one of the most common gynecologic malignancies, with limited therapeutic responses in metastatic or recurrent cases. The bacterial microbiota has emerged as a key modulator of carcinogenesis and antitumor immunity. However, the role of endometrial microbiota in ECa pathogenesis and prognosis remains poorly understood.<br><br>METHODS: We performed comprehensive multi-omics analysis integrating metatranscriptomics, transcriptomics, and targeted metabolomics from 60 ECa and 18 benign patients. RNA sequencing enabled simultaneous profiling of active tissue-resident microbiota and host gene expression. Serum metabolomics was conducted on all patients. Identified microbial-metabolite associations were validated through in vitro co-culture experiments using peripheral blood mononuclear cells (PBMCs), cancer cell lines, RNA sequencing, and live cell imaging.<br><br>RESULTS: ECa patients exhibited significantly altered microbial diversity and composition compared to benign controls. Through integrated multi-omics analysis, we identified Bacillus megaterium (BM) KCTC 3007 as a beneficial microbe associated with prolonged recurrence-free survival. In an exploratory analysis of ECa subtypes, Cupriavidus taiwanensis and Marinomonas primoryensis showed potential links to poor prognosis, although these observations warrant caution due to the limited size of certain subgroups. Tissue BM abundance positively correlated with serum trimethylamine N-oxide (TMAO) levels, particularly in postmenopausal women. In vitro experiments demonstrated that BM KCTC 3007 enhanced antitumor immunity by promoting interleukin and type I interferon expression, expanding CD8&#x2009;+&#x2009;T cell populations, and increasing immune cell-tumor cell interactions. RNA sequencing revealed activation of interferon alpha response and immune cell proliferation pathways, with IFNAR1 identified as a key upstream regulator. TMAO treatment recapitulated these immune-activating effects, enhancing CD8&#x2009;+&#x2009;T cell responses and preferentially inducing pyroptotic cancer cell death.<br><br>CONCLUSIONS: We provide the first evidence that tissue-resident BM KCTC 3007 promotes antitumor immunity in ECa through TMAO production and subsequent type I interferon-mediated immune activation. This integrated multi-omics approach establishes a complete microbe-metabolite-host mechanistic pathway and highlights the therapeutic potential of TMAO-producing probiotic strains for ECa treatment. Video Abstract.},
}
@article {pmid42010662,
year = {2026},
author = {Yuan, T and Chen, J and Zheng, H and Pu, J and Li, L and Lu, S and Sun, Y and Lin, W and Yang, J and Xu, J},
title = {A novel enterotype enriched with respiratory super-dominant pathobionts is associated with immunosuppression in pulmonary tuberculosis patients.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08165-3},
pmid = {42010662},
issn = {1479-5876},
abstract = {BACKGROUND: Perturbations of the gut microbiota in pulmonary tuberculosis (PTB) patients, often antibiotic-induced, are frequently observed; however, the defining features of this dysbiosis and its relationship with clinical phenotypes remain insufficiently characterized.<br><br>METHODS: In this cross-sectional study, we collected fecal samples from 66 PTB patients and performed 16S rRNA gene (V3-V4) sequencing. Species-level taxonomic profiling was conducted using the Human Gut Microbiome Analysis Database (HGMAD). Enterotypes were constructed, and their associations with PTB were investigated. The predictive capacity of enterotype-specific microbial signatures (enterosignatures) for clinical phenotypes was assessed.<br><br>RESULTS: Taxonomic analysis revealed significantly reduced prevalence of high-abundance bacteria group in PTB patients (43.84%) compared to healthy controls (HC, 98.01%), indicating increased microbiota heterogeneity. Known pathogenic species, predominantly common respiratory opportunistic pathogens (e.g., Haemophilus parainfluenzae, Acinetobacter baumannii, Veillonella parvula), were more prevalent in the PTB cohort (21.37% vs. 11.49% in HC). Enterotype analysis revealed a distinct cluster, designated ETE (Enterobacterales-dominated enterotype), which was predominantly observed in PTB patients and differed from the conventional Prevotella-dominated enterotype (ETP) and Bacteroides-dominated enterotype (ETB), identified in HC. ETE was significantly enriched in taxa including Acinetobacter baumannii, Enterococcus, Veillonella, Pseudomonas, and Streptococcus, exhibited lower alpha diversity, and functional inference using PICRUSt2 suggested relative lower immune-related pathways. Clinically, ETE was associated with lower cellular immunity and a trend toward higher C-reactive protein (CRP) levels. A model based on ten super-dominant respiratory pathobionts enterosignatures effectively predicted key clinical phenotypes, with area under the curves (AUCs) of 0.83 for CD4[+] T-cell count, 0.74 for CD8[+] T-cell count, 0.74 for CD4[+]/CD8[+] ratio, 0.93 for CRP, 0.78 for CA125, and 0.70 for Mtb positivity. SHapley Additive exPlanation (SHAP) analysis identified Enterobacterales and Veillonella as key negative predictors for T-cell counts, while Streptococcus and Enterobacteriaceae were positive predictors for CRP. In the CA125 model, Veillonella acted as a positive predictor and Enterobacterales as a negative predictor.<br><br>CONCLUSION: This cross-sectional study identifies a distinct, PTB-associated enterotype (ETE) characterized by enrichment of respiratory pathobionts and associated with altered immune parameters in PTB patients. Enterosignatures derive from ETE represent exploratory biomarkers with promising predictive capacity for clinical outcomes, though their generalizability warrants validation in independent, prospective cohorts.},
}
@article {pmid42010711,
year = {2026},
author = {You, C and Zhang, W and Guan, Y and Liang, Q and Nong, C and Yang, T and Li, M and Banerjee, S and Zhou, X and Wang, X and Xu, Y and Shen, Q and Wei, Z},
title = {Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02393-x},
pmid = {42010711},
issn = {2049-2618},
support = {2022YFC3501501//National Key Research and Development Program of China/ ; KJYQ2025034, KJYQ2024039//Fundamental Research Funds for the Central Universities/ ; BK20240194//the Natural Science Foundation of Jiangsu Province/ ; },
abstract = {BACKGROUND: The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking.<br><br>RESULTS: Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres.<br><br>CONCLUSIONS: Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.},
}
@article {pmid42010766,
year = {2026},
author = {Combs, D and Landeros, K and Garza, K and Azari, H and Abdelrahman, M and Albracht-Schulte, K},
title = {Exercise intensity as a modulator of gut microbiota and host metabolic health in obesity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2661415},
doi = {10.1080/19490976.2026.2661415},
pmid = {42010766},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Animals ; *Exercise/physiology ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Physical Conditioning, Animal ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiome is shaped by complex interactions among host, environmental, and lifestyle factors, with exercise emerging as a reported modulator. Growing evidence suggests that exercise intensity, ranging from low to high, can differentially influence gut microbial composition, diversity, and functional outputs relevant to metabolic health. This narrative review synthesizes current findings examining intensity-dependent microbial adaptations in the context of obesity. Across animal models (n = 17) and limited human studies (n = 5), moderate-intensity training (MIT) and high-intensity interval training (HIIT) produce the most consistent microbiota shifts, while low-intensity training (LIT) exerts minimal effects. Reported taxa associated with beneficial outcomes consistent across animal and human investigations include Akkermansia (G), and Christensenellaceae (F). Mechanistically, intensity-dependent alterations in microbial communities may influence obesity-related pathways through modulation of short-chain fatty acid (SCFA) and bile acid metabolism, gut barrier integrity, endotoxemia, and inflammatory signaling. HIIT and MIT are linked to improved expression of tight junction proteins (ZO-1, Claudin, Occludin), reducing circulating lipopolysaccharide (LPS), and increasing SCFA-producing taxa; thus, supporting a role for the gut microbiome in mediating exercise-induced metabolic benefits. However, inconsistent findings between species, interindividual variability, and considerable heterogeneity in exercise intervention duration across both animal (4-16 weeks) and human (3-12 weeks) studies, as well as limited longitudinal human studies, underscore the need for deeper mechanistic investigations. Future research should employ metagenomic and metatranscriptomic profiling, integrate sex- and diet-stratified longitudinal designs, and clarify causal links between exercise-responsive taxa, microbial metabolites, and host physiology. Collectively, these data highlight exercise intensity as a key determinant of gut microbiome dynamics and reinforce the need for integrative, translational approaches to define its therapeutic potential for obesity and metabolic disorders.},
}
@article {pmid42010947,
year = {2026},
author = {Zhang, Y and Tan, B and Zhou, Q and Xu, L and Zhou, L},
title = {Tumor-resident bacteria in gastrointestinal cancers: from regulatory mechanisms to clinical implications.},
journal = {Cancer biology &amp; medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0686},
pmid = {42010947},
issn = {2095-3941},
support = {2023ZD0501600//Non-communicable Chronic Diseases-National Science and Technology Major Project/ ; 82373080//National Nature Science Foundation of China/ ; 82403116//National Nature Science Foundation of China/ ; 2023ZT10Y094//Guangdong Pearl River Talent Program/ ; 2023QN10Y587//Guangdong Pearl River Talent Program/ ; 2022-KJXM-ZCQ-11//"the Science and Technology Empowering Inner Mongolia" Major Special Project of Inner Mongolia Autonomous Region/ ; },
abstract = {The human microbiome is increasingly recognized as a key contributor to the tumor microenvironment (TME). Advances in sequencing technologies have revealed the pivotal role of intratumoral microbiota in the development of gastrointestinal cancers. This review summarizes current knowledge on the characteristics and functional mechanisms of tumor-resident bacteria in colorectal, gastric, and hepatocellular carcinoma. We describe how these microbes affect carcinogenesis and disease progression through multiple pathways, including interactions between the microbiota and the host gut barrier, tumor cells, anti-tumor immunity, and other non-cellular components of the TME. In addition, the translational potential of intratumoral microbiota as diagnostic and prognostic biomarkers, as well as the influence on therapeutic responses, is discussed. A growing understanding of tumor-microbe interactions not only deepens insight into cancer biology but also opens new directions for innovative diagnostic and therapeutic strategies, highlighting the potential of targeting the intratumoral microbiome to improve patient outcomes in gastrointestinal oncology.},
}
@article {pmid42011428,
year = {2026},
author = {Deng, L and Yao, Y and Wang, Q and Lu, Z and Li, E and Hu, Y and Chen, J and Wang, G and Yu, T and Ji, J and Jiao, Q},
title = {Impact of gut microbiome, plasma metabolites, peripheral immune cells, and circulating inflammatory protein on chronic spontaneous urticaria: Bidirectional 2-sample Mendelian randomization study and mediation analysis.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {5},
number = {3},
pages = {100686},
pmid = {42011428},
issn = {2772-8293},
abstract = {BACKGROUND: Growing evidence links gut microbiota to chronic spontaneous urticaria (CSU), yet causality and underlying mediators remain unclear.<br><br>OBJECTIVE: We investigated causal relationships and potential mediators-specifically plasma metabolites, immune cells, and inflammatory proteins-through which gut microbes influence CSU risk.<br><br>METHODS: We applied 2-sample Mendelian randomization (MR) to genome-wide association study (GWAS) data on 430 gut microbial taxa, 1,400 plasma metabolites, 731 immune cell traits, and 91 inflammatory proteins. Analyses used inverse variance weighted, MR-Egger, weighted median, and weighted mode estimators, complemented by sensitivity, mediation, multivariable MR, and Bayesian colocalization tests for shared causal variants.<br><br>RESULTS: Eight gut taxa, 79 metabolites, 25 immune cell phenotypes, and 3 inflammatory proteins showed suggestive associated with CSU (all false discovery rate > .05). Galactonate mediated the effect of Paraprevotella on CSU, while N-acetyl leucine mediated the protective effect of Bacteroides; only the latter remained significant in multivariable MR. Immune cells and inflammatory proteins showed no significant mediation. Bayesian colocalization provided no evidence of shared causal variants between CSU and any of the 4 trait categories.<br><br>CONCLUSION: Gut microbiota may suggestively influence CSU risk via specific metabolite pathways, particularly N-acetyl leucine, though colocalization did not support shared genetic causality and no association survived multiple testing correction at false discovery rate < .05. These findings offer hypothesis-generating insights and candidate targets for further functional validation.},
}
@article {pmid42011833,
year = {2026},
author = {Yuan, BJ and Wang, YH and Lai, JR and Liu, L and Zhang, JW and Tian, HD and Johnston, RN and Liu, GR and Liu, SL},
title = {Secoisolariciresinol diglucoside resolves systemic and skin inflammation in psoriatic mice by ameliorating the gut microbiome and modulating immune responses.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04965b},
pmid = {42011833},
issn = {2042-650X},
abstract = {Psoriasis is a chronic inflammatory skin disease that often imposes enormous psychological impact on the patient, potentially leading to psychiatric comorbidities or even suicidality. The currently available treatments do not always provide satisfactory results. Our previous work demonstrates that secoisolariciresinol diglucoside (SDG) has potent anti-inflammatory effects. In this study, we aimed to assess the effect of SDG on resolving the psoriatic inflammation using an imiquimod (IMQ)-induced mouse model and elucidate the underlying mechanisms. SDG and its metabolite enterolactone (ENL) exhibited potent curative effects on the skin pathology. In association with the resolution of the psoriatic inflammation, the lignans (SDG and ENL) significantly ameliorated gut dysbiosis. In the meantime, the Treg cells and the anti-inflammatory CD163 macrophages were greatly expanded in number, while the F4/80 and iNOS macrophages, the pro-inflammatory γδ T and Th17 cells, and a broad range of inflammatory cytokines along with STAT1 were drastically decreased. These results demonstrate that SDG treatment can effectively resolve the systemic and skin inflammation in psoriasis by ameliorating the gut microbiome and modulating immune responses. Collectively, this study provides useful information for the development of curative therapeutic strategies with natural products to treat psoriasis.},
}
@article {pmid42012190,
year = {2026},
author = {Matsukawa, H and Fujita, M and Kuramoto, Y and Kuwahara, S and Tsuji, S and Takeda, Y and Son, A and Kato, T and Shirakawa, M and Yoshimura, S},
title = {Pre-existing Gut Microbiome Dysbiosis Exacerbates Neuroinflammation and Vasospasm After Subarachnoid Hemorrhage in Mice.},
journal = {Neurosurgery},
volume = {},
number = {},
pages = {},
doi = {10.1227/neu.0000000000004035},
pmid = {42012190},
issn = {1524-4040},
support = {22H04349//Japan Society for the Promotion of Science (JSPS) KAKENHI Grant/ ; 22K16699//Japan Society for the Promotion of Science (JSPS) KAKENHI Grant/ ; 25K12352//Japan Society for the Promotion of Science (JSPS) KAKENHI Grant/ ; },
abstract = {BACKGROUND AND OBJECTIVES: Delayed cerebral ischemia remains a major determinant of poor outcomes after aneurysmal subarachnoid hemorrhage (SAH), yet effective preventive strategies are limited. The gut-brain axis has emerged as an important modulator of post-SAH neuroinflammation and vascular dysfunction. We hypothesized that pre-existing gut microbiome dysbiosis (GMD) exacerbates neuroinflammation and vasospasm after SAH.<br><br>METHODS: Male C57BL/6J mice underwent broad-spectrum antibiotic-induced gut microbiome depletion or control treatment, followed by endovascular perforation SAH or control surgery. Neurological function, body weight, and mortality were assessed longitudinally. Cerebral vasospasm was quantified by anterior cerebral artery morphometry. Endothelial activation and neuroinflammation were evaluated using intercellular adhesion molecule 1 and ionized calcium-binding adapter molecule 1 immunofluorescence. Immune cell populations in the brain and spleen were analyzed by flow cytometry, and serum cytokines were measured by multiplex assays. Gut microbiome composition was assessed using 16S rRNA sequencing in microbiota-intact mice.<br><br>RESULTS: SAH alone caused minimal early changes in gut microbial diversity or composition, indicating that early post-SAH outcomes were not driven by SAH-induced dysbiosis. By contrast, pre-existing GMD did not affect initial SAH severity but significantly worsened post-SAH outcomes, including weight loss, neurological deficits, and cerebral vasospasm. Vasospasm severity correlated robustly with endothelial intercellular adhesion molecule 1 expression and cortical ionized calcium-binding adapter molecule 1-positive microglia/macrophages. GMD amplified central and peripheral inflammatory responses, characterized by increased CD86-positive macrophages and neutrophils in the brain and splenic macrophage expansion. Systemically, GMD altered cytokine profiles, with elevated CCL5 and reduced granulocyte colony-stimulating factor, and CCL5 levels correlated with both neuroinflammation and vasospasm severity.<br><br>CONCLUSION: Pre-existing GMD exacerbates neurovascular inflammation, vasospasm, and neurological impairment after SAH through dysregulated central and systemic immune responses. These findings identify the gut-brain axis as a critical modulator of delayed cerebral ischemia-like pathology and suggest microbiome-targeted strategies as potential therapeutic approaches for SAH.},
}
@article {pmid42012194,
year = {2026},
author = {Han, N and Bai, F and Wen, Q and Bi, Y and Yang, R and Han, Y},
title = {Formulation-dependent kinetics of Lacticaseibacillus paracasei Zhang in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0363725},
doi = {10.1128/spectrum.03637-25},
pmid = {42012194},
issn = {2165-0497},
abstract = {UNLABELLED: The relationship between gut microbiota and human health has become one of the focal point in medical research. Probiotics, which modulate the gut microbiome, hold considerable promise for both prophylaxis and therapeutic intervention. This requires deeper insights into the kinetic changes and molecular mechanisms upon probiotic entry into the body. In this study, we utilized advanced molecular imaging to delineate the in vivo kinetic dynamics of two Lacticaseibacillus paracasei Zhang (L. paracasei Zhang, LPZ) formulations: a liquid culture and a lyophilized powder. Our results provide new insights into the gastrointestinal transit and growth kinetics of the different probiotics formulations. Strikingly, the liquid LPZ achieved its peak growth phase within a relatively short period of 6 to 8 h post-ingestion, culminating in a 270- to 680-fold increase in residues at the 24th hour post-ingestion when compared to the lyophilized powder LPZ. Furthermore, during peak in vivo replication, LPZ enhanced gut microbial diversity and enriched beneficial commensal communities. Functionally, LPZ ingestion attenuated virulence factors while upregulating carbohydrate-active enzymes. Notably, LPZ significantly reduced xanthine levels, a metabolite associated with hyperuricemia, thereby providing a mechanistic basis for the observed relief from gout symptoms. This supports the mechanism of prior clinical findings and paves the way for future clinical trials and therapeutic use of LPZ and related probiotics.<br><br>IMPORTANCE: The innovation of this study lies in visualizing the kinetic changes of two Lacticaseibacillus paracasei Zhang (L. paracasei Zhang, LPZ) formulations (a liquid culture and lyophilized powder) within the gastrointestinal tract. It was found that liquid LPZ proliferates in vivo with a higher retention rate. Furthermore, we also found that when liquid LPZ reaches its peak proliferation phase in vivo, it not only effectively promotes the proliferation of other beneficial bacteria and the production of their metabolites but also generates more carbohydrate-active enzymes while reducing virulence factors, thereby amplifying the functions of LPZ. Meanwhile, we observed that liquid LPZ significantly reduces the production of xanthine in vivo, indicating its potential to lower uric acid. In light of the aforementioned findings, we herein propose the concept of "probiotikinetics." These results provide new insights into the intake of LPZ, along with important evidence for its application in healthy populations.},
}
@article {pmid42012708,
year = {2026},
author = {Kværner, AS and Birkeland, E and Avershina, E and Botteri, E and Bucher-Johannessen, C and Knudsen, MD and Hjartåker, A and Page, CM and Hov, JR and Song, M and Randel, KR and Hoff, G and Rounge, TB and Berstad, P},
title = {Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.},
journal = {European journal of nutrition},
volume = {65},
number = {4},
pages = {},
pmid = {42012708},
issn = {1436-6215},
}
@article {pmid42012901,
year = {2026},
author = {Bellanco, A and Yépez-Notario, C and Lozano, M and Martínez-Cuesta, MC and Requena, T},
title = {Human Gut Microbiome Can Degrade the Sweetener Acesulfame K with Potential Damaging Effects in the Intestinal Barrier Function.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c16498},
pmid = {42012901},
issn = {1520-5118},
abstract = {Acesulfame K (Ace-K) is a commonly consumed sweetener, although knowledge about the Ace-K-gut microbiota interaction remains limited. This study evaluates dose-dependent effects of Ace-K on metataxonomics, metagenomics, and metabolic activity of children gut microbiota developed in a dynamic gut simulator. An Ace-K-dose dependent increase in Anaerostipes, Coprococcus, Subdoligranulum, Blautia, Sutterella wadsworthensis, Alistipes, and Bacteroides thetaiotaomicron was observed. Butyrate showed a dose-response increase that correlated with Ace-K consumption, suggesting its microbial metabolism. Increasing bacterial taxa showed sulfatase and amidase activities potentially capable of degrading Ace-K, releasing sulfamate and acetoacetate, which species such as Anaerostipes hadrus and Intestinimonas can metabolize to produce butyrate via the butanoyl-CoA pathway. Furthermore, the Ace-K-microbiome interaction led to a dose-dependent decrease in Caco-2 epithelial integrity, possibly due to the release of sulfated metabolites. This study provides evidence of the potential risk of Ace-K consumption based on its metabolism by the human gut microbiome.},
}
@article {pmid42012979,
year = {2026},
author = {Tanes, C and Wilson, NG and Smith, M and Patel, TT and Merenstein, C and Bushman, FD and Bittinger, K and Buffenstein, R},
title = {The naked mole-rat microbiome is associated with healthy aging and social structure.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117265},
doi = {10.1016/j.celrep.2026.117265},
pmid = {42012979},
issn = {2211-1247},
abstract = {The naked mole-rat (NMR), Heterocephalus glaber, is an unusual mammal that lives underground in eusocial colonies. NMRs show remarkable longevity and are resistant to cancer, neurodegeneration, and cardiovascular disease. The gut microbiome is known to modulate human health and disease; here, we investigate the microbiome of NMRs, comparing fecal samples from individuals over different social ranks and over a span of more than three decades. In contrast to a cohort of C57BL6/J mice, which showed extensive age-related changes, we found little difference in the microbiota of NMRs from different age cohorts. Only the archaea Methanomassiliicoccus intestinalis, which was present in the NMR gut but not the murine gut, showed an increased proportion with older age. Pregnant queens were found to have higher microbial diversity, potentially a consequence of their aggressive coprophagia. Overall, these findings provide a rich and dynamic picture of the NMR microbiome and starting points for future investigation.},
}
@article {pmid42012987,
year = {2026},
author = {Good, SD and Volkmann, ER and Basnayake, C and Ross, L},
title = {A New approach and conceptual model for understanding systemic sclerosis-associated gastrointestinal symptoms.},
journal = {Expert review of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1080/1744666X.2026.2663044},
pmid = {42012987},
issn = {1744-8409},
abstract = {INTRODUCTION: Our understanding of the pathogenesis of systemic sclerosis-associated gastrointestinal (SSc-GI) disease is limited. This has hindered progress in the management of SSc-GI disease as objective measures to assess extent of disease and monitor treatment response are lacking. We propose a conceptual model for understanding pathogenic mechanisms of SSc-GI symptoms. A multi-dimensional model of understanding the etiology of symptoms may enable an improved understanding of patients' symptom experience and opportunities for development of therapies.<br><br>AREAS COVERED: We reviewed literature from the past 5&#x2009;years pertaining to SSc-GI symptoms and their etiology. When gaps in data were identified, we evaluated research from general gastroenterology and inflammatory bowel disease. We describe evolving concepts of pathologic mechanisms of SSc-GI disease, including motility, the gut-brain axis, diet, the microbiome and pelvic floor dysfunction.<br><br>EXPERT OPINION: A broad understanding of factors that contribute to symptoms is necessary to understand the experience of SSc-GI disease and develop targeted therapies that modify the SSc-GI disease course. Due to a lack of objective clinical outcome measures in SSc-GI disease, qualitative research methodologies are essential for deepening our understanding of these patient experiences and developing new outcome measures to enable trials to establish an evidence-based approach to SSc-GI disease.},
}
@article {pmid42013360,
year = {2026},
author = {Zhang, Y and Dong, Q and Li, W},
title = {Incremental value of a gut microbiome score (M-score) for predicting stroke-associated pneumonia beyond the clinical A2DS2 score: A nested case-control study.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02907},
pmid = {42013360},
issn = {1588-2640},
abstract = {Stroke-associated pneumonia (SAP) is a major complication of acute ischemic stroke. The brain-gut-lung axis suggests that post-stroke gut dysbiosis may offer independent risk information beyond clinical scores like A2DS2. The aim of this study was to evaluate the incremental predictive value of early post-stroke gut microbiome biomarkers for SAP and to construct a simplified microbiome risk score (M-score). In a prospective nested case-control study, we identified 63 SAP cases from a cohort of 551 patients with acute ischemic stroke and stool samples were collected 24-72 h post-admission. Cases were matched 1:2 (age, sex) to 126 controls. Gut microbiota was profiled via 16S rRNA sequencing. Three differentially abundant genera (prevalence ≥20%, FDR q < 0.10) were used to construct an M-score via bootstrapped regression. Independent associations were assessed with conditional logistic regression. Incremental value over the A2DS2 score was evaluated using AUC, continuous net reclassification improvement (NRI), and the Brier score. SAP cases exhibited reduced α-diversity and distinct β-diversity (both P < 0.01). Cases had higher Enterococcus and Streptococcus and lower Faecalibacterium levels (all q < 0.05). The M-score was independently associated with SAP (adjusted OR per 1-SD: 1.76, 95% CI: 1.30-2.39, P = 0.001). Adding the M-score to A2DS2 significantly improved prediction: AUC increased from 0.76 to 0.84 (ΔAUC = 0.08, P = 0.009), NRI was 0.31 (95% CI: 0.12-0.51), and the Brier score decreased from 0.18 to 0.16. Results were robust in sensitivity analyses. A gut microbiome score based on three genera provides significant independent and incremental predictive value for SAP over the A2DS2 score, enabling more precise early risk stratification after stroke.},
}
@article {pmid42013465,
year = {2026},
author = {Ofori-Amanfo, K and Dustin, M and Lim, EL},
title = {Data Science at the Interface of Air Pollution and Lung Health: Toward Precision Health.},
journal = {Annual review of biomedical data science},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biodatasci-092724-061536},
pmid = {42013465},
issn = {2574-3414},
abstract = {Air pollution is a leading cause of death, commonly linked to respiratory diseases, such as asthma, chronic obstructive pulmonary disease, and lung cancer. With a view toward precision health, efforts have been made to ascertain the relationships between air pollution and molecular dysregulation to direct risk management and prevention of pollution-promoted respiratory diseases. To this end, there have been several analyses aimed at uncovering how air pollution drives disease through dysregulation of the methylome, transcriptome, metabolome, proteome, genome, and microbiome. Here we review these studies, assess their current limitations, and discuss their contributions to research at the interface of air pollution and lung health. We highlight how large-scale analyses have elucidated the role of air pollution in dysregulating genomic stability, inflammation, and apoptotic pathways to promote respiratory diseases. Finally, we summarize opportunities for future research that may be facilitated by ongoing improvements in exposure estimates and multiomic integration strategies.},
}
@article {pmid42013483,
year = {2026},
author = {Guo, X and Li, M and Ahmad, M and Liu, X and Zhang, S and Yu, Z and Zhao, Y and Sun, H and Zhang, Y},
title = {Microbiome and metabolomics provide insights into the metamorphosis and settlement in the jellyfish Aurelia coerulea inhibited by Bacillus pacificus.},
journal = {Marine pollution bulletin},
volume = {229},
number = {},
pages = {119760},
doi = {10.1016/j.marpolbul.2026.119760},
pmid = {42013483},
issn = {1879-3363},
abstract = {Jellyfish outbreaks threaten coastal ecosystems and demand urgent control strategies, the potential for microbial-based interventions remains largely unexplored even though the key role of microbiota in marine invertebrate development. Bacillus pacificus SG15 inhibits settlement and metamorphosis of Aurelia coerulea planulae, although the underlying mechanism remains unclear. Here, we employed a combination of co-culture experiments, high-throughput sequencing, and metabolomics analyses to elucidate these mechanisms. Our results indicated that strain SG15 inhibited planulae settlement and metamorphosis and induced developmental abnormalities. Inoculation with strain SG15 reduced the abundance of Neptuniibacter, a reported potential probiotic for jellyfish, and decreased metabolites critical for metamorphosis, including all-trans-4-Oxoretinoic acid, indole-3-acetamide and indole-3-carbinol. Functional analysis revealed that strain SG15 inoculation interfered with metabolic pathways related to calcium signaling, gap junction, and nervous system development. Additionally, polyp tissues exhibited an accumulation of L-tryptophan, L-phenylalanine, and L-leucine, alongside a marked decline in the tryptophan-derived metabolite indole-3-acetamide, suggesting impaired host metabolic capacity. These metabolic shifts showed a significant correlation with changes in the abundance of Bacillus, Neptuniibacter, Marivita, Ruegeria, and Sulfitobacter. Collectively, our findings revealed that strain SG15 disrupts key host metabolic functions by altering the microbial community, thereby depriving planulae of essential compounds required for settlement and metamorphosis, providing a foundation for novel strategies to mitigate jellyfish blooms and their ecological effects.},
}
@article {pmid42013659,
year = {2026},
author = {Teijeiro, M and De Antoni, GL and Golowczyc, MA and Pérez, PF},
title = {Impact of spray-dried Lactiplantibacillus plantarum CIDCA 83114 on a murine model of giardiasis.},
journal = {Revista Argentina de microbiologia},
volume = {58},
number = {3},
pages = {100721},
doi = {10.1016/j.ram.2026.100721},
pmid = {42013659},
issn = {0325-7541},
abstract = {This study investigates the efficacy of spray-dried Lactiplantibacillus plantarum CIDCA 83114 in a murine model of giardiasis. Mice (C57BL/6) were divided into four groups: control, Giardia-only, probiotic-only, and a combined (probiotic+Giardia, PG) group. Probiotic treatment started one week pre-infection with Giardia intestinalis H7 and continued throughout the study. Infection was monitored through trophozoite counts, intestinal histology, cytokine expression and microbiome analysis. Histology revealed that the administration of strain CIDCA 83114 prior to infection, increases villus/crypt ratios compared with control infected animals. In addition, trophozoite counts in the small intestine were lower in probiotic-treated mice than in infected control animals. Probiotic-treated infected mice showed significantly higher IL-10 expression than untreated controls. Expression of the IL-12 gene was diminished in animals administered with strain CIDCA 83114 (both infected and non-infected with Giardia). In addition, Giardia infection led to a decrease in IFN-γ expression, even when the probiotic-treated animals. Expression of TNF-α increased in the groups treated only with strain CIDCA 83114 and in infected animals. Notably, the PG group exhibited lower values of TNF-α expression, potentially due to the elevated IL-10 levels detected in this group. Dysbiosis associated with Giardia infection led to an increase in Epsilonproteobacteria and Clostridium. These changes were abrogated in the group that received the probiotic strain, which, as expected, showed an increase in Lactobacillaceae. This study demonstrates that spray-dried probiotic L. plantarum CIDCA 83114 has a positive impact on key aspects of Giardia infection, supporting its potential as a preventive or therapeutic strategy for giardiasis.},
}
@article {pmid42013709,
year = {2026},
author = {Pelko, T and Jemec Kokalj, A and Regvar, M and Dermastia, M and Vogel-Mikuš, K},
title = {When "biodegradable" is not benign: Microplastic-driven disruption of soil processes and plant-microbe interactions.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142138},
doi = {10.1016/j.jhazmat.2026.142138},
pmid = {42013709},
issn = {1873-3336},
abstract = {The increasing use of biodegradable plastics (BPs) as alternatives to conventional plastics (CPs) is leading to the accumulation of biodegradable microplastics (BMPs) in terrestrial environments. Contrary to assumptions of rapid degradation, BMPs can persist in soil long enough to interact with key biological processes. This review advances the field by proposing a mechanistic framework linking BMP aging and degradation, soil physicochemical transformations, plastisphere assembly, rhizosphere interactions, and plant responses, and by critically evaluating the sources of inconsistency across studies. We show that divergent effects of BMPs can be best explained by four interacting determinants: polymer chemistry and additive composition, aging-driven surface transformations, soil physicochemical properties, and rhizosphere processes including plant-mediated effects. Through these coupled pathways, BMPs can alter aggregation, pore architecture, pH, enzyme activity, and carbon and nutrient cycling, thereby reshaping the soil environment in which microorganisms and roots interact. BMP surfaces can also act as dynamic microbial niches that promote biofilm formation, shift microbial community composition and function, and under certain conditions may facilitate pollutant transport, pathogen persistence, and horizontal gene transfer. Plant responses to BMPs are predominantly indirect and emerge from rhizosphere-mediated processes, which helps explain the wide variability in reported plant responses, ranging from subtle metabolic changes to pronounced growth inhibition. However, current evidence is constrained by short-term studies and insufficient consideration of aged materials. Biodegradability should therefore not be equated with low ecological risk in soils. Progress in this field requires integrative approaches linking BMP properties, plastisphere dynamics, and plant-soil interactions over time.},
}
@article {pmid42013750,
year = {2026},
author = {Ruíz-Valdiviezo, VM and Hernández-Lira, KV and Silva-Flores, M and Gutiérrez-Sarmiento, W and Ovando-Ovando, CI and Peña-Ocaña, BA and Jasso-Chávez, R},
title = {Biochemical and molecular mechanisms of resilience in the response of prokaryotes of an active volcano to cadmium-induced stress.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128529},
doi = {10.1016/j.micres.2026.128529},
pmid = {42013750},
issn = {1618-0623},
abstract = {The crater lake of the active volcano "El Chichón" in Mexico, represents an ecosystem characterized by changing conditions of salinity, acidity, temperature, and the concentration of different heavy metals, posing significant challenges to the abundance and diversity of microorganisms. In this study, anaerobic mesophilic and hyperthermophilic prokaryotic microbiomes isolated from the volcano-lake were evaluated to elucidate the molecular and biochemical mechanisms involved in Cd[2+] bioremoval. Cultures consumed actively carbohydrates, triacetylglycerol, acetate and methanol; the hyperthermophilic microbiome produced 50% more biomass than mesophiles at the end of the growth curve; however, the presence of Cd[2+] stimulated the biomass and methane production in the mesophilic microbiome. The relative abundance of the 16S rRNA metabarcoding analysis showed dominance of Firmicutes and Euryarchaeota in both microbiomes. The constitutive synthesis of biofilm and the overproduction of polyphosphates and thiol group molecules were protection mechanisms against Cd[2+] toxicity. Such mechanisms allowed 68-74% of Cd[2+] bioremoval (biosorption plus accumulation) at concentrations up to 500 µM CdCl2. Data suggested that the prokaryotic microbiome isolated from the extreme environment of the "El Chichón" volcano is forming a complex metabolic resilient network involving methanogenesis with phosphate and sulfur metabolism that is capable of thriving under extreme conditions of pH, temperature, and the ability for the Cd[2+] removal. This work provides for the first time, information on the mechanisms of tolerance to poly-extreme conditions; moreover, microbiomes studied here may be a promising strategy for biotechnological applications under extreme conditions.},
}
@article {pmid42013836,
year = {2026},
author = {Steinberg, R and Pust, MM and Arias-Rojas, A and Pishchany, G and Ramsey, KA and Kieninger, E and Moeller, A and Casaulta, C and Hilty, M and Latzin, P and , and , and Korten, I and Xavier, RJ},
title = {An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.019},
pmid = {42013836},
issn = {1934-6069},
abstract = {Functional studies of how early-life interventions shape the airway microbiome remain scarce. Here, we performed metagenomic sequencing of 704 longitudinal nasal swabs from infants with and without cystic fibrosis (CF) to construct and characterize a non-redundant gene atlas of the infant nasal microbiome. We aimed to determine how the nasal microbiome is perturbed by early therapies, as CF is commonly treated with inhaled hypertonic saline to improve mucociliary clearance. We found functional and compositional microbiome changes linked to inhalation therapy, including an expansion of salt-associated transporter genes and a community shift toward CF-associated microbial opportunists, including Haemophilus influenzae and fungi, carrying the identified salt-associated transporter genes with high sequence and structural identity. Hypertonic, compared with isotonic, saline accelerates H. influenzae growth and induces efflux pumps linked to antibiotic tolerance in vitro. This study establishes a reference framework for functional airway microbiome research, enabling the examination of therapeutic perturbations and their impact on microbial adaptation.},
}
@article {pmid42013837,
year = {2026},
author = {Zheng, M and Yan, H and Hao, W and An, H and Chen, X and Wu, Q and Ge, X and Ye, H and Zhou, M and Zhou, G and Yang, X and Hu, M and Zhang, P and Pan, W and Tang, R and Zheng, K and Huang, XF and Yu, Y},
title = {Gut microbiota-derived ergothioneine alleviates antipsychotic-induced synaptic and cognitive impairments.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.020},
pmid = {42013837},
issn = {1934-6069},
abstract = {Chronic antipsychotic use is associated with neuronal damage and cognitive impairment, with the gut microbiome increasingly implicated. However, the specific microbial metabolites and mechanisms involved remain unknown. Here, we demonstrate that chronic olanzapine treatment induces gut microbial dysbiosis, compromises intestinal barrier integrity, and causes cognitive deficits in mice. Multi-omics analyses reveal profound depletion of the microbiota-associated metabolite ergothioneine in blood and brain, a finding validated in the blood of olanzapine-treated patients and risperidone- and clozapine-treated mice. This deficiency correlates with a loss of ergothioneine-producing bacteria (Cyanobacteria and subordinate taxa). Fecal microbiota transplantation from olanzapine-treated mice confers cognitive impairment, while ergothioneine supplementation mitigates it. Mechanistically, ergothioneine attenuates hippocampal oxidative stress and inhibits the redox-sensitive phosphatase protein tyrosine phosphatase 1B (PTP1B). Furthermore, hippocampal neuronal-specific PTP1B deletion abolishes olanzapine-induced synaptic and cognitive deficits. Our findings identify depletion of microbiota-derived ergothioneine as a mechanism underlying antipsychotic-induced cognitive impairment, highlighting therapeutic strategies to mitigate this side effect.},
}
@article {pmid42013847,
year = {2026},
author = {Shan, Y and Huang, Y and Lee, A and Elmorsi, RM and Phan, T and Chaudhury, I and Corbiere, T and Collins, LB and Hirsch, EB and Weinberg, BA and Johnson, JM and Antonarakis, ES and Lou, E and Huang, RS},
title = {Sex-biased intratumoral microbiome influences tumor molecular and immune landscape and disease outcomes.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102757},
doi = {10.1016/j.xcrm.2026.102757},
pmid = {42013847},
issn = {2666-3791},
abstract = {The intratumoral microbiome is increasingly recognized as a regulator of cancer biology, yet sex-specific patterns and their relevance to cancer disparities remain poorly understood. We perform a multi-kingdom analysis of more than 5,000 tumors from seven datasets to identify sex-differential microbial taxa across aerodigestive and gastrointestinal cancers. We identify and validate 22 taxa with consistent sex-biased abundance, including in real-world cohort. These microbes show cancer-type- and microbe-specific associations with tumor transcriptomes, oncogenic pathways, and immune cell infiltration. Female-enriched microbes are linked to increased estrogen signaling and interferon responses, whereas male-enriched taxa show opposing patterns. In gastric cancer, intratumoral Epstein-Barr virus is enriched in males and associated with higher CD8[+] T cell infiltration and improved survival. Functional co-culture experiments demonstrate that sex-biased microbes modulate chemotherapy sensitivity. Together, these findings reveal a sex-biased intratumoral microbiome axis that shapes tumor phenotypes and disease outcomes, highlighting opportunities for microbiota-guided, sex-aware approaches in oncology.},
}
@article {pmid42013850,
year = {2026},
author = {Qin, Y and Zhang, YX and Liu, LP and Xie, YH and Ma, XY and Hao, Y and Zhao, LC and Dong, JJ and He, Y and Sun, K and Zhong, H and Zhu, S and Liu, M and Fang, JY and Zhou, CB},
title = {Distinct signatures in the human gut and oral microbiomes of gastric cancer.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102761},
doi = {10.1016/j.xcrm.2026.102761},
pmid = {42013850},
issn = {2666-3791},
abstract = {Microbiome dysbiosis is increasingly recognized as a hallmark of gastric cancer (GC). Here, we analyzed gut and oral shotgun metagenomic data from 317 individuals across two independent cohorts, with validation in a Harbin cohort. We identify 20 oral-gut shared species enriched in the gut of GC, predominantly lactic acid bacteria (LAB). While most gut microbial markers are abundant in saliva, none are significantly altered in GC. Strain-level analysis of 87 matched saliva-stool metagenomes confirms oral-gut transmission of Streptococcus species. GC-enriched LAB form robust co-abundance networks in oral and gut microbiomes, suggesting synergistic interactions. Functional analysis reveals enriched lactate fermentation pathways in GC stool, aligning with LAB dominance and previous findings on gastric microbiota. Moreover, microbiome-based classifiers achieve high predictive accuracy (area under receiver operating characteristic curve [AUROC] = 0.85 for stool, 0.87 for saliva) for GC diagnosis, highlighting translational potential. Collectively, these findings underscore the critical role of the oral-gut microbiome axis in GC.},
}
@article {pmid42013851,
year = {2026},
author = {Wang, Y and Olsen, LK and Jiao, F and Wang, C and Jiang, KX and Dou, Y and Hu, Y and Jiao, L and Chen, W and Elizarraras, JM and Khare, P and Yu, N and Zhu, H and Chen, L and Lih, TM and Eser, P&#xd6; and Martins Rodrigues, F and Shi, Z and Zhang, C and Yu, C and Heiman, DI and Liao, Y and Shafer, PW and Choi, S and Choi, JM and Savage, SR and Jaehnig, EJ and Lei, JT and Sun, Y and Peng, CW and Sun, Z and Morenkov, P and Zhang, K and Geffen, Y and Hess, J and Kumar-Sinha, C and Mani, DR and Ding, L and Getz, G and Li, QK and Omenn, GS and Le, A and Hostetter, G and Newton, CJ and Cai, S and Ketchum, KA and Robles, AI and Mesri, M and Minoo, P and Camargo, MC and An, E and Hruban, RH and Liu, Z and Thiagarajan, M and Dohlman, AB and Jin, RU and Huang, L and Chan, DW and Zhang, H and Zhang, B and , },
title = {A 15-layer multi-omics analysis of gastric cancer ecotypes provides therapeutic insights.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102756},
doi = {10.1016/j.xcrm.2026.102756},
pmid = {42013851},
issn = {2666-3791},
abstract = {Gastric cancer is marked by profound molecular and microenvironmental heterogeneity that limits therapeutic progress. Here, we present a 15-layer multi-omics atlas that integrates genomics, epigenomics, transcriptomics, proteomics, multiple post-translational modifications (PTMs), protein-protein interactions, metabolomics, and microbiome profiles from 159 primary gastric adenocarcinomas and 30 matched normal adjacent tissues. Using cell-state deconvolution, we define tumor ecotypes that refine genomic and histological subtypes by capturing distinct tumor microenvironment architectures linked to clinical outcomes and potential associations with immunotherapy response. Multi-omics integration prioritizes genomic and epigenomic aberrations and their associated vulnerabilities; defines ecotype-specific transcriptional programs, signaling pathways, PTMs, protein interaction networks, and metabolic regulation; and identifies microbiome features linked to ecotypes and resistance pathways. We further prioritize ecotype-, genomic subtype-, and cell type-specific targetable proteins using proteomic and PTM analyses within a tumor microenvironment context. This comprehensive atlas provides a systems-level blueprint for decoding gastric cancer heterogeneity and advancing precision oncology.},
}
@article {pmid42013857,
year = {2026},
author = {Schulze, L and Stahl, J and Knoedlseder, NJ and Krauss, S and Harbig, T and Nieselt, K and Brueggemann, H and Krismer, B and Peschel, A},
title = {Genetic modification of intractable bacterial clones by heat shock-facilitated phage transduction.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101406},
doi = {10.1016/j.crmeth.2026.101406},
pmid = {42013857},
issn = {2667-2375},
abstract = {Increasing recognition of commensal bacteria as essential for microbiome integrity and pathogen exclusion underscores the urgency of molecularly characterizing commensal interactions. However, many commensals cannot be transformed using available methodologies due to barriers imposed by restriction-modification (RM) systems. We developed a method for introducing plasmid DNA into otherwise intractable non-Staphylococcus aureus (NAS) staphylococci, important commensals of the human nasal and skin microbiomes, via phage transduction. We demonstrate that exposing recipient bacteria to a pulse of elevated temperature prior to phage exposure renders NAS isolates effectively and transiently amenable to transduction. Transduction of NAS mutants lacking RM systems did not respond to heat shock, indicating that transient deactivation of RM enzymes enables transduction. Our method also facilitates the transduction of representatives from other Bacillota and Actinomycetota taxa, suggesting that this approach will support research on diverse bacterial groups across a range of ecosystems.},
}
@article {pmid41874457,
year = {2026},
author = {Mohr, AE and Berryman, CE and Harris, MN and Lawrence, AB and Chakraborty, N and Campbell, R and Dimitrov, GI and Gautam, A and Hammamieh, R and Lieberman, HR and Rood, JC and Pasiakos, SM and Karl, JP},
title = {Testosterone administration partially modulates gut microbiota responses to severe energy deficit.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {330},
number = {5},
pages = {E606-E626},
doi = {10.1152/ajpendo.00291.2025},
pmid = {41874457},
issn = {1522-1555},
support = {W81XWH-14-1-0335//DOD | OSD | Defense Technical Information Center (ADD)/ ; W81XWH-17-2-0026//DOD | OSD | Defense Technical Information Center (ADD)/ ; Joint Program Committee-5//Military Operational Medicine Research Program (MOMRP)/ ; //DOE | Oak Ridge Institute for Science and Education (ORISE)/ ; T32DK137525//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; *Testosterone/pharmacology/analogs &amp; derivatives/administration &amp; dosage ; *Energy Metabolism/drug effects ; Adult ; Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; Young Adult ; Exercise/physiology ; *Androgens/pharmacology/administration &amp; dosage ; Energy Intake/drug effects ; Double-Blind Method ; },
abstract = {Severe diet- and exercise-induced energy deficit (SED) suppresses androgen production in healthy men, altering metabolism and driving muscle loss. The gut microbiota modulates host metabolism, yet the community's response to SED and any role of androgen hormones are unclear. Herein, healthy, physically active men were randomized to receive 200 mg/wk testosterone enanthate (n = 24) or placebo (n = 26) during a 28-day residential intervention that restricted energy intake and increased energy expenditure inducing a ∼2,000 kcal/day SED. Multiomic analyses revealed altered gut microbiota composition, reduced fecal short-chain fatty acids (SCFA), and shifts in bacterial metabolic pathways toward lipid utilization and mucin degradation during SED, suggesting adverse effects of SED on gut microbiota metabolic functions. Testosterone administration preserved certain SCFA-producing taxa and bioenergetic pathways without fully counteracting the effects of SED indicating a limited but potentially important interplay between androgen status and the gut microbiota under conditions of SED.NEW &amp; NOTEWORTHY This study is the first to demonstrate that testosterone administration partially preserves gut microbiota composition and metabolic function during severe energy deficit in healthy men. Using a multiomic approach, we show that testosterone modulates short-chain fatty acid-producing taxa and microbial pathways linked to host energy metabolism. These findings reveal a novel role for androgens in shaping host-microbiome interactions during catabolic stress and may inform strategies to maintain metabolic resilience.},
}
@article {pmid41959403,
year = {2026},
author = {Maier, J and Gin, C and Rabasco, J and Bass, A and Spencer, W and Duerkop, BA and Callahan, B and Kleiner, M},
title = {TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41959403},
issn = {2692-8205},
support = {R01 AI171046/AI/NIAID NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Transduction is a form of horizontal gene transfer in which bacterial DNA is packaged and transferred by virus-like particles (VLPs). Transductomics is a sequencing-based method used to detect DNA carried by VLPs. During transductomics analysis, reads from a sample's ultra-purified VLPs are mapped to metagenomic contigs assembled from the same sample's whole-community. The read mapping produces coverage patterns that require a time-consuming manual inspection and classification process which makes the method's use unfeasible for datasets with many samples.<br><br>RESULTS: We developed a novel algorithm, TrIdent (Transduction Identification), that uses pattern-matching to automate the transductomics data analysis and that is available as an R package (https://jlmaier12.github.io/TrIdent/). There is no software equivalent to TrIdent so we compared TrIdent's classifications of transductomics datasets to classifications made by human classifiers. TrIdent's classifications were generally comparable to the manual classifications on a previously generated, manually classified transductomics dataset. When applied to newly generated transductomics data from the murine microbiota, TrIdent agreed with two independent human classifiers as much as the two independent human classifications agreed with each other. TrIdent classified transductomics datasets in a fraction of the time needed by human classifiers, and the classifications produced by TrIdent are fully reproducible. We used TrIdent to explore three murine gut transductomes and found that bacterial DNA associated with the Oscillospiraceae and Turicibacteraceae families was highly enriched in the DNA packaged by VLPs as compared to the whole community metagenomes.<br><br>CONCLUSIONS: The TrIdent software is a more accessible, more efficient, and more reproducible alternative to the manual inspection of read coverage patterns previously required for transductomics data analysis. To demonstrate the application of TrIdent, we analyzed transductomics datasets from murine fecal pellets and showed that specific low abundance bacterial families appear to be heavily involved in transduction.},
}
@article {pmid42000489,
year = {2026},
author = {Della-Negra, O and Bru-Adan, V and Patureau, D and Ait-Mouheb, N and Wéry, N},
title = {Tracking antibiotic resistance genes and microbiome shifts under reclaimed wastewater irrigation: Root-associated selective modulation.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129707},
doi = {10.1016/j.jenvman.2026.129707},
pmid = {42000489},
issn = {1095-8630},
abstract = {The reuse of treated wastewater (TWW) for crop irrigation reduces pressure on freshwater resources but may also disseminate antimicrobial resistance (AMR) through the presence of antibiotics, resistant bacteria and antibiotic resistant genes (ARGs). While many studies have examined the impact of water quality on dissemination of AMR in soils, the role of plants in filtering or accumulating AMR within the soil-plant continuum remains unclear. Here, we investigated the influence of irrigation water quality, plant species, and microbial compartments (soil, rhizosphere, roots) on bacterial communities and selected ARGs under controlled mesocosm conditions. Lettuce and leek were irrigated over two consecutive years with drinking water (DW), TWW, or raw wastewater (RWW). We monitored the abundance of ARGs sul1, ermB, and intI1 and characterized bacterial community composition by 16S rRNA sequencing. Soil microbiomes were influenced by water type and probably irrigation volume, and bacterial enrichment associated with DW, TWW, and RWW were identified. Plant-specific effects on soil microbiome were observed but were minor compared to the effect of water quality. Root microbiomes appeared more resilient than soils, as most taxa enriched in TWW- or RWW-irrigated soils were less or not amplified in roots, suggesting a potential barrier effect or at least selective processes at the root interface. Only Tahibacter and Rhodanobacteraceae increased in roots, while RWW irrigation also promoted the growth of the plant-pathogen Rhizorhapis. ARGs rose significantly in soils under TWW and RWW irrigation, with distinct year-to-year dynamics, but these shifts were not observed in root communities. Overall, our results indicate that root-associated compartments may contribute to modulate the dissemination of sul1, ermB, and intI1 ARGs in the plants irrigated with TWW.},
}
@article {pmid42000492,
year = {2026},
author = {Zhao, X and Zhang, S and Lai, X and Shi, D and Yang, C and Yu, H},
title = {Natural recovery trajectory of soil chemistry and microbiome after low-temperature thermal desorption remediation.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129700},
doi = {10.1016/j.jenvman.2026.129700},
pmid = {42000492},
issn = {1095-8630},
abstract = {Urban soil contamination from historical industrial activities hinders sustainable redevelopment. Low-temperature thermal desorption is a common soil remediation strategy, offering efficient removal of volatile pollutants while limiting soil disruption. However, its ecological legacy and the potential for natural microbial recovery remain poorly understood. We tracked chemical and microbial recovery in an isolated urban brownfield for two years following remediation. Soil chemistry improved naturally over time: pH decreased from 9.1 to 8.2, total organic carbon rose from 2.3 to 5.4 g kg[-1], and carbon-to-nitrogen ratio increased from year 1 to year 2 post-remediation, although all remained below nearby urban greenspace soil (city park) soil levels. In contrast, salinity emerged as a new stressor in year 2, with electrical conductivity rising to 1.13 mS cm[-1], higher than both year 1 (0.41 mS cm[-1]) and the park (0.21 mS cm[-1]), likely due to the gradual weathering of quicklime additives applied during the thermal desorption process to enhance organic pollutant volatilization. Microbial abundance, measured by qPCR of total 16S rRNA genes, remained three orders of magnitude lower in remediated soils than park soils, but the microbial communities increased in diversity and network complexity. Functional annotations revealed a trajectory from mainly chemoheterotrophy in year 1 to a broader suite of metabolisms in year 2, though still distinct from park soils with substantially more nitrifying taxa. Collectively, these findings show that although qPCR-based microbial abundance suggests non appreciable recovery at first glance, the underlying communities exhibited clear post-remediation restructuring over two years. Persistent salinity and carbon limitation remain barriers, offering opportunities for targeted interventions-organic carbon replenishment, salinity management, and nitrogen-cycling taxa stimulation-to accelerate convergence toward resilient, multifunctional urban soils.},
}
@article {pmid42000498,
year = {2026},
author = {Wu, F and Deng, Y and Wu, Q and Chen, H and Mu, J and Zhang, Y and Meng, W and Li, N and Xie, L},
title = {Heteroaggregation with microalgae masks charge-dependent accumulation but amplifies charge-dependent toxicity of nanoplastics in mussels.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142121},
doi = {10.1016/j.jhazmat.2026.142121},
pmid = {42000498},
issn = {1873-3336},
abstract = {In natural waters, nanoplastics (NPLs) often form heteroaggregates (HAs) with microalgae. Despite surface charge being a primary driver of NPL behavior, its role in governing HA toxicokinetics and impacts in bivalves remains largely unknown. Here, the effects of positively charged polystyrene NPLs (NPL+), their negative charged counterparts (NPL-), and the pre-formed HAs (HA+ and HA-) with the microalga Chlorella salina were evaluated in the green mussel (Perna viridis) during a 21-day exposure followed by 7-day elimination. HA+ and HA- enhanced NPL uptake in digestive gland and peripheral tissues, with uptake rate constants 1.5 - 4.0 times those of NPLs alone. Although 70 - 95% of accumulated NPLs were eliminated within 24 h, higher initial burdens under HA+ and HA- produced greater residual levels. NPL+ showed stronger uptake than NPL- due to greater electrostatic affinity with negatively charged epithelial surfaces. However, this charge-related uptake advantage was attenuated in HAs, concurrent with algal-like ζ-potentials of the heteroaggregates. Biological responses paralleled toxicokinetics, with HA+ inducing the strongest effects, including hemocyte dysfunction, oxidative stress, and fungal community disruption. Overall, HAs and surface charge jointly regulated NPL accumulation and toxicity in P. viridis, highlighting the need for ecological risk assessments to consider charge effects and HA formation to avoid underestimating NPLs hazards in filter-feeding bivalves.},
}
@article {pmid42000502,
year = {2026},
author = {Wang, Z and Wang, P and Yin, B and Gao, R and Dai, P and Lin, X and Sun, C},
title = {Enantioselective alteration of soil bacterial community assembly and keystone taxa under chiral triadimefon stress.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142063},
doi = {10.1016/j.jhazmat.2026.142063},
pmid = {42000502},
issn = {1873-3336},
abstract = {Triadimefon, a representative chiral triazole fungicide, is ubiquitously applied as a racemic mixture and exhibits negative effects on microbiome in agroecosystems. However, its enantioselective effects on soil microbial community structure and assembly processes remain undefined. In this study, we investigated how bacteriome assembly responds to triadimefon at the enantiomeric level. It was found that the R- and S-enantiomers exerted distinct effects on bacterial diversity and community structure. Furthermore, deterministic processes dominated bacterial community assembly under chiral triadimefon. Co-occurrence network analysis revealed a distinct shift in microbial network across the chiral triadimefon treatments, revealing enantiomeric disparity in network organization to different enantiomers. Importantly, we identified 12 and 6 distinct key amplicon sequence variants (ASVs), respectively, selected by R- and S-enantiomers. These stereoselective key taxa are closely associated with bacterial community recombination trajectories. Overall, our research provides novel insights into understanding the enantioselective response of microbiome under chiral triadimefon and ideal targets to manipulate for contaminated situations. SYNOPSIS: Soil microbial community assembly exhibited striking differences in response to the R- and S-enantiomers of triadimefon, which are governed by the stereospecific selection imposed on the keystone taxa.},
}
@article {pmid42000515,
year = {2026},
author = {Qiu, Y and Yang, Y and Li, N and Li, X and Lu, Z and Zhou, Z and Feng, S and Liu, Y},
title = {Secondary chlorination enhanced the role of pipe materials in shaping chlorine-resistant microbiome and antibiotic resistome in secondary water supply systems.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142114},
doi = {10.1016/j.jhazmat.2026.142114},
pmid = {42000515},
issn = {1873-3336},
abstract = {Secondary chlorination is often strategically applied in secondary water supply systems (SWSSs) with insufficient disinfectant residuals to suppress microbial regrowth. However, the associated risks posed by chlorine-resistant bacteria (CRB) and antibiotic resistance genes (ARGs) remain unclear. Herein, simulated SWSSs with different pipe materials and chlorine levels were operated for 220 days. Biomass in biofilms and bulk water was markedly reduced following chlorination, and extracellular polymeric substances responded more strongly in stainless steel (SS) pipes, with polysaccharides (70.28%) exhibiting a greater reduction than proteins (37.44%). Meanwhile, chlorination reduced bacterial diversity and reshaped community structure, boosting the contributions of biofilm and particulate phases to waterborne bacteria by 11.47%-15.60% and 17.52%-22.82%, respectively. Chlorination promoted the CRB enrichment (e.g., Nevskia and Sphingomonas), with higher relative abundance in polyvinyl chloride (PVC) pipes and more taxa in SS pipes. The decline in Legionella mitigated potentially pathogenic risks, particularly in chlorinated PVC pipes, despite nine of 13 potential pathogens being chlorine-resistant. Moreover, chlorination generally reduced the ARG absolute abundance but increased their relative abundance, with sulfonamide- and multidrug-ARGs being predominant. Regarding the ARG bacterial hosts, potential pathogens (e.g., Pseudomonas and Enterobacter) posed the highest risk, followed by non-pathogenic CRB (e.g., Herbaspirillum and Sediminibacterium) and chlorine-sensitive bacteria (e.g., Runella and Isosphaera). Vertical gene transfer dominated ARG transmission, while horizontal gene transfer occurred more readily in the water phase and was promoted in chlorinated PVC pipes. These findings provide novel insights into the microbial risk and antibiotic resistome, and may guide pipe material selection and disinfection optimization within SWSSs.},
}
@article {pmid42000726,
year = {2026},
author = {Zhou, X and Zhou, D and Pu, Y and Kim, H and Sun, Z and Qi, W and Jin, J and Zhang, W and Xia, M and Wang, C and Hong, S and Nguyen, LH and Jiao, N and Zheng, Y and Liu, T},
title = {Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71981-0},
pmid = {42000726},
issn = {2041-1723},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly linked to gut microbial dysbiosis, but most studies have focused on bacteria, neglecting viruses and fungi, and their interactions. Here we show that MASLD is characterized by coordinated disruption of bacterial, viral and fungal communities and by a disturbed phage-bacteria-metabolite axis associated with disease-related bile acid changes. Integrating shotgun metagenomics, fungal ITS2 sequencing, fecal metabolomics and clinical profiling in 210 patients with MASLD and 210 age- and gender-matched healthy controls, we find reduced microbial diversity and extensive remodeling of cross-kingdom ecological networks in MASLD. Ruminococcus gnavus emerges as an enriched central hub, while Faecalibacterium prausnitzii and its associated bacteriophages are depleted. Phage-host analyses further reveal reduced lytic activity against R. gnavus and loss of sulfur amino acid metabolism-related auxiliary metabolic genes, which may impair F. prausnitzii fitness. Diminished phage control may facilitate R. gnavus expansion, alongside increased fecal isodeoxycholic acid, a secondary bile acid implicated in hepatic steatosis. A diagnostic classifier integrating bacterial and viral features with clinical parameters distinguish MASLD from controls in our cohort and maintain predictive performance in two external datasets. Together, these findings uncover a disrupted phage-bacteria-metabolite axis in MASLD and provide a multi-kingdom framework for non-invasive biomarker discovery and microbiome-targeted therapies.},
}
@article {pmid42000796,
year = {2026},
author = {Xu, P and Chen, J and Lu, X and Luo, H},
title = {Exploring the characteristics of gut microbiome changes in lung cancer patients and healthy controls.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48560-w},
pmid = {42000796},
issn = {2045-2322},
abstract = {Lung cancer is among the most prevalent and lethal malignant neoplasms worldwide. Although the role of the pulmonary microbiome in the pathogenesis of lung cancer has been examined, the structure, diversity, and composition of the gut microbiome in lung cancer remain largely unclear. The present study is chiefly concerned with the analysis of the characteristics and alterations of the gut microbiome in lung cancer patients and healthy individuals, and with the exploration of potential characteristic gut microbiome in lung cancer patients. Stool samples were collected from 40 patients with lung cancer and 20 healthy controls at the Lung Cancer Center of West China Hospital, Sichuan University. The samples were analysed using 16S rRNA gene amplicon sequencing to investigate differences in the relative and absolute abundance, diversity, and functionality of the gut microbiome between the two groups. The predominant gut microbiome communities in lung cancer patients and healthy controls were found to comprise Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. The F/B (Firmicutes/Bacteroidetes) ratio in the lung cancer group (0.73) was lower than that in the healthy control group (0.96). We found that there was no significant difference in α-diversity between LC patients and the control group (p > 0.05), whereas β-diversity of the gut microbiome revealed differences in microbial community structure between the patient and control groups (stress < 0.2). The healthy controls exhibited higher abundances of Bacteroidetes and Firmicutes as dominant bacterial groups, whereas the characteristic bacterial groups in lung cancer patients were the Ruminococcus_gnavus_group and the Prevotellaceae NK3B31 group. Studies have demonstrated that the gut microbiome of patients with lung cancer patients undergoes changes, and characteristic gut microbiome profiles may serve as potential diagnostic markers for lung cancer. Furthermore, we have revealed that impairments in normal gut microbiome function may be associated with the development and progression of lung cancer, providing valuable insights for the early prevention, diagnosis, and targeted intervention of lung cancer.},
}
@article {pmid42001039,
year = {2026},
author = {Li, S and White, JF and Zhai, Y and Li, X and Wang, K},
title = {Study on the diversity, structure, and function of endophytic bacteria in seeds of genuine medicinal plants in gansu province.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08767-5},
pmid = {42001039},
issn = {1471-2229},
support = {25YFFA043//Gansu Provincial Key Research and Development Program/ ; },
}
@article {pmid42001079,
year = {2026},
author = {Yang, Y and Kang, C and Pang, R and Huang, S and He, X and Gou, X and Yang, Y and Yan, Y and Ma, X},
title = {Dihydromyricetin exerts neuroprotective effects in acute spinal cord injury by inhibiting NLRP3/Caspase-1 inflammasome through gut microbiome modeling.},
journal = {Journal of inflammation (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12950-026-00499-5},
pmid = {42001079},
issn = {1476-9255},
support = {2024060//Chengdu Municipal Health Commission Medical Research Project/ ; 25MSZX488//Sichuan Provincial Administration of Traditional Chinese Medicine Research Project/ ; },
}
@article {pmid42001152,
year = {2026},
author = {Leroy, M and Cyriaque, V and Rattei, T and Laurion, I and Comte, J},
title = {Microbiome and plasmidome shifts drive carbon, nitrogen, and greenhouse gas dynamics within transitioning permafrost.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00892-w},
pmid = {42001152},
issn = {2524-6372},
support = {2021-PR-284297//Fonds de recherche du Qu&#xe9;bec - Nature et technologie/ ; RGPIN-2020-06876//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; RGPIN-2020-06874//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; 2021-PR-284297//Fonds de recherche du Qu&#xe9;bec - Nature et technologies/ ; },
abstract = {Thermokarst lakes contribute to greenhouse gas emissions but often experience constraints on available nitrogen. However, the interactions between carbon and nitrogen cycles in these systems, especially along the terrestrial-aquatic continuum, remain poorly understood. The increased soil-water connectivity in those systems affects organic matter processing, nutrient availability, and microbial transport. In Nunavik (Quebec, Canada), we sampled along a transect from a palsa (permafrost remnant) through an emerging thermokarst lake to peatland soils and mature lake. Using hybrid metagenome co-assemblies with gene-, plasmid-, and genome-centric approaches, we explored key biogeochemical cycles and the role of plasmids in microbial adaptation along the transect. Gene annotation, metagenome-assembled genome (MAG) reconstruction, and network analysis revealed a shift from potential for anaerobic ammonium oxidation (anammox) in palsa and emerging lake to potential for nitrification in mature lake. Potential for methanogenesis transitions from hydrogenotrophic in the palsa to methylotrophic in lakes, likely driven by a bacterial consortium degrading aromatic, peat-derived compounds. Sediments may support methane production via both hydrogenotrophic and acetoclastic potential for methanogenesis, partially fueled by the action of polysaccharide lyases. Anaerobic methane oxidation (AOM) potential seems important in both peat and the mature lake; and can be coupled with nitrification and sulfate-reducing partners through extracellular electron transfer, with cytochromes playing a central role. Notably, plasmidome shifts preceded metagenomic changes, especially in genes related to carbon and methane cycling, suggesting a role for plasmids in microbial adaptation to permafrost thaw. These findings highlight the complex microbial and plasmid dynamics that drive carbon, nitrogen, and greenhouse gas cycles in permafrost ecosystems.},
}
@article {pmid42001319,
year = {2026},
author = {Romandini, M and Hajishengallis, G and Curtis, M and Baima, G},
title = {Periodontal Medicine Rewired: Mechanisms Linking Periodontitis to Systemic Diseases.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70099},
pmid = {42001319},
issn = {1600-0765},
abstract = {Periodontitis is now recognized not merely as a localized oral condition but as a systemic disease linked to over 70 communicable and non-communicable conditions. This Review explores the key mechanistic pathways-or "gum-shots"-underpinning the systemic impact of periodontitis. Seven interwoven mechanisms are identified. The first, microbial translocation, involves oral pathobionts and virulence factors breaching anatomical barriers and gaining systemic access via hematological, respiratory, and enteral routes, contributing to tissue damage at extra-oral sites. The second, systemic (meta)inflammation, implicates both the spillover of inflammatory mediators from periodontal tissues into circulation and the immune response to translocated pathogens, fueling pro-inflammatory processes. The third, maladaptive myelopoiesis, involves the periodontitis-associated maladaptive trained immunity and aging-related clonal hematopoiesis of indeterminate potential in the bone marrow, leading to myeloid cells with heightened proinflammatory potential. The fourth, immune players trafficking, centers on the systemic repercussions of periodontally generated autoantibodies, translocated orally primed inflammatory cells, and other local immune events. The fifth, masticatory dysfunction-mediated dietary alterations, involves compromised chewing efficiency that alters dietary intake, resulting in nutritional and metabolic imbalances. The sixth, functional dysregulation of the oral microbiome, describes how periodontitis alters the metabolic activity of this densely populated microbial "superorganism", with downstream effects on both oral and systemic physiology. The final mechanism, shared underlying vulnerabilities, refers to background entities-such as biological aging, oxidative stress, psychosocial stress, (epi)genetic predispositions, certain viral infections, and potentially other as-yet-unknown contributors-that drive multi-morbidity, including periodontitis. By dissecting these interconnected pathways, this critical Review challenges the traditional dichotomy of direct versus indirect mechanisms, revealing a more intricate and dynamic interplay.},
}
@article {pmid42001402,
year = {2026},
author = {Boroumand, B and Jaberi, A and Zamani, G and Zandi, E and Zare, F and Vahedinezhad, M and Abdollahi, E and KarkonShayan, S and GhazanfarAhari, S and Sattar, M},
title = {Therapeutic Remodeling of the Gut Microbiome as a Strategy to Restore Immune Tolerance in Autoimmunity.},
journal = {MicrobiologyOpen},
volume = {15},
number = {2},
pages = {e70294},
pmid = {42001402},
issn = {2045-8827},
mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; *Autoimmune Diseases/therapy/immunology/microbiology ; *Dysbiosis/immunology/therapy/microbiology ; *Immune Tolerance ; *Autoimmunity ; Animals ; },
abstract = {Autoimmune diseases happen when the immune system, which is supposed to defend the body from infections and other harmful things, starts to attack the body's own cells by mistake. In the last few years, they seem to be getting more public, and the reasons are quite complicated. It is usually not just one factor, but a mix of genes and environmental influences, such as diet, infections, or even stress. The gut microbiome, the vast community of bacteria and other tiny organisms living in our intestines, plays an important role in shaping how the immune system behaves. When this gut microbiota becomes unstable (a state called dysbiosis), it can be associated with the onset or worsening of various autoimmune diseases. In this review, we discuss the close relationship between the gut microbiome and autoimmune disorders and focus on how the microbiome can affect immune activation, immune tolerance, and inflammation at the molecular level. The general idea is that, if we understand these interactions better, we might be able in the future to design new ways to manage autoimmune diseases earlier and maybe in a more personalized way. In the end, the review suggests that if we understand better how the microbiome is involved in autoimmune diseases, it might be possible in the future to design more personalized therapies that change gut bacteria in a smart way and hopefully improve patient outcomes.},
}
@article {pmid42001407,
year = {2026},
author = {Zhao, B and Li, D and Yang, Y and Hou, T and Hu, L},
title = {DRHIN: An Integrated and Interactive Web Server for Drug Repositioning.},
journal = {Journal of chemical information and modeling},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jcim.6c00311},
pmid = {42001407},
issn = {1549-960X},
abstract = {Drug repositioning (DR) identifies new therapeutic uses for approved drugs, reducing development burdens and offering safer treatment options for patients. While high-throughput technologies generate complex, large-scale multiomics data, existing DR tools struggle to comprehensively analyze the resulting biological networks. To address this challenge, we present DRHIN, an integrated, interactive web server for DR over heterogeneous information networks (HINs) using advanced deep learning techniques. DRHIN integrates transcriptomics, proteomics, and microbiome data, incorporating eight biological entities and 19 association types to build diverse HINs and elucidate the underlying molecular mechanisms. It includes 19 state-of-the-art graph representation algorithms, enabling flexible training, comparison, and evaluation of heterogeneous network data. The platform provides a code-free portal supporting three key predictive tasks: discovering drug-disease associations, repurposing existing drugs for new indications, and identifying potential therapies for specific diseases, making analyses accessible and reproducible. Leveraging high-performance computing, DRHIN efficiently processes million-scale networks, ensuring practical applicability in real-world scenarios. The web server is freely accessible at http://drhin.tianshanzw.cn.},
}
@article {pmid42001412,
year = {2026},
author = {Maria Lewis, B and Prashanth, A and Ramachandran, N and Sabat, S},
title = {Mutation studies on degradation of 3-phenoxybenzoic acid by Lacticaseibacillus paracasei - human gut microbiome in controlling risk for Parkinson's disease using molecular simulation dynamics.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/07391102.2026.2653065},
pmid = {42001412},
issn = {1538-0254},
abstract = {Parkinson's disease (PD) is a debilitating neurodegenerative disease affecting millions worldwide, especially the elderly. Pesticides, particularly pyrethroids like Cypermethrin, have been linked to the development of PD. Cypermethrin, when ingested, is broken down into 3-phenoxybenzoic acid (3PBA), which can lead to the dysfunction or death of dopaminergic neurons. Catechol-2,3-dioxygenase is an enzyme that breaks down 3PBA into catechol, that can further be processed and excreted by the human body. This enzyme is produced by the bacteria Lacticaseibacillus paracasei, a naturally present human gut microbe. Mutation studies were done to study the potential of the human gut microbiome in pesticide degradation improve the activity of the wild-type enzymes in degrading pesticides. The mutations were induced in two subunits of Catechol-2,3-dioxygenase using the WGS sequence of the gene coding for the same. Two subunits of the same protein i.e. Catechol-2,3-dioxygenase and NAD(+) reductase, were subjected to mutations using PyMol v3.1.0, and the crystal structures of the wild-type and mutant were docked against the ligand, 3-Phenoxybenzoic acid, using PyRx v0.8, and visualised using BIOVIA Discovery Studio Visualiser v24.1.0.23298, PyMol v3.1.0 and LigPlot + v2.2.9. The effects of mutation were further studied by analyzing the results of the molecular dynamics simulations conducted using the GROMACS software. Simulation trajectories like RMSD, RMSF, Inter and Intramolecular H-bonds, SASA, RG, PCA, FEL and FEP, all indicated better binding of the ligand (3PBA) to the active site.},
}
@article {pmid42001450,
year = {2026},
author = {Yao, J and Fei, C and Wu, H and Zhang, Z and Jiang, Z},
title = {Characterization of the Oral Bacteria in Patients With Neuroendocrine Tumors of the Pancreas.},
journal = {Cancer medicine},
volume = {15},
number = {4},
pages = {e71840},
doi = {10.1002/cam4.71840},
pmid = {42001450},
issn = {2045-7634},
support = {YKK20108//Nanjing health science and technology development special fund project plan/ ; NMUB2019134//Science and Technology Development Project of Nanjing Medical University/ ; },
mesh = {Humans ; Male ; *Pancreatic Neoplasms/microbiology ; Female ; *Neuroendocrine Tumors/microbiology/diagnosis ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Adult ; *Saliva/microbiology ; Aged ; Case-Control Studies ; Prognosis ; *Mouth/microbiology ; },
abstract = {The primary objective of this study was to investigate dysbiosis in the oral microbiota of patients with pancreatic neuroendocrine tumors (pNETs) and to identify potential biomarkers for clinical diagnosis and prognostic evaluation of pNETs. Healthy controls and pNETs patients were recruited from our hospital. Salivary flora were profiled in healthy subjects (HS group) and pNETs patients (PS group) using 16S rRNA gene sequencing. Microbial diversity was assessed by α-diversity (Tukey test) and β-diversity (Partial Least Squares Discriminant Analysis, PLS-DA). Taxonomic differences between groups were evaluated using linear discriminant analysis effect size (LEfSe). The salivary microbiota of pNETs patients showed higher abundance and diversity compared to healthy controls. Dominant bacterial phyla in both groups include Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, Fusobacteriota, Cyanobacteria, and Campilobacterota. At the genus level, Leptotrichia, Actinobacillus, and Granulicatella were more abundant in the PS group. LEfSe analysis further indicated a greater abundance of Rothia, Chloroplast, Leptotrichia, Actinomyces, and Granulicatella in the PS group. Our findings offer initial evidence suggesting a potential link between oral microbiome dysbiosis and pNETs, and identify microbial features that could be evaluated in future studies as potential biomarkers for clinical diagnosis and prognosis.},
}
@article {pmid42001830,
year = {2026},
author = {Vijayakumar, V and Rathinam, T and Deenadhayalan, SS and Edwin, ER},
title = {Human microbiome influence on head and neck cancer.},
journal = {Cancer treatment and research communications},
volume = {47},
number = {},
pages = {101218},
doi = {10.1016/j.ctarc.2026.101218},
pmid = {42001830},
issn = {2468-2942},
abstract = {Recent breakthroughs in microbiome research have identified the gut microbiota as an important regulator of systemic immunity, inflammation, and carcinogenesis. Although established risk factors for head and neck cancer (HNC) include tobacco use, alcohol use, and human papillomavirus (HPV) infection, growing data suggest that gut microbial dysbiosis may also play a role in its etiology. Changes in gut microbiota composition can have a distal influence on the head and neck region by modulating immune function, producing microbial metabolites, and disrupting epithelial barrier integrity, influencing tumor initiation, development, and therapeutic response. New research suggests that the gut microbiome plays an important role in regulating the success and toxicity of traditional HNC treatments such as chemoradiation and immunotherapy. This review focuses on current evidence linking alterations in the gut microbiome to HNC development and progression, emphasizing underlying mechanisms, diagnostic potential, and emerging microbiome-based therapeutic strategies.},
}
@article {pmid42001862,
year = {2026},
author = {Özcan, F and Arserim, NB},
title = {Antibacterial immunity in teleost fish: Integrating innate and adaptive responses for sustainable aquaculture.},
journal = {Veterinary immunology and immunopathology},
volume = {297},
number = {},
pages = {111113},
doi = {10.1016/j.vetimm.2026.111113},
pmid = {42001862},
issn = {1873-2534},
abstract = {Bacterial infections are currently the most significant hindrance to the worldwide adoption of sustainable aquaculture, causing unprecedented economical losses and challenges to food security. Teleosts have an extremely well-developed innate and adaptive immune system, but the functional integrity of these immune systems is adversely affected under universal aquaculture-related stress factors. The current review critically and comprehensively synthesizes the two most important challenges, addressing immune resilience, which include: (1) the complex functional interactions between innate and adaptive immune mechanisms, and (2) the combined modulation of these immune mechanisms under environmental factors mentioned above. Our focus primarily centers on the role of major stressors such as temperature change, water quality measures, (physiological) chronic stressing, and microbiome diversity on innate host immunity and resistance to bacterially infected diseases. Finally, we not only conclude the current state regarding the latest research progress on the role and mechanisms utilized in the transition phase from the latent to chronic infection phase based on autophagy-related responses but also emphasize the need to adopt an integrated research area named 'Eco-Immunology' to measure and develop effective interventions against fish diseases. It is the prime requirement to improve the host's resistance to diverse farming conditions to develop sustainable and effective aquaculture. This review uniquely integrates innate-adaptive immune crosstalk with environmentally driven immune reprogramming and autophagy-mediated control of chronic bacterial infections, framing teleost antibacterial immunity within an eco-immunological perspective relevant to sustainable aquaculture.},
}
@article {pmid42002154,
year = {2026},
author = {Dang, CP and Chen-Liaw, A and Xue, M and Luchak, A and Mu, K and Li, Q and Ren, MY and Lee, SH and Moayyedi, P and Griffiths, AM and Deslandres, C and Murthy, SK and Steinhart, AH and Otley, A and Dieleman, LA and Jacobson, K and Rubin, DT and Panaccione, R and Feagan, BG and Streutker, C and Mogno, I and Britton, GJ and Faith, JJ and , and Croitoru, K and Turpin, W},
title = {Pre-Crohn's Disease Stool from Discordant Siblings Promotes the Development of Colitis in Germ-Free Mice.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.03.023},
pmid = {42002154},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: The gut microbiome is implicated in Crohn's disease (CD) development. However, human microbiome studies need experimental evidence to demonstrate if specific microbial differences promote CD pathogenesis. This study aims to determine if the gut microbiome from individuals who later developed CD promotes colitis in germ-free recipient mice.<br><br>METHODS: Germ-free mice were colonized with fecal samples from 12 pairs of discordant siblings: where one sibling later developed CD (pre-CD), while the other remained a healthy matched control (HMC). After colonization, colitis was induced by T-cell transfer to assess effect of stool on multiple measures of colitis severity. Comparative analysis with human donor metadata explored transferred pathogenic traits.<br><br>RESULTS: Mice receiving pre-CD stool exhibited increased weight loss, fecal lipocalin-2, and intestinal histological damage compared to mice receiving HMC stool. Fecal metabolomic analysis revealed differences in 40 metabolites between pre-CD and HMC colonized mice. Furthermore, two metabolic pathways were shared between pre-CD participants and mice. Notably, sphingolipids showed a positive correlation between humans and mice, associated with increased colitis in mice.<br><br>CONCLUSION: This study functionally demonstrates that the stool microbiome of individuals susceptible to CD is altered years before diagnosis, exhibiting greater inflammatory potential when transferred to susceptible mice.},
}
@article {pmid42002159,
year = {2026},
author = {Liu, X and Li, S and Huang, C and Liu, Y and Dong, Y and Gong, H and Zhou, G},
title = {Iron plaque on wetland plant roots serves as a hotspot at the rhizosphere and a barrier within the endosphere for antibiotic resistance gene dissemination.},
journal = {Bioresource technology},
volume = {453},
number = {},
pages = {134648},
doi = {10.1016/j.biortech.2026.134648},
pmid = {42002159},
issn = {1873-2976},
abstract = {The iron plaque (IP) on wetland plant roots provides a crucial microenvironment for pollutant transport and transformation, yet its influence on the migration and dissemination of antibiotic resistance genes (ARGs) remains unexplored. Plasmid conjugation greatly contributes to ARG spreads. This study investigated the effect of IP formation on the plasmid-mediated ARG transfer across rhizosphere-iron plaque-root endosphere continuum and identified the key factors driving this process. Both the quantification of target genes and visual evidence demonstrated that conjugation frequencies within IP increased in a dose-dependent manner with the amount of IP formed on the root surface. In contrast, conjugation frequencies in the endosphere declined significantly as IP increased. The elevated IP content enhanced cell membrane permeability, raised reactive oxygen species (ROS) levels, and increased the activities of antioxidant enzymes including superoxide dismutase (SOD) and catalase (CAT). A significant positive correlation was observed between ROS levels and conjugation frequencies, as well as between the activities of antioxidant enzymes (SOD and CAT) and IP formation. The bacterial community structure was significantly shaped in root compartments. The transconjugal pool was phylogenetically constrained, dominated by Gammaproteobacteria such as Escherichia and Pseudomonas, which accounted for over 70% of transfer events despite representing less than 3% of the total bacterial community. Our findings imply that IP functions as both a hotspot for ARG transfer on root surfaces and a barrier against their entry into the root interior, which guide and optimize the application of IP in the phytoremediation of emerging contaminants including ARGs.},
}
@article {pmid42002228,
year = {2026},
author = {Liu, S and Huang, Z and Guo, Z},
title = {Fecal Microbiota Transplantation for gastrointestinal complications after Allogeneic Hematopoietic Cell Transplantation: a systematic review and narrative synthesis.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2026.04.016},
pmid = {42002228},
issn = {2666-6367},
abstract = {BACKGROUND: Following allogeneic hematopoietic stem cell transplantation (allo-HSCT), patients frequently develop gastrointestinal complications, including microbiota dysbiosis, infectious syndromes, and graft-versus-host disease (GVHD), which remain major contributors to post-transplant morbidity and mortality. In recent years, several studies have explored microbiome-based interventions, particularly fecal microbiota transplantation (FMT), as a therapeutic strategy for these complications in this highly immunocompromised population. However, substantial variability exists across studies with respect to clinical indications, FMT protocols, and reported outcomes.<br><br>OBJECTIVES: To systematically evaluate the reported clinical use of FMT for gastrointestinal complications following allo-HSCT, including microbiota dysbiosis, infectious complications, and GVHD. The aim was to characterize study populations, treatment protocols, and reported clinical outcomes, and to synthesize evidence regarding efficacy and safety, with a focus on indication-specific patterns and potential translational relevance for patient management in this highly immunocompromised population.<br><br>STUDY DESIGN: We conducted a PRISMA-compliant systematic review of studies evaluating FMT as a treatment in patients after allo-HSCT. PubMed, Embase, Web of Science, and the Cochrane Library were searched through October 2025. Eligible studies included randomized controlled trials, cohort studies, and prospective or retrospective single-arm studies reporting clinical outcomes following FMT. Given the marked heterogeneity in clinical indications, FMT administration strategies, and outcome definitions, study findings were synthesized using a structured narrative approach, with quantitative data summarized descriptively where appropriate.<br><br>RESULTS: Twenty studies including patients after allo-HSCT were analyzed. FMT demonstrated high and consistent response rates in non-GVHD indications, whereas GVHD cohorts exhibited more variable responses, with median CR and ORR ranging 50-55% in steroid-refractory cases. One-year overall survival was generally favorable in dysbiosis and infection groups (>70%), but more heterogeneous in GVHD. FMT was well tolerated, with predominantly mild gastrointestinal adverse events; serious events were infrequent and mostly disease-related.<br><br>CONCLUSIONS: Current evidence indicates that FMT has been explored as a context-dependent therapy for selected gastrointestinal complications following allo-HSCT, particularly in patients with aGVHD. Nevertheless, substantial heterogeneity in study design, clinical indications, and outcome assessment limits definitive conclusions regarding efficacy. Well-designed prospective studies with standardized treatment indications, outcome measures, and careful consideration of concurrent immunosuppressive therapies are required to better define the optimal role, timing, and patient selection for FMT in the post-transplant treatment setting.},
}
@article {pmid42002296,
year = {2026},
author = {Yang, X and Zhang, L and Zhou, S and Wang, Z and Lv, Q and Zhao, M and Wang, C},
title = {Mechanisms Underlying Bioactive Compounds Decline in Medicinal Blaps rhynchopetera During Artificial Rearing.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70304},
doi = {10.1111/1462-2920.70304},
pmid = {42002296},
issn = {1462-2920},
support = {2022YFC2602500//National Key Research and Development Program of China/ ; JiaoWaiSiYa[2020]619//Lancang-Mekong Cooperation Special Fund Projects/ ; SAJC202402//Chinese Academy of Sciences/ ; 2025YKZY002//Yunnan Characteristic Plant Extraction Laboratory/ ; 202449CE340005//Yunnan Provincial Science and Technology Department/ ; 202305AH340007//Yunnan Provincial Science and Technology Department/ ; },
mesh = {Animals ; *Coleoptera/microbiology/metabolism/growth &amp; development ; *Gastrointestinal Microbiome ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metabolome ; Biological Products/metabolism ; },
abstract = {Artificial rearing is essential for sustainable utilization of medicinal insects, yet its impact on bioactive compound production remains poorly understood. Here we provide preliminary evidence that rearing of the medicinal beetle Blaps rhynchopetera reshapes its gut microbiota and metabolome, beyond mere environmental effects. Metabolomic analysis revealed 727 significantly altered metabolites, with 436 compounds, many linked to analgesic and anti-inflammatory activities, markedly reduced under rearing. Network pharmacology analysis suggested that this metabolic remodelling alters the overall regulatory landscape, with reduced network complexity compared to wild counterparts. Metagenomic profiling uncovered a decline in Pseudomonadota, a phylum positively correlated with multiple bioactive metabolites. Preliminary reintroduction of four Pseudomonadota strains suggested their potential involvement in terpenoid backbone biosynthesis, a key pathway for natural product synthesis. These findings reveal an intrinsic trade-off between rearing-driven microbial homogenization and preservation of medicinal potency, highlighting the need for microbiome-informed rearing strategies.},
}
@article {pmid42002330,
year = {2026},
author = {Zhao, Y and Qiao, M and Ma, C and Hou, Q and Hu, J and Yang, J},
title = {A fructan-type polysaccharide from Lycium ruthenicum attenuates liver fibrosis via microbiota-dependent ferroptosis inhibition.},
journal = {Carbohydrate polymers},
volume = {382},
number = {},
pages = {125243},
doi = {10.1016/j.carbpol.2026.125243},
pmid = {42002330},
issn = {1879-1344},
mesh = {Animals ; *Liver Cirrhosis/drug therapy/metabolism/pathology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Lycium/chemistry ; *Ferroptosis/drug effects ; Mice ; Male ; *Polysaccharides/pharmacology/chemistry ; Mice, Inbred C57BL ; *Fructans/pharmacology/chemistry ; Liver/drug effects/metabolism/pathology ; Oxidative Stress/drug effects ; },
abstract = {Plant-derived polysaccharides represent promising candidates for hepatic fibrosis (HF) therapy through the gut-liver axis. This study investigated the structural characteristics, anti-fibrotic efficacy, and mechanisms of LRMP1, a novel polysaccharide from Lycium ruthenicum Murr. LRMP1 was identified as a homogeneous inulin-type fructan (3.055 kDa) with a → 1)-β-D-Fruf-(2 → backbone terminated by α-D-Glcp-(1 → 2)-β-D-Fruf linkages (DP 4-20). Integrated multi-omics analysis combining hepatic transcriptomics, serum metabolomics, and gut microbiome profiling revealed that LRMP1 ameliorates HF via a gut microbiota-postbiotics-ferroptosis regulatory axis. In both CCl4-induced and MCD diet-induced chronic fibrosis models, LRMP1 significantly attenuated liver injury, fibrosis, inflammation, and oxidative stress, while restoring intestinal barrier integrity. These protective effects correlated with enrichment of beneficial bacteria (Akkermansia muciniphila, Lactobacillus spp.) and pathogen depletion. Mechanistically, LRMP1 suppressed TGF-β signaling and inhibited hepatocyte ferroptosis by restoring the GPX4/SLC7A11 antioxidant system and reducing lipid peroxidation. Serum metabolomics further revealed elevated anti-ferroptotic metabolites and suppressed pro-inflammatory lipids. Crucially, antibiotic depletion abolished LRMP1's efficacy, whereas fecal microbiota transplantation and fermentation supernatant experiments confirmed that microbiota-derived postbiotics selectively protect hepatocytes from ferroptosis. These findings establish LRMP1 as a promising microbiota-targeted polysaccharide for HF intervention through the gut-liver axis.},
}
@article {pmid42002450,
year = {2026},
author = {Coleine, C and Obermeier, W and Lehnert, L and Leung, PM and Donati, C},
title = {Linking microbial function and remote sensing for understanding drylands.},
journal = {Trends in ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2026.04.002},
pmid = {42002450},
issn = {1872-8383},
abstract = {Drylands, covering over 40% of Earth's land surface, are expanding due to accelerating aridification and vegetation loss. Their microbial communities sustain essential processes such as carbon fixation, nitrogen cycling, and trace gas regulation; yet they remain largely invisible to global models. While microbiome studies reveal mechanistic details at local scales, environmental monitoring requires spatial continuity. We argue that advances in remote sensing, with its increasing resolutions, now allow microbial processes to be observed, scaled, and modeled across regions. Linking omics and spectral data can reveal microbial 'sentinels' of ecosystem change, transforming microbial ecology into a spatially predictive science. This integration provides a foundation for early-warning systems of biodiversity loss and land degradation, positioning microbes as measurable actors in Earth system dynamics.},
}
@article {pmid42002490,
year = {2026},
author = {Liao, B and Chen, L and Ruan, J and Wang, R and Hu, B and Long, R and Li, Y and Zhang, G and Yu, J and Ming Zhang, and Zhang, Y and Liao, S},
title = {Corrigendum to "Microbiome and gartynecologic cancer" [Cancer Lett. 636 (2026) 217940].},
journal = {Cancer letters},
volume = {},
number = {},
pages = {218519},
doi = {10.1016/j.canlet.2026.218519},
pmid = {42002490},
issn = {1872-7980},
}
@article {pmid42002654,
year = {2026},
author = {Martínez-Reyes, CM and González-Macedo, M and Rojas-Oropeza, M and Rodríguez-Zaragoza, S and Cabirol, N},
title = {Influence of seasonal humidity and nitrogen on soil ciliate and bacterial diversity beneath the canopy of Neltuma laevigata.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42002654},
issn = {1618-1905},
support = {PhD Grant//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; PAPIIT IN224716//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; },
}
@article {pmid42002801,
year = {2026},
author = {Luo, J and Wang, X and Ju, Y and Ji, Q and Li, R and Ruan, Y and Zhao, J and Long, Q and Shang, Y and Li, P and Cao, M and Chen, X},
title = {Dietary N-acetylcysteine enhances sperm motility by remodeling the rumen microbiome and its metabolic axis in goats.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42002801},
issn = {1674-9782},
support = {2021YFD1200403//National Key Research and Development Program/ ; GZNYJGHX-2023006//Guizhou Province Mountainous Agriculture Key Research Program/ ; Qian Kehe Platform Talent-CXTD[2023]025//Guizhou Province Mutton Sheep Genetic Improvement and Innovative Utilization Science and Technology Innovation Talent Team Project/ ; GCC[2022]021-1//Guizhou Province High-level Innovative"Hundred" Level Talent Project/ ; },
abstract = {BACKGROUND: Enhancing sperm motility is crucial for improving male fertility in ruminants. The rumen microbiota, central to nutrient metabolism of ruminants, represents a promising yet underexplored target for dietary intervention. This study investigated whether N-acetylcysteine (NAC) improves sperm motility via modulating the rumen microbiota-metabolite axis.<br><br>RESULTS: Dietary NAC supplementation significantly enhanced sperm motility in goats (P&#x2009;<&#x2009;0.05), with the optimal effect observed at 0.3%, which coincided with improvements in sperm membrane integrity, antioxidant capacity, and mitochondrial function. Functional analysis revealed that NAC-induced microbial remodeling enriched KEGG pathways involved in antioxidant, energy, and lipid metabolism. Correspondingly, beneficial bacteria such as Pediococcus pentosaceus, Bacteroides acidifaciens, and Akkermansia, among others, were significantly enriched (P&#x2009;<&#x2009;0.05). Notably, metabolic alterations in these pathways were consistently reflected in both the rumen fluid and plasma metabolomes, as evidenced by 25 conserved pathways and 2 overlapping metabolites. Collectively, these metabolic alterations ultimately enhanced sperm motility by improving sperm antioxidant status, energy supply, and lipid homeostasis.<br><br>CONCLUSIONS: Our study thus reveals that NAC enhances sperm motility via a rumen microbiome-mediated "rumen-plasma-sperm" axis. This novel insight broadens the understanding of how NAC-and potentially other antioxidants-regulates sperm motility, highlighting the promise of NAC-based dietary interventions for improving reproductive performance.},
}
@article {pmid42002816,
year = {2026},
author = {Jiang, H and Cui, Y and Lei, J},
title = {Global research on the crosstalk between microbiota - intratumoral microorganisms and liver cancer: a visualization analysis.},
journal = {Infectious agents and cancer},
volume = {21},
number = {1},
pages = {},
pmid = {42002816},
issn = {1750-9378},
support = {2020-XG-40//Lanzhou Science and Technology Bureau Project, 2020-XG-40: Development of an Intelligent Image-Assisted Diagnosis System for Early Detection and Quantitative Assessment of Therapeutic Efficacy in COVID-19 Using Deep Learning Technology and Its Clinical Application./ ; },
abstract = {BACKGROUND: In the past few decades, the field of microbiota research has experienced rapid development and growth. We have employed bibliometric methods to comprehensively visualize and analyze the global knowledge and hotspots in the field of microbiome-intratumoral microbiota in liver cancer.<br><br>METHOD: The relevant literature in this field from 2009 to 2025 was extracted from the Web of Science Core Collection Database. After the data was extracted, it was analyzed and visualized using CiteSpace, VOSviewer and R (bibliometrix) software.<br><br>RESULT: A total of 1001 publications on microbiome - intratumoral microbiota and liver cancer were published during the period 2009&#x2013;2025. Among these, China had the highest number of publications (n&#x2009;=&#x2009;495). The most prolific institution publishing on microbiome - intratumoral microbiota and liver cancer was Huazhong University of Science and Technology, China (n&#x2009;=&#x2009;29). The author with the most publications on this topic was Yu, Jun (n&#x2009;=&#x2009;14, 1.4%). The journal with the highest number of publications on this subject was Cancers (n&#x2009;=&#x2009;41, 4.1%). The top seven keywords with a frequency of 100 or more include: gut microbiota, hepatocellular carcinoma, nonalcoholic fatty liver disease, fatty liver disease, cancer, inflammation, bile acids, liver cancer, cell, and insulin resistance. Recent emerging topics include &#x201c;intratumoral microbiota&#x201d; (since 2024) and &#x201c;tumor microenvironment.&#x201d;<br><br>CONCLUSION: Current research in this field primarily investigates the mechanistic associations between gut microbiota and hepatic malignancies, with particular emphasis on hepatocellular carcinoma. The scientific frontier has progressively evolved to encompass the exploration of intratumoral microbiota and its multifaceted interactions within the tumor microenvironment.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13027-026-00750-x.},
}
@article {pmid42002835,
year = {2026},
author = {Morineau, N and Tessoulin, B and Guimard, T and Papin, M and Roquilly, A and Le Gouill, S and Montassier, E},
title = {Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659397},
doi = {10.1080/19490976.2026.2659397},
pmid = {42002835},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Piperidines/adverse effects/therapeutic use ; *Adenine/analogs &amp; derivatives/adverse effects/therapeutic use ; Male ; Female ; Middle Aged ; Aged ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism/drug effects ; Feces/microbiology ; Treatment Outcome ; *Antineoplastic Agents/adverse effects/therapeutic use ; Adult ; },
abstract = {Accumulating evidence indicates that the gut microbiome influences therapeutic efficacy and toxicity across cancer treatments; however, its longitudinal dynamics during targeted therapies remain poorly characterized. Here, we performed whole-genome shotgun metagenomic sequencing of 291 longitudinal stool samples collected over one year from 30 patients with hematologic malignancies treated with ibrutinib. Overall gut microbial diversity remained stable at the population level but exhibited markedly divergent temporal trajectories according to clinical outcome, with progressive recovery in responders and blunted or delayed restoration in non-responders. Longitudinal modeling revealed distinct species- and pathway-level microbial dynamics between patients with treatment response or nonresponse, including enrichment of saccharolytic, short-chain fatty acid-associated taxa and metabolic pathways in responders, and expansion of bile acid-modifying, proteolytic, and inflammation-associated microbial features in non-responders. Functional profiling further demonstrated opposing temporal trends in pathways related to carbohydrate fermentation, amino-acid metabolism, and secondary bile acid synthesis. In addition, both baseline microbiome composition and longitudinal remodeling were associated with the development of ibrutinib-associated diarrhea. Together, these findings reveal coordinated, outcome-specific remodeling of the gut microbiome during ibrutinib therapy and highlight longitudinal microbiome trajectories, rather than static baseline features, as potential biomarkers of treatment response and toxicity, as well as targets for microbiome-directed interventions. In conclusion, our findings highlight a potential role of gut microbiome dynamics in modulating response to BTK inhibition and support the need for larger, prospective studies to validate these observations.},
}
@article {pmid42002973,
year = {2026},
author = {Nam, K and Choi, JH and Kim, YS and Lee, S and Park, JH and Kim, H and Lee, S and Lee, Y and Lee, D and Ryou, S and Shin, JE},
title = {Impact of Portulaca oleracea L. extract in patients with irritable bowel syndrome.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2025.00200},
pmid = {42002973},
issn = {1598-9100},
abstract = {BACKGROUND/AIMS: Portulaca oleracea is known to have anti-inflammatory and immunoregulatory effects, and also showed positive effect on complete spontaneous bowel movement and bowel symptoms in patients with chronic constipation in a previous study. Thus, we aimed to investigate the impact of P. oleracea in patients with irritable bowel syndrome (IBS).<br><br>METHODS: Patients with IBS defined by ROME IV criteria were enrolled between July 2022 and April 2023. Patients were randomly assigned to P. oleracea or placebo group and took drugs for 8 weeks. Clinical data including gastrointestinal and IBS symptoms, laboratory tests including inflammatory and immunologic laboratory markers, and stool tests including fecal calprotectin and stool microbial analysis were evaluated at the baseline, week 4, and week 8.<br><br>RESULTS: A total of 108 patients were initially enrolled and 101 patients were finally included in the analysis. There was significant improvement during 8 weeks in P. oleracea group compared to placebo group in the aspect of gastrointestinal and IBS-related bowel symptoms (Gastrointestinal Symptom Rating Scale total score: from 44.1 to 31.7 vs. from 41.4 to 39.9; IBS-Symptom Severity Score total score: from 232.0 to 120.6 vs. from 202.7 to 178.2), especially in the aspect of abdominal pain. Interleukin-6 (IL-6) was significantly decreased during 8 weeks in P. oleracea group, although there was no significant difference between 2 groups. In addition, increase in IL-6 during study period was significantly associated with dysbiosis in stool microbial analysis. There was no significant adverse event.<br><br>CONCLUSIONS: P. oleracea has positive impact in patients with IBS showing improvement of immunologic cytokine and stool microbiome.},
}
@article {pmid42003036,
year = {2026},
author = {Ganamurali, N and Sabarathinam, S},
title = {Resveratrol as a Multi-Domain Modulator of Oxidative Stress, Gut Dysbiosis, and Epigenetic Remodeling in Obesity: A Systems Biology Interpretation.},
journal = {Journal of biochemical and molecular toxicology},
volume = {40},
number = {5},
pages = {e70846},
doi = {10.1002/jbt.70846},
pmid = {42003036},
issn = {1099-0461},
mesh = {*Resveratrol/pharmacology/therapeutic use ; *Obesity/drug therapy/metabolism/genetics/microbiology/pathology ; Humans ; *Epigenesis, Genetic/drug effects ; *Oxidative Stress/drug effects ; *Dysbiosis/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Systems Biology ; },
abstract = {Obesity is increasingly recognized as a chronic inflammatory redox disorder sustained by gut dysbiosis and maladaptive epigenetic programming. A "lock-in" model describes how gut dysbiosis induced reactive oxygen species (ROS) stabilize inflammatory signaling and establish epigenetic metabolic scars in adipose tissue, thereby perpetuating obesity even after the initial triggers subside. Resveratrol, a dietary stilbenoid, acts as a tri-axis therapeutic candidate by: (1) Restoring redox balance via Nrf2 activation and SIRT1 signaling, (2) Reshaping the gut microbiota to enhance SCFA production and barrier integrity, and (3) Reprogramming obesity-associated epigenetic alterations, including DNA methylation and miRNA dysregulation. By targeting oxidative, microbial, and epigenetic dimensions simultaneously, resveratrol offers a novel strategy to erase metabolic memory and disrupt obesity chronicity.},
}
@article {pmid42003076,
year = {2026},
author = {Malik, JA},
title = {Lactobacillus plantarum as a Novel Modulator of Immune and Behavioral Recovery in Substance Use Disorders: A Hypothesis.},
journal = {Current drug research reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/0125899775442579260409073358},
pmid = {42003076},
issn = {2589-9783},
abstract = {Substance Use Disorders (SUDs) are increasingly recognized as conditions driven by neuroimmune dysfunction, leading to neuroinflammation and immune dysregulation. Growing evidence highlights the microbiota-gut-brain axis as a critical regulator of central nervous system activity, particularly through the modulation of glial cells such as microglia and astrocytes. The gut microbiome provides key immunomodulatory signals, and its therapeutic exploitation through probiotics offers a promising avenue. In this study, we hypothesize that supplementation with Lactobacillus plantarum can attenuate neuroinflammation and improve immune tolerance in SUDs by restoring microbial balance and modulating neuroimmune activity via the gut-brain axis. Using an established animal model of SUD, we propose to investigate the impact of L. plantarum on gut microbial composition, systemic and central inflammatory markers, glial cell activation, and behavioral outcomes. We further suggest that probiotics containing Lactobacillus species, including L. plantarum, could serve as a transformative approach not only for SUD-associated neuroinflammation but also for other neurological disorders. Such interventions may represent a breakthrough in non-drug discovery strategies by reducing reliance on conventional pharmacological treatments. Importantly, probiotic-based therapies could enhance overall survival and quality of life in individuals with SUDs, as Lactobacillus species have been shown to suppress inflammatory pathways from early developmental stages. Lactobacillus species could regulate the gut-brain axis and impact neurodegenerative diseases. If validated, this work could position L. plantarum and related probiotic strains as novel microbiome-based adjuncts for managing SUDs and open broader therapeutic possibilities for neuropsychiatric and neurodegenerative conditions.},
}
@article {pmid42003095,
year = {2026},
author = {Aru, N and Chen, Y and Li, T and Liu, J},
title = {Metabolites and Polycystic Ovarian Syndrome: A Mendelian Randomization Study.},
journal = {Current medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298673408216260414174125},
pmid = {42003095},
issn = {1875-533X},
abstract = {INTRODUCTION: Polycystic ovarian syndrome (PCOS) is a common reproductive disorder that affects a considerable number of women worldwide. Nevertheless, the causal relationship between metabolites and PCOS remains undetermined.<br><br>METHODS: We utilized a comprehensive two-sample Mendelian randomization (MR) analysis, a genetic epidemiological approach that uses genetic variants as instrumental variables to assess causal relationships between exposures and outcomes, to examine the causal link between 1352 metabolites and PCOS. We employed complementary MR methods, such as the inverse-variance weighted (IVW) method, and conducted sensitivity analyses to evaluate the reliability of the outcomes. Reverse MR analysis was performed to evaluate the possibility of reverse causation.<br><br>RESULTS: Five metabolites were identified to be significantly associated with PCOS risk: Methionine sulfoxide levels (IVW: OR [95%]: 1.549[1.274 to 1.883], p = 1.154E-5), Theophylline levels (IVW: OR [95%]: 0.725[0.589 to 0.890], p = 0.002), 4-hydroxycoumarin levels (IVW: OR [95%]: 0.786[0.658 to 0.940], p = 0.008), Tyramine O-sulfate levels (IVW: OR [95%]: 0.699[0.568 to 0.862], p = 0.0008), and Sulfate of piperine metabolite C16H19NO3 (3) levels (IVW: OR [95%]: 1.296[1.064 to 1.579], p = 0.009). We found PCOS was significantly associated with decreased Tyramine O-sulfate levels using the IVW method (OR [95%]: 0.953[0.917 to 0.991], p = 0.015) in the reverse MR analysis. The results of the sensitivity analyses were consistent with the main findings.<br><br>DISCUSSION: This study establishes causal relationships between specific metabolites and PCOS, highlighting the significant roles of oxidative stress (methionine sulfoxide), dietary components (theophylline, piperine metabolite), and gut microbiome-derived metabolites. These findings provide novel insights into PCOS pathogenesis and identify potential targets for prevention and treatment. However, the study's limitation to European populations necessitates further validation in diverse ethnic groups.<br><br>CONCLUSION: Our MR analysis provides strong evidence supporting a causal association between metabolites and the susceptibility of PCOS.},
}
@article {pmid42003340,
year = {2026},
author = {Tong, Y and Marcelino, VR and Turnbull, R and Verbruggen, H},
title = {ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70143},
doi = {10.1111/1755-0998.70143},
pmid = {42003340},
issn = {1755-0998},
support = {2023.06155//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DE220100965//Australian Research Council/ ; RYC2023-042907-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; //The University of Melbourne's Research Computing Services/ ; },
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Genome, Plastid ; *Eukaryota/genetics/classification ; *Software ; Phylogeny ; Metagenome ; },
abstract = {Genome-resolved metagenomics has contributed greatly to discovering prokaryotic genomes. When applied to microscopic eukaryotes (protists), challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the mining and discovery of novel protistan lineages. Organellar genomes are simpler, smaller, have higher abundance than their nuclear counterparts and contain valuable phylogenetic information, but are yet to be widely used to identify new protist lineages from metagenomes. Here we present "ChloroScan", a new bioinformatics pipeline to extract eukaryotic plastid genomes from metagenomes. It incorporates a deep learning contig classifier to identify putative plastid contigs and an automated binning module to recover bins with guidance from a curated marker gene database. Additionally, ChloroScan summarizes the results in different user-friendly formats, including annotated coding sequences and proteins for each bin. We show that ChloroScan recovers more high-quality plastid bins than MetaBAT2 for simulated metagenomes. The practical utility of ChloroScan is illustrated by recovering 16 medium to high-quality metagenome assembled genomes (MAGs) from four protist-size-fraction metagenomes, with several bins showing high taxonomic novelty. The ChloroScan code (v0.1.7) is available at https://github.com/Andyargueasae/chloroscan/tree/release_v0.1.7 under Apache-2.0 licence.},
}
@article {pmid42003351,
year = {2026},
author = {Tahlan, S and Singh, S and Dey, H and Kaira, M and Pandey, KC},
title = {Molecular strategies for heterocyclic frameworks in antidiabetic drug discovery: a vision from 2020-2024.},
journal = {Future medicinal chemistry},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/17568919.2026.2658007},
pmid = {42003351},
issn = {1756-8927},
abstract = {Diabetes mellitus represents a global health crisis requiring innovative therapeutic strategies beyond traditional treatments. This comprehensive review analyzes heterocyclic frameworks developed between 2020-2024 for antidiabetic drug discovery, highlighting structure-activity relationships (SAR), molecular docking insights, and therapeutic mechanisms. Key scaffold classes emerged as potent antidiabetic agents, with benzimidazoles and triazoles demonstrating dual α-amylase/α-glucosidase inhibition (IC50 values 1.20-22.46 µg/mL), thiazolidinediones and quinazolines showing PPAR-γ agonism with improved insulin sensitivity and reduced cardiovascular risks, DPP-4 inhibitory scaffolds (pyrrolidines, pyrimidines) achieving IC50 values as low as 0.021 µM, and SGLT2-targeting heterocycles exhibiting glucose-lowering effects with cardio-renal protection. Major findings revealed that electron-donating groups (methoxy, hydroxyl) consistently enhanced binding affinity across multiple targets, halogen substitutions (fluoro, chloro, bromo) improved metabolic stability and selectivity, hybrid molecules combining multiple pharmacophores achieved superior multi-target effects, and natural product-derived heterocycles (flavonoids, coumarins, alkaloids) showed IC50values 10-100× better than acarbose. Emerging frontiers include multi-agonist therapies (GLP-1/GIP, dual SGLT1/SGLT2 inhibitors), glucokinase activators for insulin-independent glucose control, microbiome-targeting agents, and AI-driven rational drug design integrating SAR, docking, and ADMET prediction. This review provides a strategic framework for developing safer, more selective antidiabetic agents through systematic exploitation of heterocyclic chemistry, advancing toward personalized diabetes management.},
}
@article {pmid42003595,
year = {2026},
author = {Williams, MR and Rowe, HM},
title = {Bacterial alteration of redox stressors impacts environmental stability of influenza A virus.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0012526},
doi = {10.1128/msphere.00125-26},
pmid = {42003595},
issn = {2379-5042},
abstract = {Influenza A virus (IAV) causes annual morbidity and mortality and remains a constant pandemic threat due to the emergence of novel strains. Therefore, understanding the factors important in host-to-host transmission of IAV is a key control point for protecting individual and public health. Transmission is highly heterogeneous with viral factors and host inflammatory and immune factors being implicated. Also implicated is the upper respiratory microbiome. While typically thought to act indirectly on viral pathogenesis, in an immunomodulatory capacity to enhance or reduce susceptibility to viral infection, recent studies on the pathogenesis of IAV have identified direct interactions between the virus and upper respiratory pathobiont bacteria. We hypothesize that the bacterial cells and their metabolites co-shed into respiratory droplets with IAV particles alter the viability of the IAV particles in the environment, therefore altering the capacity for host-to-host transmission. In this investigation, we utilize a simplified model of fomite transmission in the absence of confounding host factors and demonstrate how oxidative stress from both the environment and the metabolic activity of Streptococcus pneumoniae contributes to the killing of IAV, while catalase or the metabolic activity of Staphylococcus aureus can protect IAV from environmental or pneumococcally produced reactive oxygen species. These findings support a mechanism for bacterial modulation of viral transmission where bacterial metabolic products present in the respiratory droplet are capable of stabilizing and destabilizing viral particles during environmental transit and therefore modulating viral transmissibility.IMPORTANCEInfluenza A virus is a major cause of illness and death every year. A key knowledge gap exists in understanding what factors modulate viral transmission. One potential mediator of viral transmission is the bacteria that are found in the human nasopharynx. However, the mechanisms responsible for bacterial modulation of viral transmission are unclear. Here, we utilize a simplified model of environmental survival where we expose viral particles to indoor environmental conditions in the presence of bacterial cells. We demonstrate that hydrogen peroxide produced by Streptococcus pneumoniae reduces viral environmental survival, while incubation with catalase or viable Staphylococcus aureus cells can protect viral particles from S. pneumoniae-mediated viability loss. This supports a model of trans-kingdom bacterial-viral interactions where bacterial metabolites produced in the respiratory droplet are capable of modulating viral environmental survival and therefore transmission.},
}
@article {pmid42003615,
year = {2026},
author = {Yamada, K and Koroleva, A and Tirkkonen, H and Siitonen, V and Laughlin, M and Moglia, A and Matroodi, S and Akhgari, A and Mazurier, G and Niemi, J and Metsä-Ketelä, M},
title = {Facultative predation expands the ecological repertoire of Streptomyces.},
journal = {mBio},
volume = {},
number = {},
pages = {e0056326},
doi = {10.1128/mbio.00563-26},
pmid = {42003615},
issn = {2150-7511},
abstract = {Microbial predators obtain energy from killing other living cells. Streptomyces are soil bacteria that are known to produce numerous catabolic enzymes and antimicrobial compounds to defend against competing organisms. Here, we demonstrate that Streptomyces are predatory bacteria that prey on Saccharomyces cerevisiae. Time-lapse fluorescence microscopy and scanning electron microscopy revealed that predation is initiated by physical contact between Streptomyces lavendulae YAKB-15 and yeast cells. Comparative transcriptomics indicated that the interaction triggered the production of numerous extracellular catabolic enzymes and natural products, while delaying morphological development. Proteomics and enzyme assays confirmed co-culture-dependent production of carbohydrate-active enzymes (CAZymes), including various glucanases, mannosidases, and chitinases, which degraded the yeast cell wall. Streptomyces lavendulae YAKB-15 destabilized yeast cell membranes through the production of two polyene antifungal agents, pentamycin and filipin III. We found that the bioactivity was enhanced by cell-associated cholesterol oxidase ChoD, putatively by modulating sterol extraction kinetics. Metabolomic analyses suggest Streptomyces assimilates yeast cell sterols as nutrients. Furthermore, we observed the depletion of yeast-derived phosphatidylcholine and phosphatidylethanolamine lipids, which points to their consumption. We show that yeast predation is a common phenomenon in Streptomyces, which changes the paradigm of how these bacteria should be considered in the soil microbiome ecosystem.IMPORTANCESoil is a rich environment for microbes, where they compete for space and resources. Streptomyces bacteria are well known for their ability to synthesize natural products, particularly antibiotics, that are used in chemical defense against competing microbes. Here, we show that Streptomyces are, in fact, predatory bacteria. Upon encountering yeast cells, Streptomyces initiate the production of numerous enzymes that digest the cell wall and cell membrane. In addition, the interaction triggers the production of natural products that destabilize the yeast cell membrane. Collectively, these actions lead to the death of yeast cells and release of cellular building blocks that Streptomyces can use as nutrients. The work fundamentally shifts the paradigm of how Streptomyces are perceived within the soil microbiome ecosystem.},
}
@article {pmid42003642,
year = {2026},
author = {Krausfeldt, LE and Subramanian, P and Doan, D and McCauley, K and Dolan, M and Hurt, DE},
title = {DiscoVir: an automated, web-based pipeline for viral metagenomics.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0008526},
doi = {10.1128/mra.00085-26},
pmid = {42003642},
issn = {2576-098X},
abstract = {DiscoVir is an automated pipeline for viral metagenomics available in National Institute of Allergy and Infectious Diseases (NIAID)'s free web application for microbiome analysis, Nephele. DiscoVir makes viral discovery, taxonomic and functional annotation, host predictions, and diversity analyses of the virome easily accessible to researchers at all levels of expertise.},
}
@article {pmid42003650,
year = {2026},
author = {Huedo, P and Astó, E and Perez, M and Rodriguez-Palmero, M and Espadaler-Mazo, J},
title = {Draft genome sequences of Lactiplantibacillus plantarum strains KABP062 and KABP063 isolated from human feces.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0019626},
doi = {10.1128/mra.00196-26},
pmid = {42003650},
issn = {2576-098X},
abstract = {We present the draft genome sequences of Lactiplantibacillus plantarum strains KABP062 and KABP063, two fecal isolates with probiotic potential.},
}
@article {pmid42003651,
year = {2026},
author = {Kocakahya, &#x130; and Şahin, G and Büyükkahraman, E and Arıkan, M},
title = {Metagenome-assembled genomes from urban pigeon feces in Istanbul, Türkiye.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0140525},
doi = {10.1128/mra.01405-25},
pmid = {42003651},
issn = {2576-098X},
abstract = {We report herein about 101 metagenome-assembled genomes (MAGs) obtained from pigeon fecal samples collected in 2025 from the Beyazıt, Kadıköy, and Beşiktaş squares of Istanbul. The MAGs were predominantly composed of members of the phyla Firmicutes, Actinobacteria, and Proteobacteria, with a lower representation of Campylobacterota and Patescibacteriota.},
}
@article {pmid42003736,
year = {2026},
author = {Xue, H and Diao, F and Yu, Q and Zhu, X and Zhong, T and Wang, L and Zhang, K and Li, D and Ji, J and Luo, J and Cui, J and Gao, X},
title = {Cotton Recruits Soil-Derived Delftia tsuruhatensis to Suppress Aphid Detoxification Via Salicylic Acid-Mediated Defense.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e75321},
doi = {10.1002/advs.75321},
pmid = {42003736},
issn = {2198-3844},
support = {2022YFF1001400//National Key Research and Development Program of China/ ; 262300421139//Natural Science Foundation of Henan Province/ ; Y2023QC23//Youth Innovation Program of Chinese Academy of Agricultural Sciences/ ; CARS-15-21//China Agriculture Research System/ ; 2022QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; //Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; },
abstract = {The synergistic defense between microorganisms and plants holds significant ecological importance in resisting pest attacks. Herbivorous insects pose a significant threat to global agriculture. While plants deploy defense hormones like jasmonic acid (JA) and salicylic acid (SA), the role of beneficial microbes in enhancing these defenses remains underexplored. This study unveils a novel tripartite interaction in which cotton actively mobilizes the soil-derived bacterium Delftia tsuruhatensis to roots and leaves upon aphid attack, reshaping its microbiome for defense. Following aphid infestation, the abundance of D. tsuruhatensis was increased significantly in both roots and leaves. Inoculation of cotton with D. tsuruhatensis significantly reduced aphid fitness, inhibiting phloem feeding, decreasing survival, prolonging nymphal development, and impairing reproduction. Mechanistically, we found that D. tsuruhatensis activates the host plant's SA signaling pathway. This plant-mediated response, in turn, effectively suppresses the expression of a key aphid detoxification gene, UGT2B17 (UDP-glucosyltransferase 2B17), compromising the insect's ability to metabolize plant defenses. Furthermore, the combination of D. tsuruhatensis and RNAi-mediated silencing of UGT2B17 synergistically enhanced aphid mortality. Our results elucidate a sophisticated defense strategy wherein the host plant leverages a beneficial microbe to augment its innate immunity through cross-kingdom gene regulation, ultimately disarming the pest's detoxification system.},
}
@article {pmid42003748,
year = {2026},
author = {Fletcher Wheeler, L and Lehmann, M and Melo-Narvaez, MC},
title = {Mechanistic Advances and Emerging Technologies Redefining Lung Aging Research.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.00912.2025},
pmid = {42003748},
issn = {1522-1563},
support = {512453064//Deutsche Forschungsgemeinschaft (DFG)/ ; 71_0011//Von-Behring-R&#x00F6;ntgen-Stiftung (Von Behring-R&#x00F6;ntgen-Foundation)/ ; LOEWE Habitat//Hessisches Ministerium f&#x00FC;r Wissenschaft und Kunst (Hessian Ministry for Science and Art)/ ; //Deutsches Zentrum f&#x00FC;r Lungenforschung (DZL)/ ; 5/2026 MR//Uniklinikum Giessen und Marburg (UKGM)/ ; 73_0031//Von-Behring-R&#x00F6;ntgen-Stiftung (Von Behring-R&#x00F6;ntgen-Foundation)/ ; },
abstract = {As the population ages, defining how biological processes change over the lifetime has become increasingly important. Acute and chronic lung diseases are more prevalent in older adults and emerging research is beginning to uncover the mechanistic and cellular pathways that link aging to conditions such as pneumonia and COPD. Additional mechanisms, particularly those involving extracellular vehicles (EVs), the microbiome, and sex differences, are now recognized as potential contributors to age-related changes in lung health yet remain underexplored. Advances in experimental models and analytical tools have accelerated progress in the field. Three-dimensional lung models such as organoids, precision cut lung slices, ECM scaffolds, and lung-on-a-chip systems offer more physiologically relevant systems than traditional two-dimensional cultures, improving translatability to in vivo biology. Meanwhile, the expansion of genomics, transcriptomics, proteomics, and metabolomics has enabled comprehensive, multi-omics approaches for mapping disease mechanisms, and such datasets are increasingly available. However, deeper integration with patient metadata and spatially resolved methods are still needed to advance precision medicine approaches to exploit aging mechanisms in chronic lung diseases. In this review, we highlight the importance of investigating EVs, the microbiome, and sex differences and their contribution of age-associated mechanism in the context of pneumonia and COPD and discuss how innovations in 3D lung models and omics technologies are reshaping our understanding of the pathological mechanisms that underlie these diseases.},
}
@article {pmid42003783,
year = {2026},
author = {Krueger, Q and Phippen, B and Reitzel, AM},
title = {Unique Transcriptional Responses by the Sea Anemone Nematostella vectensis to Individual Bacteria: Roles for Bacterial Species, Secreted Products and the Microbiome.},
journal = {Molecular ecology},
volume = {35},
number = {8},
pages = {e70339},
doi = {10.1111/mec.70339},
pmid = {42003783},
issn = {1365-294X},
support = {2044826//Division of Environmental Biology/ ; },
mesh = {Animals ; *Sea Anemones/microbiology/genetics/immunology ; *Microbiota/genetics ; Vibrio ; *Bacteria/genetics ; Transcriptome ; },
abstract = {Animal responses to bacteria, viruses and other microorganisms are important for understanding how host-microbe interactions lead to divergent molecular responses by the host and the assembly of the holobiont. The immune system of the animal and the resident microbial community are critical factors in the response, or lack thereof, by a host to a newly encountered microbe. Here, we describe the transcriptional response of the model cnidarian Nematostella vectensis when exposed to three Live Cell (LC) isolates (Bacillus velezensis, Pseudoalteromonas spiralis and Vibrio diabolicus) or their Cell Free Supernatants (CFS) with and without the native microbiome. Gene expression revealed large variation in the overall response ranging from 829 differentially expressed genes (DEGs) for antibiotically treated anemones exposed to B. velezensis to 49 DEGs in xenic individuals inoculated with V. diabolicus. The anemone's response similarly varied widely if the exposure was to live bacteria or the secreted products, especially for B. velezensis. Genes associated with the RIG-I-like immune pathway showed large differences in expression whereas the transcriptional variation for NF-kB and toll-like receptor were not significantly different. The response to each gram-negative bacteria differed from a purified bacterial ligand (lipopolysaccharide). Together, these results support the hypothesis that N. vectensis mounts unique transcriptional responses to individual bacterial species and their products, which are dependent on the presence of the native microbiome. The complexity of this molecular response further highlights the dynamic interplay between cnidarians and microbes in the assembly and maintenance of the holobiont.},
}
@article {pmid42003978,
year = {2026},
author = {Oda, Y and Miyake, M and Nishimura, N and Shimizu, T and Owari, T and Iida, K and Nakai, Y and Tanaka, N and Fujimoto, K},
title = {Changes of urinary immunity and microbiome after intravesical BCG therapy and their association with outcomes in NMIBC.},
journal = {Exploration of targeted anti-tumor therapy},
volume = {7},
number = {},
pages = {1002365},
pmid = {42003978},
issn = {2692-3114},
abstract = {AIM: Intravesical Bacillus Calmette-Guérin (BCG) is the standard therapy for non-muscle invasive bladder cancer (NMIBC); however, many patients experience recurrence or progression. We examined how urinary immune signals and the urinary microbiome change across BCG and are related to outcomes.<br><br>METHODS: In this single-center prospective cohort study, adults with NMIBC underwent transurethral resection of bladder tumor (TURBT), followed by BCG induction. Urine was collected before TURBT, before BCG, after BCG induction, and three months later. Urine sediment mRNA (PD-L1, PD-L2, CD33, and CD204) was quantified using TaqMan &#x394;Ct. The urinary microbiome was profiled using 16S rRNA gene sequencing, and diversity, composition, and taxon balance were evaluated using nonparametric tests, PERMANOVA, repeated-measures correlations, and mixed-effects models. We analyzed the relationship between the urinary microbiome and prognosis.<br><br>RESULTS: Twenty-three patients were analyzed; ten recurrences, eight progressions, and three deaths were observed. Relative to baseline, CD33 increased after BCG and after three months; PD-L2 increased immediately after BCG and returned to baseline by three months; PD-L1 and CD204 increased after BCG. Shannon alpha-diversity was unchanged, but total read count was higher at three months, with stable beta-diversity and dispersion. Higher PD-L1 expression was associated with lower Actinobacteria abundance in the bladder cancer microenvironment. A higher post-BCG Firmicutes/Bacteroidetes ratio was associated with worse prognosis, with the clearest signal for progression-free survival (PFS) observed in the univariate Cox models. Higher post-BCG Corynebacterium and Enterobacteriaceae abundance was associated with better PFS.<br><br>CONCLUSIONS: BCG was associated with higher urinary PD-L1/PD-L2 and myeloid marker transcripts, while overall community structure remained stable. These exploratory data support that pre-BCG microbial features may be related to early response, and post-BCG profiles may reflect durability and survival. Urine immune-microbiome profiling could be a feasible, noninvasive adjunct for monitoring and risk stratification in NMIBC.},
}
@article {pmid42003997,
year = {2026},
author = {Nto, NJ and Pirovano, W and Nel Van Zyl, K and Malan-Müller, S and Koch, E and Ramaboli, M and Madikgetla, D and de Leeuw, C and Lowry, CA and Hemmings, SMJ},
title = {The role of gut microbiome in the pathophysiology of PTSD, depression, and anxiety disorders.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2654224},
pmid = {42003997},
issn = {2993-3935},
abstract = {Posttraumatic stress disorder (PTSD), depression, and anxiety disorders are prevalent and often overlapping mental health conditions with complex, multifactorial etiologies. Growing evidence implicates the gut microbiome in their pathophysiology through immune modulation, neurotransmitter regulation, and bidirectional gut-brain signaling. Findings remain fragmented and difficult to reconcile due to differences in study populations, clinical contexts, and analytic methods. This structured narrative review synthesizes current evidence on gut microbial alterations in PTSD, depression, and anxiety, while examining methodological sources of heterogeneity. We searched four databases: PubMed, Scopus, Web of Science, and PsycINFO, and identified 64 eligible studies assessing the gut microbiome composition in these disorders. Sample sizes ranged from small, exploratory cohorts (≈20 participants) to large population-based datasets (>1000 participants), with most studies conducted in China. Stool sampling and DNA extraction protocols varied widely, although 16S rRNA gene amplicon sequencing of the V3-V4 region on Illumina platforms predominated. Alpha-diversity results were inconsistent, whereas beta-diversity analyses distinguished cases from controls. Across these disorders, alterations in microbial composition was observed, including enrichment of proinflammatory and depletion of beneficial bacterial taxa. The current findings indicate that that the gut microbiome represents a promising avenue for biomarker discovery and therapeutic innovation.},
}
@article {pmid42004001,
year = {2026},
author = {Yuan, Y and Ou, J and Fu, X and Tang, Y and Chen, Y and Deng, Q and Deng, Y and Sun, Y},
title = {A global-scale framework for quantifying the gut microbiome's mediating role in environmental and personal determinants of health.},
journal = {Eco-Environment &amp; Health},
volume = {5},
number = {2},
pages = {100236},
pmid = {42004001},
issn = {2772-9850},
abstract = {The human gut microbiome mediates health risks from the exposome, but research focuses on diet and lifestyle, leaving the impact of environmental characteristics unclear. Furthermore, the microbiota's quantitative, mediating role in linking the full exposome to disease is poorly understood. We conducted a global-scale association and mediation analysis of 13,463 American Gut Project participants, linking 128 environmental/personal factors to 10 gut microbial indices. We identified 390 significant but moderate associations (R[2] < 0.03, FDR < 0.05) between exposome factors and the microbiota, revealing it is influenced by numerous small, cumulative effects. Our analysis confirmed expected patterns, such as reduced gut diversity with antibiotic use and exposure to pollutants like PM2.5 and SO2. However, it also revealed counterintuitive findings, notably that several hazardous exposures, including alcohol, airborne persistent organic pollutants (POPs), and mycotoxin deoxynivalenol, were associated with increased alpha diversity (FDR < 0.05). Our mediation analysis linking these factors to 24 self-reported health outcomes identified 1129 significant pathways (p < 0.05), confirming established links such as antibiotic-associated risk for irritable bowel syndrome (IBS) and the protective effects of vegetable consumption on allergies. Our analysis also revealed striking paradoxes: exposure to POPs increased inflammatory bowel disease (IBD) risk, partly via an increase in gut alpha diversity (1.5%-15.7% mediated effect), directly challenging the "higher diversity is better" paradigm. Our global-scale analysis provides the first comprehensive map of the gut microbiome's mediating role in the human exposome, establishing a methodological blueprint for assessing the microbial contribution to the global burden of environmental disease.},
}
@article {pmid42004003,
year = {2026},
author = {Wang, B and Zhou, H and Yang, J and Fang, Y and Zi, Y and Zhang, L and Wang, J and Wang, L and He, Y and Ji, R and Lyu, T},
title = {Metabolomic and microbial responses of multilevel aquatic organisms to antibiotics in freshwater microcosm: The uniformity and specificity.},
journal = {Eco-Environment &amp; Health},
volume = {5},
number = {2},
pages = {100231},
pmid = {42004003},
issn = {2772-9850},
abstract = {The widespread presence of antibiotics in aquatic environments raises concerns about their ecological impacts. However, the molecular-level effects of antibiotics and the underlying mechanisms, particularly the responses across aquatic species, remain unclear. We established a freshwater microcosm including duckweeds (Salvinia natans), snails (Cipangopaludina cathayensis), and fish (Danio rerio) to investigate their uniform and specific responses to antibiotics (sulfamethoxazole, ciprofloxacin, oxytetracycline, and azithromycin), each at 1, 10, and 100 μg/L for 45 days. Antibiotic exposure diminished chlorophyll content in duckweeds, increased soluble sugar levels, elevated triglyceride levels in snails, and raised total bile acid concentrations in fish. Metabolomic analysis revealed that both duckweeds and fish tended to store energy to defend against antibiotic-induced stress, but through different pathways. Duckweeds accumulated sugar metabolites and downregulated antioxidants, while fish consumed primary sugars and converted them into lipid metabolites. Microbiome analysis indicated a self-coordination of gut bacteria in both snails and fish exposed to 1 and 10 μg/L of antibiotics, while dysbiosis occurred in snails at 100 μg/L, marked by increased pernicious bacteria abundance. In contrast, the abundance of probiotic bacteria increased in the fish gut due to microbial resistance to antibiotics, which played a crucial role in bile acid metabolism and positively influenced hepatic lipid metabolism via the gut-liver axis. This study uncovered the uniform and specific defense and dysregulation behaviors of multilevel aquatic organisms in response to antibiotic exposure, providing valuable insights into the selection of molecular-level endpoints for water quality benchmark development to safeguard aquatic life from antibiotic pollution.},
}
@article {pmid42004015,
year = {2026},
author = {Graham, NJ and Slavov, G and Wakelin, SA and Klápště, J and Day, NJ},
title = {Heritability of the Pinus radiata root microbiome.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1793374},
pmid = {42004015},
issn = {1664-462X},
abstract = {INTRODUCTION: Both evolutionary history and recent breeding selections can influence plant microbiomes, with closely-related individuals often having more similar microbiomes. Pinus radiata D.Don is an emerging conifer model species for investigating tree-microbiome interactions. However, little is known about how the P. radiata microbiome covaries with host genotype, especially beyond the seedling stage.<br><br>METHODS: We sampled the root microbiome of 528 individual P. radiata trees (age = 9 yrs), comprising four clonal copies each of 132 host genotypes from 28 full-sib families, from a clonal breeding trial in New Zealand. We determined whether variations in the bacterial and fungal root microbiomes were associated with host ancestry (i.e., provenance), family, and genotype.<br><br>RESULTS: Host family was associated with fungal but not bacterial root microbiome composition, whereas broader ancestry and individual genotype within families had no detectable effect on either bacterial or fungal microbiome composition. While core (in &#x2265;80% samples) amplicon sequence variants (ASVs) typically had negligible heritability, the relative abundances of 83 bacterial and 13 fungal non-core ASVs had low to moderate broad-sense heritabilities (0.2 to 0.46). Host genetic effects associated with abundances of heritable ASVs were primarily non-additive and likely involve complex gene interactions.<br><br>DISCUSSION: Our study revealed subtle host family effects for the root fungal microbiome of P. radiata, with several heritable bacterial and fungal ASVs. This study broadens our understanding of host genetic influences on the composition of the root microbiome of P. radiata and indicates there are both opportunities and challenges for including microbiome-related traits in tree breeding programmes.},
}
@article {pmid42004407,
year = {2026},
author = {Chu, D and Liu, N and Liu, Q and Li, X and Yang, H and Zhu, N and Liu, Z and Wang, R and Yuan, S and Fu, H},
title = {Diet-Driven Divergence in Gut Microbiota Variation Between Two Sympatric Gerbil Species.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73367},
pmid = {42004407},
issn = {2045-7758},
abstract = {Gut microbiota provide various benefits to their mammalian hosts; however, knowledge regarding interspecific differences in gut microecology remains limited. This study employed 16S rRNA sequencing combined with metagenomic functional prediction (potential functions or functional potential) to conduct a comparative analysis of the gut microbial composition and functional adaptability of two sympatrically distributed gerbil species with distinct diets: the herbivorous Rhombomys opimus (RO) and the omnivorous Meriones meridianus (MM). The results revealed that the omnivorous MM exhibited a level of gut microbial alpha diversity comparable to that of the herbivorous RO, whereas RO showed significant enrichment of norank_f__Muribaculaceae, a taxon associated with fiber degradation, and demonstrated higher abundance of genes related to complex fiber degradation. Notably, bacterial genera significantly enriched in the gut of MM, such as Lachnospiraceae_NK4A136_group and Desulfovibrio, may play important roles in maintaining gut health and enhancing chitin degradation efficiency. Furthermore, the abundance of genes related to monosaccharide and chitin degradation was significantly higher in MM than in RO. Functional network analysis indicated that the cellulose degradation gene networks in both gerbil species were predominantly synergistic, but the synergistic effect was stronger in RO than in MM (ratios of positive to negative correlation edges: 2.44: 1.59). Further analysis revealed that the monosaccharide and chitin degradation gene networks in MM both exhibited synergistic interaction patterns (ratios of positive to negative correlation edges: 1.69 and 2.95, respectively), whereas these two networks in RO were primarily antagonistic (ratios of positive to negative correlation edges: 0.831 and 0.73, respectively). This suggests that the gut microbiota of RO are more conducive to digesting complex plant fibers, while those of MM are better adapted for digesting starch and chitin. This differentiation in gut microbiota optimizes the utilization of different food resources by the two species, thereby promoting their sympatric coexistence. This study enhances our understanding of the adaptive mechanisms of gut microecology in rodents with different diets and provides an important foundation for further research on the microbial ecology of wild rodents and the mechanisms underlying sympatric species coexistence.},
}
@article {pmid42004633,
year = {2026},
author = {Monjardino, P and Azevedo, AR and Mendonça, D and Pozsgai, G and Borges, PAV and Frias, J and Toubarro, D},
title = {Metagenomic survey of fungal communities in compost from dairy plant wastewater sludge and garden trimmings.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e174893},
pmid = {42004633},
issn = {1314-2828},
abstract = {BACKGROUND: Composting converts organic residues into stable organic matter and nutrients under aerobic conditions, improving soil properties and microbiome balance, while mitigating environmental impacts. Although microbiomes of various compost types have been studied, information is still fragmented and often not tailored to specific raw material combinations. In particular, little is known about the fungal communities involved in composting dairy plant wastewater sludge mixed with garden trimmings. This data paper contributes to filling that gap by providing a comprehensive taxonomic inventory.<br><br>NEW INFORMATION: We provide a fungus-focused dataset from 18 compost samples generated from a 1:1 (w/w) mix of garden trimmings and dairy plant wastewater sludge, collected at three process stages (thermophilic start/end; mid-cooling and maturation) under two turning regimes. Shotgun metagenomes were taxonomically annotated against NCBI taxonomy (accessed 19 Feb 2025). Only Fungi were detected within Eukarya, spanning nine phyla; Ascomycota (60.8%), Mucoromycota (17.76%), Basidiomycota (8.50%) and Chytridiomycota (7.21%) comprised 94.27% of the taxonomic features. We report 417 genera (13 >1% relative abundance each); top: Aspergillus (17.93%), Rhizopus (8.61%), Chaetomium (4.83%), Aureobasidium (3.09%), Madurella (2.85%), Paramicrosporidium (2.71%), Rhizophagus (1.88%), Rasamsonia (1.81%), Hyaloraphidium (1.39%), Thermochaetoides (1.31%), Talaromyces (1.19%), Trichoderma (1.15%), Podospora (1.06%) comprised 49.81% of the taxonomic feature abundance. Overall 663 taxa were identified (578 species, 416 genera, 230 families, 106 orders, 48 classes and 9 phyla). The dataset (DwCA; 663 occurrences) is intended to serve as a reference for compost mycobiomes and will be available via GBIF (DOI 10.15468/nmpzwr).},
}
@article {pmid42004820,
year = {2026},
author = {Finkelstein, S and Frishman, S and Turjeman, S and Shtossel, O and Tikhonov, E and Nuriel-Ohayon, M and Pinto, Y and Popova, P and Tkachuk, AS and Vasukova, EA and Anopova, AD and Agay-Shay, K and Pustozerov, EA and Pervunina, TM and Grineva, EN and Hod, M and Schwartz, B and Hadar, E and Koren, O and Louzoun, Y},
title = {Early pregnancy is characterized by a significant decrease in the diversity of the oral microbiome and strong associations with lifestyle and conception method.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2657139},
pmid = {42004820},
issn = {2000-2297},
abstract = {BACKGROUND: Most studies of the oral microbiome during pregnancy have focused on the second and third trimesters (T2, T3, respectively). To date, no large-scale longitudinal study has examined oral microbiome development across all three trimesters, leaving early gestational dynamics largely unexplored.<br><br>METHODS: We conducted a longitudinal analysis of 346 pregnant Israeli women, validated in an independent cohort of 154 Russian women. In Israel, saliva samples were collected during T1 (11-14 weeks), T2 (24-28 weeks), and T3 (32-38 weeks); in Russia, samples were collected during T2 and T3 at similar gestational ages. Microbial profiles were analyzed for differential abundance and associations with maternal nutrition and lifestyle.<br><br>RESULTS: Significant shifts in oral microbial composition were observed as early as the transition from T1 to T2. Alpha diversity decreased progressively across pregnancy. Taxonomic changes included a reduction in Verrucomicrobiota and an increase in Synergistota. Gluten-free diet showed the strongest associations with microbiome composition across all trimesters, followed by smoking history and conception method.<br><br>CONCLUSIONS: This study provides the first large-scale evidence of significant oral microbiome changes beginning in early-mid pregnancy, characterized by reduced diversity and a directional shift toward inflammation-associated communities. Strong associations between gluten consumption and smoking suggest a lifestyle effect on the oral microbiome.},
}
@article {pmid42004950,
year = {2026},
author = {Suarez, LJ and Vargas-Sanchez, PK and Angelov, N and Mylonakis, E and Arce, RM},
title = {Host-pathogen interactions in periodontitis: an integrative interkingdom perspective.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1797726},
pmid = {42004950},
issn = {1664-3224},
mesh = {Humans ; *Periodontitis/microbiology/immunology ; *Host-Pathogen Interactions/immunology ; Microbiota/immunology ; Dysbiosis/microbiology/immunology ; Biofilms/growth &amp; development ; Animals ; Bacteria/immunology ; },
abstract = {Periodontitis is an infectious, inflammatory, non-communicable disease characterized by tissue destruction driven by host responses to dysbiotic shifts in oral microbial communities. The subgingival microbiome constitutes a complex ecosystem in which bacteria, fungi, viruses, and archaea interact via interkingdom communication to modulate the inflammatory response through molecular mechanisms that remain largely unknown. This narrative review aims to understand how functional imbalances within the microbiome alter the microenvironment and promote uncontrolled inflammation responsible for periodontal tissue damage, with implications for systemic disease. The search strategy was conducted according to the PRISM-S extension, to include studies evaluating interkingdom host-pathogen interactions at the gingiva interphase leading to microbial and immune dysbiosis. The discovery of fungi acting as opportunistic pathogens highlights their role in enhancing biofilm virulence and exacerbating host responses, contributing to the total inflammatory burden. Similarly, viruses and archaea influence bacterial metabolism through mechanisms including lysis, nutrient recycling, horizontal gene transfer, and interspecies hydrogen transfer. This interkingdom crosstalk disrupts symbiosis, facilitating enhanced biofilm formation, increased production of virulence factors, and antibiotic resistance. A better understanding of the interkingdom perspective necessitates a comprehensive polymicrobial approach to diagnosis and treatment that extends beyond simply controlling bacteria to include the modulation of interkingdom communication systems. Developing new therapeutic alternatives that address these complex interactions is essential for improving outcomes achieved with mechanical therapy and managing the interrelationships between periodontitis and other systemic diseases.},
}
@article {pmid42004962,
year = {2026},
author = {Li, J and Chen, X and Xie, X},
title = {Mechanistic insights into gut microbiota-driven autoimmunity in rheumatoid arthritis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1812972},
pmid = {42004962},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Animals ; Dysbiosis/immunology ; },
abstract = {Rheumatoid arthritis (RA) is a systemic autoimmune disease whose pathogenic drivers and initiating immune events remain incompletely understood. Increasing evidence implicates the gut-joint axis in RA, yet the mechanisms by which intestinal microbiota contribute to disease development still require integrative clarification. This review summarizes current experimental and clinical evidence on the role of gut dysbiosis in promoting autoimmunity in RA. We discuss alterations in microbial composition and their links to barrier dysfunction, immune-cell polarization, microbial metabolites, and antigen-specific immune responses. Human cohort studies and arthritis models suggest that reduced microbial diversity, loss of short-chain fatty acid (SCFA)-producing commensals, and expansion of taxa such as Prevotella copri and Collinsella are associated with impaired epithelial integrity, enhanced Th17/Tfh differentiation, reduced regulatory T- and B-cell activity, and increased autoantibody production. Mechanistic studies further support roles for molecular mimicry, microbially derived citrullinated antigens, and metabolite-mediated signaling in the breakdown of immune tolerance and persistence of synovial inflammation. We also discuss emerging microecology-based interventions, including probiotics, prebiotics, postbiotics, and fecal microbiota transplantation, together with their translational potential and current limitations. Overall, available evidence places gut microbiota-mediated immune remodeling at the center of RA pathogenesis and supports precision microbiome modulation as a promising adjunctive strategy for disease prevention and treatment.},
}
@article {pmid42005042,
year = {2026},
author = {Dalamaga, M and Liu, J},
title = {Metabolic advances in 2025: from clinical breakthroughs to molecular reprogramming.},
journal = {Metabolism open},
volume = {29},
number = {},
pages = {100442},
pmid = {42005042},
issn = {2589-9368},
abstract = {The year 2025 represented a turning point in metabolic research, marked by advances that combined unprecedented clinical efficacy with deep mechanistic insight. Landmark obesity trials redefined therapeutic expectations, with head-to-head and combination studies showing that the depth and distribution of weight loss are critical determinants of metabolic benefit across obesity and type 2 diabetes. In parallel, gene-editing studies crossed a translational threshold, showing that durable modification of metabolic pathways in humans is feasible, from bespoke correction of inborn errors to population-scale lipid lowering. Mechanistic investigations challenged long-standing assumptions about metabolic regulation. Experimental work revealed that mitochondrial electron transport functions as a dynamic redox regulator rather than a passive energy conduit, linking coenzyme Q imbalance and reverse electron transport to hepatic steatosis and metabolic dysfunction. Other studies reframed nutrient exposure and endogenous metabolites, demonstrating that non-nutritive sweeteners and cyanide exert context-dependent metabolic effects through regulated endocrine and redox pathways. At the systems level, multi-omics analyses defined reproducible microbiome-metabolome signatures associated with impaired glucose regulation, while artificial intelligence and continuous glucose monitoring exposed dynamic glycemic phenotypes invisible to conventional biomarkers. Precision-nutrition studies further showed that selective manipulation of sulfur amino acid availability can program thermogenic and metabolic responses. Collectively, these studies illustrate how metabolism in 2025 was approached as a modifiable, programmable system, shaped by clinical intervention, molecular control, and data-driven phenotyping, and point toward an era of increasingly precise and integrated metabolic medicine.},
}
@article {pmid42005241,
year = {2026},
author = {Flores Rodríguez, JC and Morán Ortega, MJ and Jimenez Ordoñez, AC and Rojas López, AK and Leyva, MC and Romero, HV},
title = {Postbiotics in Dermatology: A Literature Review of Emerging Topical Therapies for Acne, Rosacea, and Eczema.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e105440},
pmid = {42005241},
issn = {2168-8184},
abstract = {Postbiotics, defined as non-viable microbial cells and their metabolites, have emerged as topical therapies for inflammatory dermatoses and provide more clinical benefits than live postbiotics by eliminating infection risk and stability. This literature review aims to generalise existing knowledge about the effectiveness and mechanisms of action of first-line topical postbiotic treatments for acne, rosacea, and eczema. Search terms included "postbiotics" and keywords that represented the dermatological conditions of interest. Thematic synthesis was performed on the systematically extracted data. After screening, 16 studies were included in the review. Postbiotic preparations showed significant reductions in Scoring Atopic Dermatitis (SCORAD) and pruritus and improved barrier function in the skin, as well as longer remissions (p < 0.001). In acne vulgaris, postbiotics decreased inflammatory lesions by 50% to 70%, suppressed sebum secretion (42% to 72%), and stopped the growth of Cutibacterium acnes. The study concluded that topical postbiotics, reported to be effective in atopic dermatitis and acne vulgaris, have favourable safety profiles and can be integrated into treatment regimens for the aforementioned diseases. However, no interventional studies have examined rosacea, and the evidence is limited to narrative reviews in which microbiome disequilibrium remains undetermined despite a lack of clinical efficacy. Therefore, a lack of clinical trials for rosacea is a high research priority, given the substantial mechanistic rationale for this absence of high-quality pragmatic evidence.},
}
@article {pmid42005542,
year = {2026},
author = {Canha-Gouveia, A and Tenorio, CM and Rööp, T and Kõljalg, S and Smidt, I and Sepp, E and Štšepetova, J and Saare, M and Vela, S and Pérez-Prieto, I and Vargas, E and Mozas, J and Clavero, A and Sola-Leyva, A and Salumets, A and Mändar, R and Altmäe, S},
title = {Assessing endometrial microbiota in endometriosis: culturomics and sequencing analysis of receptive-phase tissue.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100593},
pmid = {42005542},
issn = {2666-5174},
abstract = {Endometriosis has been associated with alterations in the reproductive tract microbiota, yet studies focusing on the endometrial microbiome remain inconsistent, partly due to the low-biomass nature of this niche and methodological heterogeneity. In this prospective pilot study, we investigated whether the receptive-phase endometrial microbiota differs between women with and without endometriosis using a combined culturomics and 16S rRNA gene sequencing approach. Endometrial samples were collected from 20 women undergoing fertility assessment, including 10 women with a previous diagnosis of endometriosis and 10 controls with male factor infertility. Biopsies were used for culturomics and Tao brush samples for sequencing, both obtained during the mid-secretory phase. Viable bacterial growth was recovered from 19 of 20 biopsies, yielding approximately 2500 colonies corresponding to 40 non-redundant species. Direct plating and aerobic pre-incubation shared around 45% of detected species, with pre-incubation enhancing species recovery but limiting quantitative comparisons. Bacterial load estimated from direct cultures showed wide inter-individual variability and no significant differences between groups, consistent with 16S rRNA gene sequencing results, which also revealed no clear differences in microbial diversity or overall community composition within this cohort. Only a limited overlap was observed between taxa detected by culture and sequencing, highlighting the complementarity and methodological biases of each approach. Overall, this study demonstrates the feasibility of recovering viable bacteria from receptive-phase endometrial samples and supports the combined use of culturomics and sequencing as complementary tools for studying microbiota in low-biomass uterine environments. These findings should, however, be interpreted considering the exploratory design and limited sample size.},
}
@article {pmid42005840,
year = {2026},
author = {Zhgun, AA and Khomutov, MA and Avdanina, DA and Troyan, E and Dumina, MV and Ermolyuk, AA and Simonenko, N and Shumikhin, K and Khurs, EN and Zhuikova, Y and Varlamov, VP and Shitov, MV and Khomutov, AR},
title = {H-phosphinic analogs of natural amino acids: a novel and efficient treatment for preventing biodeterioration of treasured painted artworks.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1677277},
pmid = {42005840},
issn = {1664-302X},
abstract = {INTRODUCTION: Microorganisms can destroy various materials that make up objects of cultural heritage. In particular, ancient tempera paintings are made with egg yolk, animal glue, and a number of other organic materials, which serve as a good breeding ground for the development of microorganisms. Recently, the range of traditional antiseptics used to protect tempera paintings from biodeterioration has been significantly reduced because of undesirable properties associated with their interaction with painting materials and toxicity. Therefore, it is necessary to develop a new generation of antiseptics that can effectively protect paintings from destructive microorganisms.<br><br>METHODS: To solve this challenging task and protect paintings from fungal damage, we used H-phosphinic analogs of natural amino acids. Twelve different H-phosphinic analogs of natural amino acids were screened on Czapek-Dox agar medium against 11 mold fungi belonging to the genera Aspergillus, Penicillium, Simplicillium, Microascus, Cladosporium, and Ulocladium. These mold fungi are responsible for the biodegradation of tempera paintings and are the dominant representatives of the microbiome of the State Tretyakov Gallery in Russia.<br><br>RESULTS: All the studied compounds at concentrations of 0.7-2.5&#x202f;mM inhibited the mycelial growth of mold fungi. The supplementation of H-phosphinic analogs of alanine, aspartate, and valine resulted in the loss of characteristic pigmentation of Penicillium chrysogenum, which may be associated with inhibition of Ac-CoA and malonyl-CoA biosynthesis. The H-phosphinic analog of methionine protected mock layers with sturgeon glue more effectively than the other H-phosphinates and standard antiseptics, such as benzalkonium chloride or sodium pentachlorophenolate. The addition of H-phosphinic amino acid analogs to sturgeon glue did not significantly affect the spectral and surface properties of the glue applied on the layout but effectively inhibited the growth of the studied mold fungi on mock-up layers during long-term storage.<br><br>CONCLUSION: Our data provide the first evidence of the successful use of nontoxic H-phosphinic analogs of natural amino acids for protecting paintings from biodeterioration.},
}
@article {pmid42005845,
year = {2026},
author = {Berg, G and Antonietti, M and Egamberdieva, D and Korsten, L and Wicaksono, WA},
title = {Correction: Microbiome-inspired solutions to save human and planetary health.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1831892},
doi = {10.3389/fmicb.2026.1831892},
pmid = {42005845},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1744452.].},
}
@article {pmid42006274,
year = {2026},
author = {Saravinovska, K and Santi, D and Costantino, F and Prete, A and Šojat, AS and Spaggiari, G and Ivović, M and Lambrinoudaki, I and Armeni, E and Jurišić, A and Mihajlović, S and Vujović, S and Marina, LV},
title = {The impact of estrogen status on the gut microbiome: a systematic review and meta-analysis.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1780806},
pmid = {42006274},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; *Estrogens/metabolism ; Postmenopause ; *Primary Ovarian Insufficiency/microbiology/metabolism ; Premenopause ; },
abstract = {BACKGROUND: Estrogens have been proposed as modulators of gut microbiome (GM) composition, yet evidence from observational studies remains inconsistent.<br><br>OBJECTIVE: This meta-analysis aimed to systematically summarise existing evidence on GM alterations in hypoestrogenic women - post-menopausal or premature ovarian insufficiency (POI) - compared to euestrogenic pre-menopausal controls.<br><br>METHODS: PubMed, SCOPUS and Embase were searched through December 2024 for studies comparing GM characteristics between hypoestrogenic and pre-menopausal women. Primary outcome was &#x3b1;-diversity (Shannon index). Secondary outcomes included relative abundances of Bacteroidetes, Firmicutes, and the Bacteroidetes to Firmicutes ratio. Random-effects models were used for data synthesis.<br><br>RESULTS: Out of 1092 studies screened, 7 met the inclusion criteria (n = 45 women with POI, n = 1222 post-menopausal women, n = 463 eustrogenic controls). No significant differences were observed in &#x3b1;-diversity (p=0.990), Bacteroidetes (p=0.440), or Firmicutes abundance (p=0.110) between hypoestrogenic and euestrogenic groups, irrespective of POI or postmenopause. Similarly, the Bacteroidetes to Firmicutes ratio showed no significant difference between the groups (p=0.400). Study heterogeneity was high (I&#xb2; 61-99%).<br><br>CONCLUSION: Current evidence does not support consistent differences in GM diversity or major bacterial phyla between hypoestrogenic and euestrogenic women. Given the substantial heterogeneity, limited control of confounding factors, and variability in methodological quality, these findings should be interpreted with caution. High-quality, well-controlled studies are needed to better define the relationship between estrogen status and the GM.},
}
@article {pmid42006291,
year = {2026},
author = {He, H and Liu, S and Han, H and Zhou, H and Chen, Y and Tian, H and Chen, M and Wei, W},
title = {Microbial transmission among giant panda, sympatric wildlife, and domesticated animals.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115276},
pmid = {42006291},
issn = {2589-0042},
abstract = {The gut microbiome of wild animals is subject to complex influences, including cross-species transmission that risks host and environmental health. This study used 16S rRNA sequencing to profile microbial communities in giant pandas (GPs), sympatric wildlife, domesticated animals, and environmental samples from panda habitats. Results revealed significant differences in microbial community structure at both phylum and genus levels. Source Tracker analysis indicated that red pandas (RPs) serve as the primary potential microbial source for GPs (72.17%). However, the two species exhibited distinct patterns in acquiring microbes from other groups: GPs were more susceptible to potential transmission by aerobic and facultative anaerobic bacteria compared to RPs. Water and soil showed distinct microbial assembly patterns as sinks, reflecting their divergent physicochemical properties. These findings demonstrate that dietary specialization and environmental exposure collectively shape the gut microbiome, offering insights for managing microbial interactions and habitats.},
}
@article {pmid41994262,
year = {2026},
author = {Li, CM and Kenéz, &#xc1;},
title = {Effects of dietary black soldier fly larvae meal inclusion on the serum metabolome of Silkie crossbreed chickens.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1803699},
pmid = {41994262},
issn = {2297-1769},
abstract = {INTRODUCTION: Black soldier fly larvae (BSFL; Hermetia illucens) meal, an alternative to conventional dietary protein sources, such as soybean meal, is rich in medium-chain fatty acids, antimicrobial peptides and other bioactive components. These components may modulate the composition and function of the gut microbiota or, after absorption, affect host metabolic pathways. We hypothesised that the functional effects of BSFL meal would be reflected in alterations in the serum metabolite profile of Silkie crossbreed chickens.<br><br>METHODS: Serum samples from chickens fed a control soybean-based diet or a diet containing 150 g/kg partially defatted BSFL meal were analysed using untargeted liquid chromatography-mass spectrometry.<br><br>RESULTS AND DISCUSSION: A total of 3304 metabolite features were detected, of which 1341 were annotated, with 777 retained for statistical analysis. Principal component analysis and PERMANOVA revealed a clear separation between dietary groups (p = 0.001). Forty metabolites were significantly altered (FDR &#x2264; 0.05), with 31 more abundant and nine less abundant in the BSFL group. These shifts were characterised mainly by increased lipid-related metabolites, including medium-chain fatty acids (MCFAs) and phospholipids, indicating alterations in lipid metabolism. In addition, changes in amino acid derivatives and energy-related metabolites suggested the modulation of amino acid and energy metabolic pathways. Several metabolites with putative microbial origin were elevated, consistent with indirect host-microbiome metabolic interactions. These metabolic changes showed correlations with significantly higher average daily gain (p = 0.02), numerically greater final live weight, and a reduced feed conversion ratio in BSFL-fed chickens (p = 0.07 and p = 0.08, respectively). Overall, dietary inclusion of 150 g/kg BSFL meal modified systemic metabolism without detectable negative effects on performance or serum biomarkers, suggesting that this level of BSFL inclusion can be beneficial for slow-growing Silkie chickens.},
}
@article {pmid41994270,
year = {2026},
author = {Albarracín, VH and Gámez-Espinosa, E and Bingjie, M and Gomez de Saravia, SG and Jroundi, F},
title = {Editorial: Microbes and cultural heritage: from biodiversity to applications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1829794},
doi = {10.3389/fmicb.2026.1829794},
pmid = {41994270},
issn = {1664-302X},
}
@article {pmid41994275,
year = {2026},
author = {Yu, T and Yu, Y and Zhao, J and Li, H and Lu, H and Li, Y and Peng, Y and Wang, S and Wei, W and Cheng, X},
title = {Qifuyin improves physiological frailty by regulating the intestinal flora in 3xTg-AD mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753643},
pmid = {41994275},
issn = {1664-302X},
abstract = {OBJECTIVE: Alzheimer's disease (AD) is often accompanied by motor dysfunction, impaired limb strength, and gut microbiota disturbances. This study aimed to evaluate the effects of Qifuyin (QFY), a traditional Chinese medicine formula, on motor deficits, limb strength, aging, and gut microbiota composition in 3xTg-AD mice, a widely used model of AD.<br><br>METHODS: Male and female 3xTg-AD mice were administered QFY at low, medium, or high doses. Motor function was assessed using grip strength and rotarod tests. Aging was evaluated through aging scores. Gut microbiota composition was analyzed at the phylum, family, genus, and species levels. Functional profiling of microbiota was performed using KEGG, eggNOG, and carbohydrate-active enzyme (CAZyme) databases. Pearson correlation analyses were conducted to explore relationships between microbiota composition and motor performance.<br><br>RESULTS: QFY treatment significantly improved both absolute and normalized grip strength in male and female 3xTg-AD mice. Similarly, motor coordination, as assessed by latency to fall on the rotarod, was significantly enhanced in the groups of QFY. Aging scores were significantly reduced after the treatment of QFY. Microbiome analysis revealed that QFY treatment restored species diversity and improved the overall composition of gut microbiota, with significant increases in Muribaculaceae and decreases in Alcaligenaceae, Rhodanobacteraceae, and Spirochaetaceae. Principal component analysis (PCA) indicated that the gut microbiota composition of the QFY group resembled that of the control (Con) group. Functional analyses showed that treatment of QFY restored microbial pathways related to metabolism and genetic information processing, with significant correlations between microbial alterations and improved motor outcomes. Additionally, QFY modulated the abundance of key carbohydrate-active enzymes, including GH43 and GH35, which were positively correlated with grip strength and rotarod performance.<br><br>CONCLUSION: Qifuyin improves motor function, reduces aging-related deficits, and restores gut microbiota homeostasis in 3xTg-AD mice. These findings suggest that QFY may offer therapeutic potential for addressing frailty and motor dysfunction in AD, in association with alterations in gut microbiota composition and predicted microbial functions.},
}
@article {pmid41994282,
year = {2026},
author = {Wang, X and Wei, M and Yi, Y and An, J and Wang, J and Zhao, R and Su, Z and Ji, G and Zhang, X and Liu, X},
title = {Elephant-derived Bacillus licheniformis modulates immune cells shedding light on cancer resistance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753410},
pmid = {41994282},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC) is currently a leading cause of cancer-related morbidity and mortality globally, underscoring the need for innovative therapeutic strategies. Probiotic treatment is increasingly appreciated as an innovative method for ameliorating inflammation and modulating the tumor microenvironment, especially in gastrointestinal diseases. Many bacterial species isolated from human and animal sources are proven effective in potential disease treatments. Elephants, renowned for their exceptional resistance to cancer, have traditionally been linked to their TP53 gene multiplicity. However, the potential contribution of their evolutionarily-refined gut microbiota to their remarkable cancer resistance remained largely unexplored.<br><br>METHODS: Here, we investigated this underexplored avenue by analyzing the elephant gut microbiome and isolating a probiotic bacterium. We utilized whole genome sequencing (WGS) to assess its genomic profile. The in vivo efficacy was evaluated in mouse models of gut inflammation and colorectal tumors. Underlying mechanisms were investigated using transcriptomic analysis, flow cytometry, and integrative metabolomics. Finally, in vitro experimental validations were conducted on mouse and human CRC cell lines using the bacterial culture supernatant.<br><br>RESULTS: We found that elephants possess a highly specialized gut microbiome finely tuned to metabolize complex polysaccharides. WGS of the isolated Bacillus licheniformis revealed its metabolic and functioning roles and confirmed the absence of virulence factors. We demonstrated that this elephant-derived strain effectively alleviated gut inflammation and suppressed the progression of colorectal tumors in mouse models. Transcriptomic analysis and flow cytometry revealed that B. licheniformis remodeled the immune microenvironment, specifically activating tumor-infiltrating T cell response and cell cytotoxicity. Integrative metabolomics identified several key metabolites as potential soluble mediators correlated with tumor regression. Furthermore, the supernatant of B. licheniformis culture significantly enhanced cytotoxicity and upregulated p53 expression in CRC cell lines in vitro.<br><br>DISCUSSION: Collectively, these findings unveil previously unrecognized therapeutic potentials inherent in elephant-derived probiotics, suggesting a mechanism of functional immune regulation for CRC prevention.},
}
@article {pmid41994290,
year = {2026},
author = {Li, J and Xu, L and Ding, X and Qiu, N and Yue, J},
title = {Gut and skin microbial dysbiosis correlate with systemic inflammation and pruritus in immunological non-responders.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1758111},
pmid = {41994290},
issn = {1664-302X},
abstract = {INTRODUCTION: Among people living with human immunodeficiency virus (PLWH), those who exhibit immunological non-responders (INR) are highly susceptible to developing pruritus. The aim of this study was to examine the relationships among pruritus, alteration of the gut and skin microbiomes, and systemic inflammation in PLWH with INR.<br><br>METHODS: Thirty-three PLWH with INR were enrolled and divided into Pruritus (n = 18) and Control (n = 15) groups. All participants met the defining criterion of a low CD4+ T cell count (&#x2264; 350 cells/&#x3bc;l). We performed 16S rRNA gene sequencing of fecal and skin samples, and measured plasma IL-1&#x3b2; and IL-10 levels.<br><br>RESULTS: Microbiome analysis revealed specific, bidirectional patterns of microbial dysbiosis. Specifically, the skin microbiome of the Pruritus Group exhibited significantly greater microbial richness (Chao1 and Faith's Phylogenetic Diversity indices, P < 0.01), coupled with significantly lower representation of the potentially protective genus Bacillus (adjusted P<0.05), compared with that of the INR Control Group. Conversely, the gut microbiome of the Pruritus Group exhibited significantly lower alpha diversity (adjusted P<0.05). Furthermore, we identified a significant positive correlation between levels of plasma pro-inflammatory cytokine IL-1&#x3b2; and the relative abundance of the opportunistic gut genus Veillonella (adjusted P<0.05).<br><br>CONCLUSIONS: Pruritic PLWH-INRs exhibit skin microbial hyper-richness, Bacillus depletion, and reduced gut diversity, suggesting a systemic inflammatory basis linked to gut-skin dysbiosis. These findings provide new insights into the pathological process, offering a potential foundation for future microbiome-targeted therapeutic strategies as novel management avenues.},
}
@article {pmid41994309,
year = {2026},
author = {Sarkar, P and Sarkar, S and Unnisa, M and Singh, AP and Inavolu, P and Rughwani, H and Jakkampudi, A and Jaggaiahgari, S and Reddy, DN and Talukdar, R},
title = {The Jejunal Microbiota in Patients With Chronic Pancreatitis: Results From a Pilot Study.},
journal = {Gastro hep advances},
volume = {5},
number = {5},
pages = {100907},
pmid = {41994309},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Chronic pancreatitis (CP) is associated with several systemic metabolic abnormalities including diabetes. While the colonic microbiota and its association with diabetes in CP have been reported, the specific composition of the small intestinal microbiota and its function in CP remains poorly understood. In this pilot study, we primarily aimed to characterize the jejunal microbiota in patients with CP and explore potential associations with diabetes.<br><br>METHODS: Jejunal aspirates were collected in a RNAlater-containing sterile container from 29 patients with CP and 10 controls. The samples were then snap lysed followed by metagenomic DNA extraction. Next-generation sequencing was performed for the variable region 3-4 of the 16SrDNA in Illumina MiSeq. After quality control, microbial profiling and functional analysis were conducted using standard bioinformatics pipelines. We also evaluated tight junction integrity in jejunal biopsy samples using immunofluorescence. Furthermore, we assessed for plasma and stool metabolites.<br><br>RESULTS: Patients with CP exhibited higher abundances of Prevotella vespertina, Prevotella oris, and Prevotella salivae, while controls demonstrated higher abundances of Prevotella scopos, Veillonella, Rothia, and Lachnospiraceae. Immunofluorescence showed decreased expression of the tight junction protein occludin in the jejunal mucosa of CP diabetic (CPD) patients compared to endoscopic controls (EC) (p.corr. CPD-EC = 0.012). No differences were seen between CP nondiabetic and endoscopic controls, and between the CP subgroups (CPND-EC = 0.29 and CPD-CPND = 1 respectively). Overall, there were significant plasma metabolomic abnormalities in patients with CP and a trend toward reduction of butyrate in the stool samples of the CP patients with diabetes.<br><br>CONCLUSION: Our observations suggest alterations in the jejunal microbiota and mucosal barrier function in CP. These were associated with lower fecal butyrate. This may contribute to the pathogenesis of associated metabolic complications in CP. Further large-scale longitudinal and mechanistic studies are needed to validate our findings.},
}
@article {pmid41994453,
year = {2026},
author = {Zhang, W and Zhang, K and Liao, Y and Yang, Z and Xia, Z and Ke, X and Zhang, D and Chen, J and Wu, H and Hong, Y and Wang, H and Liu, Z and Suo, L and Zhang, Y and Zhang, C},
title = {Characterization of the aqueous humor microbiome in Posner-Schlossman syndrome: an exploratory metagenomic sequencing study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1780981},
pmid = {41994453},
issn = {2296-858X},
abstract = {OBJECTIVE: This study aims to characterize the aqueous humor (AH) microbiome in Posner-Schlossman syndrome (PSS) patients and evaluate its potential as a diagnostic and therapeutic target.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was performed on 59 AH samples from patients diagnosed with PSS (n&#x202f;=&#x202f;28) and myopia patients who underwent intraocular lens (ICL) implantation (n&#x202f;=&#x202f;31). Taxonomic profiling and diversity analyses were conducted to characterize the microbial communities. Interactions among microbial community members were evaluated using correlation analyses.<br><br>RESULTS: Key findings revealed that intraocular microbiomes existed in both normal and diseased eyes; however, PSS patients exhibited lower microbial diversity (Shannon index, p&#x202f;=&#x202f;0.066; Simpson index, p&#x202f;=&#x202f;0.065) and distinct community structures (PERMANOVA, p&#x202f;=&#x202f;0.05). Disease-specific microbial signatures were identified: Paeniglutamicibacter was uniquely enriched in the PSS group, whereas Escherichia coli dominated in the ICL group. Moreover, ecological network analysis demonstrated contrasting interaction patterns. The microbiomes in the PSS group formed stable, tightly connected networks with balanced positive/negative correlations, whereas those in the ICL group exhibited antagonistic relationships, suggesting competitive exclusion. These results challenge the traditional view of ocular sterility and reveal dynamic microbiome shifts associated with PSS pathogenesis. The enrichment of Paeniglutamicibacter in PSS may represent an associated microbial signature that could potentially reflect compensatory responses to chronic inflammation, although experimental validation is needed to confirm this hypothesis.<br><br>CONCLUSION: Our study provides preliminary evidence supporting the concept of intraocular microbiome dysbiosis in PSS, which requires validation in future studies. These findings suggest that potential microbial biomarkers warrant further investigation for their diagnostic and therapeutic implications.},
}
@article {pmid41994836,
year = {2026},
author = {Radhika, M and Mohan, S and Singh, HJ and Kadwe, P and Prajapati, J and Mansuri, SH and Sonis, JJ},
title = {Clinical Impact of Macronutrients and Micronutrients: A Review of Nutritional Balance, Deficiency Disorders, and Therapeutic Applications.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e105305},
pmid = {41994836},
issn = {2168-8184},
abstract = {Nutrition plays a fundamental role in maintaining human health and modulating disease risk across the life course. This narrative review synthesizes contemporary evidence on the clinical significance of macronutrients, including carbohydrates, proteins, and fats, and micronutrients, including vitamins and minerals, establishing nutritional balance as a central determinant of human health, disease susceptibility, and therapeutic efficacy. These nutrient categories function within an integrated metabolic network in which macronutrients provide energy and structural substrates, while micronutrients serve as essential cofactors and regulatory agents in enzymatic, hormonal, and cellular signalling processes. The synthesis demonstrates that nutritional imbalance, arising from either deficiency, such as iron-deficiency anaemia and vitamin D insufficiency, or excess, including high intakes of refined carbohydrates and saturated fats, constitutes a major contributor to global disease burden, particularly the phenomenon described as the double burden of malnutrition. In response to these challenges, the review highlights the role of evidence-based nutritional therapy, encompassing established dietary patterns such as the Mediterranean and Dietary Approaches to Stop Hypertension (DASH) diets, as well as the clinical implementation of medical nutrition therapy in chronic disease management. It further emphasizes a paradigmatic shift from population-level dietary recommendations toward precision nutrition, an emerging framework that integrates nutrigenomics, metabolomics, and gut microbiome profiling to inform personalized dietary interventions. By conceptualizing nutrition as a dynamic and interactive system, this review offers a comprehensive perspective that integrates biochemical mechanisms with individualized clinical care, positioning nutritional balance as a foundational component of contemporary preventive and therapeutic medicine.},
}
@article {pmid41995085,
year = {2026},
author = {Cao, Y and Chen, W and Li, Q and Liao, Y and Wang, J and Pan, L},
title = {Microbiome and Metabolomics Reveal the Effect of Rhizosphere Microorganisms on Quizalofop-p-ethyl Resistance in Polypogon fugax.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01864},
pmid = {41995085},
issn = {1520-5118},
abstract = {Plant-microbiome interactions are essential for plant health and productivity under stress; however, little is known about these interactions in response to herbicide. Here, we integrated 16S rRNA gene sequencing with nontargeted gas chromatography-mass spectrometry (GC-MS) to investigate the interactions between rhizosphere microbiomes and metabolomes in Polypogon fugax. The results indicated that quizalofop-p-ethyl-resistant (QU-resistant) P. fugax promoted microbial colonization within its microbiome, enriched the abundance of Verrucomicrobia, and increased the levels of d-proline and α,α-trehalose in the rhizosphere, potentially attracting Verrucomicrobia. Furthermore, when the rhizosphere microbiome from R3 populations was transplanted to QU-sensitive plants, the recipients exhibited enhanced antioxidant defense systems and demonstrated reduced sensitivity to QU. These results suggest that the rhizosphere microbiome of QU-resistant P. fugax contributes to its resistance against QU. Overall, our findings highlight the complex interactions among herbicide resistance mechanisms, rhizosphere microbiota, and plant responses, suggesting potential strategies for managing herbicide-resistant weed populations.},
}
@article {pmid41995217,
year = {2026},
author = {Liu, M and Yang, Z and Liu, B and Cheng, H and Qin, J and Zhang, P and Tang, T and Peng, F and Yang, J and Wei, P and Su, H},
title = {Multi-omics reveals gut microbiome- and metabolome-specific responses to sugar alcohols.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00282j},
pmid = {41995217},
issn = {2042-650X},
abstract = {The impacts of sugar alcohols (SA) utilized as low-calorie sweeteners on the gut microbiome and metabolome remain undefined. Among six SAs tested, isomalt, erythritol, xylitol and sorbitol significantly lowered fasting serum insulin and hepatic lipid levels in healthy rats, while mannitol and maltitol showed no such effect. Moreover, isomalt consumption lowered body weight gain, low-density lipoprotein and tumor necrosis factor-α, while improving high-density lipoprotein concentrations. All SAs effectively regulated gut microbiota composition and functionality. Most of the microbiota enriched by isomalt were short-chain fatty acid producers, including Faecalibaculum, Bacillus, Dubosiella and Anaerostipes, which led to a significant increase in the propionate proportion in faeces. The elevated Blautia and UCG-008 and lowered Akkermansia were the key specific responders to sorbitol, mannitol and maltitol. Notably, almost all SAs showed inhibitive efficacy on opportunistic pathogens such as Streptococcus, Staphylococcus and Ruminococcus. Dietary SAs significantly shifted stool and global metabolome profiles in rats. Isomalt and maltitol activated aldosterone-regulated sodium reabsorption and suppressed steroid hormone biosynthesis. Isomalt and sorbitol induced the thyroid hormone signaling pathway. Erythritol intake expressively triggered histamine metabolism, chemical carcinogenesis-receptor activation and folate biosynthesis. Xylitol, sorbitol and mannitol robustly promoted nucleotide metabolism, lysine biosynthesis and pyrimidine metabolism. Sorbitol and mannitol administration induced arginine biosynthesis, nicotinate and nicotinamide metabolism and terpenoid backbone biosynthesis. Additionally, stool metabolome suggested that mannitol intake attenuated ferroptosis in rats. Interestingly, structurally similar SAs, e.g. sorbitol, mannitol and maltitol, showed more shared microbiota and metabolites. This systematic comparative study identifies specific microbiota and associated metabolic pathways as responders to each SA and provides novel insights for future application in functional foods.},
}
@article {pmid41995305,
year = {2026},
author = {Haag, KL and Stein, LQ and Nunes da Silva, CG and Mazel, F and Prasad, A and Engel, P},
title = {Conserved gut microbiomes with cross-species spillover between sympatric Neotropical stingless bees and honey bees.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0248325},
doi = {10.1128/aem.02483-25},
pmid = {41995305},
issn = {1098-5336},
abstract = {Stingless bees (Meliponini) are ecologically vital pollinators with deep cultural and economic importance in the Neotropics; however, the biogeographic structure of their gut microbiota and the extent of microbial exchange with managed honey bees (Apis mellifera) remain insufficiently understood. Using full-length 16S rRNA gene sequencing of individually sampled workers from 167 colonies across Brazil, we compared gut bacterial communities of Melipona quadrifasciata and Melipona mondury with those of co-occurring A. mellifera through an integrated taxonomic, phylogenetic, and community ecological framework. The core microbiota of Melipona species was dominated by Lactobacillus, Bifidobacterium, Apilactobacillus, Bombella, and Floricoccus, whose relative abundances covaried inversely with a set of low-prevalence taxa. Although the core communities of stingless bees overlapped only partially with those of honey bees, both groups displayed comparable alpha- and beta-diversity dispersion, suggesting broadly similar assembly dynamics. Notably, 6% of all amplicon sequence variants (ASVs) were shared across hosts, encompassing nearly all canonical honey bee symbionts, consistent with frequent cross-species spillover. Among these, several Snodgrassella ASVs-typically rare in these stingless bee species-reached high abundance in M. quadrifasciata and formed a deeply divergent clade (~96% 16S rRNA identity to Snodgrassella alvi). These patterns indicate that human-mediated management practices, such as mixed apiaries and artificial feeding, create ecological opportunities for interspecific microbial exchange. Overall, our results show that stingless bee gut microbiomes are compositionally stable yet ecologically permeable, shaped jointly by long-term host specificity and recent anthropogenic contact.IMPORTANCEStingless bees are key pollinators in tropical ecosystems and hold long-standing cultural significance in the Neotropics; however, their microbiomes remain far less studied than those of managed honey bees. Understanding how gut bacterial communities vary across landscapes, and whether microbes move between native and non-native hosts, is essential for predicting the ecological consequences of increasing meliponiculture and urban beekeeping. Our study reveals that stingless bee gut microbiota are generally stable and host-associated but nonetheless acquire bacterial symbionts typical of honey bees, indicating that human management practices facilitate cross-species microbial transmission. These findings broaden current knowledge of bee-microbe evolution by showing that gut symbiont boundaries are not fixed but can become permeable under anthropogenic influence. This has important implications for pollinator health, conservation, and biosecurity as managed and native bees increasingly co-occur in human-modified environments.},
}
@article {pmid41995339,
year = {2026},
author = {Ayalew, M and Hoffman, AM and Fuller, K and Kerr, J and Lee, A and Lee, J and Martinez, ES and Ulbricht, K and Xie, X},
title = {Microbiome education at under-resourced institutions: current status, barriers, and approaches to successful implementation.},
journal = {Journal of microbiology &amp; biology education},
volume = {},
number = {},
pages = {e0028825},
doi = {10.1128/jmbe.00288-25},
pmid = {41995339},
issn = {1935-7877},
abstract = {Microbiome research offers significant promise for advancing public health, medicine, environmental science, and industry. The topic also lends itself well to engaging students and teaching a "new biology" that integrates several disciplines, including computational biology. However, access to microbiome education remains limited, particularly at under-resourced institutions. We conducted a poll showing that over 90% of faculty expressed strong interest in microbiomes; however, only 48% reported that their institutions offer related courses or modules. The most commonly cited barrier was a lack of time and/or funding for design or implementation. A secondary barrier was limited access to professional development or a supportive community of practice. Through case vignettes and reflective analysis, we explore successful efforts to incorporate microbiome education at under-resourced institutions, highlighting the role of faculty development, collaboration, curriculum design, and external funding. These cases demonstrate that implementation is possible with varying levels of investment. We conclude by emphasizing the need for innovative and collaborative strategies, along with sustained resources, to support microbiome education and empower the next generation of genomic data scientists from diverse educational backgrounds.},
}
@article {pmid41995478,
year = {2026},
author = {Conley, TE and Duncan, A and Modasia, A and Ford, AC and Pritchard, DM and Hildebrand, F and Warren, FJ and Spiller, R and Probert, CS},
title = {The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.},
journal = {Alimentary pharmacology &amp; therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70677},
pmid = {41995478},
issn = {1365-2036},
abstract = {BACKGROUND: Metabolomic analysis in irritable bowel syndrome (IBS) has identified metabotypes enriched in faecal short-chain fatty acids (SCFAs), but it remains unclear whether this reflects rapid colonic transit or if these metabolites actively contribute to pathophysiology.<br><br>AIMS: We aimed to determine whether an SCFA metabotype could be identified within a cohort of patients with moderate-severe IBS-D and assess whether this metabotype associated with greater clinical severity, alterations in gut transit time and specific microbiome features.<br><br>METHODS: This was a post hoc cross-sectional exploratory analysis of baseline data from the multicentre, randomised, placebo-controlled trial of ondansetron in IBS-D (TRITON: ISRCTN17508514). Faecal volatile organic compounds were profiled by GC-MS. The microbiome was characterised by whole-genome shotgun metagenomic sequencing. Unsupervised hierarchical clustering was used to identify an SCFA-enriched metabotype and non-negative matrix factorisation (NMF) enabled the derivation of complementary metabosignatures by assessing continuous gradients in metabolite composition.<br><br>RESULTS: A SCFA-enriched metabotype was identified in 20/63 participants (31.7%). This metabotype was associated with more severe abdominal pain, urgency, increased stool frequency and faster whole-gut transit. NMF identified three metabosignatures: S3 was typified by a high proportion of SCFAs and captured the SCFA-enriched metabotype, while S1 and S2 corresponded to the non-SCFA ("Other") metabotype. SCFA relative abundance positively correlated with symptom severity and inversely correlated with transit time. The Other metabotype and S1/S2 signatures were enriched in taxa linked to slower transit, whereas S3 showed no overlapping taxa with the SCFA metabotype.<br><br>CONCLUSION: A faecal metabotype enriched in SCFAs associated with an IBS-D phenotype characterised by pain, urgency, rapid transit and higher stool frequency.},
}
@article {pmid41995603,
year = {2026},
author = {Pu, P and Wang, Y and Liu, X and Pang, Y and Qiang, L and Wang, W},
title = {The ecological dynamics of skin microbiota in skin health and diseases.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0030525},
doi = {10.1128/cmr.00305-25},
pmid = {41995603},
issn = {1098-6618},
abstract = {SUMMARYThe skin microbiome, consisting of bacteria, fungi, viruses, and archaea, plays a crucial role in maintaining skin health by regulating immune responses, preserving barrier function, and influencing metabolic processes. Dysbiosis in the microbiome is linked to dermatological diseases such as atopic dermatitis (AD), psoriasis, and acne, with specific microbes, such as Staphylococcus aureus and Cutibacterium acnes, either promoting or protecting against disease. This review summarizes recent advances in understanding the composition and functions of the skin microbiome, its interaction with host immunity, and impact on skin health. We also discuss the implications of environmental and biological factors on microbiome stability and explore emerging therapeutic strategies targeting the skin microbiota. These insights highlight the potential of microbiome-based approaches for advancing dermatological treatment.},
}
@article {pmid41995611,
year = {2026},
author = {Elkatmis, B and Türksoy, GM and Rodríguez, E and Rahmoune, B and Koprivova, A and Kopriva, S},
title = {Sulfur as a Central Integrator of Plant-Microbe Interactions: From Nutrient Cycling to Immune Signalling and Microbiome Assembly.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag186},
pmid = {41995611},
issn = {1460-2431},
abstract = {Sulfur (S) is an essential macronutrient that underpins plant growth, stress resilience, and immunity. Beyond its role in primary metabolism, sulfur is incorporated into a diverse array of secondary metabolites that mediate plant-microbe interactions. In this review, we summarize current knowledge on how microbial sulfur metabolism contributes to plant sulfur nutrition and how plant-derived sulfur-containing compounds shape microbial community assembly and disease outcomes. Microorganisms mobilize organic sulfur in soils through sulfatase activity, volatile sulfur production, and sulfoquinovose degradation, thereby enhancing plant sulfur availability, particularly under limiting conditions. Conversely, plants deploy sulfur-rich metabolites, including volatile organic compounds, glucosinolates, and the phytoalexin camalexin, to restrict pathogens, modulate beneficial associations, and structure rhizosphere communities. These compounds act not only as antimicrobial agents but also as ecological filters that balance defense with microbiome homeostasis. Emerging evidence indicates that sulfur availability and metabolic flux influence the composition and function of plant-associated microbiota, linking primary nutrient assimilation to immune regulation. By integrating insights from sulfur biochemistry, microbial ecology, and plant immunity, we highlight sulfur metabolism as a central node in plant-microbe interactions. Understanding the dynamic exchange of sulfur between plants and their microbiota will be essential for improving crop resilience and sustainable nutrient management in sulfur-limited agricultural systems.},
}
@article {pmid41995892,
year = {2026},
author = {Ali, M and Thakali, O and Idris, O and Sherchan, S},
title = {Comparative Evaluation of DNA Extraction Workflows for Efficient Recovery of pBI143 from Wastewater.},
journal = {Food and environmental virology},
volume = {18},
number = {2},
pages = {},
pmid = {41995892},
issn = {1867-0342},
mesh = {*Wastewater/virology ; Feces/virology ; *DNA, Viral/isolation &amp; purification/genetics ; Workflow ; Tobamovirus/isolation &amp; purification/genetics ; Polyethylene Glycols/chemistry ; Maryland ; },
abstract = {This study aimed to compare the performance of polyethylene glycol (PEG) precipitation, and Nanotrap[®] Microbiome magnetic particle capture workflows for recovering novel fecal marker, pBI143 from 12 wastewater samples collected across six treatment plants in Maryland, USA. Quantitative PCR (qPCR) was used to quantify marker abundance. The Nanotrap workflow yielded significantly higher concentration of pBI143 compared to PEG precipitation workflow (p < 0.05). The Nanotrap workflow used in the study utilized both magnetic nanoparticles A and B, rather than magnetic nanoparticle A alone, highlighting the necessity of optimization based on the intended targets for enhanced recovery. The extracted total nucleic acids by the Nanotrap workflow, were further analyzed to quantify other fecal markers, crAssphage, tomato brown rugose fruit virus (ToBRFV), and pepper mild mottle virus (PMMoV). No significant differences in the concentrations of pBI143, crAssphage, and ToBRFV (p > 0.05) were observed, whereas the concentration of PMMoV was significantly lower than that of the three fecal markers (p < 0.05). Based on the concentration alone, pBI143, ToBRFV, and crAssphage were found to be a better alternative to PMMoV as an endogenous fecal marker.},
}
@article {pmid41995913,
year = {2026},
author = {Azizan, N and Al-Maleki, AR and Karajacob, AS and Loke, MF and Goh, JPE and Kallarakkal, TG and Ho, GF and Khor, HM and Ong, HC and Tay, ST},
title = {Oral microbiome profiling of primary oral candidiasis during infection and post-antifungal therapy.},
journal = {Clinical oral investigations},
volume = {30},
number = {5},
pages = {},
pmid = {41995913},
issn = {1436-3771},
mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; Male ; *Antifungal Agents/therapeutic use ; Female ; *Microbiota/drug effects ; Middle Aged ; RNA, Ribosomal, 16S ; *Mouth/microbiology ; Dysbiosis/microbiology ; Case-Control Studies ; Adult ; Aged ; },
abstract = {OBJECTIVES: Microbial dysbiosis that facilitates Candida proliferation in the oral cavity is a significant factor associated with oral candidiasis. This study aimed to gain insights into microbial dynamics of primary oral candidiasis during infection and following antifungal therapy to enhance our understanding of disease pathogenesis and treatment efficacy.<br><br>MATERIALS AND METHODS: Oral rinse samples were collected from 16 patients with primary oral candidiasis, seven of whom returned for follow-up after antifungal treatment, and from seven healthy controls. Microbiome profiling was performed using 16S rRNA gene sequencing (V3-V4 region), followed by microbial diversity and taxonomic analyses.<br><br>RESULTS: Twelve bacterial phyla and 138 genera were identified across all samples. Alpha and beta diversity analyses showed no significant differences in microbial richness or overall community structure across both infection and treatment conditions, suggesting a resilient oral microbiome. Compared to controls, oral microbiome of the patients showed a significantly higher abundance of Firmicutes and Campylobacterota, along with a lower abundance of Bacteroidota. At the genus level, Campylobacter, Staphylococcus, and lactobacilli (Lacticaseibacillus, Ligilactobacillus, and Limosilactobacillus) were present at higher abundances during oral candidiasis, while Neisseria, Prevotella, and Alloprevotella were less abundant. Following two weeks of antifungal therapy, alterations in microbial community composition and diversity were observed relative to the control group, suggesting incomplete microbiota restoration.<br><br>CONCLUSION: Microbiome analysis revealed dysbiosis with significant taxa changes during primary oral candidiasis. Clinical resolution of oral candidiasis did not correspond well with microbiota restoration, suggesting dysbiosis may persist beyond fungal clearance and contribute to delayed ecological recovery and oral homeostasis.<br><br>CLINICAL RELEVANCE: This study highlights the microbial shift during primary oral candidiasis and post-antifungal treatment. Despite clinical resolution with antifungal therapy, oral microbiome of patients with primary oral candidiasis continues to exhibit residual shifts in composition, underscoring the needs for microbiota-targeted intervention to prevent recurrence and maintain oral health. While our results provide preliminary insights into microbial dysbiosis associated with primary oral candidiasis and the effects of antifungal therapy, further validation in larger cohorts is warranted.},
}
@article {pmid41996042,
year = {2026},
author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS},
title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41996042},
issn = {1618-1905},
abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.},
}
@article {pmid41996045,
year = {2026},
author = {Mohanty, A and Pavan-Kumar, A and Chaudhari, A and Kumari, K and Kumar, P and Maurye, P},
title = {Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41996045},
issn = {1573-4978},
support = {FBT-PB1-01//Indian Council of Agricultural Research/ ; },
}
@article {pmid41996166,
year = {2026},
author = {Liu, L and Liu, L and Luo, X and Zhao, JL and Tan, X and Zhao, W and Huang, L and Yuan, Z and Li, F and Zheng, H and Xing, B},
title = {Novel Insights into Foodborne Microplastics-Enhanced Shoaling Behavior in Marine Korean Rockfish (Sebastes schlegelii): Energy Deficiency-Driven Gut-Brain Axis Dysregulation.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16888},
pmid = {41996166},
issn = {1520-5851},
abstract = {Microplastics (MPs) pollution threatens ocean health, yet their impacts on fish shoaling behavior remain poorly understood. Herein, the effects of foodborne polyethylene terephthalate debris (D-PET), PET fiber (F-PET), and tire wear particles (TWPs) at environmentally relevant concentrations (0.1 and 1 mg g[-1]) on behavioral strategies and energy metabolism-mediated gut-brain axis regulation in Korean rockfish (Sebastes schlegelii) were investigated through a 50-day exposure-depuration experiment. MPs induced boldness reduction and hyperactivity, consequently intensifying shoaling behavior in an order of TWPs > F-PET > D-PET, with the interindividual distance decreased by up to 12.14 ± 0.31%. Leachable additives from TWPs, including benzothiazolone, benzothiazole, N,N'-ditolyl-p-phenylenediamine, and N-1,3-dimethylbutyl-N'-phenyl-p-phenylenediamine-quinone, were primarily responsible for the shoaling enhancement. MPs induced hepatic mitochondrial dysfunction and apoptosis that disrupted glucose homeostasis and caused systemic energy deficiency, thereby promoting shoaling as an energetically compensatory strategy. The energy imbalance subsequently triggered oxidative neurotoxicity and perturbed serotonergic, cholinergic, dopaminergic, and GABAergic pathways. Moreover, MPs disrupted the intestinal physicochemical barrier, immune function, and reshaped microbiota, exacerbating neurotransmitter disruption via the gut-brain axis. These findings demonstrate that environmentally relevant MPs exposure can enhance fish shoaling through energy deficiency-driven gut-brain axis dysregulation, revealing the mechanisms by which MPs stress can reorganize population-level behavior and thereby expand understanding of the ecological risks posed by contaminants of emerging concerns.},
}
@article {pmid41996244,
year = {2026},
author = {Liu, X and Zeng, J and Xie, P and Shen, Q and Yuan, J},
title = {Microbial damper: Rhizosphere microbiome mitigates stress-induced plant growth-defense conflicts.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117278},
doi = {10.1016/j.celrep.2026.117278},
pmid = {41996244},
issn = {2211-1247},
abstract = {Plants face constant environmental stresses that induce conflicts between growth and defense. The rhizosphere microbiome helps resolve this conflict by enhancing nutrient-uptake efficiency and activating plant immunity simultaneously. In this review, we first outline the mechanisms and limitations of plant-intrinsic growth-defense trade-offs; we then describe the integrated support that rhizosphere microbial communities provide for plant nutrition and defense. Finally, we propose the "microbial-damper" framework and further elucidate the interactions and feedback mechanisms that constitute this system. The microbial damper is a conceptual framework describing the capacity of the rhizosphere microbiome to stabilize a plant's internal growth-defense resource allocation, which is otherwise perturbed by stresses such as nutrient imbalance and other environmental stresses. This framework highlights how the rhizosphere microbiome can reduce stress-induced plant growth-defense resource-allocation conflicts, thereby providing actionable strategies for designing sustainable agricultural systems.},
}
@article {pmid41996342,
year = {2026},
author = {Rajan, FV and Bucking, C},
title = {Effects of salinity and broad-range antibiotics on oxalate production, transport, and degradation in Poecilia latipinna.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347147},
pmid = {41996342},
issn = {1932-6203},
mesh = {Animals ; *Salinity ; *Oxalates/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Poecilia/metabolism/microbiology ; Gastrointestinal Microbiome/drug effects ; Seawater ; Biological Transport/drug effects ; Kidney/metabolism/drug effects ; },
abstract = {Oxalate is an anion that readily binds calcium and is thought to contribute to osmoregulation. This study investigated how environmental salinity influences oxalate homeostasis in euryhaline sailfin mollies (Poecilia latipinna), with a focus on the interplay between microbial symbiosis and host transport processes. Gut microbiome profiling demonstrated regional specialization, with the posterior intestine enriched in oxalate-degrading bacterial families. Community shifts across salinities suggests functional redundancy and resilience, ensuring maintenance of oxalate-catabolizing capacity. Antibiotic treatment disrupted this system, impairing microbial degradation and causing systemic oxalate stress. Oxalate concentrations were also measured in the liver, intestine, and kidney, organs central to oxalate metabolism, under freshwater and seawater conditions. Salinity induced a redistribution of oxalate among these organs, with the gut assuming an auxiliary excretory role in seawater. This functional shift parallels mammalian colon physiology and highlights the gut's role in balancing ion and oxalate flux. Expression analyses of the oxalate transporters SLC26A3 (solute carrier family 26, member 3) and SLC26A6 (solute carrier family 26, member 6) revealed organ-specific and salinity-dependent regulation. Both transporters displayed distinct responses to seawater exposure, indicating specialized roles in oxalate handling. These patterns suggest coordinated but nonredundant mechanisms that govern absorption and secretion, linking salt transport with oxalate clearance. These findings underscore the microbial contribution to oxalate balance and reveal that osmoregulatory challenges shape gut microbial composition and function. Collectively, this study presents the first comprehensive analysis of oxalate metabolism in a euryhaline teleost and demonstrates a coordinated host-microbe system that mitigates oxalate accumulation across salinities. By integrating metabolic and osmoregulatory demands, P. latipinna reallocates excretory function from kidney to gut and leverages microbial symbiosis to preserve homeostasis. These findings expand our understanding of teleost physiology and highlight oxalate metabolism as a critical axis of environmental adaptation.},
}
@article {pmid41996359,
year = {2026},
author = {Li, G and Wang, Y and Zeng, S and Li, S},
title = {Shared Genetics Implicate Gut Microbiota and Immunity in Anterior Uveitis and Inflammatory Bowel Disease.},
journal = {Ocular immunology and inflammation},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/09273948.2026.2654978},
pmid = {41996359},
issn = {1744-5078},
abstract = {PURPOSE: Anterior uveitis (AU) is a common extraintestinal manifestation of inflammatory bowel disease (IBD). This study investigates the shared genetic architecture and pleiotropic loci between AU and IBD.<br><br>METHODS: Using large-scale GWAS data from European-ancestry cohorts, we performed LD score regression to assess genetic correlations, two-sample Mendelian randomization for causal inference, and PLACO analysis to identify pleiotropic loci. Multi-trait colocalization integrating 412 gut microbiome features was conducted using HyPrColoc. Functional annotation employed FUMA and ANNOVAR, gene-based analysis used MAGMA, and drug-gene interactions were explored via DrugBank.<br><br>RESULTS: AU showed significant genetic correlations with IBD (rg&#x2009;=&#x2009;0.44, p&#x2009;=&#x2009;2.0&#x2009;&#xd7;&#x2009;10[-4]), ulcerative colitis (rg&#x2009;=&#x2009;0.52, p&#x2009;=&#x2009;6.0&#x2009;&#xd7;&#x2009;10[-4]), and Crohn's disease (rg&#x2009;=&#x2009;0.24, p&#x2009;=&#x2009;0.029). Mendelian randomization supported causal effects of genetically predicted IBD and its subtypes on AU risk. We identified 62 pleiotropic risk loci, including 18 with strong colocalization evidence. Functional and pathway analyses revealed enrichment of these loci in immune and inflammatory pathways, mainly the IL-17/IL-23 axis and NOD2 signaling. Multi-trait colocalization further linked a shared AU-IBD risk locus to the gut microbial MEP pathway. Several pleiotropic genes (e.g. JAK2, STAT3) represent potential drug targets.<br><br>CONCLUSIONS: AU and IBD share pleiotropic genetic loci involved in immune regulatory pathways and gut microbiome-associated metabolic processes, revealing a potential molecular basis for their comorbidity and highlighting actionable therapeutic targets.},
}
@article {pmid41996413,
year = {2026},
author = {He, X and Yazdy, GM and Yeoman, C and Ghanem, KG and Erchick, DJ and Taylor, A and Griffin, K and Holm, J and Ravel, J and Brotman, RM and Tuddenham, S},
title = {Comparing Asymptomatic vs Symptomatic Bacterial Vaginosis: Clinical Characteristics, Vaginal Microbiota, and Lactic Acid Profiles.},
journal = {Sexually transmitted diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/OLQ.0000000000002330},
pmid = {41996413},
issn = {1537-4521},
abstract = {BACKGROUND: Irrespective of symptoms, bacterial vaginosis (BV) has been linked to increased risk of sexually transmitted infections (STI) and HIV, yet clinical guidelines recommend treatment only for symptomatic BV (sBV). We compared demographic, clinical, and vaginal microbiota factors between asymptomatic BV (aBV) and sBV.<br><br>METHODS: Data from a previously conducted vaginitis cohort study were analyzed. Participants with Amsel-BV were classified as sBV if they reported vaginal symptoms and aBV if asymptomatic. Nugent scores were assigned. Cervicovaginal lavage fluid underwent 16S rRNA gene amplicon sequencing, broad-range qPCR, and lactic acid isomer quantitative assays. Wilcoxon rank-sum, Fisher's exact, and Chi-squared tests compared factors between aBV and sBV. Taxonomic differences were evaluated using elastic net modeling and differential abundance testing.<br><br>RESULTS: Among 70 participants with sBV and 270 with aBV, clinician-assessed abnormal discharge was more common in sBV (86%) than aBV (71%). In adjusted analyses, recent use of metronidazole or clindamycin, more sex partners, and education beyond high school were associated with increased odds for sBV, and injectable contraception with aBV. No consistent differences were observed between sBV versus aBV for other Amsel's criteria, Nugent scores, or vaginal microbiota composition. D- and L-lactic acid levels were slightly higher in sBV than aBV.<br><br>CONCLUSIONS: Although some demographic, clinical, and behavioral factors differed between sBV and aBV, no consistent differences were found in vaginal microbiota composition; lactic acid isomer levels were low in both groups. Further research is needed to understand why some experience symptoms, to identify whether other biological factors differentiate aBV from sBV, and to evaluate their respective associations with adverse reproductive outcomes.},
}
@article {pmid41996830,
year = {2025},
author = {Kreimeyer, H and Fondevila, MF and Harberts, A and Raya Tonetti, F and Schöler, D and Münte, E and Hartmann, P and Llorente, C and Hube, B and LeibundGut-Landmann, S and Stärkel, P and , and Schnabl, B},
title = {Peptide YY reduces cytotoxicity of Candida albicans in alcohol-associated liver disease.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {5},
pages = {101718},
doi = {10.1016/j.jhepr.2025.101718},
pmid = {41996830},
issn = {2589-5559},
abstract = {BACKGROUND &amp; AIMS: Transitioning from yeast to hyphal morphology enables Candida albicans (C. albicans) to secrete candidalysin, invade the intestinal mucosa and translocate to the blood stream. Patients with alcohol-associated hepatitis show increased intestinal abundance of C. albicans, and the candidalysin-encoding gene is associated with reduced survival. Paneth cell-derived peptide YY (PC-PYY) inhibits hyphal growth of C. albicans. In this study, we evaluated the potential of different C. albicans strains isolated from patients with alcohol-associated hepatitis to cause systemic infections and explored the therapeutic potential of PC-PYY in ethanol-induced liver disease in mice.<br><br>METHODS: C. albicans strains isolated from fecal samples of patients with alcohol-associated hepatitis (n = 105) were co-cultured with intestinal epithelial Caco-2 cells to assess in vitro cytotoxicity. Caco-2 cells and primary mouse hepatocytes were incubated with C. albicans in the presence or absence of PC-PYY. Mice were subjected to a chronic plus binge ethanol-feeding model.<br><br>RESULTS: C. albicans strains isolated from stool of patients with alcohol-associated hepatitis induced significant cytotoxicity in Caco-2 cells, and high cytotoxicity was associated with worse 30-day survival (log-rank p = 0.032). This cytotoxicity was primarily mediated by the hyphal form and largely driven by candidalysin. PC-PYY significantly reduced C. albicans-induced cytotoxicity in Caco-2 cells (Wilcoxon rank-sum test, p = 0.015) and in primary mouse hepatocytes (p = 0.03) compared with a scrambled peptide control, by inhibiting hyphal morphogenesis. The peptide YY-to-chromogranin A ratio in intestinal crypts was significantly increased in ethanol-fed mice compared with both isocaloric (p = 0.005) and antifungal-treated controls (p = 0.009), indicating that fungal overgrowth stimulates PC-PYY release. In ethanol-fed mice, PC-PYY administration attenuated liver injury (p = 0.032) and steatosis (p = 0.0498) and reduced fecal hyphae formation (p = 0.0159).<br><br>CONCLUSION: PYY inhibits filamentous growth of C. albicans in vitro and alleviates ethanol-induced liver disease in mice, highlighting its potential as a therapy for patients with alcohol-associated liver disease.<br><br>IMPACT AND IMPLICATIONS: Candida albicans (C. albicans) and particularly its toxin candidalysin are associated with poor outcomes in patients with alcohol-associated hepatitis but the extent to which the cytotoxicity of individual C. albicans strains influences patient survival, and the role of Paneth cell-derived PYY (PC-PYY) in this context remains elusive. This study identifies a link between the cytotoxic effect of patient-derived C. albicans strains and survival in patients with alcohol-associated hepatitis and demonstrates that PC-PYY plays a protective role in ethanol-induced liver disease by limiting candidalysin-producing hyphae. Our work provides insight into why some patients with alcohol-associated liver disease have worse outcomes and highlights the potential of PC-PYY as a therapy for patients with alcohol-associated liver disease.},
}
@article {pmid41996860,
year = {2026},
author = {Ji, Z and Fu, Z and Miao, L and Hang, D and Gu, A},
title = {Relationship between pesticide exposure, gut microbiota, and hypertension.},
journal = {Environment international},
volume = {211},
number = {},
pages = {110250},
doi = {10.1016/j.envint.2026.110250},
pmid = {41996860},
issn = {1873-6750},
abstract = {BACKGROUND: Both pesticide exposure and gut dysbiosis have been independently linked to an elevated risk of hypertension. However, the extent of interaction between these two factors remains poorly characterized in human populations.<br><br>METHODS: In a population-based study involving 218 adults from Jiangsu Province, China, we quantified pesticides in serum using LC-MS/MS and analyzed the gut microbiome via metagenomic sequencing. An environmental risk score (ERS) was created to represent pesticide exposure. We also used Mendelian randomization (MR) to identify causal gut microbial genera, multivariable regression for associations, and mediation analysis for potential pathways. Machine learning models were applied to differentiate hypertensive from non-hypertensive individuals based on a combined set of features.<br><br>RESULTS: Fourteen pesticides, notably bentazone and perfluorohexanesulfonate, were significantly associated with increased hypertension risk, and the ERS based on these pesticides further corroborated this association. Additionally, the overall microbiota composition was significantly associated with both pesticide exposure and hypertension status. Observational and MR analyses consistently identified branches of Clostridium as potentially contributors to hypertension risk. An interaction was observed between pesticide exposure and specific bacterial taxa. Specifically, high ERS combined with high Catenibacterium (both defined using a median split) abundance increased hypertension risk nearly fourfold. A neural network model achieved the best differentiation performance (AUC&#xa0;=&#xa0;0.897) for hypertension.<br><br>CONCLUSIONS: Exposure to specific pesticides, particularly bentazone, is associated with increased hypertension risk. This relationship is influenced by interactions with gut bacteria and partially mediated through alterations in the gut microbiota. These findings highlight the role of environmental chemicals and the gut microbiome in the development of hypertension.},
}
@article {pmid41997122,
year = {2026},
author = {Davar, D and Zarour, HM and Trinchieri, G},
title = {Improving immunotherapy in solid tumors using FMT.},
journal = {Cell},
volume = {189},
number = {8},
pages = {2214-2217},
doi = {10.1016/j.cell.2026.03.021},
pmid = {41997122},
issn = {1097-4172},
mesh = {Humans ; *Immunotherapy/methods ; *Fecal Microbiota Transplantation/methods ; *Neoplasms/therapy/immunology/microbiology ; Immune Checkpoint Inhibitors/therapeutic use ; Melanoma/therapy ; Animals ; Carcinoma, Non-Small-Cell Lung/therapy ; Clinical Trials as Topic ; },
abstract = {Recent clinical trials demonstrate that fecal microbiota transplantation (FMT) enhances first-line immune checkpoint inhibitor efficacy in renal cell carcinoma, cutaneous melanoma, and non-small cell lung cancer with acceptable safety. Benefit appears mediated by functional microbiome remodeling, depletion of deleterious taxa, and systemic immunometabolic modulation, supporting microbiome-directed therapeutic strategies for cancer immunotherapy.},
}
@article {pmid41997160,
year = {2026},
author = {Yu, L and Peng, S and Chen, X and Wu, T and Dong, L and Luo, J and Xu, S and Zhou, J and Zhao, X and Zheng, L and Shu, G and Wang, X and Huang, L and Chen, Q and Jiang, D and Sun, LD and Hylemon, P and Wang, XY and Sun, L and Ma, L and Zuo, D},
title = {Intestinal dysbiosis exacerbates skin inflammation via microbial metabolite-driven Th2 cell differentiation.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2026.03.019},
pmid = {41997160},
issn = {1097-4180},
abstract = {The interplay between gut microbiota and the mucosal immune system critically regulates systemic immunity and disease susceptibility. Here, we demonstrate that intestinal epithelial Toll-like receptor (TLR)4 deficiency reshaped the gut microbiome and subsequently exacerbated atopic dermatitis (AD) in mice. Mechanistically, TLR4 deficiency reduced Akkermansia muciniphila abundance and enriched choline trimethylamine-lyase (CutC)-expressing bacteria. This enhanced microbial choline-to-trimethylamine conversion and elevated circulating trimethylamine oxide (TMAO) levels. Clinically, AD patients exhibited increased plasma TMAO levels that positively correlated with disease severity and immunoglobulin E (IgE) levels. UK Biobank data also showed that higher dietary choline intake was associated with increased AD risk. TMAO promoted T helper (Th)2 differentiation by directly interacting with protein phosphatase 5 (PPP5) and enhancing PPP5-mediated dephosphorylation of PPARγ. CD4[+] T cell-specific PPARγ deletion abolished TMAO-driven skin pathology in AD mice. Our results reveal intestinal dysbiosis, as a result of innate immune deficiency, as a driver of inflammatory Th2 cells and AD pathology, highlighting a link among the gut immune environment, microbial metabolites, and skin disease.},
}
@article {pmid41997445,
year = {2026},
author = {Yu, J and Guo, C and Liu, Y and Ren, X and Guo, Y and Ran, B and Xiao, L and Kong, L and Gu, X and Jiang, C and Wu, J},
title = {The commensal microbiome in respiratory tract tumors: From oncogenic mechanisms to clinical translation.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.044},
pmid = {41997445},
issn = {2090-1224},
abstract = {BACKGROUND: The human commensal microbiome, commonly recognized as a "second genome", exerts a crucial regulatory role in host metabolism, immune homeostasis maintenance, and the progression of various diseases. Respiratory tract tumors remain a leading cause of global cancer-related deaths due to their high invasiveness and late-stage diagnosis. With the rapid development of high-throughput sequencing technology, the complex associations between microbial communities and respiratory tract tumors have been gradually uncovered. In lung cancer, distinct microbiota-related signatures, including tissue-specific and microbiota-derived ones have been identified, showing variations across cancer subtypes, anatomical sample sources, and patient demographics. These findings collectively lay the foundation for in-depth investigations into the interplay between the microbiome and respiratory tract tumors.<br><br>AIM OF REVIEW: This review aims to systematically synthesize the current understanding of the commensal microbiome across respiratory tract tumors, primarily taking lung cancer as the main example, with systematic extensions to other respiratory tract malignancies, including laryngeal carcinoma and nasopharyngeal carcinoma, focusing on clarifying the ecological characteristics of microorganisms, elucidating the mechanistic links between the microbiome and tumorigenesis as well as progression, and summarizing the translational value of the microbiome in clinical practice, including applications in diagnostics, therapeutics, and prognostic evaluation.<br><br>Emerging evidence highlights that the microbiome contributes to the initiation of respiratory tract tumors through multiple pathways: dysbiosis-induced chronic inflammation, immune system dysregulation, and metabolite-mediated epigenetic or functional alterations. Beyond tumorigenesis, the microbiome also plays a vital role in modulating the efficacy of cancer treatments, particularly conventional therapies and immunotherapies. Additionally, the microbiome provides novel opportunities for the development of diagnostic biomarkers and microbiome-targeted intervention strategies. Its prognostic potential in predicting recurrence, metastasis, and survival is increasingly recognized. These core scientific concepts collectively constitute the theoretical framework for exploring the microbiome's role in respiratory tract tumor research and clinical translation.},
}
@article {pmid41997470,
year = {2026},
author = {Saravanan, A and Bai, J and Bajaj, P and Khemmani, M and Rodriguez, A and Choudhury, S and Wolfe, AJ and Young, EE},
title = {Evidence for a shift towards a proinflammatory/pronociceptive signature of gut dysbiosis in patients with axial chronic low back pain: A preliminary cross-sectional analysis.},
journal = {The journal of pain},
volume = {44},
number = {},
pages = {106271},
doi = {10.1016/j.jpain.2026.106271},
pmid = {41997470},
issn = {1528-8447},
abstract = {Nonspecific or axial-chronic low back pain is not attributed to specific pathology yet accounts for 80%- 90% of all chronic low back pain cases and is a major cause of disability affecting one in four adults with treatment costs and lost wages totaling $100-200 billion. Despite its prevalence, there is a knowledge gap around the underlying mechanisms driving susceptibility to this type of chronic pain. Gut microbial colonization plays a role in shaping host physiology directly through interactions with host tissues and indirectly through the production of metabolites, but the role of the microbiome in the etiology of axial-low back pain is unclear. Using a cross-sectional design, in this preliminary study, patients with axial-chronic low back pain and healthy controls completed the NIH minimal dataset for chronic low back pain from the PROMIS short form followed by collection of rectal swabs and 16S rRNA sequencing and determination of microbiome composition differences between controls and patients. Our findings suggest a distinct pattern of altered colonization in axial-chronic low back pain, characterized by a specific pattern of increased formate- and succinate- producing bacterial abundance along with reduced abundance of key taxa associated with butyrate, propionate, and acetate production. A review of the literature available on metabolite production from differentially abundant bacteria suggests a proinflammatory/ pronociceptive shift in microbial colonization. These preliminary findings identify a gut dysbiosis pattern that may contribute to chronic low back pain through pro-inflammatory and pronociceptive mechanisms; however, larger, longitudinal, and metabolically profiled studies are needed to confirm causality. PERSPECTIVE: Chronic low back pain is associated with gut dysbiosis characterized by reduced abundance of butyrate and/or propionate producing bacteria combined with increased succinate- and formate-producing bacterial colonization. These data suggest a proinflammatory/pronociceptive microbial signature that may contribute to development and/or maintenance of chronic low back pain.},
}
@article {pmid41997773,
year = {2026},
author = {Han, VC and Bennett, SJ},
title = {When soils learn to suppress nematodes.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.04.002},
pmid = {41997773},
issn = {1878-4380},
abstract = {An evaluation of banana plantations, sown between 1 and 10 years ago, suggested that over time soils can become suppressive to root-knot nematodes. Lu et al. linked this transition to shifts in rhizosphere microbiomes, enrichment of free-living nematodes, and the emergence of a keystone Bacillus taxon, highlighting cross-kingdom interactions.},
}
@article {pmid41997906,
year = {2026},
author = {Tao, R and Liu, S and Crawford, J and Kramer, P and Bender, S and Tao, F},
title = {Single-cell multi-omics sequencing reveals cell-specific transcriptomic and chromatin accessibility profiles in gut microbiome metabolite butyrate-produced pain modulation.},
journal = {International journal of oral science},
volume = {18},
number = {1},
pages = {},
pmid = {41997906},
issn = {2049-3169},
support = {R01DE031255//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R01DE032061//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R03DE031822//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Chromatin/metabolism/genetics ; *Butyrates/metabolism/pharmacology ; *Transcriptome ; Single-Cell Analysis ; Male ; Mice ; Acetylation ; Multiomics ; Triglycerides ; },
abstract = {Pain is the most common symptom of temporomandibular joint (TMJ) disorders, which present significant clinical challenges due to their complexity and limited treatment options. Our previous study demonstrates that gut microbiome-derived butyrate is critical for the modulation of TMJ pain. In this study, we investigated its underlying mechanisms, and we found that oral administration of tributyrin, a prodrug of butyrate, not only significantly alleviated TMJ pain but also reversed the reduction in histone acetylation in the spinal trigeminal nucleus caudalis (Sp5C) under the TMJ pain condition. Using single-cell multi-omics sequencing, we profiled gene expression and chromatin accessibility in the Sp5C cells at the single-cell resolution. Bioinformatics analysis revealed that TMJ pain disrupted both the expression and chromatin accessibility of Nop14, Matk, Idh3b, Ndst2, and Tomm6 across four cell types in the Sp5C, and these alterations were reversed by tributyrin treatment. Specifically, Nop14 exhibited increased chromatin accessibility at its promoter region under TMJ pain condition, and knockdown of Nop14 in the Sp5C restored histone acetylation and alleviated TMJ pain. Together, our findings reveal cell-type-specific gene regulation that underlies butyrate-mediated epigenetic regulation of TMJ pain, which suggesting that targeting gut microbiome metabolites could develop a non-opioid novel therapy for TMJ disorders.},
}
@article {pmid41997944,
year = {2026},
author = {Wu, Y and Alomeir, N and Falsetta, M and Yang, R and Sun, E and Israel, AK and Fiscella, J and Wu, T and Liu, Y and Li, T and Wood, R and Kenney, M and Meng, G and Terando, S and Terio, C and Fiscella, K and Xiao, J},
title = {Cariogenic microorganisms induce oral epithelial atypia through host-microbiome-high sugar diet interactions.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00987-9},
pmid = {41997944},
issn = {2055-5008},
abstract = {Oral mucosal development during infancy is crucial because disruptions at this stage can compromise barrier function and increase susceptibility to oral diseases throughout life. The contribution of oral pathogens to oral mucosal development in infancy remains poorly understood. Here, we show that early-life co-infection with Streptococcus mutans and Candida albicans under a sucrose-enriched diet perturbs oral epithelial homeostasis and is associated with atypical hyperplasia and parakeratosis of the tongue. Using an infant rat model, we utilized OMICS data (microbiome, untargeted metabolomics, and multiplex immune profiling) together with high-dimensional mediation statistic modeling to reveal that microbial co-infection synergizes with dietary sugar to shape oral and gut microbial communities. The microbial alterations were accompanied by systemic metabolic alterations, marked by enhanced amino acid and carbohydrate metabolism, and depletion of vitamin B6 and taurine pathways. Oral microbial and metabolic changes were associated with atypical hyperplasia and parakeratosis on both dorsal and ventral surfaces of tongue mucosa. Complementary in vitro modeling revealed that sucrose-conditioned co-infection disrupted epithelial barrier integrity and orchestrated metabolic remodeling in oral epithelial cells. These findings reveal a host-microbe-diet interaction axis underlying early mucosal remodeling and provide mechanistic insight into how cariogenic microbes may influence oral mucosal disease beyond caries.},
}
@article {pmid41997961,
year = {2026},
author = {Zhao, JJ and Hu, M and Li, S and Wang, Q and Mo, Q and Yu, H},
title = {Oral microbiome signatures predict biological age and host health.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72096-2},
pmid = {41997961},
issn = {2041-1723},
abstract = {Identifying robust, non-invasive biomarkers of biological age is key to preventive medicine. While gut aging clocks exist, the oral microbiome remains underexplored as a quantitative biomarker. Using oral microbiome data from two NHANES cohorts (N = 4,675), we identified 64 age-dependent bacterial genera and developed a machine learning model predicting chronological age, with generalizability in an independent external cohort (N = 1,293). We derived an Oral Microbiome Aging Acceleration (OMAA) Score as the residual of predicted age against chronological age. The OMAA Score independently predicted all-cause mortality (HR = 1.05, P = 0.024) and frailty (OR = 1.05, P = 0.008), correlated with impaired kidney function (lower eGFR: β = -0.066, P = 5.22×10[-4]), and enhanced risk prediction for cancer (AUC 0.70 vs. 0.67, P = 0.009) and heart attack (AUC 0.79 vs. 0.76, P = 0.016) beyond conventional risk factors. Diet and medication had minimal association. The OMAA Score offers a scalable, non-invasive tool to identify high-risk individuals for age-related morbidity and mortality.},
}
@article {pmid41997995,
year = {2026},
author = {Zhong, P and Ren, A and Cui, J and Guo, C and Zhang, Y and Diao, Q and Liu, X and Zhang, N and Tu, Y and Bi, Y},
title = {Microbial landscapes in dairy cow diseases: from localized dysbiosis to inter-organ axes.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00988-8},
pmid = {41997995},
issn = {2055-5008},
support = {32222081//National Natural Science Foundation of China/ ; },
abstract = {Dairy cow health involves host-microbiome interactions. This review characterized microbial landscapes across anatomical sites in dairy cows-including the gastrointestinal tract, respiratory system, reproductive tract, mammary gland, and skin-and examines their associations with diseases. We elucidated how site-specific dysbiosis drives systemic conditions such as mastitis and ketosis through inter-organ axes. Finally, we evaluated emerging microbiome-based modulation strategies and their application prospects in dairy farming.},
}
@article {pmid41998050,
year = {2026},
author = {Gao, Y and Kim, J and Wu, R and Chowdhury, NB and Lee, JY and Nicora, CD and Moore, RJ and Monroe, ME and Jansson, JK and Burnum-Johnson, KE},
title = {Metaproteomics uncovers the functional capacity of a soil microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47816-9},
pmid = {41998050},
issn = {2045-2322},
support = {Early Career Research Program//U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research/ ; },
}
@article {pmid41998161,
year = {2026},
author = {Ji, S and Liu, Y and Xu, Y and Gao, J and Jin, J and Jiang, P and Li, Y and Su, D and Zhao, Y and Yang, S and Zhang, S and Shi, W and Zhou, Q and Zhang, M},
title = {Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41998161},
issn = {2058-5276},
support = {82322010//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbiome-host interactions can influence colorectal cancer (CRC) outcomes and the effectiveness of immunotherapy treatment, but the precise mechanisms underlying this are poorly understood. Here we analyse CRC patient cohort data and observe that Facalibacterium prausnitzii abundance in faecal samples correlates with improved CRC survival outcome and immunotherapy response. In vitro assays and experiments in azoxymethane plus dextran sulfate sodium (AOM/DSS) and Apc[min/+] mouse CRC models show that F. prausnitzii extracts have anti-tumour activity. Mass spectrometry identifies F. prausnitzii phosphoribosyl pyrophosphate synthetase (fpPRPS) as a bacterial enzyme that inhibits tumour development and promotes CD8[+] T-cell responses. Mechanistically, fpPRPS depletes ATP levels in CRC cells, which then inhibits GTP-GDP exchange on Rab11a, reprogramming CRC energy metabolism. This leads to Rab11a degradation and the disruption of PD-L1 trafficking to reduce the inhibition of T-cell responses. fpPRPS inhibition of tumour progression is PD-L1-dependent. We also show that fpPRPS and anti-PD-1 treatment synergize to promote CD8[+] T-cell responses and tumour control in mice. These findings suggest fpPRPS as a potential strategy for sensitizing CRC to immunotherapy.},
}
@article {pmid41998285,
year = {2026},
author = {Mannino, P and Park, M and Wang, MC},
title = {Organellar insights in ageing and longevity.},
journal = {Nature cell biology},
volume = {},
number = {},
pages = {},
pmid = {41998285},
issn = {1476-4679},
abstract = {Metabolic processes shape ageing and longevity at multiple levels. Emerging evidence shows that many of these processes are orchestrated within and between cellular organelles. Organelles function not only as metabolic reactors but also as signalling hubs, and their coordination plays crucial roles in maintaining cellular homeostasis and promoting organismal fitness. Rather than acting in isolation, organelles engage in dynamic crosstalk through membrane contact sites, metabolite exchange and signalling interplay. In recent years, organelles have been increasingly recognized as critical regulators of ageing and longevity. Here we summarize age-related organellar changes, highlight organelle-mediated intra- and intercellular signalling communication in lifespan and healthspan regulation, and discuss the active roles of organelles in microbiome-host interactions and transgenerational inheritance in regulating longevity. We further outline how longevity-promoting interventions influence organelles, and provide perspectives on how future technological advances may further accelerate progress in this emerging research topic.},
}
@article {pmid41998361,
year = {2026},
author = {Thiyagarasaiyar, K and Paul, D and Kerttula, J and Keski-Karhu, M and Soosaar, K and Mander, &#xdc; and Hallin, S and Machacova, K and Pumpanen, J and Siljanen, HMP},
title = {Genetic Potential for N2O Metabolism in Tree Tissues: Insights From Nitrogen Cycling Gene Prevalence and nosZ Diversity Across Tree Species.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02773-8},
pmid = {41998361},
issn = {1432-184X},
}
@article {pmid41998442,
year = {2026},
author = {Paveen, P and Ryota, K and Kumar, V},
title = {Omics-informed insights into biochar-Trichoderma interactions in plant-soil systems: mechanisms of defense and context-dependent responses.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998442},
issn = {1573-0972},
abstract = {The combined application of biochar and Trichoderma spp. represents a promising strategy for enhancing plant resilience and soil health; however, the molecular mechanisms underlying their synergistic interactions remain poorly understood and inadequately integrated. This review critically synthesizes evidence from transcriptomic, proteomic, metabolomic, and microbiome analyses to elucidate how biochar-Trichoderma interactions modulate plant defense signaling pathways and stress adaptation responses. Transcriptomic analyses reveal context-dependent activation of the jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) signaling pathways. Correspondingly, proteomic and metabolomic datasets demonstrate variable yet recurrent upregulation of pathogenesis-related (PR) proteins, reactive oxygen species (ROS)-scavenging enzymes, and phenylpropanoid-derived metabolites. Notably, accumulating evidence suggests that these molecular responses are highly context-dependent, varying substantially with soil type, biochar physicochemical characteristics, and Trichoderma strain specificity. We critically examine major methodological limitations in existing omics investigations, including inadequate reproducibility under field conditions and insufficient integration of molecular and ecological datasets. Finally, we propose a systems biology framework for designing functionally optimized biochar–microbe formulations and identify research priorities for translating insights into agronomically robust and field-deployable technologies.},
}
@article {pmid41998480,
year = {2026},
author = {Rodriguez-Martinez, AC and Nair, N and Skinner, J and Welch, AA and Malka, S and Moosajee, M},
title = {Metabolomic signatures suggest altered bile acid and energy metabolism in CRB1- retinopathies.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {3},
pages = {},
pmid = {41998480},
issn = {1573-3890},
support = {205174/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Female ; Male ; Metabolomics/methods ; *Energy Metabolism ; *Bile Acids and Salts/metabolism ; *Nerve Tissue Proteins/metabolism/genetics ; *Eye Proteins/metabolism/genetics ; *Retinal Diseases/metabolism ; Middle Aged ; Metabolome ; Adult ; Membrane Proteins ; },
abstract = {INTRODUCTION: The human CRB1 gene encodes the CRB1 protein, primarily expressed in retinal Muller cells and photoreceptors, where it regulates apical-basal polarity and cellular signalling through its role in adherence junctions and maintaining the outer limiting membrane barrier. Dysfunction of CRB1 results in a range of retinal phenotypes with few systemic implications reported. It has been suggested that disrupted Crb1 expression in the gastrointestinal epithelium of rd8 mouse models (Crb1 [-/-]) results in barrier dysfunction permitting translocation of bacteria to the retina.<br><br>OBJECTIVE: Whole metabolomic analysis in patients can provide further insights into disease pathophysiology and aid the identification of potential systemic biomarkers.<br><br>METHODS: Blood plasma from 25 molecularly confirmed CRB1-retinopathy patients from Moorfields Eye Hospital with 25 age- and gender-matched healthy controls underwent ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). MetaboLync pathway analysis identified affected metabolic pathways.<br><br>RESULTS: Of 872 compounds, 244 were significantly altered in CRB1 patients. Key findings included disrupted bile acid metabolism, with elevated primary and secondary bile acids alongside increased gut microbial phenylalanine pathway metabolites, indicative of altered gut microbiome-related metabolic activity and altered enterohepatic circulation. However, sucrose and butyrate levels remained unchanged amongst groups, suggesting absence of metabolomic evidence for severe intestinal barrier dysfunction. Reductions in antioxidants and neuroprotective agents were found alongside energy metabolism dysregulation.<br><br>CONCLUSION: These findings reveal metabolic dysregulation in CRB1-retinopathy, including altered gut microbiome-related metabolic activity, and no strong metabolomic evidence of severe intestinal barrier disruption. The reductions in antioxidants, energy pathways and neuroprotective agents highlight potential therapeutic targets to delay disease progression. Further investigation into gut microbiome composition and intestinal permeability in humans with CRB1 retinopathies is warranted.},
}
@article {pmid41998513,
year = {2026},
author = {Luo, C and Liu, D and Zhan, Z and Li, J and Lou, F and Zhong, R and Chen, L and Zhang, H},
title = {Identification of Campylobactercoli as a key pathogen in Jinhua piglet diarrhea and its the probiotic control by Enterococcus faecium.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05005-8},
pmid = {41998513},
issn = {1471-2180},
support = {32573254//National Natural Science Foundation of China,China/ ; 2021-WR-01//National High-Level Talents Special Support Program of China/ ; ASTIPIAS07//Agricultural Science and Technology Innovation Program/ ; },
}
@article {pmid41998733,
year = {2026},
author = {Xie, C and Li, N and Liu, H and Liang, S and Gao, L and Liu, Z and Mu, S and Liu, S and Wu, X},
title = {The functional evaluation of Pichia pastoris hydrolysate as a protein source partial replacement of soybean meal in diets of growing-finishing pigs.},
journal = {Porcine health management},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40813-026-00511-7},
pmid = {41998733},
issn = {2055-5660},
support = {XD C0110304//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
}
@article {pmid41998767,
year = {2026},
author = {Rungrojn, A and Chaisiri, K and Thaipadungpanit, J and Batty, EM and Blacksell, SD},
title = {Bacterial communities in Thai ticks: revealing geographical and methodological gaps in surveillance-a 25-year scoping review.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {41998767},
issn = {1348-8945},
support = {JCPET02//Royal Society of Tropical Medicine and Hygiene/ ; 220211/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Ticks serve as key vectors for a diverse range of bacterial pathogens that affect humans and animals worldwide. In Thailand, a comprehensive understanding of tick-associated bacterial diversity remains limited. This scoping review synthesises published data on tick-borne bacteria across Thailand from 2001 to 2025, focusing on bacterial diversity, host-vector associations, geographic distribution, and molecular detection methods. Literature searches in NCBI, Embase, and Web of Science identified 402 studies (272 after duplicate removal), of which 39 met the inclusion criteria. Ticks were collected from animals, humans, and the environment across four zoogeographical regions. Rhipicephalus, Haemaphysalis, Dermacentor, and Amblyomma were the most commonly studied genera. Eighteen bacterial genera, including both pathogens and endosymbionts, were identified, with Coxiella-like endosymbionts, Rickettsia, Anaplasma, and Ehrlichia being the predominant genera. Rhipicephalus ticks exhibited the highest bacterial diversity, while Rickettsia spp. were the most frequently detected pathogens. Conventional PCR remained the principal diagnostic method, with limited application of quantitative and metagenomic sequencing approaches. Geographic analysis revealed that most studies were concentrated in the Northern Peninsular and Central Peninsular regions, while the Continental section of the Indo-Chinese Mainland and Korat Plateau zones were under-represented, which may limit the accuracy of regional risk assessments, as surveillance gaps can underestimate both the diversity and prevalence of pathogenic organisms in these areas. This review emphasises the intricate nature of tick-host-pathogen interactions and highlights the importance of implementing standardised genomic surveillance nationwide within a One Health framework. The findings reveal key gaps in current surveillance efforts and advocate for incorporating genomic tick monitoring into Thailand's national One Health strategies to improve zoonotic disease preparedness.},
}
@article {pmid41998770,
year = {2026},
author = {Ng, DZW and Yap, GC and Tay, CJX and Huang, CH and Zhao, S and Low, A and Tham, EH and Loo, EXL and Shek, LP and Goh, A and Chong, KW and Goh, SH and Cheng, ZR and Van Bever, HPS and Teoh, OH and Lee, YS and Yap, F and Tan, KH and Chong, YS and Chan, SY and Eriksson, JG and Godfrey, KM and Lay, C and Knol, J and Schuster, SC and Lai, JS and Chong, MF and Lee, JWJ and Lee, BW and Chan, ECY and Ta, LDH},
title = {Maternal-prenatal gut microbiome-systemic metabolome perturbations and TH2-skewed immunity link to offspring gut microbiome disruption and atopic dermatitis susceptibility.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01655-5},
pmid = {41998770},
issn = {1756-994X},
support = {MC_UU_12011/4/MRC_/Medical Research Council/United Kingdom ; NIHR Senior Investigator (NF-SI-0515-10042) and NIHR Southampton Biomedical Research Centre (NIHR203319)//National Institute for Health and Care Research/ ; MOH-000532//Singapore Ministry of Health's National Medical Research Council Clinician Scientist - Individual Research Grant/ ; },
}
@article {pmid41998806,
year = {2026},
author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z},
title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.},
journal = {Journal of medical primatology},
volume = {55},
number = {3},
pages = {e70074},
doi = {10.1111/jmp.70074},
pmid = {41998806},
issn = {1600-0684},
support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Macaca mulatta/immunology ; *Gastrointestinal Microbiome ; *Diarrhea/veterinary/microbiology/immunology ; *Monkey Diseases/immunology/microbiology ; Longitudinal Studies ; Transcriptome ; Male ; Anti-Bacterial Agents/therapeutic use ; Female ; Chronic Disease ; Multiomics ; },
abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.},
}
@article {pmid41998859,
year = {2026},
author = {Gao, A and Luo, J and Ye, X and Hu, Y},
title = {Comments on "Gut Microbiome Signatures Differ in Cirrhosis With and Without Hepatocellular Carcinoma in a Southeast Asian Cohort".},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70395},
pmid = {41998859},
issn = {1440-1746},
}
@article {pmid41999025,
year = {2026},
author = {McMullen, E and Hafeez, DA and Pai, N and Mainville, L and Dumont, S and Julanon, N and Shenderey, R and Xiong, G and Towheed, S and Donovan, J},
title = {The Gut Microbiome as a Therapeutic Target in Alopecia Areata: Not Yet Part of the Patient Treatment Plan.},
journal = {International journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/ijd.70437},
pmid = {41999025},
issn = {1365-4632},
abstract = {Interest in the gut microbiome as a therapeutic target for treating alopecia areata (AA) has grown considerably. However, existing evidence remains limited and inconsistent. Currently, there is insufficient evidence to recommend microbiome-directed testing and therapies to patients with AA. Rigorous longitudinal studies are needed before such interventions can be recommended.},
}
@article {pmid41999204,
year = {2026},
author = {Economos, Z and Bloom, EH and Menalled, UD and Pethybridge, SJ and Ryan, MR and Casteel, CL},
title = {Cereal rye (Secale cereale) and canola (Brassica napus) cover crops reduce dry bean (Phaseolus vulgaris) herbivore damage.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70821},
pmid = {41999204},
issn = {1526-4998},
support = {//U.S. Department of Agriculture/ ; //National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Cover crops can support soil health and increase habitats for beneficial insects in diverse cropping systems. The aim of this study was to evaluate the impact of cover crop-conditioned soil on plant defense responses and insect pest damage using dry bean (Phaseolus vulgaris L.) as a model.<br><br>RESULTS: In a 2-year, multi-location field experiment comparing four cover crop treatments and a tilled control, we found that dry beans no-till planted into mechanically terminated cereal rye (Secale cereale L.) and canola (Brassica napus L.) experienced less insect damage than controls. In the laboratory, microbiome extracts from canola-enriched field soil increased dry bean jasmonic acid levels and reduced cowpea aphid (Aphis craccivora Koch) survival compared with other soil microbiome extracts. No differences in defense hormones were detected for dry bean grown in cereal rye soil microbiome extracts, however aphid survival was reduced on these plants compared to the controls.<br><br>CONCLUSIONS: Cereal rye and canola cover crops reduced insect damage in dry bean fields. Soil microbiomes associated with canola enhanced defense-related compounds in dry bean, suggesting a potential mechanism for pest suppression in the field. However, the impacts of canola varied across microbiome sources, highlighting the need for additional studies. &#xa9; 2026 Society of Chemical Industry.},
}
@article {pmid41999240,
year = {2026},
author = {Wyss, J and Baehler, S and Ferracini, J and Kroell, D and Rossier, AM and Krupka, N and Misselwitz, B and Yilmaz, B and Wiest, R},
title = {The duodenal microbiota is compartmentalized and clinically stable yet rapidly responsive to nutrient exposure.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2657053},
doi = {10.1080/19490976.2026.2657053},
pmid = {41999240},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Duodenum/microbiology ; Female ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; *Nutrients/metabolism ; RNA, Ribosomal, 16S/genetics ; Obesity/microbiology ; Intestinal Mucosa/microbiology ; Phylogeny ; Bariatric Surgery ; },
abstract = {The duodenum is one of the most nutrient-exposed and immunologically active regions of the human gastrointestinal tract, yet its microbial ecology and short-term responses to dietary stimuli remain poorly defined. Most studies rely on fasting luminal aspirates, which fail to capture mucosa-associated communities and miss rapid ecological shifts during nutrient exposure, limiting insight into the spatial organization and dynamic behavior of the upper small intestinal microbiota (SIM). To address these limitations, we performed a compartment-resolved analysis of the duodenal microbiota in 94 individuals, including healthy controls, patients with obesity before and after bariatric surgery, individuals with IBS, and subjects with other SIBO-associated risk states. Paired luminal aspirates and mucosal biopsies were obtained during upper endoscopy; bacterial load was quantified by culture, and the community structure was assessed using 16S rRNA gene sequencing and PICRUSt-based pathway inference. In addition, healthy volunteers underwent a controlled intraluminal fat challenge with dense serial duodenal sampling over 180 min to resolve short-term nutrient-driven dynamics. Across all participants, the anatomical niche emerged as the dominant ecological determinant. Mucosal communities displayed higher species richness, broader phylogenetic representation, and distinct beta-diversity signatures compared with luminal aspirates, which were narrowly dominated by Streptococcaceae. Under fasting conditions, SIM remained remarkably stable across obesity, IBS, and culture-defined SIBO, with only minor taxonomic differences in SIBO-positive individuals. In contrast, acute nutrient exposure triggered rapid microbial blooming, increased culture positivity, and a transient rise in species richness within 30-60 min, revealing a highly responsive ecosystem not captured by fasting samples. Together, these findings show that the defining feature of the human duodenal microbiota is not disease-associated dysbiosis under fasting conditions, but rather a conserved spatial architecture coupled with rapid, nutrient-driven ecological plasticity, highlighting the dynamic and compartmentalized nature of the upper small intestinal microbiome.},
}
@article {pmid41999333,
year = {2026},
author = {Tang, X and Lu, SY and Huang, JH and Cheng, ZW and Ke, YC and Ai, CF and Liu, C and Liao, HP and Zhou, SG},
title = {Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02641},
pmid = {41999333},
issn = {1520-5851},
abstract = {Phages reshape microbial community functions through auxiliary metabolic genes (AMGs) and are increasingly recognized as active drivers of microbial adaptation. Although herbicides such as glufosinate significantly inhibit soil microbes, these communities exhibit striking resilience; however, the role of phages in facilitating this rapid adaptation remains poorly understood. Here, we dissect the temporal dynamics (days 0, 15, 30, and 60) of phage-host interactions under two contrasting stressors: the microbially toxic glufosinate and the nontoxic dicamba. We find that glufosinate transiently suppresses microbial diversity, followed by a robust recovery on day 60. This successional shift coincides with an elevated proportion of putative temperate phages (74.1%) and a strategic attenuation of bacterial antiviral systems, signaling a transition from antagonistic predation to mutualistic lysogeny. Metagenomic analyses across 23 regions in China corroborate that this temperate phage recruitment is a generalized response to field-relevant glufosinate exposure. Selection for temperate phage infections arises from asymmetric fitness costs (burdening virulent phage-susceptible hosts) and prophage integration of AMGs like gdhA. Specifically, coevolution assays reveal that glufosinate selectively penalizes virulent phage-sensitive hosts, favoring the recruitment of temperate phage infections. Furthermore, in vitro validation confirms that phage-encoded gdhA provides a compensatory metabolic bypass for ammonia detoxification, directly mitigating herbicide toxicity. Collectively, these findings delineate a phage-mediated mechanism for herbicide resistance evolution in soil microbiomes, emphasizing the need for a microbiome-informed agrochemical design to manage long-term ecological resilience.},
}
@article {pmid41999406,
year = {2026},
author = {Lisco, A and Borgognone, A and Vanpouille, C and Bricker-Holt, K and Callier, V and Nason, M and Vujkovic-Cvijin, I and Macmath, D and Manion, M and Redd, AD and Galindo, F and Kalibbala, S and Ssempijja, V and Anok, A and Tomusange, S and Reynolds, SJ and Giuliano, AR and Sereti, I},
title = {Bacterial dysbiosis, cervicovaginal human papillomaviruses and inflammation persist in women living with HIV-1 after a year of antiretroviral treatment.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag211},
pmid = {41999406},
issn = {1537-6613},
abstract = {BACKGROUND: The cervicovaginal microbiome may affect HIV-1 susceptibility and can in turn influence the prevalence and clinical course of HIV-1 and other sexually transmitted diseases. As the determinants, immunological correlates and clinical effects of the dysbiosis observed in women living with HIV-1 (WWH) remain elusive, we evaluated the vaginal immunologic milieu, cervicovaginal microbiome and prevalence of human papillomaviruses (HPV) in antiretroviral-naïve WWH over their first year of antiretroviral therapy (ART).<br><br>METHODS: 83 ART-na&#xef;ve Ugandan WWH were enrolled in a longitudinal observational trial. Clinical evaluation and sampling of cervicovaginal secretions and plasma were performed at 0, 8, 24 and 52 weeks post-ART initiation. Amplification of the 16S-rRNA gene V3-V4 region was used to determine the cervicovaginal microbiome. A multiplex bead-array assay was used to quantify the concentration of biomarkers while a PCR-based hybridization assay was utilized for HPV detection and genotyping.<br><br>RESULTS: Gardnerella was the most abundant genus with a median relative abundance of 35% before ART maintaining a high prevalence throughout the study. Vaginal bacterial diversity did not change after ART, although the relative abundance of some genera, including the bacterial-vaginosis-associated bacteria Peptostreptococcus and Prevotella, decreased compared to baseline. Inflammatory biomarkers remained elevated in the cervicovaginal compartment despite prompt decreases in plasma.The prevalence of high and low-risk HPV types remained stable despite ART.<br><br>CONCLUSIONS: Suppression of HIV-1 replication is not sufficient to revert dysbiotic changes, proinflammatory immunological milieu and persistent HPV infections. Exploration of targeted strategies to restore cervicovaginal mucosal immunological functions in WWH is warranted.},
}
@article {pmid41999447,
year = {2026},
author = {Ganguly, NK and Kalra, S and Kapoor, N and Rao, P and Bakshi, M},
title = {Reconsidering Obesity in India Through a Gut-Metabolic Lens: Mechanistic Insights and the Emerging Role of Synbiotics in Individuals with the Thin-Fat Phenotype.},
journal = {Advances in therapy},
volume = {},
number = {},
pages = {},
pmid = {41999447},
issn = {1865-8652},
abstract = {India's escalating burden of obesity and metabolic disease is characterized by a distinctive "thin-fat" phenotype, in which individuals with normal or near-normal body mass index exhibit disproportionate visceral adiposity, reduced skeletal muscle mass, and heightened susceptibility to insulin resistance. Conventional obesity models centered primarily on caloric imbalance fail to adequately explain this pattern, underscoring the need for a more integrative pathophysiological framework. Emerging evidence implicates gut microbiome dysbiosis, impaired fermentation of dietary fibers, reduced short-chain fatty acid (SCFA) signaling, altered bile acid metabolism, metabolic endotoxemia, and dysregulated adipose tissue crosstalk as key contributors to metabolic vulnerability in South Asian populations. This commentary synthesizes mechanistic insights into the gut-metabolic axis and examines their relevance to India's phenotype-specific challenges. Key pathways, including SCFA-mediated incretin secretion, Toll-like receptor 4 (TLR4)-driven inflammatory signaling, angiopoietin-like protein 4 (ANGPTL4)-mediated lipid partitioning, and microbiota-dependent bile acid biotransformation, are discussed as interconnected drivers of metabolic dysfunction. Emerging clinical evidence from randomized controlled trials evaluating synbiotic and prebiotic-botanical formulations is also discussed, highlighting their potential benefits as adjuncts to lifestyle modification. Given India's dietary patterns and widespread deficiency of fermentable fiber intake, synbiotics may represent a scalable and biologically coherent strategy to support metabolic health. However, heterogeneity of formulations, interindividual microbiome variability, and limited long-term outcome data necessitate cautious interpretation. Advancing precision microbiome-targeted interventions will require population-specific research, multi-omics integration, and rigorous clinical evaluation.},
}
@article {pmid41999489,
year = {2026},
author = {Nelson, K and Peterson, N and Olson, R and Castillo, H and Antwi, C and Cromwell, S and Benbow, ME and Ayayee, P},
title = {Gut Microbial Nitrate Reduction to Ammonia: A Possible Pathway of Biological Nitrogen Provisioning in Freshwater Insects.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02771-w},
pmid = {41999489},
issn = {1432-184X},
}
@article {pmid41999613,
year = {2026},
author = {Cook, KL and Giles, ED and Sekela, JJ and Simpson, JB and Redinbo, MR and Wilson, AS and Umar, S and Befort, CA and Kimler, BF and Hursting, SD and Fabian, CJ},
title = {Weight loss and omega-3 supplementation modulate the microbiome in women with increased breast cancer risk.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1158/1940-6207.CAPR-26-0021},
pmid = {41999613},
issn = {1940-6215},
abstract = {Obesity is associated with gut dysbiosis, chronic inflammation, and insulin resistance. We assessed proportional change in fecal microbial populations in a pilot study (n=34) of peri/postmenopausal women with BMI ≥28 kg/m2 who were randomized to receive either 3.25 g/day of omega-3 fatty acids or a placebo during a weight loss intervention. Body composition was assessed using DXA, and fecal and blood samples were collected. Median weight change was -10%. Among participants who lost ≥10% of their weight, those assigned to omega-3 fatty acids showed the greatest decrease in the Firmicutes/Bacteroidetes phyla ratio and displayed favorable changes in systemic biomarkers. Notable increases in the proportional abundance of short-chain fatty acid (SCFA)-producing microbes including Phocaeicola vulgatus and Alistipes putredinis were observed in women receiving omega-3, which correlated with improvements in breast cancer biomarkers such as bioavailable estradiol, adiponectin-to-leptin ratio, and C-reactive protein levels. Women administered omega-3 fatty acids displayed increased % change in plasma SCFA propionate and decreased butyrate, suggesting intervention differentially modulated circulating bacterial-derived SCFA metabolites. High dose omega-3 fatty acids, when added to a behavioral weight loss intervention, promoted beneficial shifts to the gut microbiome and associated with improved breast cancer risk factors biomarkers.},
}
@article {pmid41999742,
year = {2026},
author = {Moyne, O and Norton, GJ and Al-Bassam, M and Lieng, C and Thiruppathy, D and Kumar, M and Haddad, E and Weng, Y and Raffatellu, M and Zaramela, LS and Zengler, K},
title = {Predicting competition and substrate preferences for targeted microbiome alteration.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.03.036},
pmid = {41999742},
issn = {1097-4172},
abstract = {Microbiome science has greatly expanded our understanding of microbial life and its roles in the environment and human health. Yet microbiome science often relies on descriptive, correlation-based approaches that limit causal insight and intentional intervention designs. Moving toward predictive and mechanistic understanding requires functional characterization of microbial interactions and metabolic preferences. Here, we present microbial interaction and niche determination (MIND), which quantifies mRNA translation prioritization to infer substrate preferences and competitive interactions in complex communities. Applied to synthetic communities, soil, human fecal samples, and a mouse model, MIND predicted microbial competition and substrate preferences, guiding precision prebiotic and probiotic interventions to selectively modulate community composition. Currently focused on competition and substrate utilization, MIND could be further extended to capture additional interactions and ecological niches. By linking functional measurements to ecological outcomes, MIND offers a broadly applicable framework for targeted microbiome manipulation and rational intervention design rooted in functional insight.},
}
@article {pmid41999744,
year = {2026},
author = {Usyk, M and Hayes, RB and Knight, R and Gonzalez, A and Li, H and Osman, I and Weber, JS and Ahn, J},
title = {Gut microbiome is associated with recurrence-free survival in patients with resected high-risk melanoma receiving adjuvant immune checkpoint blockade.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.03.041},
pmid = {41999744},
issn = {1097-4172},
abstract = {Patients with resected, high-risk melanoma receive adjuvant immune checkpoint blockade (ICB), yet clinical benefit remains unpredictable, with 25%-40% of patients experiencing recurrence. To evaluate whether pre-treatment gut microbiome (GMB) features predict recurrence, we analyzed stool samples from 674 patients enrolled in a phase 3 clinical trial, CheckMate 915, which investigated the combination of nivolumab plus ipilimumab versus nivolumab as a single agent across five geographic regions. Region-specific and cross-region meta-analyses identified pre-treatment taxa associated with recurrence, including Eubacterium, Ruminococcus, Firmicutes, and Clostridium. Recurrence prediction was strongest when the validation cohort exhibited GMB profiles similar to those in the discovery cohort. Among closely matched individuals (Jensen-Shannon divergence [JSD] ≤ 0.11), the area under the curve (AUC) for recurrence prediction ranged from 0.78 to 0.94 across regions. GMB composition remained largely stable following treatment. These findings suggest that gut bacterial markers can predict recurrence after adjuvant ICB treatment in melanoma, supporting their potential as clinically actionable biomarkers to guide personalized therapy.},
}
@article {pmid41999953,
year = {2026},
author = {Ovaska, M and Tamminen, M and Lahdenperä, M and Rautava, S and Jeevannavar, A and Isokääntä, H and Bode, L and Lagström, H},
title = {The role of human milk oligosaccharides in shaping and restoring infant gut microbiota: Population-based cohort study.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101318},
doi = {10.1016/j.ajcnut.2026.101318},
pmid = {41999953},
issn = {1938-3207},
abstract = {BACKGROUND: Infant gut microbiota colonization is important for supporting normal development and long-term health of children. Human milk oligosaccharides (HMOs) influence the composition of the gut microbiota, but their specific effects, particularly after breastfeeding, remain poorly understood.<br><br>OBJECTIVES: We aimed to deepen the understanding of how HMOs associate with the gut microbiota composition at 3 months and at 13 months of age. Additionally, we assessed the role of HMOs as microbiome-rebalancing agents in cesarean delivered infants.<br><br>METHODS: We analyzed fecal samples from infants at 3 months (n=517) and 13 months (n=522), along with human milk samples at 3 months, from a population-based cohort. Gut microbiota was profiled by 16S rRNA sequencing, and 19 HMOs quantified by high-performance liquid chromatography with fluorescent detection. Dirichlet Multinomial Mixtures clustering was used to identify bacterial fecal community types (FCTs) and multinomial logistic regression models to study the association between HMOs and FCTs. PERMANOVA and linear regression models were used to associate HMOs with gut microbiota diversity measures and Spearman correlation to bacterial genera.<br><br>RESULTS: HMOs associated with gut microbiota FCTs, diversity measures, and bacterial genera at 3 and 13 months of age. At 3 months, disialyllacto-N-tetraose (DSLNT) and the structurally related lacto-N-sialyllactose b (LSTb) showed notable associations with the gut microbiota while at 13 months, fucodisialyllacto-N-hexaose (FDSLNH) associated with multiple gut microbiota metrics. Maternal secretor status was associated with the gut microbiota beta diversity (R2=0.003, p<0.05) and decreased Shannon diversity (b=-0.24, p<0.05) at 3 months, with diminishing associations at 13 months (Observed richness, b=-11, p<0.05). While no individual HMOs showed microbiome-rebalancing effects in cesarean-born infants, infants fed by non-secretor mothers exhibited stronger cesarean-related microbiota patterns compared to those fed by secretors.<br><br>CONCLUSIONS: HMOs exhibit age-dependent and structure-specific associations with infant gut microbiota, extending beyond breastfeeding.},
}
@article {pmid42000112,
year = {2026},
author = {Cao, X and Lou, B and Sun, Z and Wei, Y and Qu, M and Xu, Y and Kang, Q and Xie, S and Wang, Q and Chen, J},
title = {Mechanism of neuroinflammation and cardiovascular toxicity induced by tributyltin: Evidence from zebrafish (Danio rerio) models and network toxicology studies.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128127},
doi = {10.1016/j.envpol.2026.128127},
pmid = {42000112},
issn = {1873-6424},
abstract = {As an antifouling agent, tributyltin (TBT) is widely used in marine anti-fouling coatings. Recent studies have demonstrated that TBT exerts toxic effects on aquatic life and can be transferred to humans via the food chain. In this study, we investigated the impact of varying TBT concentrations on the brain and heart of zebrafish, as well as the underlying mechanisms involved. These findings suggest that TBT exposure caused varying degrees of oxidative stress in the brain and heart of zebrafish, increased lipid peroxidation levels, and induced inflammatory responses, apoptosis, and histopathological damage. Additionally, TBT exposure altered zebrafish behavior, significantly reduced the expression of tight junction protein genes (zo-1, occludin, and claudin-2) in the gut and brain, and suppressed acetylcholinesterase (AChE) activity in the brain. Untargeted metabolomics and gut microbiome analysis revealed that TBT exposure significantly altered the abundance and diversity of microbial communities, leading to metabolic disturbances, with the primary differential metabolites associated with nucleotide, glycerophospholipid, and purine metabolism. Gut microbiota dysbiosis was also strongly correlated with neuro-cardiovascular toxicological responses in zebrafish. Dysbiosis increased lipopolysaccharide (LPS) secretion. In the context of blood-brain barrier disruption, circulating LPS may reach the brain, potentially contributing to neuroinflammation and subsequent neural damage. Concurrently, elevated inflammatory cytokines were associated with activation of the hypothalamic-pituitary-interrenal (HPI) axis, increasing cortisol (Cor) levels, and correlating with cardiovascular system damage. Network toxicology and molecular docking analysis revealed that strong binding affinities between TBT and core targets, including BCL2, GAPDH, IL1B, IL6, TNF, and MMP9.},
}
@article {pmid42000265,
year = {2026},
author = {Chelladurai, G and Jenivi, A and Esther Elsie, T},
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.2026.04.063},
pmid = {42000265},
issn = {0929-6646},
}
@article {pmid42000466,
year = {2026},
author = {Collins, K and Donnellan, L and Asif, Z and Chan, NSL and Subramaniam, S and Kamath, S and Ariaee, A and Abdelhafez, A and Wignall, A and Hoffman, P and Joyce, P},
title = {The gut microbiome modulates the lipase-mediated digestion of dietary lipid emulsions.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {265},
number = {},
pages = {115715},
doi = {10.1016/j.colsurfb.2026.115715},
pmid = {42000466},
issn = {1873-4367},
abstract = {The gut microbiome plays a critical role in host lipid metabolism, yet its influence on the intraluminal processes governing dietary lipid digestion, particularly lipase-mediated hydrolysis at oil-water interfaces, remains poorly understood. In this study, we combined in vivo microbiome modulation in rats with an ex vivo lipolysis model to examine how microbial perturbations affect intestinal lipid digestion. Rats were pretreated for 14 days with either broad-spectrum antibiotics or a prebiotic to induce distinct microbial profiles. Small intestinal luminal contents were collected from the jejunum and used to monitor the ex vivo digestion of coconut oil and olive oil, representing dietary lipids with varying triglyceride chain lengths. Microbial diversity was positively associated with both the rate and extent of lipid digestion. Notably, the prebiotic group showed a 3-4-fold increase in fatty acid release compared to the antibiotic group after 60 min of digestion (p < 0.0001). Physicochemical analyses indicated that prebiotic treatment enhanced emulsification efficiency, increasing the interfacial surface area available for lipase adsorption by up to 250%. Biomolecular profiling revealed marked changes in the intestinal lipidome and proteome, together with changes in endogenous bile acid and carbohydrate concentrations suggesting that microbial modulation of the luminal milieu plays a critical role in lipid emulsification and bioaccessibility. Together, these findings demonstrate that microbiome composition directly impacts the physicochemical environment of the small intestine and shapes lipid digestion outcomes, highlighting the potential of microbiome-targeted strategies to enhance digestive efficiency and metabolic health.},
}
@article {pmid41993185,
year = {2026},
author = {Kaźmierczak-Siedlecka, K and Kucharski, R and Kosiński, A and Marano, L and Makarewicz, W and Kalinowski, L},
title = {Red-complex bacteria: immunological background leading to the development of head and neck cancers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1804268},
pmid = {41993185},
issn = {1664-3224},
mesh = {Humans ; *Head and Neck Neoplasms/immunology/microbiology/etiology ; *Microbiota/immunology ; Animals ; Porphyromonas gingivalis/immunology ; Periodontitis/microbiology/immunology ; },
abstract = {Oral microbiome imbalance is involved in the development of head and neck cancers (HNCs). There is a group of oral pathogens, such as Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, that creates red-complex. Currently, the oral pathogens' role in the pathogenesis of periodontitis is well-described; nevertheless, data regarding the link between HNCs and periopathogens are still limited, especially considering T. forsythia and T. denticola. These microbes utilise various virulence factors to promote the carcinogenesis process, affecting the immunological background. This paper presents modern insights into the role of red-complex bacteria in the development of HNCs, concentrating on the immunological aspects.},
}
@article {pmid41993272,
year = {2026},
author = {Wei, Z and Hong, Q and Chen, G and Hartert, TV and Rosas-Salazar, C and Das, SR and Shilts, MH and Levin, AM and Tang, ZZ},
title = {Fast and reliable association discovery in large-scale microbiome studies and meta-analyses using PALM.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.09.717497},
pmid = {41993272},
issn = {2692-8205},
abstract = {Identifying microbial features associated with various covariates is a long-standing goal in microbiome research. Modern association studies incorporate an ever-increasing number of microbial features, covariates, and datasets from diverse cohorts. However, the complexity of microbiome data challenges analysis, often leading to poor replication of findings. We introduce PALM, a quasi-Poisson regression framework that enables fast and reliable association discovery in large-scale studies and meta-analyses. Extensive, realistic simulations demonstrate PALM's advantages in controlling false discovery rates, boosting power, improving computational efficiency, and preserving cross-study homogeneity of association effects. Three real-world applications at different scales illustrate PALM's utility, underscoring its potential to advance microbiome research.},
}
@article {pmid41993317,
year = {2026},
author = {Chaki, T and Maruyama, D and Doan, TN and Xiaoli, T and Prakash, A},
title = {Dietary tryptophan mitigates lung ischemia-reperfusion injury via microbiota-derived indole-3-propionate and aryl hydrocarbon receptor signaling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.02.714281},
pmid = {41993317},
issn = {2692-8205},
abstract = {BACKGROUND: Lung ischemia-reperfusion (IR) injury drives early morbidity after lung transplantation and cardiothoracic surgery, yet targeted preventive therapies are lacking. The gut-lung axis and microbiota-derived tryptophan metabolites, including indole-3-propionate (IPA), may regulate pulmonary immunity and inflammation. We investigated whether a tryptophan-rich (Trp-Rich) diet attenuates sterile lung IR injury by increasing microbiota-derived indole metabolites and reprogramming alveolar macrophage (AM) inflammatory responses.<br><br>METHODS: C57BL/6 mice received isocaloric tryptophan-standard (Trp-Std; 0.18%) or Trp-Rich (0.60%) diets for 14 days, then underwent unilateral left lung IR (60 min ischemia followed by 60 min reperfusion). Oxygen saturation, lung cytokines, and aryl hydrocarbon receptor (AhR) signaling readouts (Cyp1a1 / Cyp1b1) were evaluated. Gut microbiota was profiled by 16S rRNA sequencing, and targeted metabolomics quantified tryptophan metabolites in feces, portal vein (PV) plasma, and lung tissue. To further assess inflammatory priming in vivo , mice were additionally challenged with intratracheal lipopolysaccharide (LPS). Mechanistic studies compared IPA with related indole metabolites in MH-S cells and primary human AMs, including ex vivo nutritional IR, LPS stimulation, and AhR stimulation and blockade using synthetic agonists and antagonists.<br><br>RESULTS: Trp-Rich feeding improved post-IR oxygenation, reduced lung IL-1&#x3b2;, and increased pulmonary Cyp1a1 / Cyp1b1 gene expression. Trp-Rich diet remodeled the gut microbiota, including enrichment of Bifidobacterium and Lactobacillus , and increased IPA levels across feces, PV plasma, and lung tissue, with lower kynurenine/IPA ratios across matrices. In the LPS intratracheal challenge, Trp-Rich feeding reduced IL-6 levels in lung tissue and systemic plasma. Primary murine AMs isolated from Trp-Rich mice also showed reduced IL-1&#x3b2; and IL-6 release in an ex vivo nutritional IR model. Among tested indole metabolites, IPA showed the strongest dose-dependent suppression of LPS-induced cytokines and chemokines in MH-S cells and primary human AMs, remained active in the ex vivo nutritional IR model, and its anti-inflammatory effect was abrogated by AhR blockade and enhanced by co-treatment with other indole metabolites.<br><br>CONCLUSIONS: A Trp-Rich diet attenuated sterile lung IR injury, coinciding with gut microbiota remodeling, increased systemic and pulmonary IPA, reduced inflammatory priming, and reprogrammed AM responses. These data support diet- or microbiome-directed strategies targeting IPA-AhR signaling to mitigate perioperative lung IR injury.},
}
@article {pmid41993357,
year = {2026},
author = {Malarney, KP and Scott, SA and Chang, PV},
title = {A class of metallohydrolases expands bile salt hydrolase activity in the gut.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716488},
pmid = {41993357},
issn = {2692-8205},
abstract = {Bile acids are steroidal metabolites produced by host and microbial metabolism that shape gut microbiome ecology and influence host physiology [1,2] . Bile acid structural diversification requires gut microbial bile salt hydrolase (BSH) activities, which cleave the amide bond of liver-derived bile acid amidates (BAAs) [3] . Beyond this gatekeeping metabolic function, BSHs expand the bile acid pool via their amine N -acyltransferase activity to produce numerous microbially derived BAAs that signal via host receptors and are further metabolized [4,5] . To date, all BSH activity has been attributed to a family of N-terminal nucleophile (Ntn) cysteine hydrolases. However, numerous gut anaerobic bacteria possess BSH activity but do not encode bsh genes from the Ntn family. Here, we describe a previously unknown class of m etal-dependent BSHs (mBSHs) broadly distributed in the gut microbiome. These metalloenzymes have a distinct active site architecture from the canonical Ntn superfamily of cysteine hydolase BSHs (cBSHs) and are selective for taurine-conjugated BAAs. The discovery of this heretofore unappreciated class of BSHs overturns the paradigm that this important, conserved biochemical activity of the gut microbiota is provided exclusively by canonical cysteine hydrolases, greatly expands the known landscape of bile acid metabolism, and reveals a previously unrecognized link connecting host-microbiota bile acid co-metabolism with microbial taurine utilization pathways.},
}
@article {pmid41993390,
year = {2026},
author = {Hutchinson, NT and Ye, N and Jennings, M and Fang, C and Qi, N and Li, J},
title = {Engineered Lactate Catabolizing Probiotics Reveal Timescale Dependent Microbiome-Host Metabolic Coupling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.07.716956},
pmid = {41993390},
issn = {2692-8205},
abstract = {The exchange of lactate, a metabolic substrate and regulator, between the gut lumen and systemic circulation for use in host and microbial processes is well documented, but tools capable of uncovering whether this process influences host metabolic status across acute and chronic contexts are lacking. In our prior work, we engineered probiotic Bacillus subtilis PY79 to produce lactate oxidase (LOX) intracellularly, allowing it to rapidly convert intestinal lactate to pyruvate. Following oral administration, LOX reduced systemic lactate concentrations at rest and under challenge conditions, providing a platform for investigating lactate's influence on host metabolism and microbiota. In the present work, we demonstrate that acute LOX administration effectively rewired microbiota function and host energy balance, as revealed by 16S sequencing and indirect calorimetry. In silico microbial community modeling via MICOM and metagenomic inference via PICRUSt2 suggested that acute shunting of lactate to pyruvate induced microbiota remodeling towards anabolic processes, reflected by increased flux of pyruvate, acetate, and formate, alongside moderate to large increases (Cohen's d = 0.60-1.00) in pathways for fructan degradation, B-vitamin biosynthesis, and lipid synthesis. These anabolic shifts temporally aligned with transient increases in host energy expenditure (β = 1.08, p<0.05) via glucose oxidation (β = 0.01, p<0.05), hinting at functional coupling between microbial biosynthesis and host energy balance via lactate exchange. Of note, acute LOX administration also improved thermoregulation and survival following LPS-induced sepsis, demonstrating functional relevance of these metabolic effects during acute inflammatory challenge. To assess chronic effects, we administered LOX for 6 weeks during diet-induced obesity. LOX treatment persistently reduced blood lactate. However, this chronic lactate reduction did not curtail the progression of diet-induced obesity or induce sustained modulation of host energy expenditure. This disconnect between acute and chronic findings suggests that gut-centric lactate conversion affects energy balance through microbiome and/or host-dependent mechanisms, but cannot override homeostatic forces in the long term to produce clinical benefit during chronic disease. Our results validate LOX probiotics as a tool for acute metabolic augmentation, and highlight a clear homeostatic limit to gut-centric therapies. This platform may enable targeted design of probiotic interventions matched to therapeutic timescale and inform synbiotic formulations that overcome homeostatic compensation.},
}
@article {pmid41993507,
year = {2026},
author = {Coleman, I and Ma, J and Qian, G and Jiang, Y and Brown Kav, A and Korem, T},
title = {End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.06.712906},
pmid = {41993507},
issn = {2692-8205},
abstract = {The generation of Metagenome Assembled Genomes (MAGs) has become a standard and basic step in the analysis of metagenomic data. This multi-step process, which includes assembly, binning, refinement, and quality control, has many alternative approaches, algorithms, and parameters. Determining the ideal approach for a given ecosystem and study, or highlighting algorithmic gaps in need of additional research and development, requires rigorous benchmarking. We present MAG-E (MAG pipeline E valuator), a generalizable and expandable framework for end-to-end evaluation of entire MAG pipelines: from assembly, through binning, to quality control and filtering. MAG-E relies on simulations that are built to match an ecosystem of interest and provide a ground truth for accurate evaluation. To demonstrate the capabilities of MAG-E, we benchmark two assemblers, six binning algorithms, three binning modes, and three quality control and refinement methods in the context of the human gut microbiome. Our findings offer multiple insights into optimal MAG generation in this context. We find that metaSPAdes consistently outperforms MEGAHIT in terms of recall (completeness), and that COMEBin overall outperforms alternative binning algorithms, but has lower precision than SemiBin2. While multi-sample binning results in higher precision, as previously shown, single-sample binning has higher recall and leads to better overall performance with modern binners. Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance. We further show that CheckM2 systematically overestimates completeness and underestimates contamination, and that this is partially ameliorated when using GUNC. Finally, we analyze performance at the contig level, and demonstrate that binning algorithms systematically underperform for prophages and fail to bin contigs that are shared between genomes. Overall, MAG-E offers deep insights into successes and gaps in this important analytic process.},
}
@article {pmid41993513,
year = {2026},
author = {Cui, Z and Meng, CJ and Irwin, SM and Augustijn, HE and Papageorgiou, PP and Nguyen, ATP and Yu, R and Aguilar Ramos, MA and Kulik, HJ and Balskus, EP},
title = {A previously unappreciated class of metal-dependent bile salt hydrolases from the human gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716592},
pmid = {41993513},
issn = {2692-8205},
abstract = {Bile salt hydrolases (BSHs) are gut microbial enzymes that catalyze the deconjugation of glycine-or taurine-conjugated bile acids (BAs), a key step in shaping the BA pool in the human gastrointestinal tract and modulating host-gut microbiome interactions. [1-3] All known BSHs are members of the N-terminal nucleophile (Ntn) hydrolase superfamily and share a conserved architecture and mechanism involving a nucleophilic active site cysteine. [4,5] This knowledge has guided predictions and study of BSH activity in the gut microbiome [6,7] as well as the development of BSH inhibitors [8] . Here, we report the discovery and characterization of a previously unknown BSH from the human gut bacterium Bilophila wadsworthia that belongs to the metal-dependent amidohydrolase superfamily and exhibits robust and specific activity toward taurine-conjugated bile salts. We show this secreted enzyme, metalloBSH, utilizes a metallocofactor for BA deconjugation, a mechanism distinct from that of canonical Ntn-type BSHs. MetalloBSHs are conserved in B. wadsworthia and present in many other Desulfovibrionaceae found in vertebrate gut microbiomes. Analysis of multi-omic datasets indicates metalloBSHs are expressed in vivo and correlate with BA metabolism. Overall, our findings reshape our understanding of BSH activity in the gut microbiome and highlight the promise of activity guided discovery in revealing previously overlooked gut microbial enzymes.},
}
@article {pmid41993533,
year = {2026},
author = {Awan, A and Blakeley-Ruiz, JA and Kleiner, M and Hinzke, T},
title = {Area under the curve quantification outperforms spectral counting in metaproteomics, but matching between runs is detrimental.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716595},
pmid = {41993533},
issn = {2692-8205},
support = {R35 GM138362/GM/NIGMS NIH HHS/United States ; },
abstract = {UNLABELLED: Metaproteomics enables the functional characterization of microbiomes and host-microbe interactions by detecting and quantifying thousands of proteins. In data-dependent acquisition metaproteomics, protein quantification is commonly performed using either MS1-based area under the curve (AUC) or MS2-based peptide spectral counts (SpC). In AUC quantification, match between runs (MBR) is frequently employed to minimize data sparsity, yet its impact on metaproteomic data remains unclear. Understanding MBR's impact on metaproteomics data is especially important due to the high peak density in the MS1 mass spectra and the potential presence of not only proteins, but even entire organisms, in one sample and their absence in the other, which would complicate accurate feature mapping and transfer. While accurate quantification is essential for deriving meaningful biological inferences from metaproteomic analyses, systematic evaluations of AUC and SpC quantification in metaproteomics remain scarce. In this study, we used defined complex metaproteomic samples to perform a ground truth-based evaluation of AUC and SpC quantification and to determine the impact of MBR on AUC quantification. We found that MBR led to a substantial number of falsely identified proteins in complex samples. Protein identifications from an organism not present in the sample were wrongly transferred from other samples when MBR was used. We found that MBR-free AUC data had a wider dynamic range, higher quantitative accuracy, and more sensitive detection of abundance differences.<br><br>SIGNIFICANCE OF THE STUDY: Although metaproteomics is increasingly used to advance microbiome research, quantification strategies in metaproteomics are mostly selected based on convention rather than evidence, due to a lack of ground truth-based evaluation of quantification strategies in metaproteomics. Accurate protein quantification is key to deriving meaningful biological inferences from metaproteomic samples, yet it remains challenging due to their high complexity and uneven protein abundances. Here, we used defined metaproteomic samples to evaluate widely used quantification strategies in metaproteomics and to determine the effects of match between runs (MBR) on quantitative accuracy. Based on our findings, MBR adds falsely identified proteins to metaproteomic data. While MBR-free AUC offers a broader dynamic range and higher quantitative accuracy, SpC offers better proteome coverage. With this study, we provide an evidence-based framework for the informed selection of quantification strategies in metaproteomics, and highlight the strengths and limitations of these approaches with respect to proteome coverage, dynamic range, quantitative accuracy, and error propagation. Our findings also have important implications for the biological interpretation of data derived from these strategies and lay the groundwork for future studies validating quantitative approaches in data-independent acquisition workflows.},
}
@article {pmid41993548,
year = {2026},
author = {Fodor, KE and Ritter, AC and Schmieley, RA and Ricart Arbona, RJ and Miranda, IC and Lipman, NS},
title = {Microbiome-Dependent Protection Against Corynebacterium bovis -Associated Hyperkeratosis in Nude Mice (Mus musculus).},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.11.716586},
pmid = {41993548},
issn = {2692-8205},
abstract = {Corynebacterium bovis , the cause of Corynebacterium -associated hyperkeratosis (CAH), is an important pathogen in immunocompromised mice that is difficult to eliminate and can confound research outcomes. We recently observed that CAH severity varies among outbred athymic nude mouse stocks, but the relative contributions of host genetics and the microbiome remain unclear. We hypothesized that disease course and severity vary based on host genetic stock and/or microbiome composition. Three nude mouse stocks were rederived into the axenic state and either monoinfected with a pathogenic C. bovis isolate (10 [4] ; CFU) or given sterile media (n=6/group). Axenic mice were also reassociated with their source microbiome or microbiomes from three other stocks with known differences in CAH severity, then inoculated with C. bovis (n=6) or sterile media (n=2). In a separate experiment, one axenic stock was used to assess the role of C. amycolatum via monoinfection, monoinfection followed by C. bovis challenge, or addition to a nonprotective microbiome followed by C. bovis challenge. Mice were monitored daily for 21 days and scored for skin lesions (0-5). C. bovis monoinfected mice developed disease comparable in severity and timing to conventionally raised controls. Notably, reassociation with Vendor A2's microbiome prevented clinical lesions and reduced histopathologic changes across all stocks. While C. amycolatum as a monoinfection did not cause disease nor reduce disease severity following C. bovis challenge, it delayed the onset and lowered peak scores when added to a non-protective microbiome. These findings demonstrate that C. bovis can cause CAH as a monoinfection, that both host genetics and microbiome composition influence disease progression, and, together with prior work, support its role as the etiologic agent consistent with Koch's postulates. Identifying protective microbiome constituents may inform strategies to reduce disease burden in susceptible mice.},
}
@article {pmid41993554,
year = {2026},
author = {Rivas, JA and Scieszka, DP and Peralta-Herrera, E and Enriquez, CM and Merkley, SD and Nava, AL and Gullapalli, RR and Castillo, EF},
title = {Colonic metabolomic and transcriptomic alterations in a mouse model of metabolic syndrome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.02.716131},
pmid = {41993554},
issn = {2692-8205},
abstract = {UNLABELLED: Metabolic syndrome (MetS), characterized by abdominal obesity, insulin resistance, dyslipidemia, and hypertension, affects a substantial proportion of the global population and increases the risk for cardiovascular disease, diabetes, and metabolic dysfunction-associated steatotic liver disease (MASLD). Despite its prevalence, there are currently no effective pharmacological therapies targeting MetS, highlighting the need to identify novel etiological mechanisms, particularly within the gastrointestinal (GI) tract. Using a mouse model of MetS and healthy lean controls, we assessed the colonic microenvironment through metabolomic, transcriptomic, and microbiome analyses. Colonic organoids were cultured to further explore epithelial alterations. Additionally, human MetS fecal metabolomics data were cross-compared with the mouse model to validate translational relevance. MetS mice exhibited upregulation of colonic anabolic pathways, including glycolysis, the pentose phosphate pathway, and the tryptophan/kynurenine pathway, without evidence of intestinal inflammation. Microbiome analysis revealed an increased abundance of the genus Lactobacillus in MS NASH mice. Colonic organoids from MetS mice showed altered goblet cell differentiation. Comparative analysis with human MetS fecal metabolomics demonstrated similar dysregulated pathways, underscoring the translational relevance of these findings. Our study reveals significant metabolic and microbial alterations in the colon of MS NASH mice, implicating a dysfunctional GI tract as a potential etiological factor in MetS. These findings highlight specific metabolic pathways and microbial signatures that could serve as future therapeutic targets for MetS.<br><br>NEW &amp; NOTEWORTHY: This study identifies the colon as a metabolically active tissue affected in metabolic syndrome. Despite the absence of intestinal inflammation, MS NASH mice displayed altered colonic metabolism and microbiota composition, with conserved metabolite changes matching those seen in humans with metabolic syndrome. These findings highlight colonic metabolic dysfunction as a potential driver of gut dysbiosis and disease progression in metabolic syndrome and MASLD.},
}
@article {pmid41993555,
year = {2026},
author = {Herzog, HM and Fang, C and Lam, L and Jin, K and Zamarioli, A and Dinh, E and Gupta, CL and Sharma, A and Moody, T and Pierce, JL and Hohl, MS and Takimoto, SW and Lyalina, S and Wentworth, KL and Yu, K and Lu, VF and Mamikunian, I and Hunt, NK and Lynch, S and Pollard, KS and Hernandez, CJ and Perrien, DS and Hsiao, EC},
title = {Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1 [R206H] -driven heterotopic ossification.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716562},
pmid = {41993555},
issn = {2692-8205},
abstract = {UNLABELLED: Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1 [R206H] mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfrα-Cre/Acvr1 [R206H] (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1β blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions.<br><br>ONE SENTENCE SUMMARY: Antibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway.},
}
@article {pmid41993569,
year = {2026},
author = {Wang, S and Hullar, MA and Curtis, K and Kwee, S and Park, SY and Rettenmeier, C and Monroe, KR and Ernst, T and Shepard, J and Wilkens, LR and Le Marchand, L and Lampe, JW and Lim, U and Randolph, TW},
title = {Gut Microbiota Mediates the Association between Diet Quality and Ectopic Adiposity: The Multiethnic Cohort Adiposity Phenotype Study.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.10.717245},
pmid = {41993569},
issn = {2692-8205},
support = {P01 CA168530/CA/NCI NIH HHS/United States ; R01 MD018265/MD/NIMHD NIH HHS/United States ; U01 CA164973/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND: Higher-quality diets have been associated with lower levels of ectopic fat deposited in the viscera and liver, which is hypothesized to be mediated in part by the gut microbiota.<br><br>OBJECTIVES: We tested this hypothesis in a multi-ethnic imaging study using global (microbiome-wide) testing as well as a high-dimensional multiple-mediators regression framework to identify bacterial genera in the human gut that mediate the association between diet quality and ectopic adiposity.<br><br>METHODS: We analyzed the cross-sectional data of 1,400 older adults (age 60-77) from five racial/ethnic groups in the Multiethnic Cohort Adiposity Phenotype Study (2013-2016). Overall diet quality was defined by adherence to the MIND diet. The relative abundance of 151 bacterial genera was quantified from 16S rRNA gene sequencing of the stool samples. Visceral fat, liver fat, and the presence of MASLD (metabolic dysfunction-associated steatotic liver disease) were determined based on magnetic resonance imaging (MRI). We used high-dimensional mediation analysis (HDMA) to estimate gut microbial mediation in the linear regression of visceral fat or liver fat, or in logistic regression of MASLD, on the MIND adherence score, adjusted for potential confounders.<br><br>RESULTS: Higher diet quality was associated with lower ectopic adiposity: 12% less visceral fat area, 23% less liver fat, and a 49% less likelihood of having MASLD, comparing the highest to the lowest quartile of the MIND score. Using a distance-based global test, we confirmed overall significant microbial mediation of the inverse diet-ectopic fat association. From HDMA, four bacterial genera were identified as mediating the protective association with visceral fat, with the largest mediation conferred by Lachnospiraceae UCG.001 (12.2%). Two genera (Lachnoclostridium , Weissella) were shown to mediate the MIND association with both liver fat and MASLD. In particular, Lachnoclostridium mediated 13.6% of the liver fat association and 10.8% of the MASLD association, and Lachnospiraceae UCG.001 additionally mediated 12.1% of the liver fat association.<br><br>CONCLUSIONS: Our results support the hypothesis that the gut microbiota contributes to conveying the effect of diet quality on preferred body fat distribution, e.g., involving bacteria that are known to produce short-chain fatty acids (Lachnospiraceae) or secondary bile acids (Lachnoclostridium).},
}
@article {pmid41993570,
year = {2026},
author = {He, F and Bai, S and Xie, J and Zhang, Y and Xu, K and Wang, J and Ren, Y and Ren, Z and Chen, J and Wang, Y and Xie, P},
title = {Akkermansia muciniphila improving depression-like behaviors by regulating glycerophospholipid metabolism in gut-brain axis.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1790866},
pmid = {41993570},
issn = {1663-9812},
abstract = {BACKGROUND: Akkermansia muciniphila (AKK) is a potential probiotic. Our previous studies have shown that it could alleviate depressive-like behaviors (DLBs) in mice by inhibiting neuroinflammation in brain. To further explore its antidepressant effect, this study focused on the effects of AKK on the metabolic activities in gut-brain axis.<br><br>METHODS: After chronic restraint stress (CRS) depression model was successfully built, AKK was used as intervention method for 3&#xa0;weeks. The gut microbiome in feces and two intestinal permeability proteins in colon (Claudin-1, Occludin) were measured, and the metabolites in feces, colon, liver, and prefrontal cortex were also measured. In addition, two inflammation-related factors in hippocampus (Free fatty acid receptors 3 (FFAR3), phosphorylated NF-&#x3ba;B p65 (p-p65)) were measured.<br><br>RESULTS: AKK was successfully colonized in gut of chronic restraint stress (CRS) mice. The DLBs in CRS mice receiving AKK (CRS + AKK) were significantly improved, along with the improved gut microbiome. Both Claudin-1 and Occludin in colon were significantly increased in CRS + AKK mice compared to CRS mice receiving phosphate buffer saline (PBS) (CRS + p). Metabolomics analysis indicated that AKK could significantly improve the changed lipids and lipid-like molecules in gut-brain axis of CRS mice; and function analysis using differential metabolites showed that AKK could significantly improve the disordered glycerophospholipid metabolism in feces, colon, liver, and prefrontal cortex of CRS mice. Additionally, we found that FFAR3 and phosphorylated NF-&#x3ba;B p65 were increased and decreased, respectively, in hippocampus of CRS + AKK mice compared to CRS + p mice.<br><br>CONCLUSION: Our results suggested that AKK might improve the disturbances of gut microbiome, intestinal permeability, host's lipid metabolism and inflammation levels in hippocampus. Glycerophospholipid metabolism in gut-brain axis might be the important mediator in the process of AKK producing antidepressants effects.},
}
@article {pmid41993582,
year = {2026},
author = {Simões, JLB and Braga, GC and Assmann, CE and Bagatini, MD},
title = {Targeting the gut-immune-brain axis: pharmacological insights from depression in inflammatory bowel disease.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1793292},
pmid = {41993582},
issn = {1663-9812},
abstract = {Inflammatory Bowel Disease (IBD), comprising Crohn's Disease and Ulcerative Colitis, is a chronic inflammatory condition of the gastrointestinal tract with a remarkably high prevalence of psychiatric comorbidities, particularly Major Depressive Disorder (MDD). The traditional monoaminergic hypothesis of depression is insufficient to explain the complex etiology of MDD, paving the way for new paradigms, such as the inflammatory hypothesis of depression. This narrative review critically explores IBD as a human clinical model to investigate the connection between chronic inflammation and depression. It is argued that gut dysbiosis, a central feature of IBD, is a fundamental trigger that, through a compromised gut barrier, drives systemic inflammation and, subsequently, neuroinflammation. We detail the molecular and cellular mechanisms that link intestinal inflammation to central nervous system (CNS) dysfunction, including microglial activation, hypothalamic-pituitary-adrenal (HPA) axis dysregulation, and kynurenine pathway activation, which diverts tryptophan metabolism from serotonin synthesis to the production of neurotoxic metabolites. Robust epidemiological evidence demonstrating a bidirectional association between IBD and depression is discussed, suggesting a shared pathophysiology rather than a simple cause-and-effect relationship. Furthermore, we review the implications and emerging therapeutics, highlighting the antidepressant effects of immunobiologicals, such as anti-TNF therapies, and the potential of emerging interventions that target the microbiome, such as probiotics, psychobiotics, fecal microbiota transplantation, and anti-inflammatory diets. Furthermore, we address the limitations of the current literature, such as the lack of a quantitative definition for dysbiosis and the scarcity of clinical trials with integrated neuropsychiatric outcomes, and propose directions for future translational research. We conclude that IBD should be considered a systemic disease with significant psychiatric repercussions, advocating for an integrated therapeutic approach that combines immunomodulatory, neuromodulatory, and microbiological interventions to treat both gut and brain pathology effectively.},
}
@article {pmid41993584,
year = {2026},
author = {Liang, X and He, J and Wu, Q and Fu, L and Liu, Y},
title = {Gut microbiome in alcohol-associated liver disease: interactions and therapeutic strategies.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1770833},
pmid = {41993584},
issn = {1663-9812},
abstract = {Alcohol-associated liver disease (ALD), a significant cause of chronic liver disease worldwide, is strongly linked to gut microbiome dysregulation. Heavy alcohol use disrupts the gut bacterial equilibrium and damages the intestinal barrier, making it more permeable to microbial toxins (e.g., endotoxins) that trigger liver inflammation. Many studies have investigated ALD, but no single microbial marker has yet been identified as diagnostic. Results from microbiome studies on this condition have been inconsistent; consequently, scientists are developing new microbiome-based indices and multi-omics approaches to improve their ability to predict diseases. The review evaluates current findings on how disturbances in the gut microbiome and deterioration of the intestinal barrier contribute to the development of ALD. The assessment includes microbiome-based treatments such as probiotics, fecal microbiota transplantation (FMT), and bacteriophage therapy. Research indicates that probiotics and FMT treatments may enhance liver function and reduce inflammation in patients with ALD. The studies present conflicting results because researchers used different methods and worked with limited numbers of participants. Bacteriophage therapy exists as an experimental treatment method. The development of personalized microbiome treatments, along with biomarker standardization and solutions to technical and ethical challenges, will enable these strategies to enter medical practice. The review integrates existing knowledge of the gut-liver axis in ALD to demonstrate the clinical potential of microbiome-based treatments while highlighting the need for additional research to enhance treatment outcomes.},
}
@article {pmid41993800,
year = {2026},
author = {Pande, PM and Tremblay, J and St-Arnaud, M and Yergeau, E},
title = {The metatranscriptomic response of the wheat rhizosphere to drought varies with growth stages.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag065},
pmid = {41993800},
issn = {2730-6151},
abstract = {Microbes can help plant sustain abiotic stresses, such as drought. Plant-microbe interactions are, however, dynamic and the timing of the stress will affect both partners, directly and indirectly. Here, we hypothesize that the effect of drought stress on the wheat rhizosphere microbiome would change between key growth stages. We grew wheat in pots and reduced soil water content for two weeks at stem elongation, booting, or heading. We then sampled the rhizosphere soil and sequenced its metatranscriptome. The timing of the drought strongly affected the transcriptional response of the microbes, but few differentially abundant transcripts were shared across all stages. Some common patterns were, however, observed at higher taxonomical or functional levels. Drought also affected the normal succession across wheat growth stages. Many of the differentially abundant transcripts, taxa, and functions between growth stages of the control plants were not significant anymore for plants that experienced drought. Our results suggest that the timing of the drought event is paramount to the microbial rhizosphere communities and that it could explain the heightened sensitivity of younger plants to stresses.},
}
@article {pmid41993915,
year = {2026},
author = {Hoedt, EC and Burns, GL and Hedley, KE and Waller, S and Sanchez, TC and Chisolm, O and MacCallum, H and Richardson, S and Suthers, B and Pepper, E and Keely, S and Talley, NJ},
title = {Shared functional microbiome signatures in Parkinson's disease and constipation predominate irritable bowel syndrome despite taxonomic divergence.},
journal = {Brain, behavior, &amp; immunity - health},
volume = {53},
number = {},
pages = {101218},
pmid = {41993915},
issn = {2666-3546},
abstract = {BACKGROUND: Gastrointestinal dysfunction, including constipation, is a common non-motor feature of Parkinson's disease (PD) and often precedes motor symptoms. The gut microbiome interacts with the host through neural, hormonal, and immune pathways, yet whether constipation represents a cause or consequence of PD remains unclear. Therefore, we aimed to interrogate the associations between microbiome and immune alterations in relation to constipation to provide novel insight into microbiome-gut-brain axis mechanisms in PD.<br><br>METHODS: We analysed peripheral blood mononuclear cells (PBMCs) for circulating gut-homing T cell populations and used shotgun metagenomics to profile the stool microbiome composition and functional capacity in PD patients (n&#xa0;=&#xa0;18), healthy controls (n&#xa0;=&#xa0;21), and individuals with constipation-predominant irritable bowel syndrome (IBS-C; n&#xa0;=&#xa0;8). Associations between immune markers and microbial taxa were assessed, and functional pathway differences were evaluated.<br><br>RESULTS: Circulating gut-homing T cell frequencies did not differ significantly between PD and controls, but constipated PD patients showed a trend toward increased circulating gut-homing T cells. Microbiome beta-diversity analyses revealed distinct taxonomic shifts in PD and IBS-C, while functional capacity was largely conserved. Of the differential functional pathways tryptophan biosynthesis, polyamine production, and vitamin B metabolism, processes critical for neurotransmitter synthesis, epithelial integrity, and neuroimmune regulation were reduced in PD compared to IBS-C.<br><br>CONCLUSION: Our findings highlight unique microbial and immune signatures in PD, partially overlapping with IBS-C, and underscore the importance of microbial metabolic pathways in gut-brain axis disorders. Collectively our findings suggest a contribution to dopaminergic dysfunction, neuroinflammation, and impaired gut motility. Future longitudinal studies are needed to clarify causal relationships and inform targeted interventions for PD-related gastrointestinal dysfunction.},
}
@article {pmid41993944,
year = {2026},
author = {Shalmon, G and Shapira, G and Ibrahim, R and Israel-Elgali, I and Grad, M and Shlayem, R and Youngster, I and Scheinowitz, M and Shomron, N},
title = {Gut microbiota composition correlates with PBMC microRNA expression following maximal exercise testing in endurance athletes.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1734737},
pmid = {41993944},
issn = {2813-4338},
abstract = {INTRODUCTION: MicroRNAs (miRNAs) are key post-transcriptional regulators that also take part in immune responses and recovery processes following exercise. While both gut microbiota composition and peripheral blood mononuclear cell (PBMC)-derived miRNAs are known to be influenced by endurance training, potential correlations between these two systems in athletes remain largely unexplored.<br><br>OBJECTIVE: This study aimed to investigate correlations between gut microbiota composition and PBMC miRNA expression following a maximal exercise stress test in endurance athletes.<br><br>METHODS: Fifty-eight participants (22 runners, 18 cyclists, and 18 controls) underwent maximal exercise testing, with blood samples collected pre- and post-maximal exercise stress test for small RNA sequencing of PBMCs. Baseline fecal samples were analyzed via 16S rRNA gene sequencing to characterize gut microbiota. Expression data of PBMC miRNAs and microbial taxonomic profiles were integrated to assess potential correlations.<br><br>RESULTS: Thirteen significant correlations (|r| = 0.41-0.51, p < 0.005) were identified between gut bacterial taxa known to produce short-chain fatty acids (SCFAs)-including Veillonella, Blautia, Coprococcus, Butyrivibrio, Propionibacterium, and Parabacteroides-and the expression of PBMC miRNAs following a maximal exercise test. The significantly expressed PBMC microRNAs included hsa-miR-545-3p, hsa-miR-126-3p, hsa-miR-1292-3p, hsa-miR-6805-5p, hsa-miR-3668, hsa-miR-196b-5p, hsa-miR-602, hsa-miR-324-5p, and hsa-miR-365a-3p, some of which are known to modulate inflammatory pathways and immune cell signaling.<br><br>CONCLUSION: This is the first study demonstrating an association between resting gut microbiota composition and PBMC miRNA expression following maximal exercise stress test in endurance athletes. These findings raise the possibility of a complex association between gut microbial composition and PBMC miRNA expression in response to exercise. While causality cannot be inferred, the observed correlations suggest a candidate microbiota-miRNA that warrants further investigation in the context of exercise-induced immune regulation and recovery in athletes.},
}
@article {pmid41993958,
year = {2026},
author = {Meng, H and Zhao, S and Jin, H and Zhang, H and Li, Q and Zhang, L and Hu, J and Kong, F and Du, X and Li, Q and Ajwad Rahim, M and Xu, L and Xue, Y},
title = {Unveiling the Role of Rumen Microbiome in Modulating Intramuscular Fat Deposition of Pingliang Red Cattle.},
journal = {Food science &amp; nutrition},
volume = {14},
number = {4},
pages = {e71681},
pmid = {41993958},
issn = {2048-7177},
abstract = {Pingliang Red cattle is renowned for its tender meat and symmetrical intramuscular fat (IMF) deposition. Rumen microbiota are crucial for energy metabolism and nutrient acquisition in cattle, significantly influencing IMF deposition. Therefore, this study aimed to explore how rumen microbiota impact IMF deposition in Pingliang Red cattle. 34 castrated Pingliang Red cattle were subjected to the same management for 2 months, followed by centralized and unified slaughtering. Based on the measured IMF content in the longissimus dorsi, 18 cattle were selected and divided into a high-intramuscular-fat group (HIMF, n = 9) and a low-intramuscular-fat group (LIMF, n = 9). Rumen fluid was subsequently collected for metagenomic sequencing. Results showed significant differences in taxonomic abundance at both the genus and species levels, the relative abundance of carbohydrate-active enzyme (CAZy) families, and functional profiles (p < 0.05). Specific rumen microbes, such as Limosilactobacillus panis (AUC = 0.765) and Fibrobacter succinogenes (AUC = 0.753), served as potential biomarkers for HIMF deposition in Pingliang Red cattle. With the exception of Bacillus, Fibrobacter succinogenes, Limosilactobacillus panis, Prevotella intermedia, and Streptomyces exhibited positive correlations with IMF content. Functional analysis based on KEGG orthology (KO) indicated that specific enzymes promote IMF deposition by regulating the metabolism of short-chain fatty acids (SCFAs), long-chain fatty acids (LCFAs), and lipopolysaccharides, as well as insulin signaling. These findings provide a theoretical reference for regulating rumen microbial communities to improve IMF deposition.},
}
@article {pmid41993996,
year = {2026},
author = {Au Yong, SJ and Lestari Lee, AS and Subramaniyan, V and Long, CM and Husain, S and Reginald, K and Ser, HL},
title = {Gut microbiome modulation in allergic rhinitis: from current evidence to emerging therapies.},
journal = {Frontiers in allergy},
volume = {7},
number = {},
pages = {1761840},
pmid = {41993996},
issn = {2673-6101},
abstract = {Allergic rhinitis (AR) is a common inflammatory disorder of the upper airway that is primarily managed with pharmacotherapy, biologics and allergen immunotherapy. However, a substantial proportion of patients experience incomplete or insufficient symptom control, treatment-related adverse effects, or poor adherence. Increasing evidence has linked AR with alterations in microbial composition across multiple mucosal sites, including the gut, highlighting potential roles for host-microbiome interactions in the regulation of allergic inflammation, although causal relationships remain incompletely defined. This narrative mini-review synthesizes current evidence on gut microbiome-based interventions for allergic rhinitis (AR), including probiotics, prebiotics, synbiotics, postbiotics, and emerging approaches such as fecal microbiota transplantation, engineered microbes, and bacteriophage-based therapies. It examines proposed immunological mechanisms involving type 2 inflammation, regulatory immune pathways, and gut-airway axis signalling, while distinguishing clinically evaluated strategies from experimental or preclinical and assessing their translational readiness. Collectively, available evidence suggests that microbiome-targeted therapies represent a promising conceptual avenue for understanding and potentially modulating AR. However, their clinical application remains constrained by heterogeneous study designs, reliance on extrapolated data from preclinical studies, limited standardized outcome measures, insufficient long-term safety data, and evolving regulatory frameworks. Addressing these challenges through well-designed clinical trials and improved mechanistic characterization will be essential to clarify the role of microbiome-based interventions as adjunctive strategies in AR management.},
}
@article {pmid41994099,
year = {2026},
author = {Hossain, MA and Agyei, D and Reynolds, AN and Kebede, B},
title = {Legume intake on gut microbiome and glycemia in type 2 diabetes management: narrative review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1785186},
pmid = {41994099},
issn = {2296-861X},
abstract = {Legumes are rich in dietary fiber, plant proteins, micronutrients, and bioactive compounds, offering a sustainable and affordable addition to the diet. However, the extent to which legume-induced modulation of the gut microbiota contributes to glycemic regulation in type 2 diabetes (T2D), relative to microbiota-independent physiological mechanisms, remains insufficiently defined. This narrative review synthesizes current evidence on legume-based interventions and their effects on gut microbiota composition and function in relation to glycemic control. Relevant studies were identified through structured searches of MEDLINE and the Cochrane Central Register of Controlled Trials via Ovid, complemented by manual screening of reference lists. Seventeen studies (three human and 14 animal trials) were considered in this review. Human studies report that consuming legumes is associated with improved glucose tolerance and blood glucose levels, although effects on microbiota composition are variable and modest. Conversely, animal studies demonstrate improvements in insulin sensitivity, glucose tolerance, and microbial diversity with higher dose legume interventions. Legume consumption has been associated with enrichment of beneficial microbial taxa, such as Bifidobacterium, Akkermansia, Ruminococcus, and Bacteroides, as well as increased concentrations of microbial metabolites such as short-chain fatty acids (SCFAs). These microbial features are implicated in metabolic pathways relevant to insulin signaling and glycemic regulation; however, current human evidence does not establish that microbiota alterations causally mediate glycemic improvements. Well-designed, adequately powered clinical studies incorporating functional microbiome analyses and formal mediation approaches are required to clarify microbiota-dependent and microbiota-independent mechanisms.},
}
@article {pmid41994117,
year = {2026},
author = {Byrareddy, S and Kumar, N and Acharya, A and Das, R and Sardarni, U and Olasunkanmi, O and Murakonda, S and Sutar, D and Venkatesan, A and Ampasala, D and Cohen, S and Samuelson, M and Sajja, B and Dettmer, U and Ramalingam, N and Chand, H},
title = {Sex- and Age-Dependent Neuroimmune Dysregulation and Early Neurodegenerative Signatures Following SARS-CoV-2 Infection in Golden Syrian Hamsters.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9130692/v1},
pmid = {41994117},
issn = {2693-5015},
abstract = {Post-acute sequelae of SARS-CoV-2 infection, or Long-COVID, affects millions globally and is characterized by persistent symptoms affecting multiple organs, yet the underlying mechanisms remain poorly defined. Here, we used Golden Syrian Hamsters (GSH) infected with the SARS-CoV-2 to investigate how sex and age shape viral persistence, organ-specific pathology, immune responses, and neurological outcomes during acute infection and Long-COVID. We show that during Long-COVID, viral RNA persists only in the lungs of male hamsters. Lung pathology revealed sustained inflammation and tissue remodeling, with young females exhibiting greater fibrosis. Transcriptomic profiling across brain, lung, and heart identified pronounced sex- and age-dependent regulation of gene expression spanning immune, neuroinflammatory, and neurotransmitter signaling pathways. These transcriptomic alterations were accompanied by sex-specific behavioral changes and persistent microstructural remodeling in cognition-associated brain regions. Additionally, SARS-CoV-2 altered α-synuclein homeostasis and microglial activation alongside gut microbiome composition in a sex- and age-dependent manner. Together, our findings demonstrate that, in GSH Long-COVID is strongly modulated by sex and age, influencing viral RNA persistence, immune and neurobiological responses, and gut microbiota composition mirroring clinical outcomes reported in human cohorts. This study establishes SARS-CoV-2-infected GSH as a model for dissecting the mechanisms of Long-COVID and informing targeted prevention strategies.},
}
@article {pmid41994130,
year = {2026},
author = {Khan, D and Espinoza, JL and Tientcheu, PE and Otchere, ID and Mohammed, NI and Worwui, A and Nicol, MP and Kwambana-Adams, B and Antonio, M and Dupont, CL},
title = {Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8724320/v1},
pmid = {41994130},
issn = {2693-5015},
abstract = {Pneumonia is a leading cause of morbidity and mortality in children, with bacterial pathogens being important etiologic agents. Most microbiome studies in pneumonia use technologies with limited taxonomical resolution and few include lung aspirate or blood samples. In this study, we assessed the microbial communities of the nasopharynx, nasopharynx/oropharynx, induced sputum, lung aspirate and blood, and recovered metagenome-assembled genomes from the same sites using shotgun metagenomics sequencing of samples from children with severe and very severe pneumonia in The Gambia. Our data show that Proteobacteria and Firmicutes were the most common phyla across the body sites, and this was largely driven by S. pneumoniae, H. influenzae/aegyptius and M. catarrhalis. Furthermore, we observed species overlap of blood and respiratory samples with average Jaccard similarity index values ranging from 34% to 58%. We recovered 60 medium and 35 high-quality MAGs in these niches including 11 S. pneumoniae , 10 H. influenzae strains and a limosilactobacillus with less than 95% Average Nucleotide Identity to any known species in GTDB-TK. We also showed that the resistomes in our MAGs were highly species specific with more than 70% of the detected AMR genes found exclusively in a single species.},
}
@article {pmid41806005,
year = {2026},
author = {Dong, X and Zhang, T and Tang, B and Zeng, Q and Hu, Z and Huang, P and Xiong, X and Wang, X and Dong, W and Cai, Y},
title = {Microbial and metabolic profiles in autism spectrum disorder with atopic dermatitis in children.},
journal = {AMB Express},
volume = {16},
number = {1},
pages = {},
pmid = {41806005},
issn = {2191-0855},
abstract = {Atopic dermatitis (AD), an inflammatory skin disease, exhibits increased incidence with autism spectrum disorders (ASD) in children. However, the mechanism underlying the ASD-AD comorbidity remains unclear. Here, we integrated the metagenomic and metabolomics analysis to characterize the compositions and functional profiles of gut microbiome in ASD children with AD. We found significant alteration in the composition of the intestinal microbial species between ASD-AD group and ASD group based on beta diversity analysis. LEfSe analysis showed tyzzerella_nexilis, eubacterium_sp_OM08_24 and clostridium_nexile_CAG348 were significantly increased in ASD children with AD. In addition, metabolite profiles showed that differentially expressed metabolites were mainly lipids and organic acids. Meanwhile, functional profiles showed that the pathway of cholesterol metabolism and biosynthesis of unsaturated fatty acids was abundant in ASD children with AD. Furthermore, the correlation analysis revealed that bacteroides_sp_CAG443, limosilactobacillus_mucosae had a positive correlation with traumatic acid and ricinoleic acid that were decreased in ASD-AD group, respectively. Eubacterium_ramulus and lachnospiraceae_bacterium were positively correlated with 11,14-eicosadienoic acid (EDA). Taken together, our results propose that altered gut microbiota regulates metabolites to affect the development of atopic dermatitis in ASD children.},
}
@article {pmid41968359,
year = {2026},
author = {Senousy, MA and Abo-Elmaaty, RM and Nabil Omar, N and Abdelgawad, HM},
title = {Dapagliflozin-intermittent fasting combination maximizes weight and metabolic regulation through AMPK/sirtuins/clock genes and gut microbiota signaling in high-fat diet-induced obesity: a novel anti-obesity approach.},
journal = {Cell &amp; bioscience},
volume = {16},
number = {1},
pages = {},
pmid = {41968359},
issn = {2045-3701},
abstract = {UNLABELLED: Innovative and affordable treatment options are required to combat obesity and its detrimental impact on health economics. Dapagliflozin (Dapa), an antidiabetic medication, promotes weight loss; however, the extent of weight reduction may be limited. Intermittent fasting (IF) is a dietary approach regarded as a cost-effective and readily accessible regimen. This study investigated the beneficial effects of Dapa, IF, and their combination on weight loss and metabolic derangements in high-fat diet (HFD)-induced obesity in rats. Male Sprague-Dawley rats were allocated into 6 groups: groups 1 (normal control) and 2 (drug control) were administered a normal chow diet, while the obesity groups 3, 4, 5, and 6 were subjected to HFD for 8 weeks. Rats in groups 4, 5, and 6 underwent a further 8-week treatment with Dapa (5 mg/kg, p.o) daily, IF (16/8), or a combination of both, respectively. The HFD group exhibited elevated anthropometric measurements and adiposity index. Upon histopathological examination, the HFD group showed adipocyte hypertrophy, hypercellularity, and possible necrosis, along with hepatic fat accumulation and elevated serum liver enzymes. The HFD group showed a downregulation of p-AMPK/SIRT1 and an upregulation of SIRT7, GPR43, and clock genes BMAL1, CLOCK, and CRY1 expression in adipose tissue, along with a drop in the gut microbiome diversity, serum short-chain fatty acids (SCFAs), POMC, and PYY levels. Dapa and IF combination demonstrated favorable outcomes over monotherapy, as evidenced by normalized anthropometric measurements, improved histopathological and biochemical derangements, regulated p-AMPK/SIRT1, SIRT7, and clock genes expression, and restored gut microbiome and SCFA levels. Conclusively, this study suggests the concurrent administration of Dapa and IF as a new, beneficial, cost-effective anti-obesity strategy.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13578-026-01557-4.},
}
@article {pmid41981675,
year = {2026},
author = {Zhang, W and Zhao, W and Ye, L and Wang, H and Chen, Z and Liu, X and Li, Y and Zhang, Q and Zhang, H and Liu, Y and Chen, X and Chen, S and Zeng, J and Huang, R and Li, Y and He, Y},
title = {Profiling the tumor-resident microbiota in small cell lung cancer and its influence on clinical outcomes.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41981675},
issn = {1479-5876},
support = {2022YFF0705300//National Key Research and Development Program of China/ ; Fkcy2515//"Young Eagle Soaring" Youth Talent Funding Program of Shanghai Pulmonary Hospital/ ; },
abstract = {BACKGROUND: Increasing evidence has confirmed the existence of resident microbial communities within solid tumors and indicates that the tumor microbiota may represent a novel component of the tumor microenvironment, actively regulating cancer initiation, progression, metastasis, and therapeutic responsiveness. However, the role of tumor microbiota in small cell lung cancer (SCLC) has not been well explored.<br><br>METHODS: Tumor samples were collected from 71 patients with SCLC at Shanghai Pulmonary Hospital between 2019 and 2023. A comprehensive analysis of the tumor-resident microbiota in SCLC was conducted using 16&#xa0;S rRNA sequencing. The bacterial communities were profiled, and their correlation with clinical outcomes was assessed.<br><br>RESULTS: A total of 28 phyla, 79 classes, 135 orders, 251 families, and 428 genera were identified, revealing a diverse tumor microbiota in SCLC. It was shown that tumor microbiota varied markedly among patients. SCLC patients with a smoking history exhibited distinct tumor microbiota, with significantly higher abundances of Brevundimonas and Gemmatimonadetes. When patients were stratified by progression-free survival (PFS) into long-PFS (L-PFS) and short-PFS (S-PFS) cohorts, their tumor microbiota segregated distinctly. LEfSe analysis showed that Lactobacillus, Clostridium, Rothia, and Staphylococcus were selectively enriched in the L-PFS group, whereas Stenotrophomonas, Cetobacterium, and Aerococcus dominated the S-PFS group. Kaplan&#x2013;Meier analysis confirmed that carriage of Lactobacillus, Clostridium, or Staphylococcus was associated with prolonged survival relative to negative status, while positivity for Stenotrophomonas, Cetobacterium, or Aerococcus conferred a reduction in survival. Subsequent response-stratified analysis revealed that Clostridium- and Lactobacillus-positive SCLC was associated with a significantly higher response rate. Conversely, positivity for Methylobacterium, Pelomonas, Ralstonia, Bradyrhizobium, Variovorax, Microbacterium, Comamonas, or Sphingomonas markedly reduced response. The intersection of survival and response results identify Clostridium and Lactobacillus as promising prognostic tumor microbiota markers in SCLC. In vitro assays demonstrated that the Clostridium and Lactobacillus metabolites, butyrate and lactic acid, lacked direct cytotoxicity against SCLC cells. However, in the syngeneic mouse model, systemic supplementation of butyrate or lactic acid significantly potentiated the anti-tumor efficacy of standard chemotherapy. Notably, flow cytometric analysis revealed that this in vivo synergistic effect was closely associated with a profound increase in CD8&#x2009;+&#x2009;T cell infiltration within the tumor microenvironment. Furthermore, integrating these two tumor microbiota with key clinical variables (sex, age, smoking, stage, radiotherapy), we constructed three models&#x2014;therapeutic-response, 1-year PFS, and 1-year overall survival&#x2014;that maintained robust performance in both training and validation cohorts.<br><br>CONCLUSIONS: In conclusion, the tumor-resident microbiota constitutes a critical component of the SCLC tumor microenvironment, exerting profound influence on the therapeutic response and patient prognosis. In detail, Clostridium and Lactobacillus&#x2014;two pivotal tumor-resident taxa significantly linked to enhanced therapeutic responses and favorable prognosis&#x2014;indicate their potential as predictive biomarkers for treatment outcomes and patient prognosis, and highlight them as candidate targets for microbiome-directed therapeutic strategies against SCLC, which warrants further functional validation.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-08109-x.},
}
@article {pmid41993062,
year = {2026},
author = {Nuraini, P and Nelwan, SC and Pradopo, S and Pronorahardjo, AS and Andarini, PQ and Antonius, Y and Aljunaid, MA},
title = {Fractionated ethanolic red ginger extract as antibacterial agent against Aggregatibacter actinomycetemcommitans and Porphyromonas gingivalis: In silico and in vitro studies.},
journal = {Journal of oral biology and craniofacial research},
volume = {16},
number = {3},
pages = {101446},
pmid = {41993062},
issn = {2212-4268},
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease associated with oral microbiome dysbiosis, where Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis contribute through adhesion, biofilm formation, and tissue-destructive virulence factors. Although chlorhexidine is widely used as an adjunctive antimicrobial agent, its long-term use is limited by adverse effects, highlighting the need for safer natural alternatives. Red ginger (Zingiber officinale var. rubrum) exhibits antibacterial potential; however, data on fractionated extracts and their interaction with specific virulence proteins remain limited.<br><br>OBJECTIVE: To evaluate the antibacterial activity of fractionated ethanolic red ginger extract against A. actinomycetemcomitans and P. gingivalis using integrated in silico and in vitro approaches.<br><br>METHODS: Twenty-two bioactive compounds identified from the fractionated extract were analyzed via molecular docking against cytolethal distending toxin (Cdt) of A. actinomycetemcomitans and fimbrial protein Mfa5 of P. gingivalis, with chlorhexidine as reference. In vitro assays determined minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), bacterial adherence, biofilm formation, and viability.<br><br>RESULTS: Docking analysis showed that cyclooctacosane and gamma-sitosterol demonstrated binding affinities comparable to chlorhexidine toward both target proteins. The extract exhibited MIC/MBC values of 0.062/0.125&#xa0;mg/mL for A. actinomycetemcomitans and 0.031/0.062&#xa0;mg/mL for P. gingivalis. Significant reductions in bacterial adherence, biofilm formation, and viability were observed at concentrations of 0.031-0.125&#xa0;mg/mL.<br><br>CONCLUSION: Fractionated ethanolic red ginger extract demonstrates promising antibacterial activity against key periodontal pathogens by targeting virulence mechanisms related to adhesion and biofilm formation, supporting its potential as a natural adjunct in periodontal therapy.},
}
@article {pmid41993122,
year = {2026},
author = {Saez-Torillo, SN and Danielsson, R and Nguyen, TQ and Lima, J and Cleveland, MA and Roehe, R and Martínez-Álvaro, M},
title = {Predicting beef diet nutritional composition and intake from rumen metagenomic profiles.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {297-309},
pmid = {41993122},
issn = {2405-6383},
abstract = {Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (n = 70) and Charolais crossbred (n = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately postmortem and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included Mitsuokella, Selenomonas, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.},
}
@article {pmid41993168,
year = {2026},
author = {Goto, Y and Dolton, G and Thomas, H and Morin, T and Tajima, Y and Imamura, K and Sakata, S and Oka, K and Hayashi, A and Takahashi, M and Ueno, T and Sakagami, T and Tomita, Y and Sewell, AK and Motozono, C},
title = {A probiotic bacterium modulates antitumour γδ T-cell responses in lung cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1750569},
pmid = {41993168},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/immunology/therapy ; *Probiotics/therapeutic use/administration &amp; dosage ; *Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism ; Cell Line, Tumor ; Immune Checkpoint Inhibitors/therapeutic use ; Female ; Male ; *T-Lymphocytes/immunology ; *Carcinoma, Non-Small-Cell Lung/immunology ; Aged ; Middle Aged ; Gastrointestinal Microbiome/immunology ; Antigens, CD/metabolism ; Lymphocyte Activation ; },
abstract = {The link between the intestinal microflora and cancer outcomes has been recognized for over a decade. Several recent studies have demonstrated that the gut microbiome is associated with the efficiency of T-cell checkpoint blockade therapy for cancer, raising interest in strategies to harness this effect via consumption of live microorganisms (probiotics). The probiotic Clostridium butyricum strain MIYAIRI 588 (CBM588) improves response rates and overall survival in patients receiving immune checkpoint inhibitor (ICI) therapy for non-small cell lung cancer and metastatic renal cell carcinoma but the mechanism underlying this benefit remains unclear. Here, we show that CBM588 spores induce a population of Vγ9Vδ2 T-cells from the peripheral blood of healthy donors and lung cancer patients. A subset of these T-cells responded to, and directly lysed, cancer cell lines via a butyrophilin 3A-dependent mechanism. In patients taking CBM588 alongside checkpoint blockade, using samples from a cohort of 38 patients, peripheral blood Vδ2[+] T-cells expressed the activation marker CD69 more frequently than in those receiving checkpoint blockade alone and the frequency of Vδ2[+]CD69[+] cells increased following initiation of CBM588 treatment (p = 0.0041). Pleural effusions from patients receiving ICI with CBM588, although available from only three individuals, also showed a notable shift in the local γδ T-cell compartment from the expected Vδ1 dominance towards Vδ2 cells, suggesting altered recruitment or retention of Vδ2 cells at the tumour site. Across the patient cohort, higher post-treatment frequencies of CD69[+] Vδ2 T-cells were associated with improved survival and more favourable clinical outcomes. These findings provide a potential mechanism by which manipulation of the intestinal microflora might contribute to cancer prognosis through effects on immune effector cells with intrinsic anticancer properties.},
}
@article {pmid41774319,
year = {2026},
author = {Pereira, EJ and de Souza, V and da Silva Braulio, C and de Jesus Santos, AF},
title = {Epiphytic bacteria from Tacinga inamoena (K. Schum.) N.P. Taylor &amp; Stuppy improve plant growth in cucumber seedlings.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {29},
number = {4},
pages = {415-422},
pmid = {41774319},
issn = {1618-1905},
abstract = {The phyllosphere of host plants harbors microorganisms that represent a novel source of agricultural bioinputs. This unique microbiome opens a promising frontier for developing innovative agricultural alternatives. In this study, we evaluated the potential of Brevibacillus sp. UPT4 and Pantoea sp. SPM1, two epiphytic bacterial strains of Tacinga inamoena isolated from the Caatinga biome. In vitro assays exhibited plant growth-promoting traits, such as auxin production, nitrogen fixation, and tolerance to abiotic stresses. Under greenhouse conditions, cucumber plants inoculated with the strains and their consortium exhibited significant increases (p < 0.05) in shoot and root parameters, ranging from 13.58% to 194.86% when compared to the control treatment. Redundancy analysis (RDA) indicated that most of the variability observed in the biometric parameters is associated with the plant growth-promoting reported in this study. These results highlight the potential of epiphytic bacteria from semi-arid land as a promising candidate for the development of new bioinputs, offering an innovative tool for sustainable agriculture.},
}
@article {pmid41803694,
year = {2026},
author = {Sun, F and Lu, J and Qiu, J and Jiao, Y and Zhuang, J and Meng, B and Kwok, LY and Zhong, Z},
title = {Temporal dynamics and functional maturation of the infant gut microbiota during the first year of life.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41803694},
issn = {1471-2180},
support = {BR250107//the Inner Mongolia Agricultural University Young Faculty Research Capacity Enhancement Program/ ; NJYT24055//the Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {BACKGROUND: The infant gut microbiota undergoes structured, time-dependent succession during the first year of life, yet high-resolution longitudinal characterization remains limited. Here, full-length 16S rRNA gene sequencing was performed using PacBio long-read technology on 68 fecal samples from 12 exclusively breastfed infants in Hohhot, China, across six time points from birth to one year (7, 30, 60, 100, 200, and 360 days).<br><br>RESULTS: In this study, 68 fecal samples from 12 infants were analyzed. A total of 16 bacterial phyla, 192 genera and 251 species were annotated, with the dominant phyla being Firmicutes, Actinobacteriota and Proteobacteria; the dominant genera including Bifidobacterium, Streptococcus and Escherichia-Shigella; and the dominant species comprising Streptococcus_salivarius, Bifidobacterium_longum and Bifidobacterium_pseudocatenulatum. Alpha diversity generally increased by days 360, while community composition shifted from early Bifidobacterium dominance toward greater taxonomic and functional complexity. Permutational multivariate analysis of variance (PERMANOVA) revealed that host and environmental factors collectively explained 33.92% of community variation (P&#x2009;=&#x2009;0.001). Six temporal colonization patterns were observed through MaAsLin2 analyses., including mid-term explosive and sustained increasing trajectories. Functional profiling using Tax4Fun2 revealed time-specific enrichment of metabolic pathways, including fatty acid biosynthesis, xenobiotic degradation, and autophagy regulation at day 360. The findings of this longitudinal study be interpreted considering its modest sample size (n&#x2009;=&#x2009;68). Future studies with larger cohorts are needed to validate and generalize these observations.<br><br>CONCLUSIONS: These findings demonstrate that infant gut microbiota assembly follows a non-random, host-guided trajectory, with dietary transitions and microbial interactions driving structural and functional maturation, providing a high-resolution framework for understanding early-life microbiome development and its implications for infant health. However, due to the limited sample size, the relevant research results have certain limitations. In the future, it is necessary to expand the sample scale and conduct more convincing studies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04930-y.},
}
@article {pmid41803805,
year = {2026},
author = {Park, SY and Jung, MY and Nguyen, CD},
title = {Effect of biodegradable microneedle acupuncture for symptom relief moderate or milder atopic dermatitis: a study protocol for a multicenter, randomized, sham-controlled trial.},
journal = {BMC complementary medicine and therapies},
volume = {26},
number = {1},
pages = {},
pmid = {41803805},
issn = {2662-7671},
abstract = {BACKGROUND: Atopic dermatitis (AD) has no definitive cure; therefore, alternative treatments should be developed. We have demonstrated in preliminary clinical trials that Biodegradable Microneedle Acupuncture (BMA) treatment improves symptoms and is safe for mild to moderate AD.<br><br>AIMS: The study focused on evaluating the effectiveness and safety of a new medical device called BMA for AD, while also assessing its cost-effectiveness. It also explored the gut microbiome of patients with AD before and after BMA treatment.<br><br>METHODS: This multicenter, participant-assessor-blinded, sham-controlled trial will be conducted from January 10, 2025, to January 10, 2026. In total, 184 participants with AD (n&#x2009;=&#x2009;92 per group) will be recruited. Participants will be assigned randomly to two equal-sized groups: the BMA and sham groups. Treatment will be administered three times per weekduring the 4-week intervention phase. The primary outcome measure will be the objective SCORing Atopic Dermatitis index. Secondary outcome measures will include the Eczema Area and Severity Index, Dermatology Life Quality Index, Patient-Oriented Eczema Measure, and pruritus Visual Analog Scale scores. Other outcome measures will include gut microbiome, economic and safety evaluations.<br><br>DISCUSSION: This study protocol will provide an important and thorough assessment of the effectiveness of BMA treatment in improving the symptoms of moderate or milder AD. In addition, we will evaluate the safety and costeffectiveness of BMA. We will also determine the link between AD and the microbiome. This clinical trial has been registered with the Korean Clinical Trial Registry (registration number: KCT0009870; date of registration: 25 October 2024).},
}
@article {pmid41803883,
year = {2026},
author = {Wei, Z and Xu, T and Gu, X and He, Q and Feng, Q and Li, M},
title = {Single-cell RNA-seq and in vitro study reveal Fusobacterium nucleatum impairs β-cell identity in type 2 diabetes via the NF-κB-CDKN1C axis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41803883},
issn = {1479-5876},
abstract = {BACKGROUND: The pathogenesis of type 2 diabetes is characterized by insulin resistance and a progressive decline in β-cell function. A key driver of this dysfunction is the loss of β-cell identity, which reduces functional β-cell mass and leads to inadequate insulin secretion. Periodontal pathogens have been implicated in promoting insulin resistance; however, their role in the transformation of β-cell identity remains poorly understood. This study aims to investigate the impact of periodontal pathogen Fusobacterium nucleatum (F. nucleatum) on β-cell identity maintenance and the underlying molecular mechanisms.<br><br>METHOD: Single-cell RNA sequencing (scRNA-seq) data from human pancreatic islets of nondiabetic (ND), prediabetic (Pre-T2D), and type 2 diabetes (T2D) donors were analyzed to assess changes in &#x3b2;-cell proportion, differentiation trajectory, and associated molecular pathways. The Single-cell Analysis of Host-Microbiome Interactions (SAHMI) method was used to detect F. nucleatum sequences in pancreatic islets. Pearson correlation analysis identified key genes associated with the action of F. nucleatum, followed by in vitro validation using a co-culture model of F. nucleatum and MIN6 cells to elucidate the underlying mechanisms.<br><br>RESULTS: scRNA-seq analysis revealed a reduced proportion of &#x3b2;-cells and decreased expression of key &#x3b2;-cell identity-maintenance genes in the T2D group. The expression levels of transdifferentiation markers and &#x3b2;-cell disallowed genes were elevated, alongside a trend toward &#x3b1;-cell transdifferentiation. The NF-&#x3ba;B signaling pathway was significantly activated in the T2D group, accompanied by a significant increase in the SPP1 inflammatory signal, while the WNT pathway was markedly diminished. Integrated Pearson correlation and in vitro analyses identified the cell cycle regulator CDKN1C as a central mediator through which F. nucleatum promotes &#x3b2;-cell identity loss. Mechanistically, F. nucleatum activated the NF-&#x3ba;B pathway, leading to downregulation of CDKN1C expression and thereby promoting loss of &#x3b2;-cell identity, which played an important role in the progression of diabetes associated with periodontitis.<br><br>CONCLUSION: This study demonstrates that &#x3b2;-cells in T2D primarily undergo transdifferentiation towards &#x3b1;-cells, and the periodontal pathogen F. nucleatum promotes &#x3b2;-cell identity loss via NF-&#x3ba;B-mediated downregulation of CDKN1C.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07981-x.},
}
@article {pmid41917955,
year = {2026},
author = {Nazir, SM and Saied, SMM and Eskander, ME and Mansour, MM and Abdelrahman, H and Elbackly, RM and Elnawam, HM},
title = {Is apical periodontitis a matter of microbial diversity or time? A scoping review.},
journal = {Head &amp; face medicine},
volume = {22},
number = {1},
pages = {},
pmid = {41917955},
issn = {1746-160X},
abstract = {BACKGROUND: The pathophysiology of apical periodontitis is complicated involving host immunological response, virulence factors, and a diverse microbiome. Understanding how microbial diversity influences lesion size is crucial for improving therapeutic strategies.<br><br>OBJECTIVE: This scoping review aimed to have an insight through literature to determine whether primary or secondary apical periodontitis lesions of different sizes are correlated with the quantity and diversity of microorganisms or the duration of the disease.<br><br>METHODS: The Joanna Briggs Institute (JBI) methodology for conducting scoping reviews was followed. A comprehensive electronic search was conducted through PubMed, Scopus, Web of Science, and Google Scholar to identify relevant studies published up to February 2025. In addition, handsearching was performed to identify additional studies that were not retrieved in the electronic search. Eligibility criteria of the screened papers included clinical studies performed in healthy patients with symptomatic or asymptomatic apical periodontitis where microbial analysis was performed. The EndNote Web reference manager (EndNote X9; Thomson Reuters) was used to ingest articles from various sources, categorize the references, and automatically eliminate duplicates.<br><br>RESULTS: Out of 4010 papers, 132 studies met the inclusion requirements and were added to the current review. Approximately half of the papers examined bacterial diversity in endodontic infections, while just a small percentage discussed lesion size and were identified as randomized clinical trials. Brazil, USA, Germany and China were found to have the highest frequency of published articles. Fusobacteria, Streptococcus, Enterococcus faecalis and Porphyromonas species were the most detected microorganisms responsible for apical pathosis regardless of lesion size, while other microbiomes were associated with large lesions only, such as Olsenella, Lactococcus lactus and HHV-6 with 3% each and HPV with 6.1%. Other microbiomes such as Candida albicans, Filifactor alocis, HSV1, Pyramidobacter piscolens and Phocaeicola abscessus were seen only associated with small sized lesions with 4.3% each.<br><br>CONCLUSIONS: Microbial diversity and microbial load seem to be a strong determinant of apical lesion size while lesion duration could not be adequately assessed due to cross-sectional study designs. Lesion size is an important variant to be recorded to give insight into microbial diversity and provide the basis for personalized targeted antimicrobial therapies in the future. This scoping review was registered in the open science framework; DOI: 10.17605/OSF.IO/DC95Z.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13005-026-00610-4.},
}
@article {pmid41981054,
year = {2026},
author = {Mansour, NY and Ismail, MF and Sayed, NH and El-Ansary, AR and Mohanad, M},
title = {Serum metabolomics identifies gut-derived uremic toxins and bile acid dysregulation associated with chronic kidney disease severity.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41981054},
issn = {2045-2322},
abstract = {UNLABELLED: Chronic kidney disease (CKD) affects more than 700 million people worldwide, however conventional biomarkers like creatinine cannot identify early-stage disease or accurately predict progression. In this study, untargeted and targeted metabolomic approaches were combined to identify novel biomarkers relevant for CKD staging and early detection in an underrepresented Egyptian population. Untargeted ultra-high-performance liquid chromatography–mass spectrometry analyses in both ionization modes were performed on serum samples of 50 CKD patients [25 early-stage CKD (eCKD), 25 end-stage kidney disease (ESKD)] and 20 controls. Differential metabolites were determined by univariate and multivariate analyses, coupled with pathway analysis and correlations with estimated glomerular filtration rate (eGFR). Five discriminating metabolites (p-hydroxyphenyllactic acid, indoxyl sulfate, xanthurenic acid, trimethylamine-N-oxide, and glycochenodeoxycholate) were subjected to targeted LC-MS/MS validation in an independent cohort (35 eCKD, 35 ESKD, 15 controls). Gut-derived uremic toxins, bile acid and tryptophan–kynurenine metabolic dysregulation were associated with CKD severity. p-hydroxyphenyllactic acid, xanthurenic acid, glutamyl-valine and indoxyl sulfate showed strong inverse correlations with eGFR (r = -0.75 to -0.85). A five-metabolite panel (indoxyl sulfate, p-hydroxyphenyllactic acid, trimethylamine-N-oxide, glycochenodeoxycholate, xanthurenic acid), demonstrated superior discriminatory performance compared with creatinine alone for distinguishing ESKD, especially indoxyl sulfate and p-hydroxyphenyllactic acid (AUC 0.847 and 0.828, respectively vs. 0.688). This first comprehensive metabolomics study in Egyptian CKD patients identifies alterations in gut microbiome–derived metabolites and bile acid metabolism associated with CKD severity. The multi-metabolite panel demonstrates potential for non-invasive discrimination between CKD stages and supports future longitudinal metabolomic studies aimed at improving CKD risk stratification and patient management.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-44271-4.},
}
@article {pmid41982989,
year = {2026},
author = {Yoon, KN and Lee, HG and Yeom, SJ and Kim, SS and Park, JH and Song, BS and Yi, SW and Hur, TY and Eun, JB and Park, SH and Lee, JH and Kim, HB and Lee, JH and Kim, JK},
title = {Modulation of microbial community and metabolism through Lactiplantibacillus argentoratensis AGMB00912 supplementation in weaning piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {562-585},
pmid = {41982989},
issn = {2055-0391},
abstract = {Dietary supplementation effects with Lactiplantibacillus argentoratensis strain AGMB00912 (LA) on gut microbiota and metabolic functions of weaned piglets were investigated. Eight 25-day-old weaned piglets were evenly divided into a control group and an LA-supplemented group, with the LA group receiving 1.0 × 10[8] CFU/mL of LA daily for 10 days. Fecal samples taken on the 10[th] day were analyzed using 16S rRNA gene sequencing to assess microbial composition and metabolic function prediction. Supplementation with LA promoted a stable microbial environment by increasing the relative abundance of short-chain fatty acid-producing bacteria, including Faecalitalea, Catenibacterium, and Butyrivibrio, while reducing harmful genera like Treponema and Campylobacter. Administration of LA significantly influenced the metabolic activity of the microbial community, particularly by upregulating carbohydrate metabolism pathways, which enhanced the capacity for short-chain fatty acid production. This shift in microbial metabolism also extended to pathways involved in the biosynthesis of amino acids, lipids, cofactors, and vitamins, indicating an improved capacity for microbial-driven nutrient assimilation and utilization. Furthermore, LA supplementation promoted the biosynthesis of antimicrobial non-ribosomal peptides within the microbiome, crucial for inhibiting the growth of pathogenic microorganisms and maintaining microbial balance. The modulation of microbial metabolism is also predicted to reduce glycan degradation and increase peptidoglycan biosynthesis, contributing to enhanced gut barrier function and a more regulated immune response. These metabolic changes within the microbial community are predicted to stabilize the gut microbiota, providing enhanced disease resistance and supporting the overall health and growth of weaned piglets.},
}
@article {pmid41983000,
year = {2026},
author = {Lee, JY and Lim, C and Seo, YJ and Kyoung, H and Lee, S and Kim, Y and Shin, M and Song, M and Ryu, Y and Kim, JM},
title = {Multi-omics integrated approach reveals host-microbiome interactions in the adaptive mechanisms of weaning piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {603-628},
pmid = {41983000},
issn = {2055-0391},
abstract = {The weaning transition is a critical phase in piglet development, marked by physiological challenges that influence growth and health. Therefore, this study aims to investigate host-microbiome interactions during the weaning transition using a multi-omics integrated approach. Fecal samples were collected from piglets on the weaning day (W0), 7 days post-weaning (W7), and 14 days post-weaning (W14). Ileal microbiota, microbial-derived metabolites, and tissue samples (ileum, thymus, and mesenteric lymph nodes) were collected at W0 and W14. Fecal microbiota analysis revealed a more stable community at W14 than at W7, with increased presence of fiber-degrading bacteria, including Prevotella, Treponema, Muribaculaceae, and Lachnospiraceae. The ileal microbiota exhibited an adaptive pattern with increases in Lactobacillus, Clostridium_sensu stricto_1, and Enterobacteriaceae, optimized for solid feed digestion and gut stabilization. Morphological analysis of the ileum showed changes in villus architecture between W0 and W14, including increased crypt depth and villus area and decreased villus width, while villus height and goblet cell counts were numerically higher at W14. Transcriptomic profiling revealed the ileum as the primary site of molecular adaptation, with 506 differentially expressed genes (DEGs) involved in immune response pathways, including viral protein interactions with cytokine and cytokine receptor pathways and T cell receptor signaling. The thymus (158 DEGs) and mesenteric lymph nodes (30 DEGs) exhibited modulation of structural pathways linked to systemic immune development, indicating tissue-specific molecular adaptation. Integrated analysis of the host transcriptome and microbial-derived metabolites revealed upregulated glycerophospholipid and glutathione metabolic pathways in piglets 14 days post-weaning, consistent with modulation of membrane structure, barrier function, and antioxidant defense during gut adaptation. Overall, the multi-omics findings provide a comprehensive description of molecular changes associated with weaning adaptation and identify candidate targets for piglet health management during the weaning transition.},
}
@article {pmid41983002,
year = {2026},
author = {Jeong, JY and Kim, J and Kim, M and Kim, YB and Park, C and Song, J and Kim, DW and Kim, M and Park, NG},
title = {Effect of probiotics on growth performance, cytokine levels, and gut microbiome composition of broiler chickens for 7 and 35 days.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {586-602},
pmid = {41983002},
issn = {2055-0391},
abstract = {Through microbial fermentation, probiotics are essential for improving growth performance and gut health in broiler chickens. This study aimed to assess the effects of three additives on growth performance, cytokine levels, and cecal microbiota in broiler chickens. One-day-old Arbor Acres chicks (total 300) were randomized into four groups: (1) control: basal diet, (2) Bacillus subtilis (BS) + basal diet, (3) essential oil + basal diet, and (4) Bacillus velezensis + basal diet. All chickens were fed and watered ad libitum throughout the experiment. Feed intake and body weight were measured weekly. On days 7 and 35, cecal contents of one bird per replicate, based on average body weight, were collected and analyzed for microbiota using 16S rRNA gene amplicon sequencing. The BS group exhibited enhanced growth performance, including increased final body weight, average daily gain, and reduced feed conversion ratio compared to that of the other groups. On day 7, the BS group exhibited a higher abundance of Eisenbergiella (8.24%), and on day 35, there was an increased abundance of Firmicutes (99.63%) and Lachnoclostridium (1.4%). These results indicate that B. subtilis may be a promising probiotic for enhancing broiler health by modulating gut microbiota.},
}
@article {pmid41983140,
year = {2026},
author = {Liu, P and Cui, L and Peng, G and Han, X},
title = {Molecular insights into the role of vitamin D in atopic dermatitis: pathogenesis, diagnosis, and emerging therapies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1739412},
pmid = {41983140},
issn = {1664-3224},
mesh = {Humans ; *Vitamin D/metabolism/therapeutic use/analogs &amp; derivatives ; *Dermatitis, Atopic/diagnosis/etiology/therapy/epidemiology/metabolism/immunology ; *Vitamin D Deficiency/immunology/epidemiology ; Skin/immunology/metabolism/pathology ; Animals ; Receptors, Calcitriol/metabolism ; Biomarkers ; Microbiota/immunology ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by skin barrier dysfunction, immune dysregulation, and microbial imbalance. Increasing evidence suggests that vitamin D, a secosteroid hormone with pleiotropic effects, plays a key role in modulating the pathogenesis of AD. This review provides a comprehensive overview of the molecular mechanisms through which vitamin D influences skin integrity and immune function, focusing on vitamin D receptor-mediated pathways, genetic and epigenetic modifiers, and the interplay with immune cells and microbiota. We also examine the epidemiological correlations between vitamin D deficiency and AD prevalence, diagnostic considerations including biomarkers and serum 25-hydroxyvitamin D evaluation, and therapeutic strategies involving systemic and topical vitamin D interventions. The review further discusses ongoing controversies regarding optimal dosing and evaluates the limitations of current clinical evidence. Finally, emerging research directions, such as vitamin D-microbiota-skin axis and personalized vitamin D therapy, are proposed as promising avenues for advancing AD management.},
}
@article {pmid41983252,
year = {2026},
author = {O'Sullivan, TA and Nicholl, A},
title = {Exploring the dairy milk matrix beyond isolated nutrients-a narrative review.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/10408398.2026.2648097},
pmid = {41983252},
issn = {1549-7852},
abstract = {The concept of the food matrix considers individual components along with how they are structured, interact, and are modified during processing. There is increasing interest around the health effects of individual nutrients versus whole foods, creating a need to better understand how the matrix may influence health outcomes. This narrative review explores the dairy milk matrix and compares health effects with those of isolated components, with additional comparisons to plant-based milk alternatives. Comparative evidence suggests that while calcium from food and supplements generally has similar effects (depending on the form of the supplemental calcium), consumption of food-based sources such as milk may have fewer adverse effects associated with high-dose supplemental intake. Fermented milk products appear to offer additional health benefits compared with unfermented milk, likely due to bioactive compounds produced during fermentation. Structural and functional manipulation of milk proteins, such as whey and lactoferrin, can also modify matrix functionality; for example, appropriate processing conditions can preserve lactoferrin's iron-binding capacity, supporting iron transport and bioavailability. Compared with plant-based milks, which often require fortification and extensive processing, the dairy milk matrix is particularly effective at promoting nutrient absorption. Our findings highlight the importance of adopting a whole food perspective when considering milk in dietary recommendations and research.},
}
@article {pmid41983715,
year = {2026},
author = {Zhu, K and Zhao, J and Li, T and Zhang, S and Liu, C and Xu, Z and Lv, C and Zhang, G and Kang, Y and Huang, J},
title = {ROS-Responsive Hydrogel Delivering Bio-Nanoselenium for Targeted Therapy of UVB-Induced Skin Photodamage.},
journal = {ACS applied materials &amp; interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.6c00317},
pmid = {41983715},
issn = {1944-8252},
abstract = {Ultraviolet B (UVB) radiation is a major environmental factor that induces skin photodamage through oxidative stress and inflammation. To address this, we developed a reactive oxygen species (ROS)-responsive hydrogel, SeNPs@HPTA, for the intelligent delivery of biogenic selenium nanoparticles (BioSeNPs) synthesized by Bifidobacterium animalis. The hydrogel was fabricated by cross-linking phenylboronic acid-grafted hyaluronic acid (HA-PBA) with tannic acid (TA), forming dynamic boronic ester bonds that cleave under high ROS conditions to enable on-demand BioSeNPs release. Transcriptomic analysis revealed that B. lactis H15 efficiently reduces selenite (Se(IV)) to elemental SeNPs by upregulating ion transport and NADPH-regenerating pathways. In vitro, SeNPs@HPTA enhanced HaCaT cell viability, scavenged ROS, and promoted cell migration post-UVB irradiation. In vivo, topical application alleviated skin lesions, improved hydration, reduced epidermal hyperplasia, and suppressed collagen degradation. Mechanistically, the hydrogel conferred therapeutic effects by enhancing antioxidant defenses, inhibiting inflammation and attenuating ferroptosis via GPx4/Nrf2 activation. Critically, genetic knockdown of GPx4 abolished its therapeutic effects, establishing a strict dependence on this key selenoenzyme. The formulation exhibited an excellent biosafety profile. This study presents a microbiome-inspired, stimulus-responsive strategy for precise skin photodamage treatment. We anticipate this microbiome-inspired, intelligent delivery system will offer a powerful and precise strategy for treating oxidative stress-related dermatoses.},
}
@article {pmid41983734,
year = {2026},
author = {Andrade, C},
title = {Proton Pump Inhibitors and the Risk of Dementia.},
journal = {The Journal of clinical psychiatry},
volume = {87},
number = {2},
pages = {},
doi = {10.4088/JCP.26f16420},
pmid = {41983734},
issn = {1555-2101},
mesh = {Humans ; *Proton Pump Inhibitors/adverse effects ; *Dementia/chemically induced/epidemiology ; Risk Factors ; Cognitive Dysfunction/chemically induced ; Aged ; },
abstract = {Proton pump inhibitors (PPIs) are the most prescribed gastric acid suppressant drugs; the category includes omeprazole, esomeprazole, lansoprazole, dexlansoprazole, pantoprazole, and rabeprazole. In 2015, a study suggested that PPI use was associated with an increased risk of dementia. An early meta-analysis confirmed this concern, but the findings were inconsistent in subsequent meta-analyses. Also problematic is that these meta-analyses used questionable approaches, and their findings were characterized by very high heterogeneity. Notably, the high heterogeneity appeared to be driven by large studies with widely different outcomes. Nonetheless, one finding stands out in the body of research examined: older subjects who initiated and continued PPIs (implying chronic use) were at a significantly increased risk of dementia and mild cognitive impairment. Although there are causal and non-causal pathways that associate PPI use with dementia, for reasons that are explained in this article, a cause-effect relationship cannot at present be presumed; so, PPI use is best considered to be a marker of future dementia risk. However, because chronic use of PPIs has been associated with many adverse medical outcomes (eg, disturbances of the gut microbiome, orthopedic complications), and because some PPIs are associated with pharmacokinetic drug interactions (mainly inhibition of CYP2C19), it would be wise to limit the use of PPIs to the shortest duration necessary and to deprescribe PPIs when there does not appear to be need for their continuation.},
}
@article {pmid41983840,
year = {2026},
author = {Ibadullayeva, A and Khamzina, A and Smagulov, D and Khamzin, K},
title = {An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickens.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e299936},
doi = {10.1590/1519-6984.299936},
pmid = {41983840},
issn = {1678-4375},
mesh = {Animals ; Cattle/microbiology ; *Livestock/microbiology ; Camelus/microbiology ; Sheep/microbiology ; *Microbiota/genetics/physiology ; Chickens/microbiology ; Horses/microbiology ; },
abstract = {The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices.},
}
@article {pmid41983959,
year = {2026},
author = {Li, C and Yang, J and Wang, X and Tan, C and Luo, Y and Jin, Z and Zhou, X and Zhang, G},
title = {Maternal Exposure to Bisphenol A Bis(diphenyl Phosphate) Induces Offspring Colitis through Disrupting the Gut Microbiome-Metabolite Axis.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11474},
pmid = {41983959},
issn = {1520-5851},
abstract = {Bisphenol-A bis(diphenyl phosphate) (BDP) has been detected in biological organisms, but its toxicological effects remain unclear. In this study of 4376 participants, the characteristic BDP metabolite diphenyl phosphate was associated with gastrointestinal diseases via a nonlinear dose-response relationship, and was identified as a risk factor (OR = 1.02; 95% CI: 1.01-1.04; P = 0.013). Pregnant rats received 50 mg/kg/day BDP during gestation (GD 14-20) or gestation plus lactation (GD 14-PND 35). Both regimens triggered colonic inflammation and gut microbiome dysbiosis in offspring. The combined exposure group showed more severe effects, including persistent histopathological damage, elevated Il-1β and Il-6, and reduced microbial diversity. LC-MS/MS and 16S rRNA sequencing were used to assess BDP distribution and gut microbiome alterations. BDP crossed the placental barrier. SourceTracker analysis confirmed maternal microbiome transmission as the primary source (>70%) of offspring gut microbiome, accompanied by Streptococcus enrichment and Bifidobacterium depletion. Metabolite-inflammation network analysis showed positive correlations of butyrate and negative correlations of propionate with proinflammatory cytokines (IL-1β, IL-6, and TNF-α), which were subsequently confirmed by in vitro experiments. These findings demonstrate a transgenerational mechanism whereby prenatal BDP exposure induces offspring colonic inflammation via the gut microbiome-metabolite axis, informing maternal-infant intervention strategies.},
}
@article {pmid41983965,
year = {2026},
author = {Nguyen, J and Nguyen, J and Chau, T and Murphy, R and Richardson, J and Evans, E and Tiller, G},
title = {The campus microbiome: insights into soil bacterial diversity from 16S V3-V4 rRNA amplicon sequencing.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0129325},
doi = {10.1128/mra.01293-25},
pmid = {41983965},
issn = {2576-098X},
abstract = {This study consisted of characterizing soil bacterial diversity via 16S V3-V4 amplicon sequencing on CCLA's campus, with a focus on analyzing samples collected near college dormitories. The data provides a sufficient starting point for us to characterize bacterial diversity both on and off campus in Northwest Louisiana.},
}
@article {pmid41984040,
year = {2026},
author = {Sordillo, A and Heldrich, J and Turcotte, R and Sheth, RU},
title = {A Postbiotic Positively Shifts the Canine Oral Microbiome.},
journal = {Journal of veterinary dentistry},
volume = {},
number = {},
pages = {8987564261439741},
doi = {10.1177/08987564261439741},
pmid = {41984040},
issn = {2470-4083},
abstract = {The oral microbiome is an important aspect of overall oral health in dogs. To investigate the ability of a postbiotic, canine oral health postbiotic (COHP), to support oral health, a double-blind, placebo-controlled study was conducted with a dirty tooth model to assess its ability to reduce volatile sulfur compound (VSC) producing microbes that cause halitosis and modulate canine oral microbiome composition. Ten client-owned dogs were randomly split into 2 groups. The groups received either the COHP or a placebo as a powder topper on food for 7 days. Oral microbiome samples were collected on day 0 and day 7 along with the buccal gingival margin. Hydrogen sulfide (H2S)-producing colonies were quantified by plating the oral microbiome samples and counting pigment-producing colonies. Additionally, oral microbiome samples were sequenced, and taxa abundance was quantified. A trend toward a reduction in H2S-producing colonies was observed in the COHP group (P = .06), but not in the placebo group (P = .9). Canine oral health postbiotic reduced the abundance of 9 times as many taxa as the placebo, including taxa that form biofilms and produce VSCs. The placebo reduced the abundance of only one taxon, which is not associated with biofilms or VSCs. The findings provide evidence for COHP's ability to promote a positive shift in the canine oral microbiome, and, together with previous results, provides evidence that it may broadly help to maintain canine oral health.},
}
@article {pmid41984077,
year = {2026},
author = {De Wilde, M and Maarsingh, B and de Monte, LGG and Dekinga, A and Bijleveld, AI and Kressin, H and Zomer, AL and Piersma, T},
title = {Molluscivorous red knots rapidly adjust to a plant diet.},
journal = {Biology open},
volume = {15},
number = {4},
pages = {},
doi = {10.1242/bio.062365},
pmid = {41984077},
issn = {2046-6390},
support = {NZ4543.24//Universiteit Utrecht/ ; //Koninklijk Nederlands Instituut voor Onderzoek der Zee/ ; },
mesh = {Animals ; *Diet ; Feces/chemistry ; *Adaptation, Physiological ; *Feeding Behavior ; },
abstract = {Dietary flexibility is key to adjusting to environmental change. In Mauritania, the seemingly obligatory molluscivorous red knots Calidris canutus were observed to eat seagrass rhizomes. To study the ability of knots to live on plant material, we performed a diet-change experiment on captive individuals. Two groups of five were fed protein-rich pellets for 13 weeks, then plant-based pellets for 6 weeks, then reversed back to protein-rich pellets for 4.5 weeks. During the first days following the shift to the plant diet, body mass declined by 14% before increasing and stabilizing to lower levels. Faecal colour changed from green (i.e. gall, suggesting starvation) to brown and was produced in larger quantities when the birds ate plant pellets. These experimental data prove that knots can indeed live on a plant-based diet, with the observed changes suggesting that adjustments of the digestive system, i.e. gut morphology and microbiome, take only a few days.},
}
@article {pmid41984345,
year = {2026},
author = {Brienza, M and Peña-Herrera, JM and Trotta, V and Chiron, S and Sauvêtre, A},
title = {Trichoderma harzianum enhances lettuce biomass and modulates plant-soil emerging contaminant dynamics under reclaimed wastewater irrigation.},
journal = {Biodegradation},
volume = {37},
number = {3},
pages = {},
pmid = {41984345},
issn = {1572-9729},
mesh = {*Lactuca/growth &amp; development/metabolism/microbiology ; *Wastewater/chemistry ; Biodegradation, Environmental ; Agricultural Irrigation ; Biomass ; *Soil Pollutants/metabolism ; Plant Roots/metabolism/microbiology ; Soil/chemistry ; *Hypocreales ; Plant Leaves/metabolism ; Carbamazepine/metabolism ; Soil Microbiology ; Plant Growth Regulators/metabolism ; },
abstract = {The use of wastewater for irrigation in agricultural soils offers a sustainable means to reduce freshwater consumption and recycle nutrients, but also poses contamination risks associated with emerging pollutants. Furthermore, potentially toxic transformation products may form in soil and rhizosphere, and could subsequently be taken up by plants. Several products containing spores of symbiotic fungi are available and could serve as effective solutions to enhance the biodegradation of micropollutants in agricultural soils irrigated with treated wastewater. In this study, the effect of the fungus Trichoderma harzianum on the distribution of two emerging contaminants, carbamazepine and climbazole, and their main transformation products among soil and lettuce tissues was investigated under controlled conditions. Physiological effects were also investigated by quantifying phytohormones in roots and leaves. Inoculation with Trichoderma harzianum did not significantly affect the uptake of the parent compounds but increased the concentration of their transformation products in soil and reduced their levels in plant leaves after three weeks. The fungus enhanced plant biomass and altered certain phytohormones involved in defense mechanisms such as salicylic acid and microbiome recruitment in roots and soils. Findings of this study provide valuable insights that can be effectively applied to crop cultivation using reclaimed wastewater, leveraging readily available biological products for improved sustainable practices.},
}
@article {pmid41984779,
year = {2026},
author = {Sun, Z and Shi, M and Zheng, Y},
title = {Interpreting circulating microbiome-related metabolites in coronary heart disease.},
journal = {PLoS medicine},
volume = {23},
number = {4},
pages = {e1005056},
pmid = {41984779},
issn = {1549-1676},
mesh = {Humans ; Biomarkers/blood ; *Coronary Disease/microbiology/blood/metabolism/diagnosis ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Circulating microbiome-related metabolites have emerged as promising biomarkers for coronary heart disease. A recent multi-stage study in PLOS Medicine strengthens signal prioritization but highlights the persistent gap between association and causality.},
}
@article {pmid41984783,
year = {2026},
author = {Calderón-Romero, P and Valderrama, B and Bastiaanssen, TFS and Lillo, P and Thumala-Dockendorff, D and Clarke, G and Cryan, JF and Slachevsky, A and González-Billault, C and Court, FA},
title = {The neuroactive potential of the elderly human gut microbiome is associated with mental health status.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0343493},
pmid = {41984783},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Aged ; *Mental Health ; Cognition/physiology ; *Aging/psychology ; Aged, 80 and over ; Depression/microbiology ; Middle Aged ; Chile ; Cohort Studies ; },
abstract = {Ageing is usually associated with physiological decline, increased mental health issues, and cognitive. deterioration, alongside specific changes in the gut microbiome. However, the relationship between the neuroactive potential of the gut microbiome and mental health and cognition among the elderly remains less explored. This study examines a cohort of 153 older Chilean adults with cognitive complaints, assessing anthropometric data, mental health via five distinct tests, and gut microbiome composition through 16SV4 sequencing. Our findings reveal associations between anthropometric factors and depression scores in mental tests of participants with their gut microbiome composition. Notably, depression was associated with changes in the abundance of Lachnospiraceae Eubacterium xylanophilum group and Fusobacteriaceae Fusobacterium. Additionally, bacterial pathways involved in metabolising neuroactive compounds such as tryptophan, short-chain fatty acids, p-cresol, glutamate, and nitric oxide were associated with participant age, sex, and cognitive performance. Moreover, participants' sex was associated with the neuroactive potential of specific bacteria, suggesting a role of the gut microbiome in sex-related mental health differences in the elderly. Altogether, this study provides the first evidence from a South American cohort linking the inferred neuroactive potential of the gut microbiome to cognitive and psychological function in older adults with cognitive complaints, offering novel insights into microbiota-based mechanisms that may contribute to mental health and ageing.},
}
@article {pmid41984912,
year = {2026},
author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , },
title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e86058},
pmid = {41984912},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Infant, Newborn ; Female ; Infant ; Longitudinal Studies ; Prospective Studies ; Birth Cohort ; South Africa ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Observational Studies as Topic ; Rural Population ; Milk, Human/microbiology/chemistry ; Male ; Risk Factors ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.<br><br>OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.<br><br>METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.<br><br>RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.<br><br>CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.},
}
@article {pmid41985067,
year = {2026},
author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR},
title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.},
journal = {Archives of insect biochemistry and physiology},
volume = {121},
number = {4},
pages = {e70159},
doi = {10.1002/arch.70159},
pmid = {41985067},
issn = {1520-6327},
support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science &amp; Technology, New Delhi, India (INSPIRE-JRF)/ ; },
mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Microbiota ; Metagenomics ; *Culicidae/microbiology/growth &amp; development ; *Metamorphosis, Biological ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.},
}
@article {pmid41985313,
year = {2026},
author = {Khushbu, and Das, S and Debanth, N},
title = {From bench to gut: Translational horizons in probiotic nanoencapsulation for enhanced host-microbiome synergy.},
journal = {Biomaterials advances},
volume = {185},
number = {},
pages = {214871},
doi = {10.1016/j.bioadv.2026.214871},
pmid = {41985313},
issn = {2772-9508},
abstract = {Delivering viable probiotics to the gastrointestinal tract remains a challenge due to harsh physicochemical conditions and limited stability during processing and storage. Conventional microencapsulation techniques, such as spray drying, lyophilization, and emulsification, enhance survival but face scalability and efficiency constraints. Emerging nanostructured delivery platforms overcome these barriers by leveraging unique physicochemical properties of nanomaterials, including high surface area, enhanced solubility, and stimuli-responsive release. Functionalized nanocarriers enable site-specific adhesion, systemic delivery, and prolonged mucosal residence, thereby enhancing therapeutic precision and reducing off-target effects. This article highlights the potential of co-encapsulating probiotics with microbial metabolites, prebiotic carbohydrates, and polyphenolic compounds within biopolymeric matrices, which can significantly enhance translational applications and strengthen conventional probiotic nanoencapsulation strategies. This review consolidates current advancements in probiotic nanoencapsulation, emphasizing the design of multifunctional matrices that preserve microbial integrity, extend shelf life, and optimize host-microbiome interactions. By elucidating nanoparticle-probiotic interfacial dynamics, it lays the groundwork for next-generation probiotic therapeutics with improved efficacy and translational potential.},
}
@article {pmid41985330,
year = {2026},
author = {Kwiendacz, H and Cembrowska-Lech, D and Skonieczna-Żydecka, K and Klimontowicz, K and Podsiadło, K and Wierzbicka-Woś, A and Styburski, D and Kaczmarczyk, M and Gumprecht, J and Łoniewski, I and Nabrdalik, K},
title = {Multi-strain probiotic enhances metformin tolerance by modulating gut microbiome and bile acid pathways: Insight from multi-omics post-hoc analysis (ProGasMet trial).},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {198},
number = {},
pages = {119370},
doi = {10.1016/j.biopha.2026.119370},
pmid = {41985330},
issn = {1950-6007},
abstract = {BACKGROUND: Metformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear.<br><br>METHODS AND ANALYSIS: We performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline and end of treatment were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal covariate-adjusted feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score).<br><br>RESULTS: In multi-omics integration at 12 weeks, bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo.<br><br>CONCLUSION: Probiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible candidate for improved tolerability. These results support prioritising secondary bile acid-microbiome pathways for confirmation in larger trials incorporating targeted bile acid quantification and causal modelling.},
}
@article {pmid41985576,
year = {2026},
author = {Weitekamp, CA and Watson, C and Hata, E and Hester, K and Kodavanti, UP and Lau, C and Lehmann, DM and Miller, CN and Shaffer, RM and Soliman, F and Powers, M and Branch, FM},
title = {A systematic literature inventory on the interaction between dietary factors and environmental chemical exposures for nervous system health outcomes.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {213},
number = {},
pages = {116096},
doi = {10.1016/j.fct.2026.116096},
pmid = {41985576},
issn = {1873-6351},
abstract = {Environmental health research from the last seven decades suggests that dietary factors can modify adverse health outcomes associated with chemical exposures. However, the interplay between diet, chemical exposures, and health is complex and remains poorly understood. Here, to survey the existing evidence and stimulate future research, we systematically identified and cataloged available literature on the interactions between chemical exposures and dietary factors for one health outcome category, neurotoxicity. The goal of this systematic literature inventory was to identify the relationship of dietary factors on chemical exposure mediated health outcomes related to central nervous system toxicity, given the importance of the microbiome-gut-brain axis in mediating these interactions. From an initial set of 32,529 references, we identified 80 epidemiological studies, 707 toxicological studies, and 175 in vitro studies that met inclusion criteria. Study design information was captured for the 80 epidemiological studies and for 113 toxicological studies that met additional scoping criteria. The most frequently studied chemical-diet interactions across the human and animal evidence streams were metals/metalloids and micronutrients. Knowledge gaps included dietary components known to be central to microbiome function, as well as adverse dietary modifiers compared to protective dietary factors. This systematic literature inventory is intended to support future research.},
}
@article {pmid41985591,
year = {2026},
author = {Ma, R and Wang, C},
title = {Microbiome analysis reveals the positive effects of exercise on the gut microbiota in horse.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108501},
doi = {10.1016/j.micpath.2026.108501},
pmid = {41985591},
issn = {1096-1208},
abstract = {Gut microbiota is vital to host health, involving many aspects including immunity, metabolism and digestion. Exercise is recognized as a significant factor influencing the gut microbiota. However, the effects of exercise on the gut microbiota in horses remain unclear. Here, this study aims to investigate the effects of exercise on the gut bacterial and fungal communities in the horses using 16S rDNA and ITS genes amplicon sequencing. Results indicated that exercise significantly increased the ACE, Chao1 and Shannon indices of the gut bacterial community, accompanied by significant alterations in the primary components of the gut bacterial community. Conversely, exercise did not affect the diversity and abundance of the gut fungal community. Although exercise did not change the dominant bacterial phyla and genera, it resulted in significant changes in the abundance of some bacteria and fungi. Bacterial taxonomic analysis revealed that exercise significantly increased the relative abundance of 8 phyla and 187 genera, while the relative abundance of three phyla and 197 genera decreased markedly. Moreover, exercise also resulted in a significant increase in the relative abundance of five phyla and 105 genera, whereas the relative abundance of two phyla and 82 genera decreased significantly in the gut fungal community. In summary, this study indicated that exercise can affect the composition and structure of gut microbiota. Moreover, this study also conveys an important message that exercise may exert health benefits to the host by affecting the gut microbiota. Future research could investigate the effects of various types and intensities of exercise on gut microbiota to optimize health management strategies.},
}
@article {pmid41985731,
year = {2026},
author = {Lee, E and Han, K and Mun, S},
title = {CST-Based Molecular Profiling of Vaginal Microbiota Validated by qRT-PCR and 16S Amplicon Sequencing.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2026.03.015},
pmid = {41985731},
issn = {1095-9130},
abstract = {The vaginal microbiome is commonly classified into five Community State Types (CSTs) based on the dominance and relative abundance of Lactobacillus species, which play a central role in maintaining vaginal homeostasis through the production of lactic acid and hydrogen peroxide. Disruption or depletion of Lactobacillus spp. Leads to elevated vaginal pH, thereby promoting the overgrowth of anaerobic bacteria associated with bacterial vaginosis (BV). Although next-generation sequencing (NGS)-based microbiome profiling has been widely used to characterize vaginal microbial communities, its routine clinical application remains limited by high cost, long turnaround time, and reduced suitability for rapid, species-specific quantification. In this study, we developed and validated species-specific quantitative real-time polymerase chain reaction (qRT-PCR) primer sets targeting four health-associated Lactobacillus species (Lactobacillus crispatus, Lactobacillus. gasseri, Lactobacillus. iners, and Lactobacillus. jensenii) and four BV-associated bacterial taxa (Atopobium vaginae, Clostridiales genomosp. BVAB1, Prevotella bivia, and Megasphaera type 1). Quantitative results obtained by qRT-PCR were systematically compared with relative abundance profiles derived from 16S rRNA gene V3-V4 sequencing, revealing a strong concordance between the two platforms in identifying key vaginal microbial signatures. Collectively, these findings demonstrate that qRT-PCR represents a rapid, cost-effective, and sensitive approach for targeted vaginal microbiome assessment and supports its potential utility as a molecular diagnostic tool for the precise detection of vaginal microbiota imbalance.},
}
@article {pmid41985795,
year = {2026},
author = {Shen, X and Gibson-Kueh, S and Nelson, SP and Poon, ZWJ and Terence, C and Vu, NT and Carrai, M and Awate, S and Vij, S and Tan, MR and Jerry, DR and Domingos, JA},
title = {Scale drop disease virus (SDDV) infection induces intestinal dysbiosis and secondary Vibrio expansion in Asian seabass (Lates calcarifer).},
journal = {Fish &amp; shellfish immunology},
volume = {},
number = {},
pages = {111344},
doi = {10.1016/j.fsi.2026.111344},
pmid = {41985795},
issn = {1095-9947},
abstract = {Scale drop disease virus (SDDV) is a major viral pathogen causing high mortality in farmed Asian seabass (Lates calcarifer), yet its impacts on host-associated microbiota remain poorly understood. In this study, juvenile L. calcarifer were intraperitoneally challenged with 10[7] viral copies (0.1 ml SDDV), resulting in 94.2% cumulative mortality over a 24-day experimental period. A total of 36 intestinal content samples were collected at defined time points relative to challenge (dpc) from clinically healthy (H) and sick (S) fish, representing five stages: pre-infection baseline (H0 dpc), early infection (H6 dpc), peak mortality (H10 dpc and S10 dpc), declining mortality (S15 dpc) and recovery (H24 dpc). Histopathological examination revealed progressive intestinal pathology, characterised by multifocal vesicle formation and epithelial necrosis, consistent with SDDV-associated enteropathy. 16S rRNA gene sequencing demonstrated pronounced intestinal dysbiosis during infection, with a significant collapse of alpha diversity at peak mortality (10 dpc; Kruskal-Wallis test with Dunn's post-hoc comparisons, p < 0.05) where Chao1 decreased from 942 at baseline to 416 and Shannon from 4.3 to 1.9. At peak disease, the gut microbiome was overwhelmingly dominated by Vibrio (>80% relative abundance), suggesting secondary opportunistic expansion associated with virus-induced intestinal damage. Co-occurrence network analysis further revealed fragmentation of microbial interactions during peak infection, followed by partial restoration of network connectivity and re-emergence of taxa such as Photobacterium and Rhodobacteraceae during recovery from infection. Collectively, these findings demonstrated that SDDV infection induced severe intestinal pathology accompanied by dynamic restructuring of the gut microbiome in L. calcarifer, linking viral epithelial damage to destabilization of the intestinal microbial homeostasis and secondary Vibrio overgrowth. Distinct microbiome features, including reduced community diversity and Vibrio dominance at peak disease, as well as recovery-associated taxa in surviving fish, may represent potential microbial indicators of disease progression and intestinal recovery, providing a reference framework for future microbiome-informed health management strategies aimed at mitigating SDDV impacts in L. calcarifer aquaculture.},
}
@article {pmid41986005,
year = {2026},
author = {Ansari, A and Shete, O and Ghosh, TS},
title = {Artificial intelligence in microbial metagenomics.},
journal = {Progress in molecular biology and translational science},
volume = {221},
number = {},
pages = {255-276},
doi = {10.1016/bs.pmbts.2026.01.009},
pmid = {41986005},
issn = {1878-0814},
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; Microbiota/genetics ; Machine Learning ; },
abstract = {Rapid advancements in genomic sequencing technologies and similar technological advancements in the area of accessing, isolating, extracting and functional probing of microbes residing in diverse environments has resulted in a deluge of microbiome sequencing and microbial genomic sequencing data. Concomitant developments in the area of data science, specifically in the domains of advanced statistics, and artificial intelligence (AI) can facilitate mining this data to answer complex biological questions and developing translational applications in diverse areas, ranging from health-care to industrial microbiology. For most researchers, information on which AI tools address specific biological questions is scattered across disparate sources. In this chapter, we explore the various applications of AI-based methodologies (using case-studies) in answering different biological questions using microbial genomics and metagenomic data. We also discuss different AI and machine-learning (ML) based approaches to integrate metagenomic data with other "omics" data. Finally, we highlight both challenges and possibilities with this rapidly progressing field.},
}
@article {pmid41986382,
year = {2026},
author = {Dahmouni, S and Benabdelmoumene, D and Bengharbi, Z and Fodil, MK and Umar, KM and Qadi, WSM and Krache, F and Waqar, M and Tong, X and Han, R and Abu Bakar, ZH and Sarian, MN and Mediani, A and Jam, FA and Hamezah, HS},
title = {Postbiotics and paraprobiotics in food biochemistry mechanisms stability and nutritional applications.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00838-z},
pmid = {41986382},
issn = {2396-8370},
support = {DIP-2024-021//Universiti Kebangsaan Malaysia/ ; },
abstract = {Postbiotics, defined as preparations of inanimate microorganisms and their components that confer health benefits, are emerging as stable and safe alternatives to probiotics. This review summarizes recent advances in the biochemical composition, mechanisms of action, and applications of postbiotics and paraprobiotics in human and animal nutrition. It also highlights innovations in omics technologies, artificial intelligence, and sustainable production strategies that are shaping next-generation microbiome-based functional foods and therapeutic interventions.},
}
@article {pmid41986393,
year = {2026},
author = {Gimeno-Molina, B and Correia, GDS and Ng, S and Lee, YS and Bayar, E and Love, RL and Zhao, S and Mountain, KE and Teoh, TG and Brown, RG and David, AL and Lewis, HV and Terzidou, V and Botto, M and Kropf, P and MacIntyre, DA and Bennett, PR and Sykes, L},
title = {Complement and neutrophils are actively involved at the cervicovaginal interface in cases of adverse microbial composition, cervical shortening and spontaneous preterm birth.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00969-x},
pmid = {41986393},
issn = {2055-5008},
abstract = {Microbial-driven spontaneous preterm birth (sPTB) is linked to adverse vaginal microbiome and dysregulated immune responses, yet this knowledge has not translated into predictive tools or therapies. We sampled 186 high-risk pregnant women and assessed 14 complement proteins and the neutrophil immunophenotype at the cervicovaginal interface to expand potential targets. Alterations in classical and alternative complement pathway components were associated with bacterial community composition and preceded cervical shortening and sPTB. At 12[+0]-16[+6] weeks, women with Community State Type (CST) IV had significantly higher concentrations of C1q, C4, C4b, Factor B, D, C3b/iC3b, and Factor H, I than those with CST I. Women who later developed a short cervix and delivered preterm showed lower L. crispatus abundance and elevated complement activation. Neutrophils were the dominant local immune cell and exhibited enhanced activation relative to peripheral neutrophils, with altered expression of CD11b, CD62L, CD63 and CD66b. Cervical neutrophil CD63, CD66b, and CD88 differed between CST IV and CST I, though not by pregnancy outcome. Neutrophil abundance correlated with cytokines, complement proteins, and MMPs, suggesting roles in inflammation and tissue remodelling. These findings highlight a microbiota-driven complement-neutrophil axis present before cervical remodelling and sPTB, identifying potential complement-based predictors and therapeutic targets.},
}
@article {pmid41986507,
year = {2026},
author = {Venkidesh, BS and Acharya, M and Narasimhamurthy, RK and Murali, TS and Rao, BSS and Mumbrekar, KD},
title = {Multi-strain bacterial combination mitigates pelvic irradiation-induced gut damage by preserving gut integrity, inhibiting inflammation and apoptosis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47773-3},
pmid = {41986507},
issn = {2045-2322},
}
@article {pmid41986930,
year = {2026},
author = {Raghav, S and Frishman, WH},
title = {Childhood Obesity, Medications, and Surgeries.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
doi = {10.1097/CRD.0000000000001230},
pmid = {41986930},
issn = {1538-4683},
abstract = {The obesity pandemic continues to increase in prevalence in children and adolescents, with its increase outpacing the rate of adult obesity; the human developmental index, body mass index, and family income all display associations to childhood obesity. There are numerous adverse complications of childhood obesity, including cardiovascular, endocrine, and gastrointestinal manifestations. Obesity is thought to be an interaction of several different factors, such as leptin, proopiomelanocortin, glucose uptake in adipocytes, melanocortin receptor 4, protein convertase 1/3, brain-derived neurotrophic factor, fat-mass and obesity-associated gene, melanocortin receptor 4, tumor necrosis factor, interleukin-6, and long noncoding RNA. Epigenetic regulation, the unique gut microbiome role in contributing to obesity, environmental factors, and the social context of a child can precipitation of childhood obesity. In this review, we hope to explore the different medications for obesity, orlistat, glucagon-like peptide-1 agonists, liraglutide, semaglutide, exenatide, setmelanotide, metreleptin, naltrexone, lorcaserin, phentermine, metformin, fluoxetine, lisdexamfetamine, and zonisamide, while also reviewing surgeries such as the Roux-en-Y gastric bypass, laparoscopic or vertical sleeve gastrectomy, and adjustable gastric banding.},
}
@article {pmid41986966,
year = {2026},
author = {Sourij, C and Müller, A and Al-Baghdadi, A and Aziz, F and Tripolt, NJ and Pferschy, PN and Andritz, E and Kojzar, H and Stadlbauer, V and Garcia, SL and Sourij, H},
title = {Safety and efficacy of intermittent fasting with or without exercise in people living with overweight or obesity and type 2 diabetes-The INTERFAST-3 study design.},
journal = {Diabetic medicine : a journal of the British Diabetic Association},
volume = {},
number = {},
pages = {e70328},
doi = {10.1111/dme.70328},
pmid = {41986966},
issn = {1464-5491},
support = {//Austrian Science Fund/ ; },
abstract = {AIMS: Lifestyle modification, including caloric restriction and exercise, is fundamental in the treatment of people living with overweight and type 2 diabetes mellitus (T2D). The overall aim of lifestyle intervention schemes is to reduce body weight and improve glycaemic control to reduce the future risk of diabetes-associated complications. The aim of this study is to determine whether intermittent energy restriction, exercise or their combination is best suited for reaching these targets in individuals with T2D not treated with insulin.<br><br>METHODS: This randomized, controlled, monocentric parallel-group trial is designed to investigate participants living with T2D, body mass index >27&#x2009;kg/m[2], HbA1c &#x2265;53&#x2009;mmol/mol (&#x2265;7.0%) and &#x2264;86&#x2009;mmol/mol (&#x2264;10.0%) and without insulin therapy. Participants are equally and randomly allocated to one of four study groups: (1) intermittent energy restriction group, (2) exercise group, (3) combined intermittent energy restriction and exercise group and (4) control group. The intervention phase lasts 12&#x2009;weeks, followed by a two-year follow-up phase. In addition to assessing body weight and glycaemic parameters, resting energy expenditure (REE) and body composition are measured. An oral glucose tolerance test is carried out at baseline and at the end of the intervention. Additionally, stool samples for microbiome analyses and individual-related outcomes are collected, and all participants are equipped with continuous glucose monitoring (CGM). The primary outcome measure is the change in bodyweight from baseline to day 84.<br><br>TRIAL REGISTRATION: The study was registered at DRKS (Deutsches Register Klinischer Studien-German Clinical Trial Register DRKS-ID: DRKS00032036)-Date of registration: 11.10.2023.},
}
@article {pmid41987215,
year = {2026},
author = {Yan, M and Firkins, J and Guo, J and Relling, A and Yu, Z},
title = {Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02422-9},
pmid = {41987215},
issn = {2049-2618},
abstract = {BACKGROUND: Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, do not fully reflect the diverse and complex N metabolism in the rumen ecosystem.<br><br>RESULTS: To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that well-established mechanisms of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and their regulatory proteins, are absent in many of the predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria in response to ammonia availability. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes involved in N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) at 10% and 13% had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, changes in concentrate levels altered N assimilation, notably increasing expression of amino acid biosynthesis pathways.<br><br>CONCLUSION: These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.},
}
@article {pmid41987241,
year = {2026},
author = {Zhong, Y and Peng, Y and Zhang, S and Wen, L and Liu, G and Xu, B and Liang, Y and Huang, H and He, J and Feng, Y and Zeng, J and Liang, J},
title = {An integrated microbiome-drug interaction and bioinformatics approach identifies active deglycosylated and glycosidic chain metabolites of Platycodin D targeting PTPN2/HIF1A in acute lung injury.},
journal = {Biology direct},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13062-026-00779-3},
pmid = {41987241},
issn = {1745-6150},
}
@article {pmid41987825,
year = {2026},
author = {Haque, S and Ponton, F and Allen, AP and Gamage, HKAH and Encinas-Viso, F and Paulsen, IT and Dudaniec, RY},
title = {Environment and Pollen Diversity Differentially Affect the Gut Microbiomes of Introduced Honeybees and Bumblebees.},
journal = {Evolutionary applications},
volume = {19},
number = {4},
pages = {e70234},
pmid = {41987825},
issn = {1752-4571},
abstract = {Invasive species may exhibit shifts in their gut microbiome in response to novel environments and diet, but this may differ across host species and their time since colonisation. We investigate if site environmental variables and foraged pollen resources differentially shape the gut microbiomes of two bee species with contrasting introduction histories: The European honeybee, Apis mellifera (introduced 1831), and the recently invasive bumblebee, Bombus terrestris (invaded 1992). Using landscape-scale metabarcoding across the island state of Tasmania in Australia, we characterised gut bacteria (16S rRNA) and corbicular pollen diversity (ITS2) for each species. Gut bacterial composition was significantly associated with mean annual temperature for A. mellifera and with mean annual precipitation and percentage of pasture for B. terrestris. In B. terrestris, the core and facultative gut microbial diversity and richness showed associations with precipitation, foraged pollen diversity, wind velocity and temperature. Foraged pollen diversity of native plants more strongly predicted the facultative gut microbiome across species. Overall, the gut microbiome of B. terrestris showed a stronger response to abiotic and biotic predictors compared to A. mellifera. Our findings advance understanding of how environmental and dietary factors shape pollinator gut microbiomes at landscape scales, with implications for pollinator health and survival.},
}
@article {pmid41987827,
year = {2026},
author = {Bornbusch, SL and Thacher, PR and Francisque, M and DeCandia, AL and Bortner, R and Garelle, D and Kendrick, EL and Maslanka, MT and Muletz-Wolz, CR},
title = {How "pro" are probiotics for wildlife species? Novel data, lack of evidence, and future directions.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag036},
pmid = {41987827},
issn = {2730-6151},
abstract = {Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of >900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, prevalence of a potential enteric pathogen (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In black-footed ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the potential enteric pathogen. Given our findings, which reiterate concerns about the efficacy of commercial probiotics across human and animal sectors, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife under human care.},
}
@article {pmid41987828,
year = {2026},
author = {Martino, ME and Gallo, M and Nai, I and Quagliariello, A and Rovere, GD and Babbucci, M and Monticelli, G and Graziano, M and Franch, R and Racaku, M and Cardazzo, B and Milan, M and Peruzza, L and Bargelloni, L},
title = {Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag059},
pmid = {41987828},
issn = {2730-6151},
abstract = {In the context of rapidly accelerating global warming, the rising frequency of heatwaves is driving large-scale ecological shifts, profoundly affecting organismal physiology and ecosystem functioning. Thermal tolerance is a key determinant of species resilience. Evidence from diverse model systems indicates that this tolerance can be enhanced through thermal priming, a pre-adaptive process in which organisms are exposed to sublethal heat stress. Beyond intrinsic host factors, the adaptive potential of host-associated microbiomes is increasingly recognised as a critical role in shaping organismal thermal resilience. However, the extent to which microbiomes alone can enhance host thermal tolerance remains largely unknown. Here, we used the Manila clam (Ruditapes philippinarum), one of the most widely farmed bivalves, as a model system to test whether thermal pre-adaptation of the microbiome is sufficient to improve host thermal tolerance. Clams were thermally primed, their microbiota isolated, and subsequently transplanted into non-acclimated individuals, which were then exposed to simulated heatwave conditions. By integrating microbial community profiling, host physiological measurements, and transcriptomic analyses, we demonstrate that transplantation of a microbiome from animals previously exposed to heat stress is sufficient to enhance host resilience during subsequent heat stress. This effect arises from adaptive shifts in microbiome composition that promote energy conservation and survival through elevated antioxidant activity and a broad downregulation of host transcriptional pathways, placing the host in an energy-efficient, stress-mitigating state. Our findings provide novel insights into holobiont-level adaptive mechanisms to stress adaptation and hold practical potential for developing microbiome-based interventions to enhance thermal tolerance in aquaculture systems.},
}
@article {pmid41987880,
year = {2026},
author = {Cipriano, GL and Grimaldi, A and Marra, A and Quartarone, A and Maresca, G},
title = {Gut microbiota and cognitive decline: a scoping review of microbial mechanisms and adaptive responses in dementia.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1782720},
pmid = {41987880},
issn = {1663-4365},
abstract = {Dementia is a progressive disease that results in a loss of mental capacity. Some of the most affected cognitive skills are memory, orientation, and language. These skills are also associated with behavioral shifts such as increased agitation and apathy, worsening the affected person's quality of life. The most common type of dementia is Alzheimer's disease, and it is especially concerning in older adults. Alzheimer's is characterized by the formation of beta-amyloid plaques and neurofibrillary tangles that are made of hyperphosphorylated tau proteins. These plaques and tangles lead to inflammation in the central nervous system, damage to the connections between neurons, and overall degeneration of the nervous system. Newer studies have started to identify the gut microbiome and the gut-brain axis as components critical to the progression of neurodegenerative diseases. Dysbiosis, which is characterized by an imbalance or loss of microbial diversity in the gut, has been attributed to the worsening of neurodegenerative diseases. The gut microbiome has been shown to have a large impact on the brain and how it responds neurochemically. An imbalance in the gut microbiome has also been shown to lead a person to emotional and cognitive dysfunction. It has been shown that in dementia patients, there is also an associated intestinal dysbiosis and increased inflammation systemically and within the brain. Certain gut bacteria stimulate the production of pro- inflammatory cytokines and neuroinflammation, which is a defining characteristic of diseases associated with dementia. This review is focused on three main aspects in which dysbiosis is related to cognitive decline.},
}
@article {pmid41987902,
year = {2026},
author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S},
title = {Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1729497},
pmid = {41987902},
issn = {2235-2988},
mesh = {*Diarrhea/microbiology/prevention &amp; control ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Cross-Sectional Studies ; *Probiotics/therapeutic use ; Feces/microbiology ; Pilot Projects ; Female ; Prognosis ; Male ; High-Throughput Nucleotide Sequencing ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Prospective Studies ; Biomarkers/analysis ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Diarrhea is a leading contributor of mortality globally. To mitigate its disease burden, improved prognosis and alternative therapeutic approaches must be deployed. A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted with the aim of meeting the WHO's GAPPD (Global Action Plan for Pneumonia and Diarrhea) goals.<br><br>HYPOTHESIS: Next-generation sequencing is a potent tool being increasingly used for epidemiological surveillance. It can help in the comparison of the structural diversity of the gut microbiome between diarrheal and non-diarrheal samples, thereby aiding in the identification of prospective prognostic and therapeutic candidates.<br><br>AIM: The pilot study was designed to identify prospective taxa that were comparatively enriched in non-diarrheal samples and to predict gut microbial community interactions.<br><br>METHODOLOGY: 16S rRNA amplicon sequencing and subsequent analysis were undertaken for taxonomic profiling and abundance interpretation of OTUs.<br><br>RESULTS: Significant differences between the two groups with respect to structural composition was revealed. Firmicutes was the most abundant phylum in the majority of the samples. The B/F ratio was consistently <1 in all diarrheal samples. A significant difference in the mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. On the other hand, Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% of diarrheal samples; where Streptococcaceae was suppressed, Bacteroideaceae and Nocardiaceae were the most abundant. In non-diarrheal samples, where Streptococcaceae was almost completely suppressed, Bifidobacteriaceae was the most abundant and significantly suppressed other families. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% of non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples, while they were absent in diarrheal samples.<br><br>CONCLUSION: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. To our knowledge, this is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics to protect the endemic population from diarrhea and help in achieving Sustainable Development Goals 2 and 3.},
}
@article {pmid41987918,
year = {2026},
author = {Wang, Y and Ni, M and Zheng, A and Peng, Y and Liu, J and Xiong, Q and Wang, X and Savkovic, V and Kang, S},
title = {A stage-based framework to interpret regulatory T cell biology after heart transplantation.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1777360},
pmid = {41987918},
issn = {2297-055X},
abstract = {Regulatory T cells play a pivotal role in immune responses following heart transplantation, influencing the entire post-transplant process. This article examines Treg dynamics in a stage-specific framework and their clinical implications. In the early phase (0-30 days), dominated by injury-related sterile inflammation, Treg recruitment affects local inflammation resolution and tissue repair, potentially altering risks of early immune injury and rejection. The intermediate phase (1-6 months) features high acute cellular rejection risk with ongoing immunosuppression adjustments; Treg quantity, phenotype, and suppressive function are closely associated with the regulation of anti-donor immune responses. In the late phase (>6 months), chronic low-grade inflammation and progressive vascular remodeling predominate, where Tregs suppress persistent immune attacks but may promote fibrosis via repair pathways, exhibiting bidirectional effects. This article highlights Treg detection limitations, including FOXP3 specificity, epigenetic stability, and blood-graft discrepancies. Future directions encompass multimarker monitoring, dynamic risk models, Treg cell therapy, and interventions like cytokine/microbiome modulation to achieve precise immunoregulation, reduce rejection, minimize complications, and improve long-term graft survival.},
}
@article {pmid41988036,
year = {2026},
author = {Alzahrani, SS},
title = {Gut microbiome-epigenetic crosstalk in obesity and type 2 diabetes: mechanisms, evidence, and translational opportunities.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1805937},
pmid = {41988036},
issn = {1664-302X},
abstract = {Obesity and type 2 diabetes mellitus are closely linked metabolic disorders in which gut microbial alterations interact with host epigenetic regulation to influence inflammation, insulin sensitivity, and energy homeostasis. This review examines the gut microbiome-epigenetics interface in these conditions by integrating mechanistic evidence with a Scopus-based bibliometric analysis of publications from 2016 to 2025, thereby providing both disease-focused synthesis and field-level context. Bibliometric mapping identified 1,153 documents from 515 sources authored by 5,445 researchers, with a marked annual growth rate of 27.79%, indicating rapid expansion of this interdisciplinary area. Mechanistically, current evidence converges on three major epigenetic domains: DNA methylation, histone modifications, and non-coding RNA regulation. Microbiota-derived metabolites, particularly short-chain fatty acids, folate-related methyl donors, and other bioactive compounds, influence enzymes such as DNA methyltransferases and histone deacetylases, as well as downstream chromatin marks and microRNA networks relevant to metabolic dysfunction. In obesity and type 2 diabetes, recurrent findings include reduced abundance of butyrate-producing taxa and enrichment of pro-inflammatory or endotoxin-associated bacteria, although these patterns remain heterogeneous across populations, study designs, and analytical methods. Accordingly, the review emphasizes that phylum-level or taxa-level associations should be interpreted cautiously and that causality remains incompletely resolved. A key contribution of this review is the combined evaluation of mechanistic pathways, context-dependent microbial signatures, and translational limitations within a single framework. Overall, microbiome-targeted interventions remain promising but insufficiently validated, and progress toward clinical application will require longitudinal, multi-omics, and interventional studies that directly link specific taxa, metabolites, and epigenetic modifications.},
}
@article {pmid41988038,
year = {2026},
author = {Qin, H and Gong, H and Wang, X and Liu, Y and Song, W and Li, Z and Xiang, H},
title = {Rhizosphere microbial patterns and climatic correlates of phenotypic variation in Rosa roxburghii.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1762588},
pmid = {41988038},
issn = {1664-302X},
abstract = {Plant phenotypic variation represents an important expression of diversity among populations and their responses to heterogeneous environments. However, the factors associated with such variation remain incompletely characterized. In this study, we examined eight phenotypic traits of Rosa roxburghii across environmentally heterogeneous sites and characterized rhizosphere bacterial and fungal communities using 16S rRNA and ITS high-throughput sequencing. Marker taxa were identified, and statistical analyses were applied to explore associations between microbial patterns, climatic context, and phenotypic traits. Our results revealed significant differences among populations in fruit length, fruit width, and stem diameter. Microbial community analyses indicated inter-population divergence in both bacterial and fungal communities, with fungi showing relatively stronger compositional differentiation. Using complementary analytical approaches (LEfSe, LASSO, and sPLS-DA), we identified a consensus set of 12 marker taxa, including six bacterial and six fungal genera. Correlation analyses suggested that fungal markers exhibited broader associations with phenotypic traits than bacterial markers, and regression analyses indicated that fungal markers were statistically associated with variation in fruit size. Stem diameter showed associations with both climatic variables and microbial markers. Overall, phenotypic variation in R. roxburghii was associated with patterns in rhizosphere microbial communities and climatic context, highlighting complex relationships that warrant further investigation. This study contributes descriptive insights into plant-microbe and environment-phenotype associations and provides a foundation for future work aimed at elucidating underlying mechanisms.},
}
@article {pmid41988103,
year = {2025},
author = {Cheng, C and Ma, H and Zhong, Y and Uhlemann, AC and Feng, X and Hu, J},
title = {BIOMARKER DETECTION FOR DISEASE CLASSIFICATION IN LONGITUDINAL MICROBIOME DATA.},
journal = {The annals of applied statistics},
volume = {19},
number = {2},
pages = {943-966},
pmid = {41988103},
issn = {1932-6157},
support = {P30 CA013696/CA/NCI NIH HHS/United States ; R01 AI143886/AI/NIAID NIH HHS/United States ; },
abstract = {The microbiome has been found to have a close relationship with human health. Advancements in sequencing technologies have enabled in-depth studies of microbial communities and their associations with various diseases. When analyzing microbiome data, it is common to perform compositional scale normalization to ensure statistical validity. This requires special treatment to address the unique characteristics of microbiome data. Furthermore, biomedical studies often involve repeated measurements of microbial samples, which adds complexity to the data analysis. In this paper we focus on a liver transplant microbiome study. The main objective is to investigate the association between the colonization status of multidrug-resistant bacteria (MDRB) and the longitudinal microbial abundance profile. To accomplish this, we employ a regularized functional logistic regression model in our analysis. Specifically, we utilize the log-contrast model with a low-rank approximation to handle the compositional covariates and nonconvex penalties to select the important components in the covariate space. We propose an efficient estimation algorithm and establish the oracle property of the estimator. We name this new development as Functional Compositional data Quadratic Method (FCQM). We demonstrate the promise of the proposed method with extensive simulation studies and the liver transplant application.},
}
@article {pmid41988382,
year = {2026},
author = {Dong, H and Cao, H and Gong, Y and Zhao, Z and Wang, K and Zhang, X and Zhang, F},
title = {Chronic kidney disease as an active driver of digestive tract tumors: mechanistic insights and emerging management strategies.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1797181},
pmid = {41988382},
issn = {2296-634X},
abstract = {Digestive tract tumors (DTT), particularly gastric cancer (GC) and colorectal cancer (CRC), remain among the leading causes of cancer-related morbidity and mortality worldwide. Accumulating epidemiological evidence indicates that patients with chronic kidney disease (CKD) exhibit a significantly increased risk of developing gastrointestinal malignancies and experience worse clinical outcomes. However, the biological mechanisms underlying this association have not been comprehensively synthesized. In this review, we integrate clinical and experimental evidence to delineate how CKD functions as a systemic pro-tumorigenic condition rather than a passive comorbidity. We highlight three interrelated mechanistic axes linking CKD to DTT: (i) persistent systemic inflammation and oxidative stress, (ii) metabolic and endocrine dysregulation driven by uremic toxin accumulation, vitamin D deficiency, and mineral imbalance, and (iii) immune perturbations associated with dialysis modalities and post-transplant immunosuppression. These processes converge to disrupt gastrointestinal barrier integrity, reshape the gut microbiota, impair antitumor immune surveillance, and promote malignant transformation and tumor progression. Importantly, we discuss how CKD-specific interventions, including dialysis strategies, kidney transplantation, dietary management, and modulation of gut microbiota, may further modify gastrointestinal cancer risk. Finally, we propose CKD-oriented preventive and screening strategies for GC and CRC, emphasizing the need for risk stratification based on renal function, proteinuria, and metabolic profiles. By framing CKD as an active driver of gastrointestinal carcinogenesis, this review provides a novel integrative framework that synthesizes interconnected mechanistic pathways and explicitly links them to CKD-specific clinical management strategies, a translational perspective that informs early detection, prevention, and integrated care of DTT in patients with CKD.},
}
@article {pmid41988384,
year = {2026},
author = {Zhang, C and Tang, X and Chen, S and Akanyibah, FA and Mao, F},
title = {The role of extracellular vesicles in the transport and regulation of novel inflammatory mediators in IBD and its associated CRC.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1760517},
pmid = {41988384},
issn = {2296-634X},
abstract = {Inflammatory bowel disease (IBD), comprising ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammation of the gut characterized by an imbalance in the intestinal microbiome and ecology. IBD raises the risk of developing colorectal cancer (CRC). CRC is one of the most commonly diagnosed cancers in the world, with high incidence rates. Extracellular vesicles (EVs) play a crucial role in intercellular communication and are vital for maintaining intestinal homeostasis. Recent research highlights novel inflammatory mediators, such as specialized pro-resolving mediators (SPMs), damage-associated molecular patterns (DAMPs), alarmins, non-coding RNAs (ncRNAs), and metabolic intermediates, as crucial in the pathophysiology of IBD and CRC. These novel inflammatory mediators are transported by EVs, influencing the pathogenesis of IBD and associated CRC. Therefore, this article examines the role of novel inflammatory mediators transported by EVs in the pathogenesis of IBD and related CRC, as well as the interaction between EVs and the tumor microenvironment. We also review new research on EV use as a diagnostic indicator and on the potential of EVs, such as mesenchymal stem cell-derived EVs (MSC-EVs), as therapeutic delivery channels for cancer treatment targeting unique inflammatory mediators.},
}
@article {pmid41988471,
year = {2026},
author = {Gonzalez, AM and Townsend, JR and Sapp, PA and Edwards, C and Kirby, TO and Wright, J and Lamendella, R and Esposito, R},
title = {Effect of AG1[®] supplementation on nutritional adequacy and gut microbial composition in trained adults.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1783951},
pmid = {41988471},
issn = {2296-861X},
abstract = {BACKGROUND: Dietary supplements that combine vitamins, minerals, phytonutrients, prebiotics, and probiotics have gained popularity among health-oriented consumers seeking convenient ways to fill nutritional gaps and support gut health.<br><br>METHODS: This randomized, double-blind, placebo-controlled crossover study examined the effects of two weeks of the nutritional supplement (AG1[&#xae;]) on gut microbial composition, nutritional adequacy, and tolerability. Twenty resistance-trained men (n = 10; 26.4 &#xb1; 6.5 y) and women (n = 10; 26.9 &#xb1; 5.3 y) supplemented daily with either AG1[&#xae;] or placebo (PL) for 14 days. Following a 2-week washout, participants crossed over to the other condition. Participants provided stool samples for gut microbial composition analysis, completed the Digestion-associated Quality of Life Questionnaire (DQLQ), and completed a 24-h dietary intake assessment at the beginning and end of each 14-day supplementation period. Outcomes were analyzed using repeated-measures and multivariate statistical approaches for dietary intake, gut microbiota, metabolomics, and questionnaire data.<br><br>RESULTS: AG1[&#xae;] did not produce large, global shifts in microbial alpha or beta diversity, supplementation was associated with selective enrichment of key bacterial taxa commonly linked to gut health, including Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus, and Bifidobacterium animalis. AG1[&#xae;] supplementation significantly improved nutritional adequacy by increasing the total number of micronutrient Estimated Average Requirements (EARs) met compared to placebo (2.8; p = 0.0011), with no significant differences in digestive quality of life between groups (p = 0.777). Vitamins A, C, and E were the most common nutrient gaps filled by AG1 supplementation.<br><br>CONCLUSIONS: Two weeks of AG1[&#xae;] supplementation improved micronutrient adequacy in healthy resistance-trained adults by reducing nutrient gaps. Supplementation also selectively enriched key beneficial gut microbial taxa and putative microbial functional without inducing major disruptions to overall community structure. Importantly, AG1[&#xae;] was well tolerated and did not negatively impact digestion-associated quality of life.<br><br>CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier: NCT06521424.},
}
@article {pmid41988516,
year = {2026},
author = {Liang, Y and Chen, H and Ren, G and Jiang, G},
title = {Research progress on the role and therapeutic applications of traditional Chinese medicine in radiation enteropathy.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1747735},
pmid = {41988516},
issn = {1663-9812},
abstract = {Radiation enteropathy (RE) is a debilitating complication following radiotherapy, with currently limited treatment options. Multi-target intervention strategies such as Traditional Chinese Medicine (TCM) botanical formulas and acupuncture have been investigated as potential complementary approaches for its management. This review systematically synthesizes the evidence on TCM botanical formulas (e.g., Modified Baitouweng Decoction, Xihuang Pill, TJ-14) and acupuncture for the treatment of RE. Existing studies suggest multiple mechanisms of action, including anti-inflammatory and antioxidant effects, regulation of apoptosis and proliferation, restoration of intestinal barrier integrity, and modulation of gut microbiota. Clinical studies have reported improvements in symptoms and reductions in inflammatory markers, while preclinical models have demonstrated protective effects against radiation-induced intestinal injury. However, the current body of evidence is generally constrained by methodological limitations. Many clinical studies have small sample sizes and lack rigorous designs (e.g., absence of randomized controls), while mechanistic research often provides limited causal inference and relies on models with questionable clinical relevance, resulting in a significant translational gap. Based on this appraisal, we critically evaluate the limitations of existing research and propose future directions. These include: (i) employing CRISPR-based microbiome editing to investigate causal mechanisms; (ii) developing pharmacokinetic-pharmacodynamic (PK-PD) models for dose individualization; and (iii) utilizing innovative trial designs such as Bayesian adaptive trials to bridge the gap between empirical practice and evidence-based medicine. Rigorous further investigation is essential to define the role of these TCM interventions within the integrative treatment strategy for RE.},
}
@article {pmid41988525,
year = {2026},
author = {Kong, L and Wang, C},
title = {A machine learning model integrating gut microbiota biomarkers for predicting neurological recovery after cerebral hypoxia-ischemia: a single-center study augmented with public data.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1756017},
pmid = {41988525},
issn = {1663-9812},
abstract = {OBJECTIVE: To evaluate the predictive value of gut microbiota biomarkers for neurological recovery after cerebral hypoxia-ischemia and to develop a clinically oriented, validated machine learning (ML) for early outcome prediction.<br><br>METHODS: In this single-center cohort study, 772 patients (2022-2024) were stratified according to 1-year neurological outcomes into favorable (n = 538) and poor recovery (n = 234) groups, gut microbiota composition, microbial metabolites, systemic inflammatory and oxidative stress markers, and selected gene expression profiles were assessed using blood and fecal samples. Microbial profiling was assessed via 16S rRNA sequencing and whole-genome sequencing. LASSO regression, random forest (RF), and neural networks models were constructed and evaluated using internal validation strategies and augmented with publicly available datasets.<br><br>RESULTS: Patients with favorable neurological recovery exhibited significantly higher levels of short-chain fatty acids, increased superoxide dismutase activity, and upregulated neuroprotective gene expression, along with reduced pro-inflammatory cytokines and harmful metabolites (all P < 0.001). Microbiota analysis demonstrated enrichment of beneficial taxa (e.g., Bifidobacterium longum) and depletion of pro-inflammatory species (e.g., Clostridium difficile). Across ML approaches, IL-6 consistently emerged as a key predictive feature, with RF confirmed its prelative importance. The neural network model showed stable predictive performance across validation analyses, indicating robustness for high-dimensional biomarker integration.<br><br>CONCLUSION: Gut microbiota-associated biomarkers, when combined with systemic inflammatory indicators such as IL-6, enable robust early prediction of neurological recovery following cerebral hypoxia-ischemia. ML-based integration of multi-modal biomarkers may facilitate clinically applicable prognostic assessment, while also providing a foundation for future investigations into microbiota-targeted interventions.},
}
@article {pmid41988834,
year = {2026},
author = {Taléns-Visconti, R and Diez-Sales, O and Nácher, A},
title = {Cosmetic Interventions for Skin Microbiome Modulation: Current Strategies and Future Directions.},
journal = {Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)},
volume = {32},
number = {4},
pages = {e70352},
pmid = {41988834},
issn = {1600-0846},
mesh = {Humans ; *Microbiota/drug effects/physiology ; *Skin/microbiology/drug effects ; *Cosmetics/pharmacology ; Dysbiosis ; Probiotics ; Prebiotics ; Skin Microbiome ; },
abstract = {BACKGROUND: Human skin harbors a highly diverse and dynamic microbiome that maintains barrier function and homeostasis, while endogenous/exogenous factors and cosmetic products modulate microbial balance. Dysbiosis contributes to inflammatory diseases like atopic dermatitis and acne; however, evidence for microbiome-targeted cosmetics remains preliminary. This article critically examines the impact of cosmetic products on the skin microbiota, distinguishing between potentially harmful formulations and those specifically developed to preserve microbial balance, collectively termed "microbiome-friendly" cosmetics.<br><br>MATERIALS AND METHODS: This narrative review synthesizes clinical, microbiological, and mechanistic studies on the skin microbiome's composition, endogenous/exogenous determinants, dysbiosis in skin diseases, and the impact of conventional and microbiome&#x2011;targeted cosmetics. Databases were searched up to January 2026 for peer&#x2011;reviewed studies, with emphasis on human clinical trials and systematic analyses.<br><br>RESULTS: Most conventional cosmetics do not induce major dysbiosis in healthy skin when properly formulated. For advanced formulations, including ingredients such as probiotics, prebiotics, postbiotics, and paraprobiotics, early clinical and microbiological studies report promising benefits without compromising microbial diversity. However, evidence is limited by heterogeneous designs, small sample sizes, and the lack of standardized criteria for "microbiome&#x2011;friendly" claims.<br><br>CONCLUSIONS: The evidence indicates that informed cosmetic selection and use of skincare products support microbiome balance as a complementary skin health strategy as may be key for both preventative and therapeutic strategies in managing skin disorders, just as allowing a dynamic understanding of the skin microbiome to improve human health.},
}
@article {pmid41989100,
year = {2026},
author = {Yang, J and Du, H and Tao, F and Ashraf, MA and Gao, X and Huang, X and Zhu, K and Li, G and Zheng, J and Bonfante, P and Cardinale, F and Liu, J},
title = {Rhizosphere microbial shifts drive amygdalin detoxification and jasmonate-mediated alleviation of peach autotoxicity.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag095},
pmid = {41989100},
issn = {1751-7370},
abstract = {Plant-associated microbes play essential roles in maintaining plant health and modulating responses to environmental stresses. Autotoxicity from allelopathic compounds is a major constraint on perennial crop production, yet the potential for plants to recruit microbiota to counteract such toxicity remains understudied. Our research combined field sampling from a multi-replant peach system, multi-omics, pot, and hydroponic experiments to elucidate plant-microbe interactions that alleviate amygdalin-induced autotoxicity. Metabolomic analysis of peach orchard soils showed that amygdalin accumulated progressively in the rhizosphere with longer continuous cultivation. Exogenous amygdalin inhibited plant growth, with stronger suppression observed in sterilized soil, suggesting a protective role of soil microbes. Amygdalin application altered rhizobacterial community structure and enriched several taxa, including Burkholderia-Caballeronia-Paraburkholderia and Sinomonas. In vitro assays confirmed that amygdalin serves as a selective substrate for these enriched bacteria. We further found that three strains isolated from the amygdalin-stressed peach rhizosphere significantly alleviated autotoxic inhibition, and their co-inoculation showed the greatest enhancement of plant performance. Metabolomic and transcriptomic analyses revealed activation of plant jasmonic acid (JA) pathway. Its involvement was confirmed by the alleviation of amygdalin-induced stress upon exogenous JA application and by the attenuation of microbiota-mediated stress relief upon JA pathway inhibition. Our study reveals a critical mechanism by which host plants enrich specialized microbes that can alleviate autotoxicity by direct amygdalin degradation, activation of the JA pathway, and modulation of redox homeostasis in peach. These findings provide new insights into plant-microbe interactions in perennial systems and highlight the potential of microbiome-informed microbial interventions for mitigating replant disease.},
}
@article {pmid41989132,
year = {2026},
author = {Parhi, P and Banerjee, A and Thatoi, H},
title = {The role of gut microbiome in chemoresistance property development in colorectal cancer tissue and its novel therapeutic strategies.},
journal = {Journal of chemotherapy (Florence, Italy)},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/1120009X.2026.2653339},
pmid = {41989132},
issn = {1973-9478},
abstract = {Colorectal cancer remains the second contributor to cancer-related mortality worldwide. Despite various advances in chemotherapeutic approaches, chemoresistance still poses a significant risk, hampering the effectiveness of the treatment. Recent researches have explored the crucial role of dysbiotic gut microbiota in the progression of CRC. Specific dysbiosed gut microbiota plays a key role in enhancing chemoresistance in CRC patients through different mechanisms by metabolizing drugs, and modulating the immune system, creating a barrier between CRC tissue and chemotherapeutic drugs. Various microbial genes have been linked to chemoresistance that code for different enzymes, resulting in the degradation of chemotherapeutic drugs, thus reducing drug's efficiency and identifying these genes can provide insight into various resistance pathways. Therefore, identifying the microbial signature for predetection of chemoresistance in patient, prevention of colonizing chemoresistance inducing bacteria and interventions like modification of gut flora for enhancing the effectiveness of chemotherapeutics is essential to overcome these challenges.},
}
@article {pmid41989202,
year = {2026},
author = {Mankel, D and Maierhaba, Y and Momjian, C and Calabrese, F and Duhamel, S and Marlow, J},
title = {Dual-BONCAT reveals distinct subpopulations of anabolically active cells.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0239125},
doi = {10.1128/aem.02391-25},
pmid = {41989202},
issn = {1098-5336},
abstract = {Bio-orthogonal non-canonical amino acid tagging (BONCAT) has emerged as a prominent molecular technique that enables microbial ecologists to visualize and identify metabolically active cells in cultures and complex microbial communities. To date, researchers have used just one non-canonical amino acid (ncAA) in a given experiment; here, we validate a novel approach using two different ncAAs in a single experiment. This advancement facilitates the detection of differentially active subpopulations within the same experimental context, thereby reducing the uncertainty and variability associated with parallel treatments and providing precise spatial information about organisms that are active under distinct conditions or at different times. We show that both ncAAs can be taken up by E. coli cultures and by constituents of the Little Sippewissett Salt Marsh microbiome, resulting in fluorescence signals that are significantly higher than background and ncAA-free control experiments, as well as differential labeling patterns reflective of distinct subpopulations. As a proof of concept, we implemented this "dual-BONCAT" approach in salt marsh sediments, adding one ncAA during daytime hours and the other at night. Subpopulations of cells that were anabolically active during the day and/or night were distinguishable by both fluorescence microscopy and by fluorescence-activated cell sorting. Subsequent high-throughput 16S rRNA gene amplicon sequencing of active subpopulations revealed that Methylobacterium, potentially feeding on plant exudate carbon, was preferentially active during the day, while sulfur-cycling taxa dominated the night-active population. Dual-BONCAT offers an important advancement in multiplexing substrate analog probing techniques, providing a more realistic understanding of metabolic activity under distinct environmental conditions.IMPORTANCEMicrobial communities are complex and dynamic, with different groups of microbes active under distinct conditions. Bio-orthogonal non-canonical amino acid tagging (BONCAT) uses synthetic amino acids to tag newly made proteins, allowing researchers to see and identify the active subset of a community. While BONCAT studies to date have used a single synthetic amino acid to evaluate cell activity in a single experimental context, here, we introduce a new approach, "dual-BONCAT," using two synthetic amino acids to track differential responses to changing conditions. After validating the approach with E. coli, we deployed it in a salt marsh sediment community, finding that organisms potentially feeding on plant root sugars were more active during the day, while microbes likely metabolizing sulfur were more active at night. We believe dual-BONCAT will prove useful in many studies, as it illuminates microbial community responses to changing conditions, which has important implications for ecosystem dynamics.},
}
@article {pmid41989380,
year = {2026},
author = {Hontelez, S and Guthrie, M and Stobernack, T and van Baarlen, P and Rousseau, C and Boks, MP and Pereira, RR and Boekhorst, J and Kleerebezem, M},
title = {Microbiome signatures correlate with diet-mediated ADHD symptom reduction.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659400},
doi = {10.1080/19490976.2026.2659400},
pmid = {41989380},
issn = {1949-0984},
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology ; Child ; Male ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; *Diet ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8-10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut-brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.},
}
@article {pmid41989563,
year = {2026},
author = {Saini, V and Verma, A and Kumari, S and Chaudhary, S and Mishra, A and Kumar, A and Jha, HC},
title = {The gut microbiome axis: how Lactobacillus-fermented soymilk orchestrates health.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {41989563},
issn = {1432-072X},
support = {2103365//PMRF (IN)/ ; IITI/CRDT/2022-23/05//CRDT-IIT Indore/ ; ANRF/PAIR/2025/000018/PAIR-A(G)//Anusandhan National Research Foundation (IN)/ ; },
}
@article {pmid41989595,
year = {2026},
author = {Walker, MR and Schwarzfischer, M and Scharl, M},
title = {The cancer-microbiome axis: Mechanisms and emerging therapeutic strategies.},
journal = {Seminars in immunopathology},
volume = {48},
number = {1},
pages = {},
pmid = {41989595},
issn = {1863-2300},
}
@article {pmid41990128,
year = {2026},
author = {Giagnoni, L and Deb, S and Tondello, A and De Noni, M and Borella, M and Stevanato, P and Cecchinato, A and Squartini, A and Spanu, C},
title = {The legacy of raw milk storage temperature is associated with cheese microbiome composition, notwithstanding pasteurization and starter addition.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag046},
pmid = {41990128},
issn = {1574-6968},
abstract = {Using DNA metabarcoding, we assessed the relative impact of two variables: (a) raw milk storage temperature and (b) cheese maturation duration, on a semi-fresh cheese bacteriome composition under authentic factory-scale industrial conditions. The study is compared to a prior literature report run at a high-quality milk facility, whilst in the present case, milk from an average-quality farm, better reflecting typical local standards, was used. We tested three milk storage temperatures (4 °C, 7 °C, 9 °C) and sampled cheese at six maturation stages (0, 10, 25, 30, 45, and 60 days). Results showed that raw milk storage temperature was the variable most strongly associated with microbial community composition across the sampled stages, exceeding the variation associated with maturation time. Even the pasteurization step and the addition of a Streptococcus thermophilus starter culture did not erase the microbial 'memory' of initial milk conditions. Interestingly, the cheese bacterial community shaping associated with different milk tank temperatures was moreover compositionally uncoupled from the dominant taxonomical pattern of the starting milk. Additionally, the study provided insights into balancing milk quality and storage temperatures to prevent spoilage by psychrotrophic pseudomonads. Under the conditions tested here, the findings suggest that the 4°C storage benchmark may warrant re-evaluation.},
}
@article {pmid41990265,
year = {2026},
author = {Liang, CL and Chen, Y and Lu, C and Liu, H and Qin, F and Dai, S and Qiu, F and Chen, H and Lu, W and Bromberg, JS and Dai, Z},
title = {High Humidity Exacerbates Psoriasiform Skin Disease Relapse by Increasing Tissue-Resident Memory T Cells via Altering Skin Microbiota.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04061},
doi = {10.1002/advs.202504061},
pmid = {41990265},
issn = {2198-3844},
support = {82104867//National Natural Science Foundation of China/ ; 82004377//National Natural Science Foundation of China/ ; 2023B1212060063//Science and Technology Planning Project of Guangzhou/ ; 2025A03J1082//Science and Technology Planning Project of Guangzhou/ ; 2022A1515011704//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A1515010807//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A1515010295//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2026A1515012112//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
abstract = {Psoriasis recurrence remains a common and difficult medical problem, while environmental humidity appears to have an impact on psoriasis morbidity. However, it remains unknown whether and how high humidity impacts psoriasis relapse. Using unique mouse models of psoriasis relapse, we found that high humidity exposure exacerbated psoriasis recurrence by increasing skin-resident memory CD8[+] T (TRM) cells through a mechanism depending on its upregulation of IL-15Rα on keratinocytes. Keratinocyte-specific knockout of IL-15Rα or administrating soluble sIL-15Rα to block IL-15 abrogated these effects. Moreover, the effects of high humidity on psoriasis relapse, IL-15Rα expression and skin TRM cell formation were attributed to cutaneous Staphylococcus nepalensis since its recolonization or its specific metabolite, asymmetric dimethylarginine (ADMA), upregulated IL-15Rα expression on keratinocytes, increased skin CD8[+] TRM cells and worsened psoriasis relapse. However, treatment with mupirocin, an antibiotic, alleviated recurrent psoriasis. In vitro experiments showed that culture supernatant of Staphylococcus nepalensis upregulated IL-15Rα expression on keratinocytes, while IL-15Rα-expressing keratinocytes promoted formation of CD8[+] TRM phenotypes. Finally, high humidity also aggravated psoriatic skin lesions in humanized mice. Thus, our findings enhanced a new understanding of how climatic factors govern psoriasis recurrence and unveiled a role for IL-15Rα-expressing keratinocytes in skin CD8[+] TRM formation and psoriasis relapse.},
}
@article {pmid41990601,
year = {2026},
author = {Kholif, AE and Olafadehan, OA and Anele, UY},
title = {Tannins in ruminant feeding: effects of tannin type and dosage on rumen fermentation, production performance, health, and sustainability.},
journal = {Research in veterinary science},
volume = {206},
number = {},
pages = {106181},
doi = {10.1016/j.rvsc.2026.106181},
pmid = {41990601},
issn = {1532-2661},
abstract = {Tannins are plant-derived polyphenolic compounds of variable molecular weights that have attracted considerable attention as natural feed additives in ruminant nutrition. Their ability to modulate rumen microbial ecology, improve nutrient utilization, mitigate enteric methane (CH4) emissions, and promote animal health has positioned them as potential tools for improved, sustainable ruminant production systems. This review critically evaluates and synthesizes published evidence on the effects of tannins on rumen fermentation dynamics, nutrient digestibility, hematological and biochemical parameters, production performance, and overall health status of ruminants. A systematic literature search was conducted using Scopus, Web of Science, ScienceDirect, Google Scholar, and PubMed, targeting peer-reviewed English-language studies published between January 2000 and September 2025. Search terms were organized using Boolean operators across tannin chemistry and type, ruminant species, and production-, environmental-, or health-related outcomes. Studies were included if they reported in vitro or in vivo responses of ruminants to tannins, while non-ruminant studies, conference abstracts, and non-English publications were excluded to ensure comprehensive comparability. Collectively, available evidence indicates that hydrolyzable tannins generally exert more consistent positive effects on feed intake, nutrient digestibility, and CH4 mitigation than condensed tannins, although responses remain highly dependent on tannin source, chemical structure, diet composition, dietary inclusion level, and the extent of animal adaptation. Low to moderate inclusion levels (generally <3% of dietary dry matter [DM]) were associated with neutral to beneficial effects on feed intake, rumen fermentation characteristics, nitrogen utilization, and animal performance. In contrast, higher rates (>5% of dietary DM) frequently impair digestibility, depress feed intake, compromise nitrogen efficiency, and reduce productive performance, indicating dose-dependent responses. Besides nutritional modulation, other ancillary benefits of tannins include reduced internal parasite burden and decreased incidence of ruminal bloat. Positive changes in hematological and biochemical indices further suggest potential improvements in physiological response and health status at moderate levels, although high rates may induce adverse metabolic alterations. In summary, tannins represent a promising nutritional strategy for improving the sustainability of ruminant production systems; however, their successful application depends on careful selection of tannin type, strategic dosage optimization, and feeding strategy. Future research should prioritize defining optimal inclusion thresholds, elucidating rumen microbiome adaptation mechanisms at the molecular level, and assessing long-term production and health outcomes under practical production conditions.},
}
@article {pmid41990662,
year = {2026},
author = {Wen, X and Fu, Y and Xiang, L and Liao, M and Harindintwali, JD and Wang, Y and He, C and Gao, Z and Jiang, J and Jiang, X and Wang, F},
title = {Rhizosphere reprogramming by integrated bio‑organic fertilizer and seed coating mitigates atrazine phytotoxicity in soybeans.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142058},
doi = {10.1016/j.jhazmat.2026.142058},
pmid = {41990662},
issn = {1873-3336},
abstract = {The widespread use of atrazine in maize fields poses a persistent threat to subsequent soybean production due to its soil persistence and phytotoxicity. Here, we present an integrated field strategy by synergistically combining a vermicompost-based bio-organic fertilizer with a targeted seed coating, both delivering the efficient atrazine‑degrading Paenarthrobacter sp. AT5. This synergy thereby provides a dual guarantee of precise rhizosphere colonization and a conducive soil environment for atrazine degradation. The combined treatment significantly reduced atrazine concentrations in roots, stems, and leaves by 38.8%, 23.2%, and 35.5%, respectively, while elevating hydroxyatrazine to 8.2-31.0 times the levels in the atrazine-only treatment. Soil atrazine residues decreased while hydroxyatrazine accumulated, particularly in the rhizosphere. Microbiome analyses revealed that the combined treatment enriched key bacterial genera, including Flavobacterium and Bacillus, potentially harboring atrazine-degrading capabilities, and increased the abundance of the functional gene trzN. In parallel, it restored deterministic community assembly processes and re-established cooperative interactions within the rhizosphere bacterial network. Together, these findings elucidate the mechanistic basis by which synergistic inoculation mitigates atrazine phytotoxicity under field conditions and highlight a scalable, microbiome-based strategy for sustaining soybean productivity in herbicide-impacted agroecosystems.},
}
@article {pmid41990710,
year = {2026},
author = {Moeckli, B and Rocha, M and Wassmer, CH and El Hajji, S and Collet, TH and Lacotte, S and Toso, C},
title = {Maternal obesity and the intergenerational risk of cancer: Epidemiologic evidence and mechanistic insights.},
journal = {Cancer epidemiology},
volume = {102},
number = {},
pages = {103079},
doi = {10.1016/j.canep.2026.103079},
pmid = {41990710},
issn = {1877-783X},
abstract = {Over recent decades, the prevalence of obesity has markedly surged. While excess maternal weight is a well-established risk factor for adverse pregnancy outcomes, growing evidence suggests that maternal obesity may also increase the long-term risk of cancer in offspring. This comprehensive review synthesizes epidemiological and experimental data linking maternal obesity to heightened cancer susceptibility in the next generation. Observational studies demonstrate increased risks of childhood leukemia and colorectal cancer in offspring of obese mothers, whereas preclinical models support associations with breast, liver, colon, and pancreatic cancers. Mechanistically, maternal obesity induces epigenetic reprogramming, immune dysregulation, and vertical transmission of a dysbiotic gut microbiota, which may lead to persistent alterations in metabolic and inflammatory signaling pathways in offspring, thereby promoting a pro-tumorigenic environment and potentially increasing cancer susceptibility. Given the global burden of obesity, this intergenerational risk has critical public health implications. Lifestyle modifications, weight-loss interventions, and targeted approaches such as probiotic supplementation may offer promising strategies to mitigate cancer risk in offspring, but require scientific confirmation in further studies. Future research should prioritize mechanistic dissection of exposure windows, identification of predictive biomarkers, and the development of effective, scalable preventive therapies.},
}
@article {pmid41990750,
year = {2026},
author = {Gonzalez Pastor, B and Shkoporov, AN and Hill, C},
title = {Not just passengers: Phages as agents of genetic exchange in fecal microbiota transplantation.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.017},
pmid = {41990750},
issn = {1934-6069},
abstract = {Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection and is increasingly being explored for other microbiota-associated diseases. However, general research has largely focused on bacterial engraftment, overlooking the contribution of the gut virome. In this perspective, we highlight phage-mediated horizontal gene transfer (HGT) as a potentially influential process occurring following FMT. Donor-derived phages may potentially influence community structure, engraft in resident bacteria, and modulate microbial functions or host physiology. In addition, temperate phages are well-equipped to mobilize bacterial genes, such as metabolic functions, stress-response traits, and antibiotic resistance determinants, raising the possibility that gene flow could well contribute to FMT outcomes. We propose a conceptual model in which phages act as bidirectional mediators of adaptation, not only accompanying bacterial communities but also influencing gut ecosystems in subtle, yet potentially consequential, ways.},
}
@article {pmid41990911,
year = {2026},
author = {Espín-Sánchez, D and Russo, L and Diambra, L and Mannino, MC and Scorsetti, AC and Huarte-Bonnet, C and Pedrini, N},
title = {Host transcriptional and microbiome metatranscriptomic changes in soybean plants carrying the insect-pathogenic fungus Beauveria bassiana as an endophyte.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108629},
doi = {10.1016/j.jip.2026.108629},
pmid = {41990911},
issn = {1096-0805},
abstract = {Entomopathogenic fungi, such as Beauveria bassiana, have been naturally isolated from various plant species and have also been introduced as endophytes to enhance plant health and resilience. These fungal endophytes are often associated with improved plant defense against insect pest herbivory. This study aimed to assess the endophytic capacity of B. bassiana ARSEF 2860 in soybean plants and to investigate the associated changes in gene expression and leaf microbiome activity one-week post-inoculation. The results showed that B. bassiana successfully colonized the leaves, stems, and roots of soybean plants and induced gene expression changes in both the host leaves and their associated microbiome. In the soybean leaves, the fungal endophyte down-regulated genes related to responses to far-red light and the abscisic acid pathway, while up-regulating genes involved in photosynthesis, lipid and carbohydrate biosynthesis, and stress response. Additionally, plant inoculation with B. bassiana was associated with a reduction in total microbiome transcript abundance. This shift was characterized by a relative decrease in reads mapping to potentially pathogenic bacteria, alongside a relative increase in transcripts from bacteria commonly associated with beneficial functions. Total fungal reads were also lower in B. bassiana-colonized plants compared to control samples, with plant-pathogenic fungal reads being reduced. These findings highlight the role of entomopathogenic fungal endophytes to promote plant growth by potentially enhancing photosynthesis and strengthening plant defense mechanisms. The shift in the microbial activity highlights the capacity of endophytes to modulate plant-associated microbiota towards communities that may enhance health and resilience.},
}
@article {pmid41991203,
year = {2026},
author = {Sefer, AP and Aydiner, EK},
title = {From bench to bedside: advances in standardized oral immunotherapy and early predictors of persistent cow's milk allergy in children.},
journal = {Allergologia et immunopathologia},
volume = {54},
number = {S Pt 1},
pages = {18-27},
pmid = {41991203},
issn = {1578-1267},
support = {//None./ ; },
mesh = {Humans ; *Milk Hypersensitivity/therapy/immunology/diagnosis ; *Desensitization, Immunologic/methods/standards ; Child ; Animals ; *Allergens/immunology/administration &amp; dosage ; Administration, Oral ; Immunoglobulin E/immunology ; Cattle ; },
abstract = {Immunoglobulin E (IgE)-mediated cow's milk allergy (CMA) remains the most prevalent pediatric food allergy and a major cause of early-life anaphylaxis, with a substantial proportion of children developing persistent disease despite traditional avoidance-based management. Oral immunotherapy (OIT) has emerged as a proactive strategy that modulates the allergic immune response through controlled and sustained allergen exposure, shifting immunity from T-helper (Th) 2-dominant pathways toward a more regulatory and tolerogenic profile. Current evidence from randomized trials and real-world cohorts demonstrates that cow's milk oral immunotherapy (CM-OIT) achieves desensitization in most treated children, reduces accidental reaction risk, and improves quality of life, although sustained unresponsiveness remains variable and protocol-dependent. Marked heterogeneity exists across protocols regarding dosing, antigen formulation, maintenance targets, and escalation speed, reflecting differing therapeutic philosophies rather than standardized practice. Safety concerns, including dose-related reactions and rare cases of eosinophilic esophagitis, underscore the need for careful patient selection, optimization of comorbid atopic diseases, and shared decision-making. Advances in precision immunology, including component-resolved diagnostics, epitope mapping, basophil activation testing, and emerging transcriptomic and microbiome signatures, now enable the earlier identification of children at high risk of persistent CMA who may benefit most from OIT, while low-risk phenotypes can be safely observed. Adjunctive biologic therapy, particularly anti-IgE agents, has improved tolerability and expanded eligibility in high-risk patients. This review synthesizes current evidence on efficacy, safety, biomarkers, protocols, and adjunctive strategies, emphasizing a personalized, risk-adapted approach to CM-OIT and outlining future directions toward standardized formulations, biomarker-guided stratification, and integrated biologic-assisted immunomodulation.},
}
@article {pmid41991444,
year = {2026},
author = {Simpson, RC and Cutler, HB and James, DE and Masson, SWC},
title = {The gut microbiome as an effector of metabolic disease gene variants.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2026.03.011},
pmid = {41991444},
issn = {0168-9525},
abstract = {Here, we discuss emerging studies that have identified overlap in the genetic drivers of the gut microbiome and metabolic disease, and we evaluate the possibility that some genes affecting host metabolic function do so by first manipulating the microbiome.},
}
@article {pmid41991448,
year = {2026},
author = {Diab, E and Thome, NU and Elsayed, SS and Raaijmakers, JM and van Wezel, GP},
title = {Chemical dialogues at the crossroads of host-bacteria interactions.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.013},
pmid = {41991448},
issn = {1878-4380},
abstract = {Microbiomes are now recognised as the second genome of eukaryotes, providing diverse life-support functions for their hosts. The impact of microbiome members on the growth and health of their hosts is determined by chemical cues from the host that modulate microbial physiology, virulence, and the biosynthesis of specialised metabolites. In this review, we provide a cross-kingdom comparison of the role of human and plant molecules in regulating bacterial gene expression. We highlight specific feedback loops and discuss common mechanisms of bidirectional cueing in human- and plant-associated bacteria. Despite the different taxonomies of human- and plant-associated bacteria, we find striking functional similarities in the chemical dialogues at the crossroads of host-bacteria interactions.},
}
@article {pmid41991462,
year = {2026},
author = {Zang, Y and Guo, Z and Ledesma-Amaro, R and Xin, Y and Wu, Y and Gu, Z and Zhang, L},
title = {Engineering Bacillus subtilis as a sustainable platform for the production of functional bile acids.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2026.03.021},
pmid = {41991462},
issn = {1879-3096},
abstract = {Bile acids and their derivatives are key regulators of host metabolism, immunity, and microbiome interactions, with growing therapeutic potential. Conventional production methods of bile acids relying on animal extraction or chemical synthesis are inefficient, costly, and environmentally unfriendly. Microbial synthesis offers a sustainable alternative but is limited by the absence of genetic tools for native anaerobic producers. Here, we reconstructed the bile acid 7α-dehydroxylation pathway in Bacillus subtilis, a safe and tractable host. We characterized the key Bai enzymes and performed comprehensive analyses of the bile acids generated through in vitro assays and whole-cell catalysis. Multiple intermediates and end products, including cholyl-CoA, 3-oxo-cholic acid, 3-oxo-4,5-6,7-didehydro-deoxycholic acid, 3-oxo-4,5-dehydro-deoxycholic acid, 3-oxo-deoxycholic acid, and deoxycholic acid, were identified. This work establishes a functional heterologous platform for bile acid biosynthesis, enabling sustainable production and future applications in therapeutics and microbiome engineering.},
}
@article {pmid41991481,
year = {2026},
author = {Pyrzanowska, KI and Smith, EN and Ramalingam, C and Greig, M and Gandhi, RA and Heyes, S and Sanger, D and Smith, T and Partridge, DG and Stafford, GP},
title = {A Survey of the Microbiome, Culturome and ARG Profile of a Cohort of Chronic Diabetic Foot Lesions.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {134},
number = {4},
pages = {e70203},
doi = {10.1111/apm.70203},
pmid = {41991481},
issn = {1600-0463},
support = {BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NIHR203321//NIHR Sheffield Biomedical Research Centre/ ; },
mesh = {*Diabetic Foot/microbiology ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Aged ; Female ; *Bacteria/isolation &amp; purification/genetics/classification/drug effects ; Anti-Bacterial Agents/pharmacology ; Cohort Studies ; Drug Resistance, Bacterial ; Adult ; },
abstract = {This study aimed to analyse the microbiome of chronic infected diabetic foot ulcers (DFUs) using parallel methods: traditional culture (the culturome), 16S rRNA gene sequencing (the microbiome) as well as the Antibiotic Resistance Gene (ARG) profile of isolated strains. Swab samples were collected in parallel from affected ulcers. The microbiome sequencing results identified that all patients had a polymicrobial flora with the five most frequent genus level OTUs as Escherichia, Staphylococcus, Streptococcus, Pseudomonas and the anaerobe Anaerococcus. Microbiological culture from the same swabs identified multiple species in all but two patient samples and revealed the most common isolates as CoNS Staphylococcus (17%), Enterococcus faecalis (14.3%), Corynebacterium spp. (10.7%), Anaerococcus spp. (7%), Staphylococcus aureus (8%) and Pseudomonas aeruginosa (6%). Enteric pathogens such as Klebsiella spp. were also frequently isolated. Attempts to revive anaerobes were largely unsuccessful, identifying a limitation in clinical microbiology storage protocols. Genome sequencing of 55 isolates revealed a high number of ARGs relating to β-lactams and tetracyclines, indicating multi-drug-resistant organisms (MDROs). This was confirmed by phenotypic antimicrobial susceptibility data that included several highly resistant Gram-negative bacteria. Overall, our data add to the picture of DFU microbiome as complex and displaying high levels of anti-microbial resistance (AMR).},
}
@article {pmid41991624,
year = {2026},
author = {Garg, PM and Malhotra, A},
title = {Emerging role of non-coding RNAs as biomarkers and therapeutic targets in preterm infants with necrotizing enterocolitis.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41991624},
issn = {1530-0447},
abstract = {Necrotizing enterocolitis (NEC) is a leading cause of morbidity and mortality in preterm infants, marked by intestinal necrosis, inflammation, hemorrhage, and impaired repair. Despite advances in neonatal care, early diagnostics and targeted therapies remain limited. Emerging evidence shows that non-coding RNAs (ncRNAs), including microRNAs, long ncRNAs, and tRNA-derived fragments, regulate key inflammatory, cell-death, angiogenic, and immune pathways in NEC. Distinct ncRNA signatures correlate with histopathology, and plasma-derived exosomal ncRNAs show promise as early biomarkers. Human milk exosomal microRNAs exhibit protective effects, while ncRNA-microbiome interactions may influence disease susceptibility. Larger studies using high-throughput sequencing are needed to advance biomarker-driven precision care.},
}
@article {pmid41991647,
year = {2026},
author = {Liu, CC and Grencewicz, D and Chakravarthy, K and Li, L and Liepold, R and Wolf, M and Marcho, LM and Sangwan, N and Tzeng, A and Hoyd, R and Jhawar, SR and Grobmyer, SR and Al-Hilli, Z and Sciallis, AP and Spakowicz, D and Ni, Y and Eng, C},
title = {Breast tumor microbiome regulates anti-tumor immunity and T cell-associated metabolites.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48719-5},
pmid = {41991647},
issn = {2045-2322},
support = {K01AG070310/AG/NIA NIH HHS/United States ; Innovator Award (1046611)//American Lung Association/ ; Research Scholar Award (RSG-23-1023205)//American Cancer Society/ ; P30CA016058//National Institutes of Health, United States/ ; 8UL1TR000090-05/TR/NCATS NIH HHS/United States ; GRAYFDN1908CE//Gray Foundation/ ; },
}
@article {pmid41991788,
year = {2026},
author = {Imran, H and Nouha, F and Wael, T and Haroun, BA and Wissal, M and Thouraya, BH and Darine, T},
title = {Mesorhizobium inoculation and Water-nitrogen regimes enhance Potato-chickpea intercropping performance and Rhizosphere microbiome diversity.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41991788},
issn = {1573-0972},
}
@article {pmid41991820,
year = {2026},
author = {Akuaka, GO and Haris, H and Zarkasi, KZ and Furusawa, G and Lau, NS and Madukpe, VN},
title = {Quantifying the contribution of the rare biosphere and functional potential to the compacted clay baseliner of sanitary landfill.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41991820},
issn = {1573-0972},
}
@article {pmid41991911,
year = {2026},
author = {Liu, Y and Huang, P and Zhang, C and Dong, Q and Wang, X and Tian, F and Zhao, J and Sun, Z and Chen, L and Chen, W and Zhai, Q},
title = {A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71929-4},
pmid = {41991911},
issn = {2041-1723},
support = {32425044//China National Funds for Distinguished Young Scientists/ ; 2022YFD2100703//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
abstract = {Cheese has been consumed globally over millennia and serves as a natural reservoir of diverse microorganisms. Chinese traditional cheeses rely on natural fermentation and have unique physiochemical and microbial characteristics compared to European cheeses. However, there is a major knowledge gap in the understanding of Chinese cheese microbiome. Here, we present a curated Cheese microbiome catalog (cCMC) consisting of 3327 high-quality metagenome-assembled genomes, recovered from metagenomic sequencing of 235 Chinese cheese samples covering all traditional artisanal cheese-producing regions in China, together with 198 publicly available non-Chinese cheese metagenomic datasets. This catalog represents 395 nonredundant species spanning 50 families, including 85 putative novel species. We identified six lactic acid bacteria species enriched in Chinese cheeses, and confirmed that the unique presence of Acetobacteraceae contributes to improving the nutritional quality of Chinese cheese. A total of 8851 biosynthetic gene clusters were detected from cCMC, with over 57% classified as novel. We demonstrated that SNP-level variations among different Lactobacillus helveticus strains are associated with differences in β-galactosidase thermostability. Using the cCMC database, we developed a synthetic microbial community as the starter culture for Qula, a yak milk-based Chinese cheese produced by the Tibetans. Overall, the cCMC provides a comprehensive resource of cheese to enable future attempts on large-scale industrial production of naturally fermented cheeses with distinctive ethnic features.},
}
@article {pmid41992000,
year = {2026},
author = {Schneider, SM and Fan, C and Wang, Y and Jenq, RR and Watowich, SS},
title = {Microbiota and immune-related adverse events in cancer immunotherapy.},
journal = {Nature reviews. Cancer},
volume = {},
number = {},
pages = {},
pmid = {41992000},
issn = {1474-1768},
abstract = {In response to treatment with immune checkpoint inhibitors (ICIs), patients with cancer can develop immune-related adverse events (irAEs), which are off-target toxicities affecting non-tumour tissues. Development of an irAE can require cessation of ICI treatment and cause additional morbidities, unrelated to cancer. Although the mechanisms that drive irAEs remain largely unknown, thus limiting treatment strategies, emerging evidence implicates tissue microbiomes, particularly in the gastrointestinal tract, lung and skin, as potential mediators. Here we review evidence that supports roles for the microbiome in irAEs. We focus on ICI colitis, a common irAE that has strong association with the gut microbiome. We examine clinical and preclinical studies that shed light on the immune and microbial drivers of ICI colitis and discuss current experimental treatments. By summarizing recent findings, we aim to encourage research into therapies that reduce irAE risk and severity while preserving anti-tumour efficacy of ICI treatment.},
}
@article {pmid41992021,
year = {2026},
author = {Chioccioli, S and Meriggi, N and Monroy, MM and Renzi, S and Cerasuolo, B and Caderni, G and De Filippo, C},
title = {Combination of a pesco vegetarian diet with non-steroidal anti-inflammatory drugs reduces colorectal cancer risk and modulates gut microbiota in PIRC rats.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48074-5},
pmid = {41992021},
issn = {2045-2322},
abstract = {Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide, with genetic predispositions such as Familial Adenomatous Polyposis (FAP) contributing significantly to early-onset disease. This study investigated the synergic chemopreventive potential of two non-steroidal anti-inflammatory drugs (NSAIDs), acetylsalicylic acid (ASA) and sulindac (SU), in combination with a pesco-vegetarian diet (PVD), using Apc-mutated PIRC rats, a well-established model of CRC. Animals were treated over three months with two doses of ASA (800 and 1600 ppm) or a single low dose of SU (80 ppm), and tumour burden and gut microbiota composition were assessed. Results confirmed the robust protective effect of the PVD diet in reducing the intestinal tumorigenesis, particularly in the colon, independent of pharmacological treatment. ASA treatment, especially at the higher dose, significantly reduced tumour incidence in both dietary groups, with additive effects seen in combination with PVD, while SU did not show a significant protective effect. Microbiota analysis revealed distinct shifts in bacterial composition associated with both dietary and pharmacological interventions. Notably, taxa such as Roseburia and Colidextribacter, previously linked to intestinal homeostasis and anti-inflammatory activity, were modulated by ASA and diet, suggesting a microbiome-mediated chemoprevention although mechanistic effect still need to be understood. These findings underscore the independent and complementary roles of diet and pharmacological interventions in CRC prevention and highlight the gut microbiota as a promising target for future personalised preventive strategies.},
}
@article {pmid41992275,
year = {2026},
author = {Won, S and Hong, J and Kim, H and Lee, J and Ko, YC and Yang, B and Kim, SH and Koh, SS and Park, J and Guak, GO and Lee, GI and Choi, Y and Lee, SH and Kang, G and Cho, S and Kim, H},
title = {Mycobacterium tuberculosis infection disrupts gut and respiratory microbial communities and networks with incomplete restoration after two months of treatment.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00834-4},
pmid = {41992275},
issn = {1757-4749},
support = {2022-ER2004-01//Korea National Institute of Health/ ; },
}
@article {pmid41992364,
year = {2026},
author = {Cummins, C and Sutton, W and McLeod, T and Dallas, JW and Ghotbi, M and Vargas-Gastélum, L and Alexander, NR and Rurik, AJ and McGinnity, D and Reinsch, SD and Sandonato, P and Arbour, J and Freake, M and Ashley, A and Ternes, W and Culp, E and Spatafora, J and McPhail, K and Stajich, JE and Hardman, R and Walker, DM},
title = {Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis).},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41992364},
issn = {2524-4671},
support = {EF-2125067//National Science Foundation/ ; EF-2125066//National Science Foundation/ ; EF-2125065//National Science Foundation/ ; },
}
@article {pmid41794765,
year = {2026},
author = {Wu, G and Zhang, J and Yan, S and Liu, N and Chen, W and Wu, F and Wang, Z and Zhang, J and Yang, Y and Deng, Y and Qiu, X and Liu, J and Shi, L and Cui, X and Wan, R and Li, X and Han, Y and Yang, G},
title = {Circadian rhythms and microbiota: molecular crosstalk and its implications for health and disease.},
journal = {Biology direct},
volume = {21},
number = {1},
pages = {},
pmid = {41794765},
issn = {1745-6150},
abstract = {UNLABELLED: Circadian rhythms, evolutionarily conserved 24-hour oscillations, exert precise regulatory control over microbial communities across host niches including the gastrointestinal tract, oral cavity, urinary bladder, and skin. This bidirectional interplay is critical to host physiology: host circadian clocks shape the composition and functional rhythms of resident microbiota, while microbiota-derived signals reciprocally modulate circadian entrainment and tissue-specific rhythmicity. Circadian disruption from shift work, irregular feeding, light pollution, or sleep deprivation trigger microbial dysbiosis and circadian misalignment, contributing to metabolic diseases, gastrointestinal disorders, neuropsychiatric conditions, cardiovascular diseases, and dermatological or reproductive disorders. Mechanistically, this crosstalk is mediated by rhythmic hormonal secretion, microbial metabolites, epigenetic regulation, and immune signaling. Therapeutic strategies such as time-restricted feeding, probiotics, melatonin, and polyphenol-rich diets show promise in restoring temporal homeostasis. This review synthesizes current evidence on circadian-microbiota interplay, elucidates its roles in physiology and disease, and highlights translational opportunities for chrono-microbiome-based interventions to optimize host health.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13062-026-00748-w.},
}
@article {pmid41929220,
year = {2026},
author = {Pedreros, MB and Irigoyen, MF and Simoes-Barbosa, A and Riestra, AM and de Miguel, N},
title = {Chemotaxis and selective interactions of Trichomonas vaginalis with the vaginal bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41929220},
issn = {2692-8205},
abstract = {Trichomonas vaginalis is an extracellular parasite that inhabits the human genital tract, yet little is known about how it senses and responds to the complex vaginal microbial ecosystem. Here, we show that T. vaginalis exhibits chemotactic behavior on semisolid surfaces, forming multicellular assemblies that coordinate collective migration. Parasite colonies display both positive and negative chemotactic responses, indicating the ability to detect and react to diffusible signals. Different parasite strains display marked mutual avoidance between neighboring colonies, highlighting specific recognition mechanisms. Furthermore, we show that T. vaginalis is strongly attracted to acidic environments, revealing a niche-adapted pH taxis. Given that vaginal bacteria critically shape local pH, we examined parasite responses to representative members of the vaginal microbiota. T. vaginalis exhibited preferential chemotactic migration toward Lactobacillus gasseri, a hallmark species of eubiotic community state types (CSTs), over Gardnerella vaginalis, which is associated with dysbiotic CST-IV communities, while showing no detectable attraction to Escherichia coli. This selective migration correlated with a robust chemotactic response to lactic acid, a major metabolite produced by lactobacilli. Additionally, when the parasite is co-cultured with the equal number of L. gasseri and G. vaginalis, T. vaginalis exhibits a clear preferential binding to L. gasseri, as demonstrated by flow cytometry and fluorescent microscopy. We show that co-culture of T. vaginalis with either L. gasseri or G. vaginalis results in enhanced parasite growth only in the presence of L. gasseri. Collectively, these findings reveal pH taxis; bacteria-directed migration and preferential association with Lactobacillus as previously underappreciated behavioral traits of T. vaginalis. Such behaviors may destabilize protective microbial communities and drive the transition toward a CST-IV-type dysbiotic state which is frequently associated with trichomoniasis.},
}
@article {pmid41979573,
year = {2026},
author = {Serrage, HJ and Farrar, MD and McBain, AJ and Pennock, J and O'Neill, C},
title = {Skin Staphylococcus species differentially modulate keratinocyte cytokine secretion in response to UVB.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0154925},
doi = {10.1128/aem.01549-25},
pmid = {41979573},
issn = {1098-5336},
abstract = {Skin acts as the body's first line of defense against environmental insults including ultraviolet radiation (UVR) from sunlight and engages in a dynamic dialog with the resident skin microbiota, increasingly recognized for its role in shaping and educating the immune responses of the skin in both health and disease. However, how or indeed if the resident skin microbiota mediates inflammatory responses to sunlight remains unclear. To address this, we investigated the effects of five abundant members of the skin microbiota on cytokine secretion in human primary keratinocytes exposed to a single dose of UVB. Co-culture of primary keratinocytes with a defined five-species skin commensal community resulted in a broad increase in the secretion of innate immune mediators including interleukin-6 (IL-6), independent of UVB exposure. In the absence of UVB, Staphylococcus epidermidis was the dominant species, followed by Staphylococcus hominis within the five-species community. UVB induced a marked shift in community composition, characterized by increased proliferation of S. hominis and reduced S. epidermidis abundance, as confirmed by species-specific growth curve analyses. Assessment of species-specific effects using mono-associated host cells revealed S. epidermidis as the predominant contributor to the enhancement of immune mediator secretion. Without the presence of additional community members, UVB amplified S. epidermidis-induced cytokine secretion. However, co-culture of S. epidermidis with S. hominis attenuated the heightened inflammatory response to UVB typically associated with S. epidermidis, likely due to the reduced abundance of S. epidermidis following UVB exposure. These findings suggest that the resident skin microbiota may contribute to our inflammatory response to sunlight.IMPORTANCEThis study reveals that the skin microbiome may play a role in shaping inflammatory responses to UVB exposure. It provides evidence of organisms capable of both amplifying and mitigating inflammatory responses to UVB, highlighting the importance of microbial composition in photoprotection. These findings suggest individual responses to sunlight may be influenced not only by skin type but also by specific microbes present on the skin.},
}
@article {pmid41979582,
year = {2026},
author = {Smółka, L and Strugała, M and Kursa, K and Pomianowski, B and Blady, K and Bratek, K},
title = {The impact of the gut microbiome on the development of atherosclerosis and peripheral arterial disease: A narrative review.},
journal = {Przeglad epidemiologiczny},
volume = {79},
number = {4},
pages = {580-594},
doi = {10.32394/pe/214773},
pmid = {41979582},
issn = {0033-2100},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology ; *Peripheral Arterial Disease/microbiology ; *Dysbiosis ; },
abstract = {Atherosclerosis is a chronic, progressive process affecting medium and large arteries, while peripheral artery disease (PAD) represents one of its clinical manifestations in the limb arteries. Although classical risk factors such as poor diet, hypertension, diabetes, and smoking are well established, increasing evidence indicates that the gut microbiome is an important and modifiable contributor to vascular pathophysiology. This paper reviews current knowledge on the role of the gut microbiome in the initiation and progression of atherosclerosis and PAD, with emphasis on bacterial metabolites, proinflammatory mechanisms, and potential therapeutic interventions. Gut dysbiosis-an imbalance in the intestinal microbial community-has been associated with increased cardiovascular risk. Patients with vascular diseases show higher levels of pro-atherogenic taxa, including Enterobacteriaceae, Streptococcus spp., Lachnoclostridium, and Family XI, alongside a reduction of beneficial short-chain fatty acid (SCFA)-producing bacteria such as Roseburia, Faecalibacterium, Coprococcus2, and Ruminococcaceae. Two key microbial metabolites influence vascular health. Trimethylamine N-oxide (TMAO), formed from choline and L-carnitine via microbial and hepatic metabolism, promotes endothelial dysfunction, inflammation, and platelet reactivity, thereby accelerating atherosclerosis. Conversely, SCFAs-acetate, propionate, and butyrate-exert anti-inflammatory effects, improve insulin sensitivity, and enhance nitric oxide synthesis, resulting in vascular protection. Therapeutic strategies targeting the gut microbiota show promising potential. These include the use of probiotics and prebiotics (notably Lactobacillus rhamnosus GG), adherence to a Mediterranean diet, and fecal microbiota transplantation (FMT), all aimed at restoring eubiosis and a favorable intestinal metabolic profile. In summary, the gut microbiome appears to be a key modulator of the pathogenesis of atherosclerosis and PAD. Targeted modulation of gut microbial composition and activity may emerge as an innovative and effective strategy for the prevention and treatment of cardiovascular diseases.},
}
@article {pmid41979594,
year = {2026},
author = {Ager, EO and Nickodem, CA and Brown, J and Jendza, J and Neeno-Eckwall, E and Schuldes, M and Dittoe, DK and Hite, JL},
title = {Diet-vaccine interactions: SQM Iron and Salmonella vaccination shape poultry gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0012726},
doi = {10.1128/aem.00127-26},
pmid = {41979594},
issn = {1098-5336},
abstract = {UNLABELLED: Vaccines to prevent Salmonella are rapidly gaining traction in the poultry industry. Yet how these interventions interact with other management strategies to influence the broader gut microbial community, rather than Salmonella per se, remains poorly understood. Understanding these effects is critical because shifts in the microbiome can alter nutrient metabolism, immune function, and pathogen dynamics in ways that could either enhance or suppress management strategies aimed at improving bird health and food safety. Here, we examine how a live-attenuated Salmonella vaccine (AviPro Megan Vac 1) and iron supplementation, two widely adapted management strategies, individually and jointly shape the cecal microbiome of broiler chickens. Specifically, we compare standard iron supplements (FeSO4) with a polysaccharide-complexed iron supplement (SQM Iron) which uses a complexation process that "hides" iron from Salmonella via time- and tissue-specific release of this critical nutrient. Using 16S rRNA gene sequencing, we found that while overall microbial diversity was unchanged, both interventions induced reproducible shifts in community composition, including enrichment of taxa linked to fermentation and short-chain fatty acid production. Vaccination alone promoted Bacillota genera associated with gut homeostasis, whereas iron supplementation altered competitive dynamics by reducing Streptococcus and favoring several rare taxa. Strikingly, combining these treatments suppressed several beneficial fermentative genera, and Staphylococcus was markedly increased, revealing nonadditive effects. These findings illuminate the potential of integrated strategies, combining immune stimulation with precision micronutrient supplementation, to improve poultry health and food safety. However, these results also underscore the intricate microbial trade-offs that must be carefully navigated to avoid unintended consequences in modern production systems.<br><br>IMPORTANCE: Globally, non-typhoidal Salmonella (NTS) is a persistent food safety challenge and pre-harvest control is an industry priority. While Salmonella vaccines are rapidly gaining adoption, their interactions with other common management practices such as nutritional strategies remain unclear. Iron metabolism is particularly important, as it influences host immunity, pathogen colonization, and shapes the gut microbiome. This study investigates how live-attenuated Salmonella vaccine (AviPro Megan Vac 1) and iron-based nutritional management interact to shape the cecal microbiota of broiler chickens. Specifically, we focus on SQM Iron, with a complexation process that enables time- and tissue-specific release of this critical nutrient. Our findings indicate that targeted combinations of immune stimulation and micronutrient supplementation can selectively remodel the poultry gut microbiome, with potential implications for nutrient utilization, microbial metabolism, and integrated, non-antibiotic approaches to reduce Salmonella burden while supporting flock health.},
}
@article {pmid41979614,
year = {2026},
author = {Ibrahim, MN},
title = {The Immune Cost: How Virtual Life Becomes a Modifiable Risk Factor for Immune Dysregulation.},
journal = {Clinical laboratory},
volume = {72},
number = {4},
pages = {},
doi = {10.7754/Clin.Lab.2025.250624},
pmid = {41979614},
issn = {1433-6510},
mesh = {Humans ; Risk Factors ; *Stress, Psychological/immunology ; Gastrointestinal Microbiome/immunology ; *Immune System/immunology ; },
abstract = {BACKGROUND: The emergence of technology-based lifestyles has led to what may be called "virtual isolation," as people spend more and more time in front of screens and less and less time in the world. Though the psychological consequences of this isolation are broadly appreciated, the biological impact of such isolation, especially on the immune system, has not been well-studied.<br><br>METHODS: This letter synthesizes interdisciplinary research in neuroendocrinology, psychoneuroimmunology, and microbiome science to explore the biological implications of digital isolation on immune system regulation.<br><br>RESULTS: Long-term digital immersion has been linked to higher levels of the stress hormone cortisol, disrupted sleep and reduced oxytocin signaling - all which disarray both innate and adaptive immune function. The lack of social bonding in the real world limits the sharing of microbes and gut microbiome diversity, making immune homeostasis even worse. Digital addiction is also associated with raised inflammatory indicators and increased sus-ceptibility to infections and immune dysregulation.<br><br>CONCLUSIONS: The virtual bubble is nice, psychologically, but carries an insidious and deepening challenge to the integrity of the immune system. Tackling digital over exposure is essential to restore immunological balance, particularly in a post-pandemic society prone to stress-driven immunosuppression.},
}
@article {pmid41979934,
year = {2026},
author = {Mertz, L},
title = {Suite of Ingestible Devices Opens Window to the Gut Nervous System, Microbiome.},
journal = {IEEE pulse},
volume = {17},
number = {1},
pages = {26-32},
doi = {10.1109/MPULS.2026.3659238},
pmid = {41979934},
issn = {2154-2317},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Optogenetics ; Animals ; *Gastrointestinal Tract/innervation ; },
abstract = {Ingestible capsules reveal gut neural signaling and microbiome dynamics through sensing and optogenetics.},
}
@article {pmid41980076,
year = {2026},
author = {Liu, J and Zhang, J and Hu, S and Jiang, M and Lin, X and He, P and Peng, C},
title = {Endogenous Mechanisms of Selenium-Induced Antagonism against Cadmium Toxicity in Crops: Integration and Reconstruction of a Multilevel Defense Network.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17688},
pmid = {41980076},
issn = {1520-5118},
abstract = {Selenium (Se) orchestrates a multilevel endogenous defense network in crops against cadmium (Cd) toxicity. This network operates from rhizosphere immobilization (e.g., Cd-Se complexes, microbiome interactions, iron plaque, and root exudates) and subcellular sequestration via transporter regulation (e.g., OsNramp5, OsHMA3) to antioxidant enhancement and selenoprotein activation. Critically, Se acts as a signaling initiator, engaging pathways (e.g., GATA3-COMT1-melatonin) to systemically reprogram stress responses. This review highlights that Se's antagonistic efficacy is form-, dose-, and genotype-dependent, providing a mechanistic basis for precision agronomic strategies. Future efforts must bridge laboratory findings to field applications by elucidating molecular switches and developing integrated predictive technologies.},
}
@article {pmid41980084,
year = {2026},
author = {Aragón, M and Spyridis, H and Mostard, P and Reichelt, M and Gershenzon, J and Dicke, M and Kloth, KJ},
title = {Jasmonic and Salicylic Acid Pathways Shape the Rhizosphere Microbiome, affecting Aphid Herbivory and Soil-Mediated Insect-Plant Interactions in a density-dependent manner.},
journal = {Plant &amp; cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcag048},
pmid = {41980084},
issn = {1471-9053},
abstract = {Aboveground induction of plant defense pathways can shape root-associated microbial communities. However, whether these changes are pathway-specific and how they affect plant growth and resistance remains unclear. We evaluated how induction of the Jasmonic Acid (JA) and Salicylic Acid (SA) defense pathways shapes the root microbiome of Brassica oleracea, and whether these soil-mediated shifts affect plant growth and resistance to herbivory in a subsequent generation using a plant-soil feedback (PSF) approach. In the conditioning phase, defense pathways were induced either through foliar application of methyl jasmonate (MeJA) and SA solutions, or through herbivory by caterpillars (JA) and aphids (SA). Both pathways led to distinct shifts in microbial communities, with bacterial and fungal composition varying by pathway identity and induction method. JA induction resulted in more differentially abundant ASVs than SA, particularly with Proteobacteria depletion. Conversely, Planctomycetota (bacteria) and Mortierellomycota (fungi) were enriched under both pathways, suggesting that these represent general stress-responsive groups. In the feedback phase, JA- and SA-conditioned soils had no effect on resistance under high aphid pressure, whereas under low aphid density, plants grown in SA-conditioned soil exhibited reduced phloem feeding and lower aphid population development. Together, our results indicate that benefits provided by the defense-shaped root microbiome depend on pest pressure intensity and arise from overall community shifts rather than specific taxa enrichment. Our findings underscore the complex interactions between plant-defense pathways, rhizosphere microbes, and herbivores.},
}
@article {pmid41980215,
year = {2026},
author = {Zhang, L and Dove, A and Du, J and Yang, D and Su, Q and Huang, X and Wang, J and Yue, J},
title = {The Lung-Brain Axis in Cognitive Impairment and Dementia: Mechanisms and Therapeutic Prospects.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0095},
pmid = {41980215},
issn = {2152-5250},
abstract = {The lung-brain axis has been recognized as a critical interface linking lung health to cognitive disorders, including cognitive impairment, Alzheimer's disease, and dementia. Epidemiological and clinical evidence shows a close association between compromised lung health-including chronic obstructive pulmonary disease (COPD), asthma, obstructive sleep apnea (OSA), and pulmonary infections-and cognitive impairment and dementia. Potential mechanisms include established factors (systemic inflammation and immune crosstalk, hypoxic injury, and air-pollutant-induced neurotoxicity) and exploratory mechanisms (lung microbiome dysregulation). Notably, lung-centric strategies targeting the lung-brain axis involve repurposing pulmonary medications, intervening in shared mechanisms, and employing non-pharmacological strategies. Furthermore, realizing this promise will require future randomized controlled trials (RCTs) to develop comprehensive management strategies and alleviate the global burden of cognitive impairment and dementia.},
}
@article {pmid41980217,
year = {2026},
author = {Yagi, M and Mizukoshi, R and Ito, K and Isogai, N and Funao, H and Fujita, R},
title = {Microbiome-Linked Metabolic Architecture of Accelerated Biological Aging in Humans.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0237},
pmid = {41980217},
issn = {2152-5250},
abstract = {Biological aging is a major determinant of frailty, functional decline, and vulnerability to age-related diseases; however, its upstream metabolic and inflammatory signatures remain incompletely understood. We investigated biological aging using an integrated multi-omics approach in a clinically enriched human cohort. In this prospective study, 120 patients with adult spinal deformity (ASD) and 480 age- and sex-matched healthy controls were included for comparison of PhenoAge. Within the ASD cohort, high-resolution plasma metabolomics and targeted proteomics were performed to characterize metabolic and inflammatory correlates of biological aging. A composite trimethylamine N-oxide (TMAO) Pathway Index (TPI) was constructed using standardized methylamine-related metabolites. Biological age was significantly elevated in ASD compared with matched controls. Within the ASD cohort, metabolomic profiling revealed enrichment of methylamine-related and glycation-associated metabolites among the strongest correlations of PhenoAge. The TPI showed a strong, age-independent, near-linear association with PhenoAge. In sensitivity analyses adjusted for age, sex, BMI, smoking status, and eGFR, this association remained significant (β = 2.92, 95% CI 0.74-5.10, p = 0.009). Targeted proteomic analyses showed that tumor necrosis factor-α was selectively associated with both PhenoAge and the TPI, whereas associations with interleukin-1β, interleukin-6, and adiponectin were limited. Higher PhenoAge was also associated with reduced physical performance, increased frailty, and impaired health-related quality of life. These findings support an exploratory, hypothesis-generating framework in which methylamine-related metabolism and chronic inflammatory signaling are associated with biological aging in ASD. Because of the cross-sectional design, these results should be interpreted as associative rather than causal.},
}
@article {pmid41980282,
year = {2026},
author = {Sun, W and Wang, Y and Bao, J and Tong, Z and Zhang, J and Huang, M and Chen, H},
title = {Environmental concentration of chlorantraniliprole induces dysbiosis of gut microbiota and metabolism in crayfish (Procambarus clarkii).},
journal = {Ecotoxicology and environmental safety},
volume = {316},
number = {},
pages = {120139},
doi = {10.1016/j.ecoenv.2026.120139},
pmid = {41980282},
issn = {1090-2414},
abstract = {The widespread application of chlorantraniliprole (CAP) in rice-crayfish co-culture systems poses a potential threat to the health of the non-target crustacean Procambarus clarkii. However, the sub-chronic effects of environmentally relevant concentrations of CAP on intestinal health remain poorly understood. In this study, we conducted a 14-day exposure experiment at two environmentally realistic CAP doses (0.05 and 0.5 mg/L) to investigate its effects using an integrated approach combining histopathology, biochemical assays, 16S rRNA gene sequencing, and untargeted metabolomics. Our results demonstrated that CAP exposure induced dose-dependent intestinal damage, ranging from villi degeneration to severe enterocyte dissolution and cytoplasmic vacuolation. This structural compromise was accompanied by significant CAP accumulation and oxidative stress, as evidenced by the suppression of antioxidant enzymes (SOD, CAT) and the depletion of GSH, along with increased lipid peroxidation (MDA). Furthermore, CAP exposure caused significant gut microbiota dysbiosis, characterized by an increased Firmicutes/Proteobacteria ratio, reduced alpha diversity, and taxon-specific, dose-dependent shifts in genus abundance. Metabolomic analysis revealed substantial reprogramming of the host-associated metabolome, with the high-dose group exhibiting a distinct profile and a stronger disruption in amino acid metabolism pathways. Crucially, Mantel test analysis revealed a dose-dependent intensification of the microbiota-metabolite correlation, indicating that the dysbiotic gut microbiome actively mediated the host's metabolic dysfunction under high-level CAP exposure. Our findings provide a comprehensive perspective on the intestinal toxicity of CAP in crayfish, highlighting the gut microbiome as a key mediator of pesticide-induced metabolic dysregulation.},
}
@article {pmid41980294,
year = {2026},
author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Glucose metabolism's impact on Blastocystis presence in the human gut.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106647},
doi = {10.1016/j.clnu.2026.106647},
pmid = {41980294},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.<br><br>METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.<br><br>RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.<br><br>CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.},
}
@article {pmid41980384,
year = {2026},
author = {Ye, W and Yan, Y and Dai, J and Wang, P and Jiang, H and Yao, W and Zheng, W},
title = {Subacute dimethylated monothioarsenate (DMMTA) exposure induces hepatotoxicity and disrupts the gut microbiota-bile acid-liver axis: A multi-omics study in mice.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142031},
doi = {10.1016/j.jhazmat.2026.142031},
pmid = {41980384},
issn = {1873-3336},
abstract = {Dimethylated monothioarsenate (DMMTA), an emerging thiolated organic arsenical frequently detected in rice, exhibits in vitro cytotoxicity comparable to trivalent inorganic arsenic. However, its in vivo hepatotoxicity and underlying mechanisms remain largely unknown. Here, a 28-day subacute DMMTA exposure study was conducted in C57BL/6 mice, integrating hepatic transcriptomics, targeted bile acid metabolomics and 16S rRNA microbiome profiling to elucidate DMMTA-induced perturbations along the gut-liver axis. Phenotypically, DMMTA induced an atypical hepatotoxicity characterized by paradoxical liver atrophy coexisting with severe steatosis, alongside inflammatory infiltration and a non-monotonic elevation of liver ALT activity. Mechanistically, DMMTA critically impaired hepatic detoxification and redox homeostasis, evidenced by the inhibited nuclear translocation of Nrf2 and the concerted suppression of downstream xenobiotic-metabolizing genes (e.g., Gsts, Ugts). Targeted metabolomics revealed a profound disruption of enterohepatic circulation, marked by a 29% reduction in the primary to secondary bile acid ratio and 6.0-fold increase in toxic accumulation of 6,7-diketo LCA. Concurrently, microbiome profiling identified a highly selective dysbiosis driven by the massive expansion of Negativibacillus (71.1-fold) and the depletion of Blautia (20.3-fold). Multi-omics integration (Procrustes, M[2] < 0.46, P < 0.05) robustly linked these microbiota shifts to the accumulation of hepatotoxic secondary bile acids. Collectively, this study challenges the traditional "low toxicity" paradigm of organic arsenicals and highlights the gut-liver axis as a central mediator of DMMTA hepatotoxicity, providing vital mechanistic evidence to refine environmental risk assessment for rice-based diets.},
}
@article {pmid41980702,
year = {2026},
author = {Chlebicz, M and Reese, TA},
title = {The Trouble with "Clean" Mice: How Infection History Alters Host Immune Responses.},
journal = {Annual review of virology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-virology-092623-094931},
pmid = {41980702},
issn = {2327-0578},
abstract = {Laboratory mice are widely used in biomedical research due to their low cost, genetic tractability, and ease of manipulation. To reduce experimental variability, they are typically housed under specific pathogen-free (SPF) conditions that limit microbial exposure. While this approach minimizes confounding infections, it also creates an immunological environment that differs markedly from that of humans, reducing the translational relevance of mouse immune studies. This limitation has driven the development of alternative models known as "dirty" or microbially experienced (ME) mice. Despite methodological differences, ME models demonstrate that lifelong microbial exposure profoundly shapes immune development. Although immune maturation in these mice is often attributed to microbiome changes, persistent exposure to endemic rodent viruses and other pathogens also may drive sustained immune activation. Here, we review the immune implications of the various ME models and highlight the critical role the virome plays in aligning mouse immune responses more closely with those of humans. Through harnessing microbial experience as a complementary tool to traditional SPF housing conditions and germ-free models, researchers can more faithfully model a mature, pathogen-shaped immune system.},
}
@article {pmid41980780,
year = {2026},
author = {Dai, DLY and Manus, MB and Hoskinson, C and Jiang, J and Sbihi, H and Miliku, K and Campisi, SC and Korczak, DJ and Duan, Q and Moraes, TJ and Mandhane, PJ and Finlay, BB and Simons, E and Lishman, H and Patrick, DM and Subbarao, P and Azad, MB and Chawes, B and Bønnelykke, K and Sørensen, SJ and Thorsen, J and Stokholm, J and Petersen, C and Turvey, SE},
title = {Breastfeeding may lessen socioeconomic disparities in child health through differences in the infant gut microbiome.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102755},
doi = {10.1016/j.xcrm.2026.102755},
pmid = {41980780},
issn = {2666-3791},
abstract = {Lower familial socioeconomic status (SES) is linked to increased childhood disease risk. Since SES has no inherent biological basis, identifying how it becomes physiologically embedded is essential for equitable intervention. Using data from the Canadian CHILD birth cohort (n = 2,752) with replication in the Danish Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC2010) cohort (n = 681), we analyze modifiable pathways linking SES to child health and find that the infant gut microbiota plays a key mediating role. Breastfeeding is associated with a stabilized infant microbiota, buffering against environmental impacts and reducing health risks in lower SES contexts. The presence of Bifidobacterium infantis, enriched through breastfeeding, is linked to protection against adverse outcomes from SES. Together, these results suggest that improving breastfeeding rates and restoring breastfeeding-enriched microbes, like B. infantis, may help buffer early biological impacts of social inequality and support healthier trajectories for children growing up in industrialized settings.},
}
@article {pmid41980904,
year = {2026},
author = {Bebelman, S and Artuyants, A and Nijmeijer, B and Fitzgerald, S and Henry, C and Blenkiron, C},
title = {Evaluating Sequencing Strategies for Endometrial Microbiome Profiling in Endometrial Cancer: A Comparative Study of Short- and Long-Read 16S rRNA Approaches.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {9},
number = {4},
pages = {e70540},
pmid = {41980904},
issn = {2573-8348},
support = {//Cancer Research Trust New Zealand/ ; //Cancer Society of New Zealand/ ; //Maurice and Phyllis Paykel Trust/ ; },
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/pathology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; New Zealand ; *Endometrium/microbiology/pathology ; Middle Aged ; Pilot Projects ; *High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics/isolation &amp; purification ; *Bacteria/genetics/isolation &amp; purification/classification ; Aged ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Endometrial cancer (EC) is the most common gynaecological malignancy globally, with rising incidence and notable disparities in outcomes. In New Zealand, EC rates have increased significantly, particularly among Māori and Pacific women, who face higher risks of advanced disease and poorer outcomes. Microbial dysbiosis has been implicated in EC pathogenesis, but characterising the uterine microbiome is challenging due to low microbial biomass and high contamination risk.<br><br>AIMS: This study aimed to pilot a protocol that could inform the preparation of a larger cohort trial. Short-read Illumina MiSeq and long-read Oxford Nanopore Technologies (ONT) 16S rRNA gene sequencing were investigated to profile the uterine microbiome in people with EC.<br><br>METHODS AND RESULTS: Uterine and vaginal swabs were analysed to assess platform performance in terms of DNA recovery, sequencing success, diversity metrics, and taxonomic resolution. The impact of sample freezing or immediate lysis prior to DNA extraction was also evaluated. ONT sequencing provided enhanced species-level resolution and improved detection of low-abundance taxa but showed variable performance in low-yield samples. Freezing prior to cell DNA extraction modestly increased bacterial 16S copy numbers and improved community consistency. Contamination was a problem across both platforms, particularly in low-biomass samples, but can be minimised during data analysis.<br><br>CONCLUSION: This study provides practical guidance for sequencing platform selection and sample handling in uterine microbiome research. Our findings support future efforts to elucidate microbial contributions to EC pathogenesis and highlight the importance of rigorous contamination control. Importantly, this is the first presentation of a New Zealand cohort and contributes valuable data from an underrepresented population and informs future research in diverse clinical settings.},
}
@article {pmid41980940,
year = {2026},
author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z},
title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00986-w},
pmid = {41980940},
issn = {2055-5008},
support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.},
}
@article {pmid41980958,
year = {2026},
author = {Kim, NH and Oh, J and Lee, JH and Lee, S and Jung, ES and Suh, DH and Kang, HJ and Kim, B and Kim, HS and Jung, HR and Kim, H and Yun, INR and Ji, Y and Cho, SY and Lee, SW},
title = {A colon mimetic screening approach reveals Lactobacillus fermentum as a microbiome-based therapy for COPD.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00978-w},
pmid = {41980958},
issn = {2055-5008},
support = {RS-2024-00439165//Korean Health Industry Development Institute/ ; RS-2023-NR077159//National Research Foundation of Korea/ ; 2024ER080601//National Institute of Health research project/ ; },
abstract = {Chronic obstructive pulmonary disease (COPD) remains a major health burden with few effective therapies, particularly for emphysema. The gut-lung axis and microbial metabolites, such as short-chain fatty acids (SCFAs), have emerged as modulators of lung inflammation. We investigated the therapeutic effects of Lactobacillus fermentum HEM20792 (LF), identified through a colon mimetic personalized pharmaceutical meta-analytical screening (PMAS) platform using fecal samples from severe COPD patients. LF and Lactobacillus sakei HEM20224 (LS) were orally administered to smoke-exposed mice, followed by lung function testing, histopathology, RNA sequencing, single-cell transcriptomics, and fecal microbiome/SCFAs analyses. LF attenuated emphysematous changes, improved compliance, and reduced macrophage and IL-17+ lymphocyte infiltration. Single-cell analysis showed restoration of alveolar macrophages and reduction of pathogenic C1q[+] macrophages, while transcriptomics revealed normalization of NF-κB and arachidonic acid pathways and attenuation of IL-17- and SPP1-associated signaling. LF also increased fecal SCFAs levels. These findings provide preclinical evidence for LF as a promising microbiome-based therapeutic candidate for COPD.},
}
@article {pmid41980965,
year = {2026},
author = {Arp, G and Levy, S and Jiang, AK and Dufault-Thompson, K and Zhong, A and Grant, M and Li, Y and Jiang, X and Hall, B},
title = {SpiR is a gut microbial enzyme that drives cholesterol conversion.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41980965},
issn = {2041-1723},
support = {R35-GM155208//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Cholesterol/metabolism ; Humans ; Phylogeny ; *Eubacterium/enzymology/genetics ; *Bacterial Proteins/metabolism/genetics ; Oxidation-Reduction ; },
abstract = {The gut microbiota contributes to cholesterol homeostasis by converting cholesterol into coprostanol, a non-absorbable sterol excreted in the feces. However, the enzymes mediating this process remain poorly defined. Here, we identify spiR, a steroid Δ[5-4] isomerase/3-keto reductase from Eubacterium coprostanoligenes that catalyzes the initial oxidation of cholesterol to cholestenone, a requisite step in coprostanol production. We confirm that SpiR oxidizes both cholesterol and pregnenolone, and stereospecifically reduces 3-keto-steroids to 3β-hydroxylated forms. We show that SpiR preferentially binds to cholesterol over related steroids and functions as an NAD(H)-dependent homodimer. Through phylogenetic analysis, we show that spiR clusters with known Δ[5-4] isomerases and is restricted to an uncultured clade within Acutalibacteraceae, where it frequently co-occurs with species encoding ismA, a gene previously implicated in cholesterol conversion. We analyze a multi-omic dataset from three human cohorts and find that spiR homologs were strongly enriched in individuals exhibiting cholesterol conversion. We also show that spiR homologs have a greater predictive power for cholesterol conversion than ismA homologs, establishing them as superior markers of microbial cholesterol metabolism. Our findings refine the enzymatic model of cholesterol metabolism in the gut and establish spiR as a critical biomarker and mechanistic driver for microbiome-mediated cholesterol reduction.},
}
@article {pmid41981035,
year = {2026},
author = {Faber, Q and Baker, CCM and West, JR and Doherty, SJ and Ernakovich, JG and Barbato, RA},
title = {Antimicrobial resistance varies with warming in active layer soil and permafrost.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46295-2},
pmid = {41981035},
issn = {2045-2322},
support = {PE 0602144A Program "Defense Resiliency Platform Against Extreme Cold Weather"//United States Department of Defense/ ; },
}
@article {pmid41981092,
year = {2026},
author = {Lenonyane, CK and Tsholo, K and Molale-Tom, LG and Bezuidenhout, CC and Olanrewaju, OS},
title = {Plant spatial compartmentalization buffers bacteriome structure and function under antibiotic stress.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46797-z},
pmid = {41981092},
issn = {2045-2322},
support = {D15022[CRP 2308]//International Atomic Energy Agency/ ; },
abstract = {Agricultural antibiotic contamination poses increasing threats to crop productivity and ecosystem stability through disruption of the plant-associated microbiome. While antibiotic impacts on bulk soil and rhizosphere communities are documented, the extent to which spatial compartmentalization across the plant-soil continuum buffers these effects remains poorly understood. Here, we investigated how compartment-specific selective pressures influence bacterial community assembly, functional resilience, and interaction networks under antibiotic stress. Lettuce (Lactuca sativa) was grown under five treatments in a completely randomized greenhouse design: T1 (sulfamethoxazole [SMX], 3 mg kg[-1] + manure + plant), T2 (trimethoprim [TMP], 3 mg kg[-1] + manure + plant), T3 (manure + plant, antibiotic-free control), T4 (manure only, plant-free control), and T5 (soil only, negative control). Bacterial communities were profiled across bulk soil, rhizosphere, and endosphere compartments using full-length 16 S rRNA gene sequencing. Spatial compartmentalization emerged as the primary driver of bacteriome structure and functional potential, surpassing antibiotic treatment effects across all analytical approaches. PERMANOVA revealed significant compartment-driven community structuring (R[2] = 0.189, P = 0.001), while treatment effects were non-significant (R[2] = 0.145, P = 0.116). Endosphere communities exhibited substantially lower alpha diversity than bulk soil and rhizosphere (P = 0.0001), with significant treatment × compartment interactions (P = 0.007). Antibiotic treatments selectively enriched xenobiotic degradation (P = 0.042) and secondary metabolism functions, particularly in bulk soil, without systematically increasing pathogen-associated or resistance-related functions. Network analysis revealed reduced bacterial connectivity under antibiotic pressure, yet cooperative interactions dominated across all treatments. Compositional differential abundance testing (ALDEx2) detected no significantly altered taxa for primary antibiotic contrasts (T1 vs. T3, T2 vs. T3), indicating context-driven rather than antibiotic-driven compositional changes. Functional diversity was significantly structured by compartment (Shannon P = 0.0017; richness P = 0.0039), while core plant-beneficial functions remained stable across treatments, with large effect sizes (Cohen's d ≥ 0.8) restricted to antibiotic degradation and secondary metabolism pathways. Our findings demonstrate that plant-microbe spatial structuring provides an ecological buffer that maintains core bacteriome functions against pharmaceutical disturbance, preserving plant-beneficial capabilities despite compositional shifts. The selective enrichment of antibiotic degradation pathways suggests potential for microbiome-assisted mitigation of pharmaceutical residues in agricultural systems. These results provide insights for developing compartment-specific microbiome management strategies that integrate with One Health approaches to enhance agricultural resilience under increasing pharmaceutical pressure in agroecosystems.},
}
@article {pmid41981263,
year = {2026},
author = {Zeng, S and Wang, S},
title = {Intergenerational dialogue via the gut microbiome and breast milk.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41981263},
issn = {1869-1889},
}
@article {pmid41981284,
year = {2026},
author = {Mukhopadhyay, M},
title = {Host-microbiome maps.},
journal = {Nature methods},
volume = {23},
number = {4},
pages = {679},
doi = {10.1038/s41592-026-03074-1},
pmid = {41981284},
issn = {1548-7105},
}
@article {pmid41981309,
year = {2026},
author = {},
title = {The gut microbiome as a fingerprint of antibiotic use history.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41981309},
issn = {1546-170X},
}
@article {pmid41981378,
year = {2026},
author = {Almohmadi, NH and Al-Kuraishy, HM and Hussein, KS and Turkistani, AM and Yousef, FM and Al-Gareeb, AI and Abdelaziz, AM and Elewa, YHA and Batiha, GE},
title = {The Gut-Brain Axis: A Critical Link between Type 2 Diabetes and Parkinson's disease.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41981378},
issn = {1867-1314},
}
@article {pmid41981415,
year = {2026},
author = {Byrd, MC and Han, S and Osazuwa-Peters, O and Bhaumik, D and Weatherspoon, D and Schlecht, NF and Osazuwa-Peters, N},
title = {Oral microbiome diversity, community- and taxon-level differences by oral human papillomavirus (HPV) and race/ethnicity.},
journal = {Infectious agents and cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13027-026-00757-4},
pmid = {41981415},
issn = {1750-9378},
}
@article {pmid41981426,
year = {2026},
author = {Muzhabaier, K and Li, Y and Wang, F and Guo, X and Chen, Q and Zhang, X and Cao, L},
title = {[Differential analysis of gut microbiome in patients with periprosthetic joint infection, aseptic failure, and osteoarthritis].},
journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery},
volume = {40},
number = {4},
pages = {548-556},
doi = {10.7507/1002-1892.202601002},
pmid = {41981426},
issn = {1002-1892},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Prosthesis-Related Infections/microbiology ; Female ; Middle Aged ; Aged ; *Osteoarthritis/microbiology ; Dysbiosis/microbiology ; Prosthesis Failure ; Arthroplasty, Replacement, Knee/adverse effects ; },
abstract = {OBJECTIVE: To explore the differences in gut microbiota diversity and structural characteristics among patients with periprosthetic joint infection (PJI), aseptic failure (AF), and osteoarthritis (OA), and to analyze the association between gut microbiota dysbiosis and the occurrence of PJI, thereby providing a new theoretical basis for elucidating the pathogenesis and treatment strategies of PJI in clinical practice.<br><br>METHODS: The study enrolled patients with PJI and AF admitted between February 2024 and December 2024, as well as OA patients admitted in February 2024. A total of 52 PJI patients, 19 AF patients, and 29 OA patients who met the selection criteria were included in the analysis. Significant differences were observed among the three groups in terms of gender, age, surgical site, preoperative C-reactive protein levels, and erythrocyte sedimentation rate (P<0.05), while no significant difference was found in American Society of Anesthesiologists (ASA) classification and body mass index (P>0.05). Among the PJI patients, infection staging was as follows: 9 cases in the acute phase, 28 cases in the delayed phase, and 15 cases in the chronic phase; 23 cases were accompanied by sinus tract formation. Fecal samples were collected at different time points: for the PJI group, samples were obtained preoperatively and on postoperative days (7&#xb1;1) and (14&#xb1;1); for the AF group, preoperatively and on postoperative day (7&#xb1;1); and for the OA group, preoperatively only. Metagenomics next-generation sequencing were employed to analyze gut microbiota &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) and differential bacterial genera (screened using the LEfSe algorithm).<br><br>RESULTS: Analysis of gut microbiota diversity showed that the preoperative &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) in the PJI group were significantly lower than those in AF group and OA group (P<0.05). Compared with the AF group on postoperative day (7&#xb1;1), the &#x3b1;-diversity indices in the PJI group on postoperative day (7&#xb1;1) were lower, but the difference was not significant (P>0.05); by postoperative day (14&#xb1;1), these indices further decreased, and the difference was significant (P<0.05). In the PJI group, no significant difference was observed in any of the indices across different time points postoperatively (P>0.05). Analysis of gut microbiota structural characteristics revealed that the PJI group exhibited characteristic dysbiosis both before and after operation. Preoperatively, the PJI group was characterized by enrichment of Pseudomonadota (relative abundance 13.19%), Enterobacteriaceae (Escherichia 3.26%, Klebsiella 1.90%), and opportunistic pathogens such as Enterococcus faecium (0.43%), while the relative abundances of Firmicutes (51.83%) and Bifidobacterium (0.24%) decreased. Postoperatively, the &#x3b1;-diversity in the PJI group further declined, with increased relative abundances of Escherichia and Klebsiella, and the relative abundance of Firmicutes decreased to 40.24%. LEfSe analysis of preoperative gut microbiota composition between the PJI group and AF group indicated that the AF group was predominated by Firmicutes, Bifidobacterium, and Roseburia preoperatively, with greater postoperative microbial stability compared to the PJI group.<br><br>CONCLUSION: Patients with PJI exhibited a gut microbiota profile characterized by reduced diversity and enrichment of opportunistic pathogens. Postoperative antibiotic treatment further aggravated this dysbiosis, providing new clinical insights into the role of gut microbiota imbalance in the pathogenesis and progression of PJI.},
}
@article {pmid41981555,
year = {2026},
author = {Bangera, SR and Subbiah, R and Govindaraj, S and Ibegbu, C and Reznik, D and Read, TD and Hartman, TJ and Paul, S and Torres-Patarroyo, N and Lymon, KJ and Ciers-Davis, NA and Nguyen, ML and Bruner, DW and Flowers, L and Velu, V and Xiao, C},
title = {Characterizing Oral Microbiome and Periodontal Disease in Oral HPV-Positive (COMP-HPV) individuals with HIV: an observational longitudinal study protocol.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08193-x},
pmid = {41981555},
issn = {1472-6831},
support = {P51 OD011132/CD/ODCDC CDC HHS/United States ; R01 DE032243/DE/NIDCR NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; R01 CA285198/CA/NCI NIH HHS/United States ; },
}
@article {pmid41981595,
year = {2026},
author = {Liang, L and Cao, S and Zhao, Y and Liu, B and Wang, J and Gong, P and Wang, Y and Hao, G and ZhangMu, X and Lu, N and Zhang, H and Wu, S and Kuang, F and Zhang, H},
title = {Neonatal sevoflurane exposure disrupts the lung-brain axis and drives microglial neuroinflammation and cognitive deficits.},
journal = {Journal of neuroinflammation},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12974-026-03808-0},
pmid = {41981595},
issn = {1742-2094},
support = {82101345//National Natural Science Foundation of China/ ; 82201414//National Natural Science Foundation of China/ ; 82271231//National Natural Science Foundation of China/ ; 82171170//National Natural Science Foundation of China/ ; 25YXYJYB00143//Science and Technology Plan in Xi'an of China/ ; },
abstract = {BACKGROUND: Neonatal sevoflurane exposure in mice induces microglial activation and long-term cognitive deficits, a finding that raises significant concerns for pediatric anesthesia. The lung-brain axis, a critical pathway mediating pulmonary-central nervous system communication, is indispensable for maintaining organismal homeostasis. However, existing research on anesthetic neurotoxicity has focused predominantly on central mechanisms, with insufficient attention to the lung-a major immune organ with extensive bidirectional crosstalk with the brain. Herein, we aim to explore the lung-brain interactions underlying long-term cognitive sequelae of neonatal sevoflurane exposure.<br><br>METHODS: C57BL/6J mice were selected and exposed to 3% sevoflurane for 2&#xa0;h daily on postnatal days 6-8. Upon reaching adulthood, cognitive function and microglial activation status were evaluated. At 4 weeks post-exposure, 16S rRNA gene sequencing and metabolomic analysis were performed respectively to characterize the structure of the pulmonary microbiota and the metabolite profile. Proximity ligation assay (PLA), fluorescence lifetime imaging microscopy-fluorescence resonance energy transfer (FLIM-FRET), and co-immunoprecipitation (COIP) were employed to investigate the molecular mechanisms by which lung-derived metabolites mediate brain effects. Additionally, rescue experiments were conducted by administering the sphingosine-1-phosphate receptor modulator FTY720 and Moce to validate the aforementioned effects.<br><br>RESULTS: Repeated neonatal sevoflurane exposure impaired adult cognitive function, induced microglial activation, and was concurrent with pulmonary microbiome dysbiosis and metabolic alterations. Notably, sphingosine-a key membrane lipid-was significantly decreased. Intratracheal administration of FTY720, a sphingosine analog, alleviated neuroinflammation and ameliorated cognitive deficits. Mechanistically, sevoflurane exposure upregulated HDAC1 and downregulated KLF4, whereas FTY720 significantly rescued these sevoflurane-induced expression aberrations, implicating the HDAC1/KLF4 axis in the regulation of neuroinflammation. Additionally, MOCE significantly alleviated neuroinflammation and ameliorated cognitive deficits.<br><br>CONCLUSIONS: Developmental sevoflurane exposure induces microglial activation and cognitive decline via a pulmonary dysbiosis-sphingosine reduction cascade. The sphingosine-1-phosphate receptor modulator FTY720 mitigates this impairment by regulating microglial activation and neuroinflammation. These findings reveal novel mechanisms of anesthetic neurotoxicity and identify potential neuroprotective targets for pediatric anesthesia.},
}
@article {pmid41981681,
year = {2026},
author = {Brachmann, S and Kiesewetter, KN and Liddicoat, C and Wallace, KJ and Breed, MF and Eisenhauer, N and Barnes, AD},
title = {Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00896-6},
pmid = {41981681},
issn = {2524-6372},
support = {UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; },
abstract = {BACKGROUND: Forest restoration has primarily been evaluated through changes in aboveground communities, while belowground microbial communities-critical drivers of ecosystem functions-remain less understood. Moreover, studies of soil microbes have focused largely on community structure, which does not necessarily reflect the recovery of functional capacity and stability.<br><br>METHODS: To determine how forest restoration affects microbial community structure and function and how microbial diversity relates to ecosystem multifunctional potential and stability, we analysed soil microbial communities from 79 urban forest restoration sites across New Zealand, spanning 0-63&#xa0;years since initial plantings. Shotgun metagenomic sequencing was used to characterize taxonomic composition and functional potential, with diversity quantified using alpha and beta metrics. To evaluate links between diversity and ecosystem function, we assessed ecosystem multifunctional potential (EMF) which describes the ecosystem's capacity to simultaneously provide multiple functions, and we developed a novel functional insurance (FI) index grounded in ecological theory as an indicator of functional stability and resilience. To calculate FI in microbial systems from sequencing data, we quantified functional overlap by estimating over 250 million species-function correlations per sample.<br><br>RESULTS: Contrary to our expectations, only beta diversity, not alpha diversity, was positively associated with EMF and FI, indicating that community composition and dissimilarity rather than species richness underpins microbial functional capacity and stability. EMF and FI were positively correlated, showing that high functional diversity and functional overlap can co-occur in microbial systems. In addition, archaeal turnover increased with closing forest canopies, contributing to higher EMF and FI, while bacterial turnover was only weakly associated with restoration parameters. Notably, restoration time did not play a role in shaping microbial diversity, EMF and FI.<br><br>CONCLUSIONS: Our findings demonstrate that microbial compositional turnover, rather than increases in species richness, are critical for restoring soil ecosystem functions. Incorporating microbial functional metrics like the FI index into restoration frameworks that recognise both above and belowground dynamics could promote resilient and multifunctional urban forests.},
}
@article {pmid41981684,
year = {2026},
author = {Clough, J and Mikac, KM},
title = {Metagenomic profiling of bacterial and fungal microbiota and putative pathogens of southern greater gliders (Petauroides volans).},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00564-7},
pmid = {41981684},
issn = {2524-4671},
}
@article {pmid41981689,
year = {2026},
author = {Zhang, Y and Li, H and Yu, F and Gao, M and Wang, Y and Xin, S and Yang, J and Wang, Z and Xiang, L and Ru, Q and Jiang, N},
title = {The role of Traditional Chinese Medicine in the management of liver disease: targeting gut microbiome.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {41981689},
issn = {1749-8546},
support = {ZDYN-2024-A-116//Clinical Collaboration Program on Viral Hepatitis between Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; GZY-ZJ-KJ-23070//The Science and Technology Department of the State Administration of Traditional Chinese Medicine and Zhejiang Provincial Administration of Traditional Chinese Medicine co-built the Science and Technology Plan Project/ ; },
abstract = {In recent years, liver disease have become a major contributor to global morbidity and mortality, with current clinical treatments often limited by late diagnosis and rapid progression. This review aims to explore the underexplored role of gut microbiota (GM) in liver disease pathogenesis, and to highlight how Traditional Chinese Medicine (TCM) offers a novel therapeutic approach through indirect modulation of the GM. While conventional pharmacological strategies focus on direct organ-targeting interventions, TCM emphasizes a holistic, multi-target approach that aligns with the complex GM-liver axis. Specifically, we examine the interactions between GM and various liver diseases (alcoholic liver disease, non-alcoholic fatty liver disease, cirrhosis, acute liver injury, autoimmune hepatitis, and hepatocellular carcinoma) and focuses on the indirect axis of "TCM-GM-liver," aiming to elucidate its scientific implications from the perspective of indirect pharmacology. Unlike current research that broadly addresses GM-derived metabolites, this review innovatively details how TCM and natural products regulate specific bacterial phyla and their representative genera to influence disease progression. In conclusion, we emphasize that GM metabolites serve as critical intermediate substances in TCM-mediated hepatoprotection. By elucidating these mechanisms, this review provides a theoretical foundation for developing microbiota-guided therapeutic strategies and advancing novel drug discovery for liver diseases.},
}
@article {pmid41981704,
year = {2026},
author = {Li, M and Wu, S and Zi, X},
title = {Identification of silage bacterial clusters and analysis of their microecological characteristics.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00891-x},
pmid = {41981704},
issn = {2524-6372},
abstract = {BACKGROUND: Enterotypes refer to the different bacterial clusters in the gut microecosystem, which are closely related to host physiology, digestion, disease, and other phenotypes. However, whether there are clear clusters in the silage microecosystem, and the fermentation quality and characteristics of unique cluster silage remain unknown. To determine whether distinct bacterial clusters exist in the silage microecosystem and to characterize their fermentation properties, we analyzed the bacterial community composition and fermentation quality of 156 silage samples, and further explored their underlying microbial ecological features.<br><br>RESULTS: We confirmed three distinct clusters in the silage microbiome, which were named according to their dominant bacterial taxa: the E-cluster (characterized by a higher abundance of unclassified Enterobacteriaceae (UG)), the P-cluster (enriched with Pseudomonas and Janthinobacterium), and the L-cluster (dominated by Lactobacillus). These microbial clusters were closely associated with fermentation quality: the L-cluster exhibited superior silage quality compared to the E- and P-clusters. Meanwhile, the microbial functional profiles differed significantly among the three clusters of silage. Numerous pathways were significantly enriched in the P-cluster, such as the Biosynthesis of other secondary metabolites, etc. Moreover, bacterial co-occurrence networks of three clusters silage displayed cooperative interactions mainly, P-cluster silage network was more complex and tighter, E-cluster silage has more functional microbial units and more stable. Furthermore, the assembly of microbial communities in the three silage clusters was dominated by stochastic processes. Specifically, the E-cluster and L-cluster were governed by ecological drift, while dispersal limitation was more influential in the P-cluster.<br><br>CONCLUSIONS: Overall, we found in our study that the silage microbiome can be divided into three clusters, and different clusters have significant differences in fermentation quality, microbial diversity and compositions, functional profiles, microbial network characteristics and community assembly mechanisms. These results could broaden our comprehension of the silage microbial ecology processes and also provide a scientific basis on which to develop a method to precisely regulate silage quality.},
}
@article {pmid41981741,
year = {2026},
author = {Chen, Y and Wang, YT and Hu, JY and Wang, EC and Jia, XH and Wang, J and Min, GT and Jin, WL and Jiang, L},
title = {Modulating the gut microbiota to enhance immune checkpoint inhibitor efficacy in colorectal cancer: mechanisms, therapeutic strategies, and clinical perspectives.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2652476},
pmid = {41981741},
issn = {1949-0984},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Colorectal Neoplasms/microbiology/immunology/drug therapy/therapy ; *Gastrointestinal Microbiome/drug effects ; Immunotherapy/methods ; Animals ; Bacteria/classification/metabolism/genetics ; Extracellular Vesicles ; },
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, yet their efficacy in colorectal cancer (CRC) remains limited to a minority of patients with microsatellite instability-high (MSI-H) tumors, leaving the majority with microsatellite stable (MSS) disease unresponsive. The gut microbiota, a key regulator of host immunity, has emerged as a pivotal determinant of ICI response. This review delineates the dual role of the gut microbiome-encompassing specific bacterial strains, their metabolites, and bioactive components such as extracellular vesicles (EVs) and outer membrane vesicles (OMVs)-in either enhancing or impairing ICI efficacy through complex interactions with the host immune system. We further explore the emerging concept of gut microbiota circadian rhythms and their potential to inform personalized chrono-immunotherapy paradigms. Furthermore, we synthesize promising microbiota-targeting strategies as adjunctive approaches to overcome resistance and augment ICI efficacy in CRC. Finally, we present selected clinical evidence and outline future perspectives to expand the clinical benefit of immunotherapy in CRC patients.},
}
@article {pmid41981758,
year = {2026},
author = {Murtaza, G and Hassan, NE and Ahmed, Z and Elmenofy, W and El-Mogy, MM and El-Ganainy, S and Kesba, HH and Hamed, LMM and Iqbal, R and Ullah, S},
title = {Microbiome-metabolite signaling drives aluminum stress alleviation in soybean under intercropping and selenium nanoparticle application.},
journal = {Plant signaling &amp; behavior},
volume = {21},
number = {1},
pages = {2657733},
pmid = {41981758},
issn = {1559-2324},
mesh = {*Glycine max/drug effects/microbiology/metabolism/physiology ; *Aluminum/toxicity/metabolism ; *Selenium/pharmacology ; *Microbiota/drug effects ; *Nanoparticles/chemistry ; *Stress, Physiological/drug effects ; Rhizosphere ; *Signal Transduction/drug effects ; Oxidative Stress/drug effects ; },
abstract = {Aluminum (Al) toxicity and soil-borne pathogens severely constrain legume productivity in acidic soils, yet the signaling mechanisms underlying intercropping-mediated stress alleviation remain insufficiently understood. Here, we investigated whether soybean-sorghum intercropping under Al stress (SSAl), alone or combined with selenium nanoparticles (SSAl + Se), modulates rhizosphere signaling networks and plant defense responses. Integrated 16S rRNA microbiome sequencing and rhizosphere metabolomics were employed to decipher microbe‒metabolite interactions associated with Al detoxification and disease suppression. Compared with monoculture soybean under Al stress (MSAl), SSAl and SSAl + Se significantly reduced Al accumulation (16.9% and 57.4%, respectively) and Fusarium wilt incidence (10.9% and 34.4%, respectively), accompanied by enhanced root growth. These treatments attenuated oxidative stress, as evidenced by decreased O2[-], H2O2, and malondialdehyde (MDA) levels, while stimulating antioxidant enzyme activities (SOD, POD, and APX), indicating reinforcement of redox homeostasis. In the rhizosphere, NH4[+]-N and available K levels increased, with NH4[+]-N positively correlated with urease activity and negatively correlated with Al accumulation, suggesting nitrogen-mediated modulation of Al dynamics. Microbiome analysis revealed enrichment of beneficial taxa, including Streptomyces, Intrasporangium, and Sphingomonas, which are positively associated with antimicrobial and stress-related metabolites such as 15-methyl palmitate, lactucin, and sordarin. These coordinated shifts in the microbial community structure and metabolite profiles indicate that the activation of rhizosphere chemical signaling restricts pathogen proliferation and enhances Al detoxification. Collectively, our findings demonstrate that selenium nanoparticles potentiate intercropping-induced rhizosphere reprogramming, linking redox regulation, nitrogen transformation, and microbiome-metabolite signaling to improve aluminum stress tolerance and disease resistance in soybean. This study provides mechanistic insight into how nano-enabled agronomic strategies influence plant signaling networks under edaphic stress.},
}
@article {pmid41981872,
year = {2026},
author = {Janković, SM},
title = {Clinically significant interactions between drugs, microbiome, and sex.},
journal = {Expert opinion on drug metabolism &amp; toxicology},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/17425255.2026.2660706},
pmid = {41981872},
issn = {1744-7607},
abstract = {INTRODUCTION: There are multiple interactions between drugs and the human microbiome that can influence drug effects and pharmacokinetics, but few clinical studies have examined the influence of sex on these interactions.<br><br>AREAS COVERED: Literature for this narrative review was searched in PubMed and Google Scholar without language restrictions and for the time period from 2015 to the present. Focus of the search was on clinical trials and observational studies in the human population.<br><br>EXPERT OPINION: Current knowledge about the clinically significant effects of microbiomes on drug metabolism and treatment outcomes in humans is very scarce, while the question of sex differences remains unanswered. Both population pharmacokinetic studies, including microbiome composition and sex as covariates, and clinical studies of treatment outcomes will be necessary to fill this knowledge gap.},
}
@article {pmid41981895,
year = {2026},
author = {Bright, R and Macowan, MG and Tian, K and Fitzsimmons, T and Wilson, RL and Roberts, CT and Christophersen, CT and Bartold, PM and Kidd, SP and Zilm, PS},
title = {Periodontitis during pregnancy: The effect on the gut microbiome and intestinal inflammation.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70132},
pmid = {41981895},
issn = {1943-3670},
support = {190-2027//Australian Dental Research Foundation/ ; },
abstract = {BACKGROUND: Periodontitis has been epidemiologically associated with adverse pregnancy outcomes, but causality remains difficult to establish in humans due to confounding factors. This study uses a controlled murine model to examine the effects of experimentally induced periodontitis on the composition of the gut microbiota and gastrointestinal inflammation during pregnancy.<br><br>METHODS: Periodontitis was induced in pregnant BALB/c mice via oral inoculation with Porphyromonas gingivalis and Fusobacterium nucleatum before conception (n&#xa0;=&#xa0;20 per group). Pregnancy outcomes, gut histology, systemic inflammatory markers, and microbiome composition, assessed by 16S rRNA sequencing, were evaluated at gestational Day 18.<br><br>RESULTS: Periodontitis was confirmed by significant alveolar bone loss. While fetal and placental weights were modestly increased in periodontitis-positive mice, there were no changes in implantation rates or placental efficiency. Systemic inflammatory markers, including C-reactive protein and interleukin-33, were reduced, suggesting pregnancy-specific immunomodulation. Histological analysis revealed significant inflammation in the jejunum and colon of periodontitis-exposed mice. Despite this, alpha and beta diversity metrics of the gut microbiota remained essentially unchanged. Taxonomic shifts were observed at the genus level, with reductions in protective taxa, such as Akkermansia muciniphila and increases in potentially pro-inflammatory genera, like Desulfovibrio.<br><br>CONCLUSIONS: Periodontitis during pregnancy alters gut microbial composition and increases gastrointestinal inflammation without overtly impairing pregnancy outcomes in mice. These findings suggest an association between oral inflammation, intestinal inflammatory changes, and systemic inflammatory modulation during pregnancy. Further studies are warranted to explore long-term maternal and offspring consequences and their relevance to human pregnancy.<br><br>PLAIN LANGUAGE SUMMARY: This study explored how periodontitis during pregnancy can influence the gut and immune system. Periodontitis is already associated with poor pregnancy outcomes, but establishing cause and effect in humans is difficult. To investigate this, the researchers used a controlled mouse model. We induced periodontitis in pregnant mice and examined its impact on the gut microbiome, intestinal health, and immune responses. The results revealed that periodontitis does not stay confined to the mouth; it disrupts gut bacterial balance, causes gut inflammation, and modifies immune pathways. Notably, these effects occurred during pregnancy, a time when the immune system is already adapting. The findings suggest that oral infections during pregnancy can have widespread effects, impacting gut health and immune regulation. This may help explain the link between periodontitis and human pregnancy complications. Overall, the study underscores the importance of oral health during pregnancy and supports the idea that treating periodontitis might also safeguard gut and immune health, leading to better outcomes for both mothers and their babies.},
}
@article {pmid41982387,
year = {2026},
author = {Huang, P and Du, M and Liu, Y and Han, Z and Wan, Q and Liang, F and Han, W},
title = {Phase variation in Bacteroides fragilis governs susceptibility to a microvirus and drives its evolution.},
journal = {Engineering microbiology},
volume = {6},
number = {1},
pages = {100252},
pmid = {41982387},
issn = {2667-3703},
abstract = {The interaction and co-evolution between human gut bacteria and their phages shape the dynamic gut microbiome, exerting a significant impact on human health. However, the underlying mechanisms are largely unexplored. In particular, a bacteria-phage interaction model of the Bacteroidota phylum and the Microviridae phages is lacking, limiting our understanding of their ecological roles in human gut. In this study, we isolated a Bacteroidota-infecting Microviridae phage φHBP1 from human feces. Infection of its host Bacteroides fragilis with φHBP1 drives multiple genomic structural variations, which are correlated with host resistance to φHBP1. In turn, our phage evolution assay in B. fragilis H1 obtained φHBP1 mutants that carry mutations within the capsid and pilot proteins and can reinfect the resistant bacterial population. Together, our findings provide novel insights into an antagonistic co-evolution mechanism between gut phage and bacteria, and hold important implications for diversifying phages through evolution to target resistant bacteria in phage therapy.},
}
@article {pmid41982457,
year = {2026},
author = {Shi, S and Wang, S and Li, S and Lu, R and Pan, S and Chen, F and He, X},
title = {Severe periodontitis patients with well-controlled type 2 diabetes display a distinct subgingival microbiome with increased Saccharibacteria compared to systemically healthy controls.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1814983},
pmid = {41982457},
issn = {2235-2988},
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/microbiology ; Middle Aged ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Periodontitis/microbiology/complications ; *Gingiva/microbiology ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Dysbiosis/microbiology ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; DNA, Ribosomal/chemistry/genetics ; Dental Plaque/microbiology ; Aged ; },
abstract = {INTRODUCTION: Type 2 diabetes mellitus (T2DM) is a major systemic risk factor that exacerbates periodontitis, with microbial dysbiosis recognized as an important mechanism. However, whether a well-controlled diabetic state still exerts a distinct influence on the subgingival microbiome remains to be fully elucidated.<br><br>METHODS: This study compared the subgingival microbiota composition in patients with generalized Stage III/IV periodontitis, categorized into a systemically healthy Control group (n = 30) and a well-controlled T2DM group (HbA1c < 8%, n = 30). Subgingival plaque samples were collected using curettes from the deepest diseased sites. The V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina NovaSeq 6000 platform.<br><br>RESULTS: Demographic characteristics and periodontal parameters were comparable between groups, except for glycemic indices. Alpha and beta diversity analyses demonstrated no significant differences in overall microbial diversity or community structure (ANOSIM, P > 0.05). However, the T2DM group exhibited a distinct diabetic-associated microbial signature. The T2DM group showed a significant enrichment of the phylum Saccharibacteria (formerly TM7), particularly Nanosynbacter lyticus. In contrast, the phylum Actinomycetota, predominantly represented by the genus Actinomyces, was significantly reduced in the T2DM group. Notably, classical "Red Complex" pathogens were not identified as discriminative biomarkers between the groups. Additionally, correlation analysis revealed that Saccharibacteria abundance was positively associated with HbA1c and fasting blood glucose levels.<br><br>DISCUSSION: These findings demonstrate that even with adequate glycemic control, the diabetic microenvironment exerts a unique selective pressure on the subgingival microbiome, favoring the expansion of specific epibiotic bacteria like Saccharibacteria while reducing commensal Actinomyces.},
}
@article {pmid41982475,
year = {2026},
author = {Wang, Y and Wang, Y and Jin, H},
title = {Update on the Etiology and Pathogenesis of Erythrodermic Psoriasis.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {581723},
pmid = {41982475},
issn = {1178-7031},
abstract = {Erythrodermic psoriasis(EP) is a rare, life-threatening variant affecting 75%-90% of the body surface area. Characterized by widespread erythema and potential systemic symptoms like fever and lymphadenopathy, it severely impairs patient quality of life. The pathogenesis of erythrodermic psoriasis is not fully understood. It is a multifactorial, multistep process suspected to result from an abnormal immune response induced by both genetic and environmental factors. Key contributors to erythrodermic psoriasis onset include specific gene polymorphisms, altered expression of adhesion molecules, dysregulated cytokine activity, and abnormal activation of T cell subsets. Additionally, imbalances in the skin microbiota and external factors, such as infections and medications, play important roles in disease onset and progression. Distinct from prior reviews that primarily emphasize clinical features and treatment, this review integrates recent mechanistic advances across genetic, immune, environmental, and microbiome domains to provide an updated, systems-level framework for understanding erythrodermic psoriasis and to highlight potential therapeutic implications.},
}
@article {pmid41982769,
year = {2026},
author = {Zhang, D and Sheng, J and He, P and Wang, J and Zhou, M and Sun, Y and Cao, Y and Jiang, Y and Jia, H and Wang, L and Xu, X and Teng, Y},
title = {Dietary fiber supplementation mitigates gestational diabetes risk and preterm birth via gut microbiota modulation: a randomized controlled trial.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1794560},
pmid = {41982769},
issn = {1664-2392},
mesh = {Humans ; Female ; Pregnancy ; *Dietary Fiber/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Diabetes, Gestational/prevention &amp; control/microbiology/diet therapy ; Adult ; *Dietary Supplements ; *Premature Birth/prevention &amp; control/microbiology/epidemiology ; Gestational Weight Gain ; Infant, Newborn ; Pregnancy Outcome ; },
abstract = {BACKGROUND: Gestational Diabetes Mellitus (GDM) poses severe health risks to mother and child, yet effective, non-invasive preventive strategies remain elusive. While the gut microbiota is known to influence glucose metabolism, its potential as a therapeutic target and predictive biomarker in high-risk pregnancies is underexplored. This study investigated whether soluble dietary fiber supplementation could remodel the gut microbiome to prevent GDM and improve pregnancy outcomes.<br><br>METHODS: We performed a single-center, randomized controlled trial with 98 pregnant women at elevated risk for GDM. For 5 weeks, from 20 to 24[+6] weeks of pregnancy, participants were randomly assigned to either a fiber group (getting soluble fiber supplements every day) or a control group (getting normal care). Clinical outcomes encompassed OGTT results, gestational weight gain (GWG), and delivery outcomes. We used 16S rRNA sequencing to look at changes in gut flora. Furthermore, we developed a novel nomogram integrating clinical variables with microbial signatures to predict GDM risk.<br><br>RESULTS: Although GDM incidence did not statistically differ, the fiber group exhibited significantly improved glycemic excursions (predominantly lower 1h-PG, and reduced whole-OGTT glucose AUC and iAUC), reduced GWG during the 5-week intervention period (1.83 vs. 2.54 kg; P = 0.016), and a complete absence of preterm births (0% vs. 12.0%; P = 0.040). Microbiome analysis revealed that fiber intake enriched Bifidobacterium and Limosilactobacillus while suppressing Phascolarctobacterium. Functional prediction indicated a downregulation of inflammation-related pathways (HIF-1, AMPK) in the Fiber group. Crucially, a prediction model combining clinical factors with a specific "micro-balance" (Bifidobacterium ratio) achieved superior predictive accuracy (AUC 0.821) compared to clinical factors alone.<br><br>CONCLUSIONS: Preliminary findings suggest that dietary fiber supplementation serves as a potent "biotic" intervention in high-risk pregnancies, improving 1-hour postprandial glucose homeostasis and eliminating preterm birth in this cohort. The mechanism appears associated with the specific enrichment of Bifidobacterium. Additionally, we validated a novel clinical-microbial nomogram, suggesting that integrating gut microbiome data can significantly enhance GDM risk stratification. Future extensive research is need to confirm these results.},
}
@article {pmid41982876,
year = {2026},
author = {Ren, J and Lan, Z and Wang, C and Zhu, J and Li, M and Xu, J and Lu, Y and Tu, J and Zhang, X and Boskovic, L and Huang, J and Hu, X},
title = {Metagenomic next-generation sequencing and conventional microbiology for microbial profiling in biliary tract infections: a comparative study with clinical stratification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1799474},
pmid = {41982876},
issn = {1664-302X},
}
@article {pmid41982878,
year = {2026},
author = {Yu, Y and Li, X and Shahzad, AS and Zhuang, S},
title = {Short-term calcium peroxide application promotes soil microbial interactions to improve peanut yield in acidic soils.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780622},
pmid = {41982878},
issn = {1664-302X},
abstract = {The deterioration of soil microorganisms stands as a key barrier to the sustainable cultivation of peanut. Peroxides such as hydrogen peroxide (H2O2) and calcium peroxide (CaO2) with antimicrobial efficacy may inhibit soil pathogens and improve microbial community, but their effects on the soil properties, microbiome and peanut yield are still unclear. In this study, a field experiment was conducted to investigate the effects of CaO2 (CP, with application rate of 4.5 t ha[-1]) and H2O2 (HP, with application rate of 22.5 t ha[-1]) and no peroxide application (CK) on physicochemical properties, microbial communities and network structures of acidic soils in which peanut had been cultivated for 13 years. Compared with CK, calcium peroxide application significantly increased soil pH. Hydrogen peroxide showed a similar trend, but not significant. Principal co-ordinates analysis (PCoA) indicated that peroxides application significantly affected the fungal community structure, while it had a weaker impact on the bacterial community. With peroxides application, soil harmful fungus Fusarium and the fungal functional group associated with plant pathogen declined. Network co-occurrence analysis showed that peroxides enhanced bacterial network interactions, with bacterial stability increasing markedly by 2.19- and 1.40-fold in calcium peroxide and hydrogen peroxide treatments, respectively. Peanut yield was correlated with the microbial network properties, and significantly increased by 31.7% in calcium peroxide. Random forest model analysis further revealed that bacterial stability, soil pH, bacterial negative cohesion, and complexity were key factors for peanut yield. In conclusion, short-term calcium peroxide application increased soil pH and bacterial stability, thereby promoting peanut yield in acidic soils.},
}
@article {pmid41982910,
year = {2025},
author = {Santos, S and Salinas, I and Almeida, N and Caicedo, A},
title = {The role of microbiota dysbiosis in Parkinson's disease: Pathophysiology and therapeutic opportunities.},
journal = {Engineering microbiology},
volume = {5},
number = {3},
pages = {100222},
pmid = {41982910},
issn = {2667-3703},
abstract = {Parkinson's disease (PD) is a chronic, progressive neurodegenerative disorder characterized by debilitating motor and non-motor symptoms. Its etiology is multifactorial, with no single definitive cause identified, although aging is a significant risk factor. Additional risks include genetic predisposition, family history, and environmental factors such as pesticide exposure and Helicobacter pylori infection. Dysbiosis of the gut microbiota, and in particular bacterial imbalances, has been implicated in the disruption of the gut-brain axis, contributing to both systemic and neuroinflammation. Environmental factors such as antibiotic exposure and toxins can precipitate microbial dysregulation, potentially accelerating PD progression. Understanding the mechanisms of the gut-brain axis and identifying strategies to preserve a healthy microbiome are essential for developing novel therapeutic approaches. This review synthesizes current therapeutic strategies and ongoing research focused on restoring gut-brain balance to combat PD. These approaches include fecal microbiota transplantation, dietary interventions, and probiotic therapies, all of which show promise in mitigating both motor and non-motor symptoms. Furthermore, we emphasize the urgent need for continued research into probiotics and innovative therapeutic approaches for gut-brain axis modulation, presenting novel opportunities for effective PD management.},
}
@article {pmid41982913,
year = {2025},
author = {Hu, M and Xu, S and Xu, R and Qi, X and Yu, X and Wang, J and Li, Y and Liu, Y and Xi, G and Yu, J and Shi, M},
title = {Analysis of single-cell RNA sequencing data to examine the gastric inflammation-to-cancer transition and evaluation of the effect of probiotic on precancerous lesions.},
journal = {Engineering microbiology},
volume = {5},
number = {3},
pages = {100208},
pmid = {41982913},
issn = {2667-3703},
abstract = {Gastric cancer (GC) is the fifth most prevalent malignancy globally. However, its heterogeneity and asymptomatic early-stage development hinder timely diagnosis and effective treatment. Here, we employed single-cell RNA sequencing to delineate the transitional features of pit mucous cells (PMCs) during the gastritis-to-cancer transition and identified 100 core genes. Characterization of the gene set revealed the role of ribosomal protein small subunit and ribosomal protein large subunit in inflammation-to-cancer transition, which promoted ribonucleoprotein complex biogenesis and cytoplasmic translation. External validation using independent cohorts confirmed that this core gene set discriminated disease progression (AUC > 0.7) and was significantly enriched in GC tissues (p < 0.01). Moreover, we evaluated the therapeutic intervention effects of C. butyricum and synbiotics (Weichanghao®) using a rat model of gastritis and demonstrated the targeted suppression of inflammation-to-cancer transition genes. Our findings establish the basis for early diagnosis of GC through PMC-driven molecular dynamics. Additionally, we propose microbiota-based strategies to prevent the inflammation-to-cancer transition in preneoplastic stages. Furthermore, our results highlight that dysbiosis of the gastric microbiome can be addressed using probiotic supplementations and the core gene set may provide labeling for the evaluation of probiotics-based treatment.},
}
@article {pmid41965542,
year = {2026},
author = {Priya, S and Sridhar, SB and Shareef, J and Wadhwa, T and Balusamy, B and Meenakshi, DU and Sundram, S and Malviya, R},
title = {Epidemiology, diagnosis and emerging therapies for Lyme disease of the Northern Hemisphere.},
journal = {International journal of emergency medicine},
volume = {19},
number = {1},
pages = {},
pmid = {41965542},
issn = {1865-1372},
abstract = {BACKGROUND: Lyme disease is the most widespread tick-borne infection in the Northern Hemisphere and is challenging to diagnose and treat due to its changing clinical presentation, antigenic variation, tissue tropism, and the expanding distribution of vectors. This review includes ecology, pathogenesis, diagnostics, treatment, post-treatment, prevention, and novel translational approaches.<br><br>METHODS: A literature review was conducted to include literature published between January 2000 and March 2026 in PubMed/MEDLINE, Scopus, and Web of Science, with landmark studies used where applicable. Original research, clinical trials, systematic reviews, and major public health reports were prioritised.<br><br>RESULTS: Two-tier serology is the most common diagnostic technique, but it has limited sensitivity in early infection and does not distinguish between active and past infection. Culture and PCR are only useful in a few instances. The use of new technologies such as multiomics biomarkers, metagenomics, T-cell assays, and AI-enhanced diagnostics is promising but has not yet been tested in a prospective multicentre study. Most of the early and disseminated disease can be treated with standard antibiotics, whereas the long-term therapy of PTLD is not justified and can cause more adverse effects. These preventive and curative advancements involve VLA15 vaccination, anti-tick and reservoir-specific approaches, microbiome-engineered vectors, and anti-persister/ biofilm.<br><br>CONCLUSION: Lyme disease requires combined prevention, improved diagnostics, enhanced biomarker research, and well-designed PTLD trials. The short-term benefits will be based on the optimisation of existing diagnostics and vector control, and the long-term benefits will be based on rigorous validation of vaccines, biomarkers, and specific therapies.},
}
@article {pmid41975041,
year = {2026},
author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , },
title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41975041},
issn = {1532-1827},
support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; },
abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).<br><br>METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.<br><br>RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa&#xa0;-notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.<br><br>CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.<br><br>PROSPERO: CRD42023433704.},
}
@article {pmid41975112,
year = {2026},
author = {Liu, J and Sun, X and Yuan, P and Qin, Y and Wu, W and Fan, Y and Zhang, Y and Zou, L and Ren, C and Li, S},
title = {Clinical response and risk factors of fecal microbiota transplantation in children: a systematic review and meta-analysis.},
journal = {European journal of pediatrics},
volume = {185},
number = {5},
pages = {},
pmid = {41975112},
issn = {1432-1076},
support = {No.ZF2025046//the Hebei Provincial Department of Finance/ ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/adverse effects/methods ; Child ; Risk Factors ; *Clostridium Infections/therapy ; *Inflammatory Bowel Diseases/therapy ; *Autism Spectrum Disorder/therapy ; Treatment Outcome ; },
abstract = {UNLABELLED: The objective of this study is to investigate the clinical response and incidence of adverse events (AEs) following fecal microbiota transplantation (FMT) in children, across various diseases, populations, and treatment protocols. A systematic search was conducted across eight major Chinese and English databases, identifying 47 studies up to August 28, 2025, for inclusion. Study quality was assessed using the Quality Assessment with Diverse Studies (QuADS) tool. Single-arm rates were pooled via meta-analysis employing the Freeman-Tukey double arcsine transformation, followed by extensive subgroup comparisons to identify influencing factors. FMT demonstrated efficacy in pediatric recurrent Clostridium difficile infection (rCDI), inflammatory bowel disease (IBD), and autism spectrum disorder (ASD), although a higher incidence of AEs was observed in children with IBD. Subgroup analyses revealed that the use of donor feces from relatives or friends was associated with a higher clinical response rate in rCDI. The presence of comorbidities such as IBD diminished the response rate in rCDI patients. Younger age in rCDI and IBD patients showed a trend towards higher clinical response rates, though this did not reach statistical significance. No statistically or clinically significant differences were found in other subgroup comparisons. Meta-regression suggested IBD to be a risk factor for FMT-related AEs.<br><br>CONCLUSION: This study innovatively delineates the efficacy-safety profile of pediatric FMT and outlines a pathway for optimizing individualized treatment regimens, providing crucial evidence-based guidance for clinical practice.<br><br>TRIAL REGISTRATION: This study has been registered on the PROSPERO database (CRD42024614196).<br><br>WHAT IS KNOWN: &#x2022; Fecal Microbiota Transplantation (FMT) demonstrates preliminary therapeutic potential in several pediatric diseases. &#x2022; Existing evidence remains fragmented, with limited systematic data on factors modifying efficacy and safety in children.<br><br>WHAT IS NEW: &#x2022; The study revealed FMT's high efficacy across rCDI, IBD, and ASD, and identified IBD as a risk factor for elevated FMT-related adverse events in pediatric patients. &#x2022;&#xa0;Notably, related/friend donors improved rCDI response rates, while comorbidities like IBD reduced rCDI treatment efficacy.},
}
@article {pmid41975182,
year = {2026},
author = {Kleinbölting, N and Fiore, A and Cangioli, L and Visca, A and Huang, L and Hett, J and Costanzo, M and Sevi, F and Tabacchioni, S and Aprea, G and Mengoni, A and Pihlanto, A and Neuhoff, D and Sczyrba, A and Schlüter, A and Bevivino, A},
title = {Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47528-0},
pmid = {41975182},
issn = {2045-2322},
support = {818431//Horizon 2020 Framework Programme/ ; },
abstract = {Beneficial microbial consortia provide an eco-friendly alternative to conventional inorganic fertilizers and can serve as a complementary management tool for enhancing soil fertility and crop productivity. This study aimed to assess the impact of microbial consortia application on the indigenous maize rhizosphere microbiome under different fertilization regimes in organically managed fields in Germany. Three experimental microbial consortia (MC_B, MC_C, MC_C_AMF) and one commercial product (Micosat F) were tested in combination with three fertilization levels (unfertilized, 110 kg nitrogen ha[- 1], and 200 kg nitrogen ha[- 1]) in a split plot design. The diversity, composition and functional potential of the maize rhizosphere microbiome were analyzed at different maize growth stages. Fertilization levels exerted a stronger influence than microbial consortia, significantly shaping community composition and functional traits of the indigenous soil microbiome. Increasing fertilization intensity altered the abundance of specific plant growth-promoting (PGP)-determinants, either stimulating or suppressing potential PGP bacteria. In contrast, microbial consortia application did not impact PGP-associated abundance profiles. Overall, the results indicate that multifunctional microbial consortia can act as effective biofertilizers in sustainable maize cultivation without compromising resident microbiome diversity, thereby reducing long-term ecological risks on natural biodiversity.},
}
@article {pmid41975257,
year = {2026},
author = {Tang, Z and Zhuang, D and Duan, X and Gong, Q and Tian, C and Jiang, P and Yu, J and Li, F and Zhao, F and Shi, G and Yang, H and Du, Q and Li, T and Ye, Z and Zhang, Z},
title = {MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06444-w},
pmid = {41975257},
issn = {1471-2105},
}
@article {pmid41975274,
year = {2026},
author = {Nikolaidis, M and Hu, C and Juran, BD and McCauley, BM and Schlicht, EM and Bianchi, JK and Ali, AH and Tragaki, V and Atkinson, EJ and Johnson, S and Mars, RA and Eaton, JE and Carey, EJ and Franke, A and Schramm, C and Kashyap, PC and Go, YM and Tran, V and Teeny, S and Jones, DP and Grant, CW and Athreya, AP and Miller, GW and LaRusso, NF and Gores, GJ and Karlsen, TH and Hov, JR and Amoutzias, GD and Lazaridis, KN},
title = {Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655793},
pmid = {41975274},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolome ; Female ; Male ; Middle Aged ; Feces/microbiology/chemistry ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Liver Cirrhosis, Biliary/microbiology/metabolism/pathology ; *Cholangitis, Sclerosing/microbiology/metabolism/pathology ; Aged ; },
abstract = {Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are rare, idiopathic, chronic cholestatic liver diseases that respond differently to limited medical therapies and often lead to liver transplantation. We examined the compositional and functional differences in the gut microbiome, mycobiome, and metabolome of these diseases to better understand their impact on pathogenesis and outcomes. Stool sample metagenomes and metabolomes from patients with PSC (n = 245), PBC (n = 280) and matched controls (n = 245 and n = 278, respectively) were analyzed by shotgun sequencing and ultrahigh-resolution mass spectrometry. Comparisons were conducted with covariate-adjusted linear models. The gut microbiomes of patients with PSC and PBC were characterized by reduced diversity and increased abundance of pathobionts and virulence factors, coupled with altered microbial metabolism, including a reduction of short-chain fatty acids and B-vitamins. Untargeted stool metabolomics supported these results. Patients were stratified into groups using their microbial signatures, and each group had distinct patterns of microbiome-related changes. Cox regression analysis revealed that pathogenic microbial species were predictive of hepatic decompensation, whereas beneficial species had a protective effect. Based on previous groundwork and our new results, microbiome-based interventions such as probiotics, short-chain fatty acid supplementation, and phage therapy represent promising therapeutic options for cholestatic liver diseases.},
}
@article {pmid41975478,
year = {2026},
author = {Zhang, H and Mao, W and Lai, Z and Zhu, Y and Dong, J and Li, L and Xie, F and Zhu, W and Shen, J and Mao, S},
title = {Integrated metatranscriptomics identifies Lachnospiraceae as keystone taxa regulating rumen biohydrogenation and milk ω-6/ω-3 polyunsaturated fatty acids ratio in dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02397-7},
pmid = {41975478},
issn = {2049-2618},
support = {2022YFD1301001//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Enhancing milk nutritional quality through increased ω-3 polyunsaturated fatty acid (PUFA) content and a reduced ω-6/ω-3 PUFA ratio represents a significant opportunity for improving dairy products. While ruminal biohydrogenation substantially influences milk fatty acid (FA) composition, the specific microbial mechanisms regulating the milk fat ω-6/ω-3 PUFA ratio remain poorly characterized. This study aimed to identify key microbial taxa and metabolic pathways controlling this nutritionally relevant parameter, thereby establishing a foundation for targeted microbiome interventions to optimize milk FA profiles.<br><br>RESULTS: Analysis of 95 Holstein cows revealed that rumen bacterial community composition explained 41.0% of the variation in the milk &#x3c9;-6/&#x3c9;-3 PUFA ratio. Comparative analysis of cows with contrasting phenotypes (high-ratio, HFR; low-ratio, LFR) demonstrated distinct FA profiles across rumen fluid, serum, and milk, with &#x3b1;-linolenic acid (ALA, C18:3 C9,12,15) and linoleic acid (LA, C18:2 C9,12) emerging as critical determinants. Integrated metatranscriptomic and amplicon sequencing identified members of the family Lachnospiraceae, particularly Butyrivibrio and Eubacterium genera, as central regulators of PUFA metabolism. Notably, HFR-associated microbiomes showed enrichment of FA isomerase gene transcripts. Experimental validation using isolated strains demonstrated that B. hungatei preferentially hydrogenated ALA, while Eubacterium_I efficiently metabolized LA, establishing a mechanistic basis for differential substrate biohydrogenation that influences the final &#x3c9;-6/&#x3c9;-3 PUFA ratio.<br><br>CONCLUSIONS: Collectively, these results indicate that rumen microbial community structure and transcriptional activity are closely associated with variation in the milk &#x3c9;-6/&#x3c9;-3 PUFA ratio. Members of Lachnospiraceae appear to contribute to substrate-specific biohydrogenation processes that may influence downstream milk FA composition. These findings provide a multi-omics framework for understanding microbiome-lipid interactions and support future efforts to develop microbiome-targeted strategies for improving dairy nutritional quality. Video Abstract.},
}
@article {pmid41975790,
year = {2026},
author = {Goh, CJ and Park, J and Kim, Y and Park, D and Kim, J and Kwon, SJ and Kim, MJ and Lee, MS},
title = {Machine Learning-Based Lung Cancer Classification Using Blood-Derived Microbial DNA: A Comparative Analysis of Taxonomic Profiling Strategies.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {7},
pages = {},
pmid = {41975790},
issn = {2075-4418},
abstract = {Background: Blood-derived circulating cell-free microbial DNA (cfmDNA) has emerged as a potential non-invasive biomarker source for cancer detection. However, low biomass and high susceptibility to analytical variability raise concerns regarding the stability and interpretability of inferred microbial signatures. This study aimed to evaluate how different taxonomic profiling strategies influence downstream machine learning-based classification and feature interpretation in lung cancer. Methods: cfDNA sequencing data from 168 individuals (80 lung cancer patients and 88 non-cancer controls) were analyzed using two taxonomic profiling workflows: a Bracken-based abundance estimation approach and a BLAST-refined alignment-based strategy. Microbial profiles derived from each pipeline were evaluated using supervised machine learning models within a nested cross-validation framework. Feature stability and fold-change trends were compared across profiling strategies. Results: A Random Forest model achieved robust classification performance under both workflows (AUC 0.852 for Bracken-derived data and 0.906 for BLAST-derived data). However, substantial pipeline-dependent variation was observed in feature selection patterns and quantitative fold-change directionality. Although 13 genera were consistently selected across cross-validation folds in both workflows, the magnitude and direction of abundance differences were not uniformly concordant. Conclusions: Blood-derived microbial DNA profiles can support machine learning-based lung cancer classification; however, feature-level interpretation remains sensitive to taxonomic assignment strategy. These findings underscore the importance of pipeline-aware interpretation and methodological transparency in low-biomass blood microbiome research.},
}
@article {pmid41975843,
year = {2026},
author = {Koskinas, N and Gouva, M and Konstanti, Z and Sintou, E and Mantzoukas, S and Zagorianakou, N},
title = {Oral Self-Care as a Preventive Strategy in Medicated Older Adults: Biological Mechanisms, Genetic Susceptibility, and Public Health Implications.},
journal = {Healthcare (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {41975843},
issn = {2227-9032},
abstract = {Global population aging has led to a substantial increase in the number of older adults receiving long-term pharmacological treatment, often involving polypharmacy. Long-term medication use is often linked to negative oral health outcomes, such as xerostomia, periodontal disease, dental caries, and changes in the oral microbiome, even if it is necessary for treating systemic conditions. The general health, nutritional state, and quality of life of elderly people are all significantly impacted by these diseases. This narrative review integrates recent data on biological causes, genetic vulnerability, and public health consequences to investigate oral self-care as a preventive strategy in older persons on medication. The effects of long-term medication therapy on oral tissues, salivary function, inflammatory responses, and microbial balance are given special attention, as is the role of genetic variants linked to immunological and inflammatory pathways on individual variability. The review also evaluates oral self-care interventions aimed at reducing medication-related oral complications, such as the use of fluoride, mechanical plaque control measures, and caregiver-assisted oral care practices. Oral self-care is viewed from a public health perspective as a scalable and affordable strategy for reducing oral health disparities in older populations. The results highlight the significance of preventative, individualized, and integrated oral health interventions within larger healthcare frameworks for older persons taking long-term medications.},
}
@article {pmid41975975,
year = {2026},
author = {Szala, &#x141; and Staninska-Pięta, J and Piotrowska-Cyplik, A},
title = {Microbiome of Bovine Milk and Factors Influencing Its Composition.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41975975},
issn = {2076-2615},
support = {MEiN/2023/DPI/2870//Ministry of Science and Higher Education/ ; },
abstract = {The bovine milk microbiome is a complex and dynamic microbial ecosystem, comprising both commensal and pathogenic bacteria. Its composition is shaped by endogenous factors, including udder physiology, lactation stage, and health status, particularly mastitis, as well as by exogenous factors, such as housing conditions, farm infrastructure, milking practices, and post-milking processing. Mastitis not only alters milk quality but also induces persistent dysbiosis that may persist even after clinical recovery, highlighting the need for continuous microbiome monitoring to ensure milk safety. Advances in molecular and metagenomic techniques have enabled the detection of microbial taxa that are difficult to identify using traditional culture-based methods. However, challenges remain due to low microbial biomass, reagent contamination, and the inability to distinguish live from dead bacteria, all of which complicate accurate characterization. Environmental contamination from skin, air, and equipment, along with microbial shifts during transport, storage, pasteurization, and product separation, further modulate microbial communities. While mastitis-related changes in milk microbiota have been extensively studied, the effects of other bovine diseases and systemic health conditions remain largely unexplored, constituting a critical knowledge gap. Understanding the factors that shape milk microbial communities is essential for ensuring dairy product safety, optimizing herd management, and developing microbiome-based innovations in milk production.},
}
@article {pmid41975980,
year = {2026},
author = {Idowu, PA and Chauke, C and Mpofu, TJ},
title = {Integrated Stress Physiology and Mitigation Strategies for Heat Stress in Layer Chickens-Review.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41975980},
issn = {2076-2615},
abstract = {Heat stress is a major constraint to global egg production, as rising temperatures increasingly challenge the physiological limits of commercial layer chickens. This review integrates current advances in stress physiology to demonstrate that heat stress is not merely a thermoregulatory problem but a multi-systemic disruption involving neuroendocrine overload, metabolic imbalance, oxidative damage, immune suppression, and gastrointestinal barrier breakdown. These interacting pathways collectively impair egg production, shell quality, feed efficiency, and hen welfare. The review also synthesizes emerging mitigation strategies across environmental control, nutritional interventions, genetic and breeding innovations, welfare-oriented housing systems, and precision monitoring technologies. Studies indicate that targeted cooling, antioxidant, and electrolyte supplementation, the selection of heat-tolerant strains, enriched environments, and sensor-based early-warning systems can significantly enhance egg-laying hen resilience. Remaining gaps include a limited understanding of multi-stressor interactions, microbiome-mediated thermal tolerance, and the large-scale implementation of precision tools. The review provides a forward-looking framework for improving heat resilience in modern layer systems.},
}
@article {pmid41976013,
year = {2026},
author = {Srisa, A and Kamonpatana, P and Promhuad, K and Wongphan, P and Seubsai, A and Klinmalai, P and Harnkarnsujarit, N},
title = {Plant-Derived Functional Ingredients in Pet Nutrition: Phytochemical Classification, Mechanisms, Efficacy, and Application in Dogs and Cats.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41976013},
issn = {2076-2615},
support = {project no. FF(KU) 51.67//Kasetsart University Research and Development Institute (KURDI)/ ; },
abstract = {This review classifies plant-derived functional ingredients in pet food according to phytochemical groups and application forms, including direct oral supplementation and incorporation into complete diets. Polyphenols and plant extracts exert prominent antioxidant (singular), anti-inflammatory, immunomodulatory, and microbiome-regulating effects. Microalgae and omega-3 sources support lipid metabolism, cardiovascular function, and skin integrity. Cannabinoids demonstrate dose-dependent responses in dogs, while cats generally tolerate long-term administration and exhibit notable benefits in chronic pain management. Combinations of botanical extracts with complementary bioactives and fermented botanical preparations exhibit multi-target functionality, with dogs showing pronounced biochemical and microbiome modulation, whereas cats display more behavioral and functional improvements. Phytochemicals operate through integrated multi-level regulation, including activation of antioxidant enzymes, modulation of inflammatory cytokines and T-lymphocyte ratios, microbial metabolic shifts toward short-chain fatty acid production, and regulation of lipid metabolism. Dogs demonstrate marked effects on hepatic function, reproductive resilience, microbiome diversity, CD4+/CD8+ balance, and cholesterol control. In contrast, cats show greater benefits in inflammation reduction, pain relief, intestinal integrity, and long-term safety. These species-specific responses underscore the importance of precision formulation and highlight the emergence of plant-based "pharma-pet nutrition" integrating nutritional and biochemical strategies for targeted health promotion.},
}
@article {pmid41976101,
year = {2026},
author = {Wang, E and Han, X and Sun, W and Zheng, C and Du, W},
title = {Replacing up to 50% of Corn Silage with Triticale Silage Alters the Fecal Microbiome but Not Milk Yield or Composition in Mid-Lactation Holstein Cows.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41976101},
issn = {2076-2615},
abstract = {Diversifying forage sources may improve the sustainability and flexibility of dairy production. In a 60 d feeding trial, 72 mid-lactation Holstein cows were assigned to three treatments (24 cows/group) and fed a total mixed ration in which corn silage represented 41.16% of dietary dry matter in the control diet; 25% or 50% of this corn silage fraction was replaced with triticale silage (TS) on a dry matter basis. The study evaluated whether partial TS substitution could maintain lactational performance while affecting fecal fermentation and microbiota. Replacing corn silage with TS did not affect milk yield, 4% fat-corrected milk, major milk components, or metabolic indicators. However, 50% replacement increased fecal bacterial richness and diversity, as reflected by ACE, Chao1, and Shannon indices, and altered the overall microbial community structure. This treatment also changed fecal volatile fatty acid profiles, including increasing the proportions of branched-chain volatile fatty acids. Overall, TS can replace up to 50% of the corn silage fraction in the ration of mid-lactation cows without compromising milk production or composition, while modifying hindgut microbial ecology and fermentation patterns, thereby offering greater ration flexibility when corn silage availability is limited or costly.},
}
@article {pmid41976282,
year = {2026},
author = {Klus, W and Ossowska, J and Kowalcze, K and Kiliszczyk, A and Paziewska, A},
title = {Pathogenesis, Diagnostic Pathways, and New Therapeutic and Nutritional Strategies for Pancreatic Cancer-Associated Cachexia.},
journal = {Cancers},
volume = {18},
number = {7},
pages = {},
pmid = {41976282},
issn = {2072-6694},
abstract = {Background/Objectives: Pancreatic cancer-associated cachexia (CAC) is a complex, multifactorial and multi-organ metabolic syndrome affecting approximately 80% of patients with pancreatic ductal adenocarcinoma (PDAC). Recent epidemiological data show that cachexia is a primary cause of mortality in PDAC, directly accounting for approximately 30% of cancer-related deaths and significantly limiting the tolerability of cancer therapy and is associated with adverse effects of treatment. It is defined by systemic weight loss, skeletal muscle atrophy (sarcopenia), and adipose tissue depletion, often driven by systemic inflammation and metabolic dysregulation. Methods: The literature was searched in PubMed and Scopus using combinations of keywords. The search covers the literature between 2016 and 2026, but papers before this period were also included because of their historical importance. Studies with higher evidential value, such as prospective studies, randomized controlled trials, and meta-analyses, were prioritized and emphasized in our analysis. Results: CAC in PC arises from a systemic inflammatory response driven by tumor-host interactions and the release of pro-inflammatory mediators, such as growth differentiation factor 15 (GDF-15) and parathyroid hormone-related protein (PTHrP), which promotes anorexia and weight loss. The most commonly used diagnostic criteria include unintentional weight loss of more than 5% of body mass within 6 months, a body mass index (BMI) below 20 kg/m[2], or weight loss greater than 2% in the presence of sarcopenia. Emerging evidence supports the use of AI-based body composition analysis and novel biomarkers, including GDF-15 levels, to improve the detection and monitoring of cachexia. This review highlights that, despite the absence of pharmacological agents specifically approved for CAC in the United States and Europe, current guidelines recommend multimodal supportive care, including low-dose olanzapine, nutritional support, and exercise-based interventions. Furthermore, we identify recent phase 2 trials targeting the GDF-15 pathway, such as the GDF-15 inhibitor ponsegromab, which have demonstrated significant improvements in body weight and physical activity, suggesting a potential breakthrough in targeted therapies for CAC. Conclusions: CAC in PDAC represents a critical unmet medical need in oncology. It manifests as a lethal systemic pathology that demands early identification and targeted personalized pharmacological and nutritional interventions. Early diagnosis and targeted intervention represent promising strategies for improving survival and quality of life in this high-risk patient population.},
}
@article {pmid41976434,
year = {2026},
author = {Li, X and She, M and Yi, L and Zhou, G and Lian, Y and Yang, C and Wu, Y and Liu, Y and Han, Y and Li, J},
title = {Surfactin-Producing Bacillus velezensis A1 Inhibits Lactic Acid Bacteria in Jiang-Flavor Baijiu Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976434},
issn = {2304-8158},
support = {32021005//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; BK20233003//Jiangsu Basic Research Center for Synthetic Biology/ ; BK20202002//Natural Science Foundation of Jiangsu Province/ ; JUSRP124034//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Lactic Acid Bacteria contribute to heightened acidity in the fermentation process of Jiang-flavor Baijiu due to their production of lactic acid. High-temperature Daqu may act as a reservoir for beneficial microorganisms and antimicrobial compounds. In this study, we utilized 16S rRNA and ITS amplicon sequencing to identify microbial taxa in high-temperature Daqu that inhibit the primary lactic acid bacterium involved in Jiang-flavor Baijiu fermentation, Acetilactobacillus jinshanensis, followed by the selection of antagonistic strains. The strain exhibiting the strongest antagonistic activity was identified as Bacillus velezensis based on whole-genome sequencing. Genome analysis revealed 12 secondary metabolite biosynthetic gene clusters, from which one lipopeptide was identified. This lipopeptide was demonstrated to antagonize A. jinshanensis AJS1 by disrupting the cell membrane and inducing leakage of intracellular contents. Collectively, strain A1 and its secondary metabolites exhibit considerable promise as antagonistic agents to mitigate acidity increases triggered by A. jinshanensis AJS1 during the fermentation of Jiang-flavor Baijiu.},
}
@article {pmid41976554,
year = {2026},
author = {Liu, M and Kong, W and Zhang, T and Wu, Z and Zeng, X and Guo, Y and Pan, D},
title = {Alcohol-Induced Acute Liver Disease in Mice: A Comparison of the Preventive Effects of Fermented Milk from Lactobacillus delbrueckii Subsp. bulgaricus or Lacticaseibacillus casei.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976554},
issn = {2304-8158},
support = {32272339, 32372355//National Natural Science Foundation of China/ ; D26C200002//Natural Science Foundation of Zhejiang Province/ ; BF2025322//Jiangsu Provincial Frontier Technology Research and Development Program/ ; },
abstract = {Fermented milk is rich in probiotics, peptides, vitamins, and minerals, which are used as routine food supplements and are of great benefit for regulating human health. This study explored the mechanism of Lactobacillus delbrueckii ssp. bulgaricus CGMCC 21287 or Lacticaseibacillus casei CGMCC 15956 fermented milk for alleviating acute alcoholic liver injury. We found that fermented milk was associated with reduced activation of TLR4/NF-κB pathways, alleviating alcohol-induced liver inflammation. Meanwhile, the two probiotics regulated different intestinal microbial communities in mice. The LC group specifically increased the abundance of probiotics such as Roseburia, unidentified_Lachnospiraceae, and Allobaculum, and decreased the abundance of pathogenic bacteria such as Enterococcus and Shigella. The LB group increased the abundance of Adlercreutzia and Ruminococcus, thereby increasing butyric acid, acetic acid, and valeric acid levels and decreasing lipopolysaccharide (LPS) production. These results suggest that daily intake of fermented milk can attenuate alcohol-induced acute liver injury in mice via the gut-liver axis, though differences exist in the mechanisms of action and areas of emphasis.},
}
@article {pmid41976908,
year = {2026},
author = {Oommen, TT and Philips, CA and Ahamed, R and Theruvath, AH and Tharakan, A and Rajesh, S and Augustine, P},
title = {Palliative Healthy Donor Stool Transplantation (pFMT) in Patients with End-Stage Alcohol-Related Cirrhosis and Severe Unstable Decompensations-A Cohort Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {7},
pages = {},
pmid = {41976908},
issn = {2077-0383},
abstract = {Background and Aims: Severe alcohol-associated hepatitis (SAH) can trigger unstable decompensations in cirrhosis patients. They experience high rates of emergency department visits and hospitalization. We evaluated real-world clinical outcomes following palliative-faecal microbiota transplantation (pFMT) compared to best supportive care (BSC) in this critically ill population. Patients and Methods: From July 2021 to April 2024, 28 patients on pFMT were compared with 37 on BSC. Patients on pFMT received nasoduodenal healthy donor stool infusion daily for 5-days. Patients were followed up for portal hypertension-related events, infections, hospitalizations, extrahepatic organ failure and 6- and 12-months survival. 16S rRNA sequencing on stool samples collected at baseline and on follow up were analysed for changes in relative abundance (RA) of bacterial communities. Results: Patients were matched for age, type of decompensation and liver disease severity at enrolment. Twelve-month survival was 64.3% in pFMT versus 51.4% in BSC groups. pFMT dramatically reduced hospital readmissions (mean 0.76 ± 0.76 vs. 2.29 ± 1.27, p < 0.001). Unstable decompensations beyond 3 months occurred in 14.3% of pFMT versus 64.9% of BSC (p < 0.001). Organ failures were lesser with pFMT: acute kidney injury 7.7% versus 93.8% (p < 0.001), hepatic encephalopathy 7.1% versus 68.2% (p < 0.001). Infection burden was significantly lower (53.6% vs. 83.8%, p = 0.008), particularly infections requiring admission (17.4% vs. 66.7%, p < 0.001) with pFMT. Microbiome analysis revealed progressive expansion of Gram-negative genera in BSC, and beneficial Actinobacteria in pFMT-treated patients at 3, 6, and 12 months. Conclusions: Palliative FMT represents a unique disease-modifying intervention in end-stage alcohol-related cirrhosis, preventing organ failure progression, reducing healthcare utilization, and improving survival trajectories.},
}
@article {pmid41977084,
year = {2026},
author = {Crișan, IM and Crețu, A and Bucur, SM},
title = {Observational Study of the Association Between Oral Helicobacter pylori, Fixed Orthodontic Appliances, and Gastric Cancer Risk.},
journal = {Journal of clinical medicine},
volume = {15},
number = {7},
pages = {},
pmid = {41977084},
issn = {2077-0383},
abstract = {Background:Helicobacter pylori is a well-established risk factor for gastric carcinogenesis. Increasing evidence suggests that the oral cavity may serve as an extragastric reservoir for the bacterium, potentially contributing to persistent infection and reinfection. Orthodontic appliances can modify oral biofilm ecology and may facilitate bacterial colonization. This study aimed to investigate the association between oral H. pylori colonization and gastric cancer, while exploring the potential modifying role of fixed orthodontic appliances. Materials and Methods: In this cross-sectional observational study, 212 participants were recruited from gastroenterology and dental clinics between January 2023 and March 2025. Oral samples were collected and analyzed for H. pylori DNA using polymerase chain reaction (PCR). Gastric diagnoses were established through endoscopic examination and histopathological evaluation, classifying participants into gastric cancer, precancerous gastric lesions, non-atrophic gastritis, and control groups. Demographic, clinical, and oral health variables were recorded. Multivariable logistic regression models were used to evaluate the association between oral H. pylori detection and gastric cancer while adjusting for potential confounders, including age, sex, smoking status, oral hygiene indicators, and socioeconomic factors. Results: Oral Helicobacter pylori DNA was detected in 35/54 (64.8%) patients with gastric cancer, 30/56 (53.6%) with precancerous lesions, 21/52 (40.4%) with non-atrophic gastritis, and 15/50 (30.0%) controls. Gastric H. pylori infection was identified in 41/54 (75.9%) gastric cancer cases compared with 18/50 (36.0%) controls. Oral H. pylori positivity was more frequent among patients undergoing active orthodontic treatment (22/36, 61.1%) than among those without orthodontic appliances (79/188, 42.0%). In multivariable analysis, oral H. pylori positivity remained independently associated with gastric cancer (adjusted OR 3.02, 95% CI 1.51-6.03, p = 0.002). Conclusions: Our findings support an association between oral-gastric microbial interactions and H. pylori-associated disease, and suggest that the oral cavity may serve as a potential reservoir for gastric infection dynamics. The presence of orthodontic appliances may be associated with altered oral microbial ecology and could be linked to sustained H. pylori colonization.},
}
@article {pmid41977121,
year = {2026},
author = {Kamiński, J and Piotrowicz-Cieślak, AI},
title = {Effects of Inorganic Fluoride and the Fluoroquinolone Antibiotic Pefloxacin on the Growth and Microbiome Structure of Eruca sativa L.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977121},
issn = {1422-0067},
support = {UMO-2019/35/B/NZ7/04394//National Science Centre/ ; },
mesh = {*Microbiota/drug effects ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Pefloxacin/pharmacology ; Rhizosphere ; *Fluorides/pharmacology ; Soil Microbiology ; Bacteria/genetics/drug effects/classification ; *Sodium Fluoride/pharmacology ; Plant Roots/microbiology/drug effects/growth &amp; development ; },
abstract = {Environmental contamination with fluorinated compounds has increased markedly due to their widespread use in industry, medicine, and agriculture. Fluoride ions and fluoroquinolone antibiotics may enter soils through fertilizers, wastewater, and manure application, where they can interact with plant-associated microbial communities. In the present study, we investigated the effects of inorganic fluoride (applied as sodium fluoride, NaF) and the fluoroquinolone antibiotic pefloxacin on the growth and microbiome composition of Eruca sativa L. Plants were cultivated under controlled conditions and exposed for four weeks to NaF or pefloxacin at equimolar concentrations of 10 and 20 µM/kg soil. Morphological parameters, including biomass accumulation, root length, leaf dimensions, and leaf area, were not significantly affected by either treatment. Nevertheless, increased variability of growth traits was observed, particularly in plants exposed to NaF. High-throughput sequencing of the 16S rRNA gene revealed pronounced, treatment-specific alterations in both rhizosphere and phyllosphere bacterial communities. The rhizosphere microbiome was relatively stable at higher taxonomic levels but exhibited selective enrichment of Actinomycetota, including the class Thermoleophilia, under NaF exposure. In contrast, the phyllosphere microbiome showed strong sensitivity to fluoride, with a marked increase in Betaproteobacteria, dominated by Burkholderiales. Changes induced by pefloxacin were weaker and more diffuse. Our results demonstrate that plant-associated microbiomes respond to fluorinated compounds at concentrations that do not induce visible plant stress. The phyllosphere microbiome, in particular, represents a sensitive indicator of fluoride exposure and may serve as an early-warning system for environmental contamination.},
}
@article {pmid41977129,
year = {2026},
author = {Liu, Z and Wang, X and Li, L},
title = {Lysine Propionylation as a Metabolically Coupled PTM: Mechanisms, Functional Consequences, and Therapeutic Potentials.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977129},
issn = {1422-0067},
support = {32570698//the National Natural Science Foundation of China/ ; DUT24YG126//the Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; *Lysine/metabolism ; *Protein Processing, Post-Translational ; *Acyl Coenzyme A/metabolism ; Animals ; Acylation ; Acetylation ; Fatty Acids, Volatile/metabolism ; },
abstract = {Lysine propionylation (Kpr) is a metabolically coupled lysine acylation that links propionyl-CoA availability to the molecular regulation of gene expression and protein function. Although lysine acetylation (Kac) is the most extensively characterized, recent proteomic and metabolic studies suggest that Kpr is more frequent than previously appreciated, occurs at defined lysine sites, and displays tissue-resolved and context-dependent patterns. Kpr often co-varies with other short-chain acylations such as Kac and lysine butyrylation (Kbu); however, emerging genomic-scale evidence indicates mark-biased genomic distributions and functional associations, suggesting that Kpr is not simply an extension or alternative to Kac. Notably, propionyl-CoA, the direct acyl donor for Kpr, can be influenced by microbiome-derived short-chain fatty acids (SCFAs), implying that interventions modulating SCFA availability (e.g., dietary manipulation) may provide an actionable route to tune Kpr and related acylations. Here, we summarize recent advances in propionyl-CoA sources and compartmentalization, the enzymatic writers/erasers/readers, the molecular mechanisms underlying Kpr, and the functional consequences of Kpr in physiology and disease.},
}
@article {pmid41977159,
year = {2026},
author = {Suturina, L and Belkova, N and Sidorova, T and Smurova, N and Igumnov, I and Lazareva, L and Danusevich, I and Nadeliaeva, I and Sholokhov, L and Belenkaia, L and Atalyan, A},
title = {Gut Microorganisms as Markers of Hyperandrogenemia in Premenopausal Women with Polycystic Ovary Syndrome.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977159},
issn = {1422-0067},
support = {126020216231-0//Ministry of Science and Higher Education of the Russian Federation/ ; 1022040800022-7-3.2.2;3.2.24//Ministry of Science and Higher Education of the Russian Federation/ ; &#x410;&#x410;&#x410;&#x410;-&#x410;20-120120790036-3//Ministry of Science and Higher Education of the Russian Federation/ ; &#x410;&#x410;&#x410;&#x410;-&#x410;18-118011990043-5//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/microbiology/complications ; *Gastrointestinal Microbiome ; Adult ; Premenopause ; *Hyperandrogenism/microbiology ; RNA, Ribosomal, 16S/genetics ; Biomarkers ; Case-Control Studies ; Young Adult ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Previously, the role of decreased biodiversity of gut microbiota in polycystic ovary syndrome (PCOS) was demonstrated, but the objective criteria for assessing the representation of microorganisms associated with hyperandrogenemia (HA) were limited. A total of 175 premenopausal women (26 women with PCOS and HA and 149 women without HA, including 19 healthy controls) were recruited during the Eastern Siberia PCOS Epidemiology and Phenotype (ESPEP) Study (2016-2019). Methods included a questionnaire survey, clinical examination, pelvic U/S, blood and feces sampling. Gut microbiome was analyzed by high-throughput sequencing of the V1-V3 of the variable regions of the 16S rRNA gene (Illumina MiSeq, San Diego, CA, USA). Amplicon libraries of 16S rDNA were processed using the QIIME2 bioinformatics pipeline. All data were analyzed using R 3.6.3. The gut microbiocenosis in women with HA was characterized by a higher representation of Lactobacillus and a lower prevalence of the Clostridia class. For Faecalibacterium, Christensenellaceae_R-7_group, and [Eubacterium] eligens group the cut-off values of their relative presence, associated with HA, were estimated as: ≤0.043%, ≤0.039%, and ≤0.02%, respectively. Conclusions: Women with PCOS-associated HA demonstrate a lower prevalence, predominantly, of Clostridia class gut microorganisms, compared with those without any forms of HA. The study presents the quantitative criteria for assessing the representation of gut microorganisms, negatively associated with hyperandrogenic phenotypes of PCOS. The threshold values proposed may be useful to justify the administration of probiotics in PCOS patients with HA.},
}
@article {pmid41977176,
year = {2026},
author = {Wang, X and Wu, F and Liu, J and Hong, X and Dong, S},
title = {Application and Potential of Local Drug Delivery Systems for Antibacterial Treatment of Periodontitis.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977176},
issn = {1422-0067},
support = {jcsz2023481-10//the Healthcare Talent Development Project of the Finance Department of Jilin Province/ ; },
mesh = {Humans ; *Periodontitis/drug therapy/microbiology ; *Anti-Bacterial Agents/administration &amp; dosage/therapeutic use ; *Drug Delivery Systems/methods ; Animals ; Nanoparticles/chemistry ; Biofilms/drug effects ; },
abstract = {Periodontitis (PD) is a chronic inflammatory disease characterized by the progressive destruction of periodontal supporting tissues. As one of the most prevalent chronic diseases, PD affects more than 743 million people globally, some with serious systemic health implications. Plaque accumulation constitutes the key driver of periodontitis, initiating host inflammatory cascades and compromising periodontal microbiome equilibrium. Conventional treatment methods, such as scaling and root planing, are limited by a constrained operative field, resulting in blind spots that impede the complete eradication of bacterial biofilms and the modulation of the inflammatory microenvironment. Therefore, employing new therapeutic strategies (e.g., drug delivery systems) is essential. This review focuses on local drug delivery systems for the treatment of PD, including fibers, strips and films, microspheres, gels, nanoparticles, and vesicle systems, to deliver drugs directly into the periodontal pockets, targeting inflammation and providing sustained antibacterial effects while reducing systemic side effects. The characteristics and clinical implications of each type of local drug delivery system are discussed, along with emerging technologies such as 3D printing and nanotechnology.},
}
@article {pmid41977259,
year = {2026},
author = {Amaradasa, BS and Chretien, RL and Lowman, S and Mei, C},
title = {Transcriptomic and Root Microbiome Responses of Lettuce to Beneficial Endophytic Bacteria in Hydroponic Systems.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977259},
issn = {1422-0067},
support = {2021B-570//the U.S. Department of Agriculture's (USDA) Agricultural Marketing Service/ ; },
mesh = {*Lactuca/microbiology/genetics/growth &amp; development ; *Plant Roots/microbiology/genetics/growth &amp; development ; Hydroponics/methods ; *Microbiota/genetics ; *Transcriptome ; *Endophytes/physiology ; *Pseudomonas/physiology ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; },
abstract = {Controlled environment agriculture (CEA) relies on hydroponic systems to achieve high yields, yet optimizing plant performance remains a challenge. Beneficial endophytic bacteria offer a sustainable solution by promoting growth and nutrient uptake. Here, we investigated the mechanistic basis of growth enhancement in lettuce (Lactuca sativa) inoculated with Pseudomonas psychrotolerans IALR632 in a nutrient film technique (NFT) system. Growth measurements showed significant increases in shoot and root biomass and leaf greenness. RNA-seq profiling at 4, 10, and 15 days after transplanting revealed dynamic transcriptional reprogramming, with 38, 796, and 7642 differentially expressed genes, respectively. MapMan and GO analyses indicated up-regulation of pathways related to cell wall remodeling, lipid metabolism, nitrogen assimilation, and stress adaptation, alongside modulation of ethylene signaling. Root bacterial microbiome through 16S metabarcoding sequencing demonstrated distinct community shifts, confirmed by analysis of similarity (ANOSIM) (R = 1, p = 0.028), with enrichment of genera linked to nutrient cycling and plant growth promotion. These findings provide integrated molecular and ecological evidence that IALR632 enhances lettuce growth by coordinating host gene expression and rhizobiome restructuring, offering a mechanistic framework for microbial inoculant strategies in hydroponic horticulture.},
}
@article {pmid41977298,
year = {2026},
author = {Cycoń, M},
title = {Molecular Monitoring in Soil Bioremediation: From Genetic Potential to Verified Pathway Operation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977298},
issn = {1422-0067},
mesh = {*Biodegradation, Environmental ; *Soil/chemistry ; *Soil Pollutants/metabolism ; *Soil Microbiology ; },
abstract = {Sequence-based tools have greatly improved the molecular description of soil bioremediation, but detection alone cannot confirm that a contaminant is being degraded by a defined pathway. In soils, bioavailability limitations, redox microsites, relic DNA, gene mobility, and community restructuring can decouple gene presence from reaction flux. This review synthesizes an operational framework that separates three inferential levels: pathway potential, in situ activity, and verified pathway operation. The framework links inoculant fate, functional gene abundance, gene expression, pathway reconstruction, stable isotope probing, and targeted chemical analysis under explicit quality assurance, quality control, and decision rules. Particular attention is given to distinguishing parent compound loss from mineralization and detoxification and to using isotopic attribution when functional redundancy or inoculant-native overlap obscures agency. Instead of being presented as conceptually new, these principles are organized into a practical workflow for soil systems. This structure clarifies what can be discerned from genes, transcripts, proteins, metabolites, and transformation products at each evidentiary tier and provides a conservative basis for integrating multi-omics with mechanistic and quantitative interpretation.},
}
@article {pmid41977315,
year = {2026},
author = {Prasad, YM and Gowda, SR and Shantamurthy, N and Sehar, AEJS and Razack, SA and Srichairatanakool, S and Ravikumar, Y},
title = {Computational Identification of Triphala-Derived Sterol Compounds as Putative Agonists of the Human Takeda G Protein-Coupled Receptor (TGR5).},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977315},
issn = {1422-0067},
support = {11/2025//Chiang Mai University/ ; },
mesh = {Humans ; *Receptors, G-Protein-Coupled/agonists/chemistry/metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; *Sterols/chemistry/pharmacology ; Plant Extracts/chemistry/pharmacology ; },
abstract = {The presence of an unbalanced gut microbiome and the dysregulation of bile acid signalling are considered pivotal causes of various inflammation-based diseases. The Takeda G protein-coupled receptor (TGR5), TGR5 is a bile acid-responsive receptor that modulates inflammatory signalling pathways, making it an enticing molecular target for the discovery of novel anti-inflammatory agents. Herein, a comprehensive in silico approach was employed to identify potential TGR5 agonists from sterol-rich phytocompounds present in Triphala, a traditional polyherbal formulation. Using in silico computational methods, such as molecular docking and molecular dynamics simulations (MDS), we screened the putative agonistic potential of 10 phytocompounds obtained from Terminalia chebula, Terminalia bellirica, and Phyllanthus emblica against the crystal structure of human TGR5 (PDB ID: 7XTQ). Based on binding energy and molecular interactions, ergosterol (-12.34 ± 0.17 kcal/mol) and stigmasterol (-10.35 ± 0.04 kcal/mol) were predicted to be the top and best compounds. Furthermore, the stability of these two compounds in the docked complex was analysed using MDS for 200 ns. The mean Cα RMSD values were 0.22 ± 0.02 nm for both ergosterol- and stigmasterol-bound complexes, compared to 0.21 ± 0.02 nm for the unbound apo protein. Further, the molecular mechanics/Poisson-Boltzmann surface area (MMPBSA) analysis revealed that ergosterol exhibited binding free energy (-139.868 ± 12.318 kJ/mol) comparable to that of the co-crystallised ligand R399 -93.424 ± 8.919 kJ/mol. In silico ADMET predictions indicated acceptable drug-like properties and low toxicity for both compounds. Collectively, these computational findings suggest that ergosterol is a promising putative TGR5 agonist, warranting further experimental validation of its potential role in modulating inflammation-related pathways.},
}
@article {pmid41977345,
year = {2026},
author = {Ifrach, C and Levy-Turgeman, R and Szitenberg, A and Kesten, I and Pitashny, M and Levin-Iaina, N and Segev, Y and Yagil, Y},
title = {Gut Microbiome Signatures Distinguish Susceptibility from Disease Development in Type 2 Diabetes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977345},
issn = {1422-0067},
support = {N/A//Institutional funds/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology/etiology ; Rats ; Disease Susceptibility ; RNA, Ribosomal, 16S/genetics ; Male ; Feces/microbiology ; *Diabetes Mellitus, Experimental/microbiology ; Disease Models, Animal ; },
abstract = {Individuals may be prone or resistant to the development of type 2 diabetes. The basis for susceptibility is in part genetic, but environmental factors are likely to come into play. The gut microbiome stands at the interface of genetics and the host microenvironment. Its role in mediating susceptibility to diabetes, however, has not been resolved. Here we investigated whether the gut microbial composition contributes to susceptibility to diabetes, as distinct from disease development. We hypothesized that distinct microbial signatures modulate sensitivity or resistance to a diabetogenic diet (DD) and that separate signatures are linked to disease development. To test this hypothesis, we studied the Cohen diabetic rat model, comprising a diabetes-sensitive strain (CDs/y) and a diabetes-resistant strain (CDr/y). When exposed to DD, diabetes develops in CDs/y but not in CDr/y rats; on a regular diet (RD), both strains remain metabolically normal. To establish the contribution of the gut microbiome to susceptibility, we studied the fecal microbial composition in young, metabolically healthy CDs/y and CDr/y rats, using 16S rRNA gene sequencing, measures of α- and β-diversity, and differential taxonomic abundance. We found distinct, strain-specific gut microbiota profiles that differentiated diabetes-sensitive from -resistant animals, indicating an association between microbial composition and susceptibility. To test causality, we co-housed sensitive and resistant animals to allow passive microbial cross-transfer and fed the animals with DD. Co-housing led to partial convergence of microbial communities and significantly attenuated the diabetic phenotype in CDs/y rats, supporting a contributory and causal role for the gut microbiome in modulating sensitivity to diabetes. The resistance phenotype, on the other hand, remained unchanged. To distinguish between the contribution of the gut microbiome to susceptibility to diabetes as opposed to the development of the disease, we studied the gut microbial profiles across strains after feeding with DD or RD and the development of diabetes in CDs/y but not in CDr/y. We found distinct taxonomic signatures that differentiated diabetic from non-diabetic animals. These findings demonstrate that the gut microbiome contributes to susceptibility to diabetes with separate pathways from those linked to the development of diabetes and may represent an important modifiable determinant of diabetes risk and a target for early intervention.},
}
@article {pmid41977499,
year = {2026},
author = {Shetty, S and Luca, R and Rodriguez, SH and Skondra, D},
title = {A Potential Gut-Retina Axis in Retinopathy of Prematurity: Emerging Perspectives on Microbiome-Mediated Modulation of the IGF-1-VEGF Pathway.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977499},
issn = {1422-0067},
mesh = {Humans ; *Retinopathy of Prematurity/metabolism/microbiology/pathology/etiology ; *Gastrointestinal Microbiome ; *Insulin-Like Growth Factor I/metabolism ; Animals ; *Vascular Endothelial Growth Factor A/metabolism ; Signal Transduction ; *Retina/metabolism/pathology ; Infant, Newborn ; Dysbiosis ; },
abstract = {Retinopathy of prematurity (ROP) is a leading cause of childhood blindness characterized by disrupted physiologic vascularization followed by pathologic neovascularization, classically organized around the insulin-like growth factor-1 (IGF-1)-vascular endothelial growth factor (VEGF) axis in the retina. Increasing evidence suggests that early-life gut dysbiosis may act as an upstream modifier of this biphasic process. In this review, we synthesize human cohort studies, multi-omics analyses, and experimental animal models examining associations between the neonatal gut microbiome and ROP. Preterm infants who develop severe ROP demonstrate enrichment of facultative anaerobes and reduced acquisition of obligate anaerobes, alongside altered predicted metabolic capacity. Microbiome-derived metabolites, including short-chain fatty acids, bile acid derivatives, and lipid mediators, have been shown in experimental systems to influence systemic IGF-1 production, hypoxia-inducible factor-1α stabilization, and VEGF signaling. Rodent oxygen-induced retinopathy models offer a translation framework to assess the functional link between microbial perturbation and retinal angiogenic responses. Collectively, these findings support a conceptual microbiome-IGF-1-VEGF-retina axis in which early intestinal dysbiosis may modulate inflammatory tone, metabolic signaling, and retinal vascular development. Although current evidence remains largely associative, integrating microbiome profiling with mechanistic and longitudinal studies may clarify potential causal pathways and identify novel biomarkers or preventive strategies for severe ROP.},
}
@article {pmid41978089,
year = {2026},
author = {Singar, S and Kachouei, AA and Lantigua-Somoano, L and Manley, D and Cardinale, A and Sadikan, MZ and Kadyan, S and Shahamati, D and Dias, L and Wood, A and Chavarria, C and Rosenkranz, SK and Akhavan, NS},
title = {Ultra-Processed Foods and the Cardiovascular-Kidney-Metabolic Continuum: Integrating Epidemiological, Multi-Omics, and Translational Evidence.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978089},
issn = {2072-6643},
mesh = {Humans ; *Cardiovascular Diseases/epidemiology/etiology ; *Fast Foods/adverse effects ; *Metabolic Syndrome/epidemiology/etiology ; Metabolomics ; *Kidney Diseases/epidemiology/etiology ; Translational Research, Biomedical ; *Food Handling ; Proteomics ; Food, Processed ; Multiomics ; },
abstract = {Cardiovascular-kidney-metabolic (CKM) syndrome integrates excess adiposity, metabolic dysfunction, kidney impairment, subclinical cardiovascular diseases, and clinical events along a staged continuum that invites unified prevention and treatment. Ultra-processed foods (UPFs) are a complex, high-prevalence exposure that may influence risk across CKM stages through nutrient profiles, additives, processing-induced compounds, and packaging-related contaminants. This review synthesizes epidemiologic, mechanistic, and translational evidence with attention to exposure definition and analytic rigor. We summarize NOVA-based UPF operationalization across dietary assessment tools, highlighting misclassification of mixed dishes, brand heterogeneity, and energy under-reporting, and we propose further examination of energy-adjusted models, calibration, and harmonized metrics. Observational studies consistently associate higher UPF intake with adiposity, diabetes, chronic kidney disease, cardiovascular events, and mortality, with modest to moderate effect sizes that are heterogeneous across populations. Mechanistic data from metabolomics, lipidomics, proteomics, and the gut microbiome converge on pathways of inflammation, lipid metabolism, oxidative and metabolic stress, and intestinal barrier dysfunction; in selected cohorts, multi-omics modules account for a substantial minority of UPF-outcome associations. We outline quality-control pipelines, batch-effect prevention/correction, and multiple-testing control necessary for reproducible diet-omics. Translationally, targeted lipidomic and proteomic panels show promise for CKM risk stratification and monitoring but require validation, clinical thresholds, and guideline endorsement. Equity and global context, including differences in product mix, food systems, and care capacity, modify population impact. We conclude with a research agenda prioritizing harmonized exposure metrics, error-aware modeling, standardized multi-omics workflows, and adequately powered, stage-specific interventions capable of testing mediation and prognostic utility.},
}
@article {pmid41978103,
year = {2026},
author = {Lim, MJS and Parlindungan, E and See, E and Gan, CH and Yap, R and Yong, GJM},
title = {Diet, the Gut Microbiome, and Estrogen Physiology: A Review in Menopausal Health and Interventions.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978103},
issn = {2072-6643},
support = {C240314055//Agency for Science, Technology and Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; *Menopause/physiology ; *Estrogens/physiology/metabolism ; *Diet ; Phytoestrogens/administration &amp; dosage ; Probiotics/administration &amp; dosage ; Women's Health ; },
abstract = {Menopause represents a key transitional phase in women's health, characterized by declining estrogen levels and increased risk for cardiometabolic, musculoskeletal, and urogenital disorders. Beyond its endocrine roots, emerging evidence highlights the gut microbiome as a critical modulator of systemic hormonal balance. This review synthesizes current understanding of the bidirectional relationship between estrogen and the gut microbiome and its implications for women's health during menopause. Evidence from current studies reveals distinct findings across populations, reflecting the complexity of estrogen regulation in part by the gut microbiome (i.e., estrobolome). While no ideal gut microbial composition has been identified for women across stages of perimenopause, likely due to geographically unique gut microbiome profiles among healthy women, greater microbial diversity has been positively associated with improved estrogen regulation. Conversely, reduced diversity and altered Firmicutes/Bacteroidetes ratios have been linked to biomarkers of inflammation during perimenopause, which is a key driver across many perimenopausal symptoms. Although hormone replacement therapy remains the primary clinical intervention during perimenopause, we highlight emerging evidence on the adjuvant potential of diet, synbiotics, phytoestrogens, and strain-specific probiotics in modulating the estrogen-gut microbiome axis for improved health span trajectories and better symptom management. Future longitudinal studies integrating diet, gut microbiome profiles and symptom trajectories are essential to clarify these mechanisms across ethnicity and geography. Ultimately, understanding localized diet-microbiome interactions will enable the development of accessible, personalized, and non-hormonal strategies to complement and increase agency in proactive management during the perimenopausal transition.},
}
@article {pmid41978124,
year = {2026},
author = {Matera, M and Biagioli, V and Palazzi, CM and Meocci, M and Pedaci, F and Besostri, A and Zerbinati, N and Di Pierro, F},
title = {A One Health Decalogue for Breastfeeding: Microbiota-Targeted Strategies for Infant Gastrointestinal and Neurodevelopmental Health.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978124},
issn = {2072-6643},
mesh = {Humans ; *Breast Feeding ; Infant ; Probiotics/administration &amp; dosage ; Female ; *Gastrointestinal Microbiome/physiology ; Milk, Human/microbiology ; *Infant Health ; Infant, Newborn ; *Child Development ; Maternal Nutritional Physiological Phenomena ; *Gastrointestinal Tract/microbiology ; Infant Nutritional Physiological Phenomena ; },
abstract = {Background/Objectives: Breastfeeding represents a critical developmental window during which maternal biology, environmental exposures, and nutrition converge to influence infant gastrointestinal health and long-term developmental trajectories. From a One Health perspective, breastfeeding can be conceptualized not as a static nutritional act, but as a dynamic and modifiable biological system in which maternal factors shape early-life microbiota assembly and immune programming. This narrative review explores how microbiota-oriented strategies during breastfeeding may foster a favorable trajectory of infant health, potentially extending to transgenerational outcomes. Methods: This narrative review is structured around a ten-point decalogue addressing interconnected domains relevant to the maternal-milk-infant microbiota axis, including maternal diet, microbial diversity, environmental exposures, psychological stress and probiotic use. Current mechanistic and clinical evidence was examined to evaluate how these domains may modulate microbiota composition and function during breastfeeding. Attention was given to probiotic supplementation, including strain specificity, timing of administration, and clinical context, as well as to the broader implications of a One Health framework. Results: Available evidence suggests that maternal nutritional patterns, environmental and psychosocial exposures, and targeted microbiota-modulation strategies may influence the composition and functional properties of human milk and the developing infant microbiota. Probiotic use during breastfeeding appears to have strain-specific and context-dependent effects, with potential benefits in selected clinical scenarios. However, findings remain heterogeneous, and uncertainties persist regarding optimal strains, timing, and long-term outcomes. Conclusions: Breastfeeding can be understood as a dynamic biological interface shaped by maternal and environmental factors. Integrating microbiota-oriented strategies within a One Health framework may support infant gastrointestinal health and possibly contribute to longer-term developmental trajectories. Nevertheless, careful interpretation of the current evidence is warranted to avoid reductionist, supplement-centered approaches and to prevent maternal overmedicalization or blame.},
}
@article {pmid41978132,
year = {2026},
author = {van Wees-Jansen, ERPC and Hutten, BA and Nieuwdorp, M},
title = {The Broad Effect of Iodine in Graves' Hyperthyroidism and Its Relationship with the Gut Microbiota.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978132},
issn = {2072-6643},
mesh = {Humans ; *Graves Disease/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Iodine/administration &amp; dosage ; Diet ; Thyroid Hormones/biosynthesis ; },
abstract = {Thyroid disorders are among the most common endocrine disorders worldwide and are classified as noncommunicable diseases. These disorders are associated with significant morbidity, impaired quality of life, and considerable socioeconomic burden. Like other noncommunicable diseases, thyroid disorders arise from complex interactions between genetic susceptibility and environmental factors, including diet and lifestyle. Despite growing interest in lifestyle-based approaches to noncommunicable disease prevention and management, thyroid disorders have received comparatively limited attention in this context. Graves' disease, the most common cause of hyperthyroidism, is a relevant condition for exploring dietary interventions. Current treatment strategies-anti-thyroid drugs, radioactive iodine and thyroidectomy-have remained largely unchanged for decades. Long-term remission following drug therapy is achieved in no more than approximately 50% of patients, while all treatment modalities carry potential adverse effects. These limitations underscore the need for alternative or adjunctive therapeutic strategies. Iodine intake plays a central role in thyroid hormone synthesis. Indeed, observational studies have shown inverse associations between iodine intake and remission rates, as well as achievement of euthyroidism, medication requirements and thyroid autoantibody titers. These findings suggest that dietary iodine restriction may enhance treatment efficacy and reduce medication-related risks. Beyond its direct effects on thyroid hormone synthesis, iodine may influence Graves' disease through indirect mechanisms involving the lipid profile and the gut-thyroid axis. Autoimmune thyroid diseases are associated with a dyslipidemic profile and with gut microbiota dysbiosis; the latter characterized by increased potentially pathogenic bacteria and reduced beneficial bacteria such as Lactobacillus and Bifidobacterium.},
}
@article {pmid41978138,
year = {2026},
author = {Kase, BE and Liese, AD and Zhang, J and Murphy, EA and Steck, SE},
title = {Association Between the Dietary Index for Gut Microbiota (DI-GM) and Colorectal Cancer in the PLCO Cohort.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978138},
issn = {2072-6643},
support = {U01 CA272977-01/CA/NCI NIH HHS/United States ; P20 GM155896/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/epidemiology/microbiology/prevention &amp; control ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; *Diet ; Aged ; Incidence ; Risk Factors ; Proportional Hazards Models ; Follow-Up Studies ; Cohort Studies ; },
abstract = {OBJECTIVES: The study aimed to examine the association between a dietary index for gut microbiota (DI-GM) and the risk of incident colorectal cancer (CRC). Clarifying the role of diet-induced alterations in the composition and function of gut microbiota on the development of CRC can contribute to prevention efforts.<br><br>METHODS: Participants from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening trial enrolled in the intervention arm and who completed baseline assessments were included in the analysis (n = 55,685). The DI-GM is a literature-derived index used to score diet quality in terms of maintaining healthy gut microbiota. A time-dependent Cox model stratified by follow-up years (<5 and &#x2265;5 person-years) was used to evaluate the relationships between the dietary patterns and risk of incident CRC.<br><br>RESULTS: A total of 735 incident CRC were identified over 650,470 person-years of follow-up. During < 5 years of follow-up, those with higher diet quality (DI-GM scores above 67th percentile) had an 18% lower risk of incident CRC (HRadjusted = 0.82, 95% CI: 0.63, 1.07) compared with those with lower diet quality (DI-GM scores below the 67th percentile), though effect estimates were imprecise. During &#x2265; 5 years of follow-up, there was no association between incident CRC and DI-GM (HRadjusted = 1.01, 95% CI: 0.80, 1.26).<br><br>CONCLUSIONS: Diet quality measured using the DI-GM was associated with the risk of CRC in the first five years of follow-up in a large prospective cohort study. A diet that enhances the composition and function of gut microbiota may contribute to reduction in CRC risk.},
}
@article {pmid41978161,
year = {2026},
author = {Gala, RM and Schoeman, J and Revuelta Iniesta, R and van den Brink, M and Lovell, AL and Huibers, MHW and , },
title = {Establish Global Nutrition Research Strategies: The Meeting Report of the First SIOP Nutrition Research Forum.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978161},
issn = {2072-6643},
mesh = {Humans ; *Neoplasms/therapy ; Nutritional Status ; Child ; Global Health ; *Biomedical Research ; Pediatrics ; *Medical Oncology ; *Nutritional Sciences ; Congresses as Topic ; },
abstract = {Despite strong evidence linking nutritional status to treatment efficacy and survival in pediatric cancer, significant knowledge gaps and practice variation persist globally. On 24th October 2025, the International Society of Paediatric Oncology (SIOP) Nutrition Network, in collaboration with Prinsess Máxima Center for Paediatric Oncology and the International Initiative for Pediatrics and Nutrition (IIPAN), convened the first global SIOP Nutrition Network Research Forum. The forum brought together 54 international experts from high-income countries and low- and middle-income countries to define global nutrition research strategies for pediatric oncology. The forum addressed six emerging domains: body composition and treatment outcomes; microbiome, micronutrient status and metabolic health; prehabilitation and rehabilitation strategies; validation of nutritional assessment tools, guideline development for high-income settings; insights from international multicentric research initiatives-the International Atomic Energy Agency (IAEA), SIOP Nutrition Network, the Adapted Resource and Implementation Application (ARIA) guide nutrition portal, the International Collaboration on Nutrition in Cancer (ICONIC) WHO knowledge portal; and IIPAN and the World Cancer Research Fund (WCRF) for funding strategies. Delegates identified three priority working groups, namely prehabilitation optimization, pharmacokinetics, and advocacy, with each outlining collaborative nutrition research priorities for the next five years. This forum represents a critical point in pediatric oncology nutrition research as it established the first coordinated and internationally endorsed roadmap to bridge gaps in cancer care and ensure standard nutrition care worldwide. The research priorities and collaborations will help in creating evidence to improve cancer treatment and survival rate for children globally.},
}
@article {pmid41978176,
year = {2026},
author = {Frye, BM and Cooper, H and Negrey, JD and Sutphen, C and Nagpal, R and Kim, J and Barcus, RA and Lockhart, SN and Whitlow, CT and Tooze, JA and Yadav, H and Craft, S and Register, TC and Shively, CA},
title = {Dietary Pattern-Induced Gut Microbiota Differences Are Associated with White Matter Volume Changes in Middle-Aged Female Macaques.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978176},
issn = {2072-6643},
support = {R01 HL122393/HL/NHLBI NIH HHS/United States ; RF1 AG077443/AG/NIA NIH HHS/United States ; P30CA012197//National Cancer Institute's Cancer Center/ ; USDA-ARS-447044//United States Department of Agriculture/ ; USDA-ARS-448763//United States Department of Agriculture/ ; USDA-ARS-440658//United States Department of Agriculture/ ; FDOH-24A05//Florida Department of Health/ ; FDOH-23A02//Florida Department of Health/ ; IDSA-ALZ-ID-0000000028//Infectious Diseases Society of America/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; *Diet, Western/adverse effects ; *Diet, Mediterranean ; *White Matter/diagnostic imaging ; Amino Acids, Branched-Chain/blood ; Fatty Acids, Volatile/metabolism ; Macaca fascicularis ; Insulin/blood ; Insulin Resistance ; Feces/microbiology/chemistry ; Lipopolysaccharide Receptors/blood ; },
abstract = {Background/Objectives: Western and Mediterranean diets have divergent effects on the brain. The gut microbiome may mediate diet effects, and specific microbes may be particularly significant contributors to these processes. Oscillospira, a genus of gut-dwelling bacteria, has been implicated as a key microbial target. Other peripheral contributors may include short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), insulin resistance, and microbial translocation. Methods: We determined the effects of long-term (31 months, ~9 human years) consumption of a Mediterranean or Western-type diet on Oscillospira abundance, fecal SCFAs, plasma BCAAs, soluble CD14 (sCD14), and insulin responses in a randomized trial of 38 middle-aged female cynomolgus macaques (Macaca fascicularis). We determined diet effects and associations between dependent variables. For variables that were affected by diet composition and significantly associated with Oscillospira, we tested whether Oscillospira abundance mediated the effects of diet. Results: The Mediterranean diet resulted in higher Oscillospira (p = 0.004) and SCFAs (acetate p = 0.002; propionate p = 0.049) and lower BCAAs (isoleucine p = 0.035; leucine p = 0.007; valine p < 0.001). The Western diet increased insulin resistance (p = 0.040) and WM loss (p = 0.011). Oscillospira abundance was negatively associated with BCAAs (leucine p = 0.007; valine p = 0.005) and insulin resistance (insulin AUC: p = 0.024; increase in insulin AUC from pretreatment: p = 0.020), with trends for isoleucine (p = 0.066) and sCD14 (p = 0.103). Oscillospira abundance was positively associated with acetate (p = 0.032) and WM volume changes (p = 0.012). Oscillospira abundance significantly mediated the effects of diet on white matter volume changes (p = 0.020) and on insulin resistance (insulin AUC: p = 0.012 at study end; increase in insulin AUC during study: p = 0.020), presenting potential pathways through which diet may influence the brain. Conclusions: These findings suggest that diet-driven differences in Oscillospira are linked to metabolic regulation and white matter integrity, and Oscillospira may mediate the relationships. The results highlight a potential role for diet-microbiome interactions in shaping metabolic and brain aging trajectories.},
}
@article {pmid41978177,
year = {2026},
author = {Chan, MX and Hoh, CY and Teh, YY and Toh, XY and Ismail, NAS},
title = {Effects of Probiotic Supplementation on Core Symptoms of Autism Spectrum Disorder in Children.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978177},
issn = {2072-6643},
support = {no//Faculty of Medicine, Universiti Kebangsaan Malaysia/ ; },
mesh = {Humans ; *Probiotics/administration &amp; dosage/therapeutic use ; *Autism Spectrum Disorder/therapy/microbiology ; Child ; Adolescent ; *Dietary Supplements ; Gastrointestinal Microbiome ; Treatment Outcome ; Male ; Child, Preschool ; Female ; Randomized Controlled Trials as Topic ; },
abstract = {Background/Objectives: Increasing evidence implicates the microbiome-gut-brain axis in Autism Spectrum Disorder (ASD) pathophysiology, prompting interest in probiotics as a therapeutic strategy, although findings remain inconsistent. This systematic review aimed to evaluate the clinical efficacy of probiotic supplementation on core ASD symptoms, examine the outcome measures used, and provide insights into optimal probiotic interventions. Methods: This review was conducted in accordance with PRISMA 2020 guidelines. PubMed, Scopus, Web of Science, Ovid, ProQuest, and Wiley Online Library were searched for studies published between January 2015 and July 2025. Randomized, non-randomized, and open-label clinical studies evaluating oral probiotic supplementation in children and adolescents with ASD were included. Outcomes assessed core symptom domains using validated instruments. Study selection, data extraction, and risk-of-bias assessment (RoB 2 and ROBINS-I) were performed independently by multiple reviewers. Due to methodological heterogeneity, the findings were synthesized narratively. Results: Fourteen studies involving 924 children and adolescents with ASD across seven countries or regions were included, of which ten were randomized controlled trials. Eight studies reported significant improvement in core ASD symptoms, predominantly within the social and communication domain. The most frequently used assessment tools were the Social Responsiveness Scale (SRS), Autism Treatment Evaluation Checklist (ATEC), and Autism Diagnostic Observation Schedule (ADOS). Lactobacillus reuteri supplementation for at least three months was consistently associated with improvement in social behavior. Conclusions: L. reuteri supplementation possibly improves social and communication function in children with ASD. However, there is limited high-quality evidence on this. Evidence for other core domains remains limited and inconsistent, highlighting the need for well-designed, multicenter trials using standardized outcome measures and strain-specific hypotheses.},
}
@article {pmid41978283,
year = {2026},
author = {Sun, Y and Fu, C and Wang, Y and Peng, L and Li, S and Zhao, M and Wang, S and Shen, J and Cheng, L},
title = {ZmPHR1 and ZmPHR2 Mediate Metabolic and Microbial Regulation of Maize Adaptation to Phosphorus Heterogeneity.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70527},
pmid = {41978283},
issn = {1365-3040},
support = {328017493//Deutsche Forschungsgemeinschaft (DFG)/ ; 2366//Deutsche Forschungsgemeinschaft (DFG)/ ; 2023YFD1700203//National Natural Science Foundation of China and the National Key Research and Development Program of China/ ; 31972496//National Natural Science Foundation of China and the National Key Research and Development Program of China/ ; 32130094//National Natural Science Foundation of China and the National Key Research and Development Program of China/ ; },
abstract = {Spatial heterogeneity of soil phosphorus (P) severely constrains maize productivity, yet the regulatory mechanisms underlying plant adaptation to heterogeneous P supply remain poorly understood. This study reveals the distinct roles of the transcription factors ZmPHR1 and ZmPHR2 in mediating metabolic and rhizosphere microbial responses to heterogeneous P supply in maize (Zea mays L.). Using split-root systems combined with multi-tissue metabolomics and microbiome analysis, we show that mutation of ZmPHR2 severely impaired shoot development, photosynthetic efficiency and systemic P allocation. In contrast, ZmPHR1 mainly influenced root morphological plasticity. Loss of ZmPHR2 led to widespread repression of leaf metabolites, including organic acids and glutathione, and disrupted key pathways such as alanine, aspartate and glutamate metabolism. In root exudates, sphingolipid and histidine metabolism were critical for asymmetric root proliferation. Both mutations abolished differential root growth in P-rich patches and altered bacterial and fungal community composition and network structure. Our findings decipher a ZmPHR1/2-mediated adaptive framework integrating metabolic reprogramming and microbiome assembly, providing a mechanistic basis for breeding P-efficient maize suited to heterogeneous soils.},
}
@article {pmid41978401,
year = {2026},
author = {Wen, Q and Zhang, L and Qin, A and Li, X},
title = {[Small intestinal bacterial overgrowth and inflammatory factor expression levels in patients with asymptomatic hyperuricemia].},
journal = {Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences},
volume = {58},
number = {2},
pages = {313-318},
pmid = {41978401},
issn = {1671-167X},
mesh = {Humans ; *Hyperuricemia/microbiology/blood/complications ; Interleukin-6/blood ; C-Reactive Protein/metabolism/analysis ; Male ; Female ; Interleukin-1beta/blood ; Tumor Necrosis Factor-alpha/blood ; Middle Aged ; Adult ; *Intestine, Small/microbiology ; Breath Tests ; Case-Control Studies ; Aged ; *Blind Loop Syndrome/epidemiology ; },
abstract = {OBJECTIVE: To analyze the incidence of small intestinal bacterial overgrowth (SIBO) in patients with asymptomatic hyperuricemia (HUA) and the serum levels of C-reactive protein (CRP), interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) in patients with asymptomatic HUA and SIBO.<br><br>METHODS: A total of 87 asymptomatic HUA patients and 40 healthy controls from Shanxi Fenyang Hospital from June 2023 to June 2024 were selected as the study subjects, and the baseline data, laboratory indicators were collected. Lactulose methane-hydrogen breath test (LHBT) was used to detect the occurrence of SIBO, and the asymptomatic HUA patients was divided into SIBO-positive group and SIBO-negative group according to the test results of LHBT. The positive rate of SIBO in the asymptomatic HUA patients was analyzed, and the concentrations of H2 and CH4, the levels of CRP, IL-1&#x3b2;, IL-6 and TNF-&#x3b1; at each time point between the asymptomatic HUA patients and the healthy controls were compared, and the levels of CRP, IL-1&#x3b2;, IL-6 and TNF-&#x3b1; were compared between the SIBO-positive group and the SIBO-negative group. Multivariate Logistic regression analysis was performed to analyze the influencing factors of SIBO in asymptomatic HUA. Spearman rank correlation analysis was used to analyze the correlation between CRP, IL-1&#x3b2;, IL-6 and TNF-&#x3b1; levels and SIBO in asymptomatic HUA patients.<br><br>RESULTS: The positive rate of SIBO in the asymptomatic HUA patients was 58.62%, which was higher than that in the healthy controls (20.00%), and the difference was statistically significant (&#x3c7;[2]=16.431, P < 0.001). There were significant differences in exhaled H2 concentration between the asymptomatic HUA patients and the healthy controls at 0, 30, 60 and 90 min (P < 0.05), and there was no significant difference in exhaled CH4 concentration at each time point (P>0.05). The levels of CRP, IL-1&#x3b2;, IL-6 and TNF-&#x3b1; in the asymptomatic HUA patients were significantly higher than those in the healthy controls (P < 0.05). The serum levels of CRP, IL-1&#x3b2; and IL-6 in the SIBO-positive group were significantly higher than those in the SIBO-negative group (P < 0.05), while the levels of TNF-&#x3b1; were not significantly different between the two groups (P>0.05). Multivariate Logistic regression ana-lysis of the influencing factors of SIBO in the asymptomatic HUA showed that increased IL-1&#x3b2; (OR=1.332, 95%CI: 1.005-1.764, P=0.046) and increased IL-6 (OR=1.586, 95%CI: 1.216-2.069, P=0.001) were independent risk factors for SIBO in the HUA patients. In asymptomatic HUA patients with SIBO, the LHBT set value was positively correlated with serum IL-1&#x3b2; (r=0.594, P < 0.001).<br><br>CONCLUSION: Asymptomatic HUA patients are more likely to develop SIBO than healthy people, and SIBO in asymptomatic HUA patients is closely related to the level of inflammatory factors, so attention should be paid to the detection and intervention of SIBO in asymptomatic HUA patients.},
}
@article {pmid41979145,
year = {2026},
author = {Alderete, TL and Holzhausen, EA and Liang, D and Jones, RB and Lurmann, F and Goran, MI and Chang, HH and Sarnat, JA},
title = {Early-Life Air Pollution Exposure Is Associated with the Infant Gut Microbiome and Fecal Metabolome in the First Two Years of Life.},
journal = {Research report (Health Effects Institute)},
volume = {},
number = {237},
pages = {1-58},
pmid = {41979145},
issn = {1041-5505},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Feces/chemistry/microbiology ; Female ; *Metabolome/drug effects ; Infant ; Male ; *Air Pollution/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Pregnancy ; Particulate Matter/adverse effects/analysis ; *Environmental Exposure/adverse effects ; California ; Prenatal Exposure Delayed Effects ; Infant, Newborn ; },
abstract = {INTRODUCTION: Obesity is a major public health concern because it increases the risk of numerous diseases, including cardiovascular disease and type 2 diabetes. Ambient and near-roadway air pollution has been associated with childhood obesity risk, independent of diet and physical activity. However, the biological mechanisms underlying these relationships remain unclear. Based on our previous work and existing literature, we hypothesized that exposure to air pollutants alters the developing infant gut microbiome and fecal metabolome, with implications for childhood obesity risk. In this study, we aimed to determine whether prenatal or early-life exposure to ambient air pollution and near-roadway air pollution is associated with the gut microbiome and fecal metabolome during the first 2 years of life.<br><br>METHODS: Our analysis had two components, both of which examined participants from the Southern California Mother's Milk Study, a Latino cohort in which we collected detailed information regarding maternal and child health during the first 24 months of life. Residential-based estimates of exposure to ambient particulate matter (particulate matter &#x2264;2.5 &#xb5;m and &#x2264;10 &#xb5;m in aerodynamic diameter: PM2.5 and PM10, respectively), nitrogen dioxide (NO2), and ozone (O3), as well as near-roadway air pollution (NOx), were modeled using residential address histories. High-throughput metagenomics and metabolomics were performed on stool samples collected at 1, 6, 12, 18, and 24 months of age. Overall, our sample included 207 unique individuals with gut microbiome data and 127 unique individuals with fecal metabolomics data. In the first analysis component, we examined the cross-sectional associations of pre- and postnatal exposure to ambient and near-roadway pollutants with the infant gut microbiome and fecal metabolome at 1, 6, 12, 18, and 24 months of age. In the second analysis component, we examined the longitudinal associations of pre- and postnatal exposure to air pollutants with the trajectory of the developing infant gut microbiome and fecal metabolome.<br><br>RESULTS: Our findings indicate that exposure to air pollutants during prenatal and postnatal periods is associated with significant changes in the developing gut microbiome and its metabolic output, as evidenced by perturbations in the fecal metabolome. These molecular alterations were evident in both cross-sectional and longitudinal analyses. The results suggest that early-life exposure to air pollution can disrupt the developmental trajectory of the gut microbiome, potentially leading to changes with substantial health implications. These findings underscore the importance of mitigating air pollution exposure during critical developmental periods to protect and promote gut health and overall well-being in infants.<br><br>CONCLUSIONS: We identified gut microbes and fecal metabolites associated with early-life exposure to air pollution. Many of these markers of gut bacterial composition and function have been linked to childhood obesity. These findings contribute to our understanding of mechanisms underlying the obesogenic effects of air pollutants in early life. Future work in this cohort will include integrated mixture and multi-omics analyses to explore the joint impact of air pollution exposure on the gut microbiome and fecal metabolome.},
}
@article {pmid41979351,
year = {2026},
author = {Zhang, R and Li, Y and Zhao, X and Degen, AA and Liu, X and Lian, J and Li, Y and Wu, Y and Shang, Z},
title = {Five-year fertilization alters soil microbial composition and functionality in sandy grassland.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0296325},
doi = {10.1128/spectrum.02963-25},
pmid = {41979351},
issn = {2165-0497},
abstract = {UNLABELLED: The impacts of reclamation and fertilization of sandy grassland on soil microbial communities and functional groups related to carbon (C) and nitrogen (N) cycling are not well understood. To fill this gap, three types of fertilizers, namely, chemical fertilizer (CF), manure (M), and chemical fertilizer plus manure (CF_M), were applied annually for five years to reclaimed sandy cropland planted to maize. Nearby sandy grassland without fertilizer and maize was included as a control. Soil microbial communities and processes, soil properties, and aboveground biomass (AGB) were determined. Soil microbial Chao richness was lowest in soil without fertilizer and maize. Fungal Shannon diversity was lowest with chemical fertilizer plus manure, while soil microbial Chao richness and bacterial Shannon diversity were not influenced by fertilization. Reclamation and fertilization increased AGB, which was greatest with chemical fertilizer plus manure and was more than seven times greater than that of sandy grassland. Soil extracellular enzyme activities increased with chemical fertilizer plus manure. Fertilization enhanced C cycle functional groups by decreasing soil bulk density and elevating soil total N, total carbon, Firmicutes abundance, and bacterial Chao richness, but lessened N cycle functional groups by decreasing Nitrospirota abundance. Microbial functional category groups associated with C and N cycles responded differently to reclamation and fertilization of sandy soil, which, in turn, affected soil carbon sequestration and nutrient availability.<br><br>IMPORTANCE: Reclamation and fertilization of sandy grassland altered biogeochemical functions by influencing microbial communities and functional category groups related to carbon (C) and nitrogen (N) cycling. Reclamation and fertilization could lead to the reduction of soil C content and insufficient soil N by altering functional category groups, which would be a potential risk leading to sandy grassland degradation. These findings not only improve our understanding of the consequences of sandy grassland reclamation and fertilization on ecosystem processes, but are also important for predicting soil C sequestration and nutrient cycling and for developing strategies to prevent degradation of sandy grassland.},
}
@article {pmid41979517,
year = {2026},
author = {Pioppi, A and Gomes, SIF and Nicolaisen, M and Xu, X and Kovács, &#xc1;T},
title = {Successive cultivation under drought selects for specific microbiome members in the wheat rhizosphere.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag037},
pmid = {41979517},
issn = {1574-6941},
abstract = {Growing knowledge on plant microbiomes demonstrates the contribution of the host plant during microbiome assembly, especially under stress conditions commonly threatening crops. To dissect the influence of a plant on its microbiome, repeated cycling of microbiomes can be utilized to enhance functional properties in the enriched microbial communities. We used such a successive cultivation approach for wheat (Triticum aestivum) microbiome under drought conditions and selected lineages for drought resilience and susceptibility, with and without enriching the starting community with a library of bacterial isolates obtained from wheat. Significant differences in the rhizosphere microbiome between selection regimes were confirmed through 16S rRNA gene amplicon sequencing. Notably, replicate lineages of each selection regime showed convergence to similar microbiomes. Specific genera were abundant depending on the selection regimes; Stenotrophomonas under drought resilience, while Rahnella under drought conditions when the strain library was added initially. Applying Stenotrophomonas or Rahnella as single inoculum did not improve drought resilience in wheat. We hypothesize that complex microbiome dynamics take place during successive cultivation, which underscores the importance of considering complex plant-microbiome systems for studying plant stress resilience. Successive cultivation remains a valuable approach for observing rhizosphere microbiome changes under different conditions.},
}
@article {pmid41787255,
year = {2026},
author = {Wang, J and Yang, F and Hao, S and Dong, C and Tian, Y and Xu, Y and Yang, S and Yang, H and Xiao, X and Zheng, T and Zuo, H and Pei, X and Zhao, X},
title = {Machine learning model integrating oral microbiota and clinical features for predicting osteoporosis and bone loss in high-altitude populations.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41787255},
issn = {1471-2180},
support = {2024YFHZ0043//Science and Technology Department of Sichuan Province/ ; 2024YFFK0184//Science and Technology Department of Sichuan Province/ ; 2024NSFSC0563//Science and Technology Department of Sichuan Province/ ; XZ202301ZY0049G//Science and Technology Department of Tibet Autonomous Region/ ; HN240302C//the Project of Institute of Health New Productivity/ ; 2023SY-04//the Discipline Revitalization Project of Public Health Laboratory Sciences/ ; },
abstract = {BACKGROUND: Osteoporosis and bone loss (OP&amp;BL) are major public health challenges, especially in high-altitude environments with chronic hypoxia. Current diagnostic methods, based on low-altitude populations, are impractical for large-scale screening in resource-limited, high-altitude settings. This study developed a machine learning-based predictive model for OP&amp;BL by integrating oral microbiota data with clinical and questionnaire variables.<br><br>METHODS: We analyzed data from 560 Tibetan adults residing at high altitudes. Bone health status (OP&amp;BL vs. normal) was determined by dual-energy X-ray absorptiometry. Oral microbiota profiles were characterized via 16&#xa0;S rRNA sequencing. After feature selection using elastic net regression, five machine learning models, namely Logistic Regression (LR), Na&#xef;ve Bayes (NB), Random Forest (RF), Support Vector Machine (SVM), and Extreme Gradient Boosting (XGB), were trained (60%, 337/560) and validated (40%, 223/560).<br><br>RESULTS: Feature selection identified nine predictors: Age, Gender, BMI, oral microbial genera Abiotrophia, Frequency of spicy food consumption (H23), Tooth brushing frequency (J5), Frequency of sweet-drink consumption (J3b), Current marital status (Separated/Divorced, A5_3), and frequency of numbing food consumption (H27). The LR model demonstrated good and stable performance with an AUC of 0.885 (95% CI: 0.823&#x2013;0.937) on the test set, along with good calibration and the highest net clinical benefit. SHAP analysis indicated that oral factors Abiotrophia and Tooth brushing frequency together accounted for nearly 10% of the model&#x2019;s total predictive contribution.<br><br>CONCLUSIONS: We developed a machine learning model integrating oral microbiota and clinical data for predicting OP&amp;BL in people living above 3500&#xa0;m. This model could offer a promising non-invasive tool for early screening in resource-limited settings and highlights the potential role of oral factors in high-altitude bone health.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04718-0.},
}
@article {pmid41969125,
year = {2026},
author = {van der Molen, MK and van de Sande, M and Zandt, MI' and Saccomandi, T and Baartman, SL and Zhao, H and de Arellano, JV},
title = {Declining Ecosystem Respiration Linked to Nitrogen Deposition: Insights From a 26-Year FLUXNET Record.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70849},
pmid = {41969125},
issn = {1365-2486},
support = {NWO 2025//Ruisdael Observatory/ ; 184.034.015//Ruisdael Observatory/ ; },
mesh = {*Nitrogen/metabolism/analysis ; Netherlands ; *Soil/chemistry ; *Ecosystem ; *Soil Microbiology ; *Carbon Cycle ; *Forests ; Hydrogen-Ion Concentration ; Pinus ; Carbon/metabolism ; },
abstract = {Long-term carbon flux measurements at the FLUXNET site Loobos, a Pine forest in the Netherlands, reveal a counter-intuitive decline in total ecosystem respiration (TER) by tens of percents between 1997 and 2021. This trend cannot be explained by temperature variability or methodological changes alone. Instead, our findings point to a biogeochemical mechanism: despite a doubling of soil organic matter stocks, ecosystem respiration appears limited by decomposition rates rather than substrate availability. Soil incubation experiments indicate that microbial activity is limited by substrate quality and strongly acidic conditions (pH = 2.9), associated with large nitrogen deposition. Glucose addition experiments confirm the presence of an active microbiome, but its activity is suppressed under the present acidic soil conditions. These results raise concerns about ecosystem health under conditions of nitrogen deposition and the long-term sustainability of the observed carbon sink. Loobos may serve as an early indicator of broader ecosystem responses to environmental disturbances, as similar negative TER trends have been observed at other long-term FLUXNET sites. To advance understanding of the global carbon cycle, it is essential that observed flux trends are attributed and corroborated by changes in carbon and nitrogen stocks, and that models are continuously confronted with observational data. We therefore discuss the need of periodically measuring pH as soil acidification can be a limiting factor and suggest the need to introduce this variable in model representations of TER near regions sensitive to nitrification.},
}
@article {pmid41969207,
year = {2026},
author = {Saha, P and Roy, S and More, M and Bose, D and Trivedi, A and Brooks, BW and Syn, WK and Diehl, AM and Chatterjee, S},
title = {Underlying MASLD-induced gut microbiome dysbiosis and intestinal inflammation are key to poor outcomes in vibriosis infections in a preclinical model.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2652474},
doi = {10.1080/19490976.2026.2652474},
pmid = {41969207},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Mice ; Disease Models, Animal ; *Vibrio Infections/microbiology/pathology/complications ; Vibrio vulnificus/physiology ; Mice, Inbred C57BL ; Male ; Humans ; Inflammation/microbiology ; *Non-alcoholic Fatty Liver Disease/microbiology/complications ; Intestines/microbiology/pathology ; Female ; Liver/pathology ; Anti-Bacterial Agents ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading cause of chronic liver disease globally, especially in developed countries, including the United States. The etiology of MASLD is closely associated with several other cardiometabolic conditions and can further aggravate to more severe stages of liver disease, including steatohepatitis and cirrhosis. Moreover, patients with underlying MASLD conditions have altered gut microbiome signatures and intestinal homeostasis, leading to gut barrier dysfunction, thereby making them more vulnerable to acute gastrointestinal infections like non-cholera vibriosis. However, the exact role of the gut microbiome and intestinal pathophysiology in increasing susceptibility to infection in patients with MASLD remains poorly understood. In this study, we used oral inoculation of the bacterium Vibrio vulnificus to investigate the pathophysiological outcomes in both control and diet-induced MASLD mouse cohorts. Our results showed that non-cholera vibriosis in mice with underlying MASLD caused increased liver damage, an inflammatory surge, followed by the onset of fibrotic lesions compared to the chow-diet fed control mice, depicting a worsened outcome. Depletion of the gut bacteriome by antibiotic treatment and following fecal microbiota transplantation in these mouse cohorts showed decreased pathophysiology in the livers, indicating that an altered gut microbiome in MASLD could be a key factor in the increased likelihood of non-cholera vibriosis in patients with MASLD.},
}
@article {pmid41969232,
year = {2026},
author = {Du, Y and Zhao, M and Zuo, Z and Sun, Y},
title = {Bioelectric Profiling of Atopic Dermatitis: From Molecular Barrier Defects to Closed-Loop Theranostic Strategies.},
journal = {Experimental dermatology},
volume = {35},
number = {4},
pages = {e70250},
doi = {10.1111/exd.70250},
pmid = {41969232},
issn = {1600-0625},
support = {81741128//the National Natural Science Foundation of China/ ; 81401553//the National Natural Science Foundation of China/ ; //National Innovation and Entrepreneurship Program of Northwestern Polytechnical University/ ; W007101//Innovation Program for the Undergraduate International Student of the School of Life Science and Technology, NPU/ ; 23JRRA701//Gansu Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *Dermatitis, Atopic/physiopathology/diagnosis/therapy ; Filaggrin Proteins ; Dielectric Spectroscopy ; Cytokines/metabolism ; Skin ; Theranostic Nanomedicine ; Animals ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory dermatosis characterised by skin barrier disruption and immune dysregulation. Current clinical scoring systems (e.g., SCORAD) often fail to quantify subclinical pathophysiology or characterise the biopharmaceutical interface. This review synthesises the 'bioelectric profile' of AD, integrating electrical impedance spectroscopy (EIS) and current perception threshold (CPT) to construct a precision phenotyping framework. Evidence indicates that EIS non-invasively quantifies barrier integrity, with specific parameters (e.g., EIS[diff]) that correlate positively with terminal differentiation proteins such as filaggrin, serving as a surrogate marker of molecular permeability. Concurrently, neuroselective CPT assessment reveals abnormal C-fibre sensitisation in non-lesional skin, distinguishing extrinsic from intrinsic AD phenotypes. Furthermore, we explore reciprocal interactions between bioelectric parameters, Th2/Th22 cytokines (e.g., IL-31, IL-13) and the microbiome. Finally, we discuss translating these signatures into closed-loop theranostic strategies for feedback-controlled drug delivery. This bioelectric panorama provides a unique biophysical perspective on AD pathogenesis and a theoretical foundation for future precision medicine.},
}
@article {pmid41969349,
year = {2026},
author = {Cheng, L and Wang, J and Sun, J and Xu, S and Zhao, G and Li, M},
title = {Integrated multi-omics of the ruminal microbiome and host metabolome reveals compensatory growth in response to dietary energy restriction and re-alimentation in growing beef bulls.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {265-281},
pmid = {41969349},
issn = {2405-6383},
abstract = {Understanding the mechanisms of dietary energy on compensatory growth in beef cattle is crucial for improving feed efficiency and mitigating the environmental footprint of beef production. The objectives of the study were to investigate the effects of dietary energy restriction and subsequent re-alimentation on growth performance, nutrient digestibility, ruminal microbiome, plasma metabolites, and nitrogen metabolism in growing beef bulls. Twelve 6-8-month-old Simmental crossbred bulls (initial body weight: 226 ± 24 kg) were randomly allocated to two groups (n = 6 per group): the dietary energy restriction group (REC) was fed a diet containing 9.25 MJ/kg metabolizable energy (ME) for 4 weeks (energy restriction period), followed by a 2-week re-alimentation period with a 10.29 MJ/kg ME diet, while the control group (CON) was fed the 10.29 MJ/kg ME diet consistently throughout the experimental period. Dietary energy restriction significantly decreased body weight and average daily gain (ADG) compared to CON (P < 0.05). However, no significant differences were observed by the end of the re-alimentation period (P > 0.05), demonstrating successful compensatory growth through dietary energy modulation. Ruminal propionate, total volatile fatty acids, ammonium nitrogen, and microbial crude protein (MCP) concentrations significantly decreased in the energy restriction treatment compared to CON (P < 0.05), but MCP exceeded the levels in CON after dietary energy re-alimentation (P < 0.05). Energy restriction also significantly increased urinary nitrogen excretion (P = 0.002), driven by imbalanced amino acid metabolism and significantly increased urinary urea (P = 0.038), which significantly reduced protein synthesis and nitrogen retention (P = 0.017). Metagenomics analysis revealed that energy restriction significantly increased the relative abundances of Limosilactobacillus, Enterococcus, and Aliarcobacter (P < 0.05), while decreasing those of Gemmatirosa and Mesorhizobium (P < 0.05). Dietary energy re-alimentation significantly increased the relative abundance of Gramella, Acetobacter, Phaeobacter, and Flammeovirga (P < 0.05). These bacteria are associated with pathways related to amination, transamination, and microbial protein synthesis. Integrated multi-omics revealed shifts in the ruminal microbiome and host metabolome, particularly in pathways related to ruminal urea hydrolysis, biosynthesis of glutamate, glutamine, and alanine, and post-absorptive amino acid metabolism, which collectively enhanced protein synthesis and compensatory growth. These findings establish a practical feeding strategy to optimize feed efficiency and enhance compensatory growth in beef bulls via short-term dietary energy manipulation.},
}
@article {pmid41969353,
year = {2026},
author = {Wei, Y and Wei, Y and Liu, C and He, Y and Ruan, S and Huang, Y and Wang, L and Yang, X and Yi, H},
title = {Biosynthetic reuterin improved the intestinal health in pigs.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {212-227},
pmid = {41969353},
issn = {2405-6383},
abstract = {This experiment aimed to study the effects of dietary supplementation with biosynthetic reuterin (RT) from Escherichia coli cells on the growth performance and intestinal health of pigs. A total of 72 pigs (Duroc × Landrace × Yorkshire, 21 d old, 5.7 ± 0.3 kg weight) were randomly divided into basal diet group (CON), basal diet supplemented with 5 × 10[10] colony-forming unit (CFU)/kg Lactobacillus reuteri group (LR), and basal diet supplemented with 50 mg/kg reuterin group (RT) with 6 pens (4 pigs per pen) per group for a 14-d period. One piglet was randomly selected from each pen on the 15th d for sampling. The results showed that the addition of RT to the diet significantly improved the growth performance of piglets, specifically increasing average daily gain (ADG; P = 0.004), and reduced diarrhea rate (P = 0.012), improved the intestinal morphology by significantly increasing villus height and the villus height to crypt depth ratio (P < 0.05), and enhanced intestinal barrier and immune functions by upregulating the expression of related genes (ZO1, MUC1, pBD2, and PR39; P < 0.05). Simultaneously, RT upregulated TLR gene expression and activated the MAPK signaling pathway (P < 0.05). Combined analysis of microbiome and non-targeted metabolomics showed that RT improved metabolism by affecting the relative abundance of Phascolarctobacterium succinatutens YIT12067 (known for succinate production and impacting energy metabolism) and Holdemanella (implicated in carbohydrate metabolism and immune modulation) in pigs (P < 0.05). In addition, RT significantly reduced the deposition of intestinal collagen (P < 0.05). In conclusion, this study demonstrated that biosynthetic RT effectively improved the growth and intestinal health of pigs, which may provide some theoretical basis for the RT production as a feed additive.},
}
@article {pmid41969354,
year = {2026},
author = {Dayan, J and De Cesare, A and Soglia, F and Zampiga, M and Indio, V and Antenucci, EL and Petracci, M and Sirri, F},
title = {Nutritional alternatives to commercial lipid sources: Impact of the dietary inclusion of black soldier fly (Hermetia illucens) larvae oil on broiler chicken productivity, breast meat quality traits and caeca microbiome.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {255-264},
pmid = {41969354},
issn = {2405-6383},
abstract = {Protein production from poultry, particularly broiler chickens, is considered a key component of future global food security, due to its relatively high sustainability. However, the use of resources such as soybean oil remains a concern. Black soldier fly (Hermetia illucens [HI]) larvae oil represents a promising alternative due to a relatively rapid rearing cycle and ability to utilize organic waste as growth substrates. This study investigated how replacing a commercial lipid source such as soybean oil, with HI larvae oil affects broiler growth performance, meat quality traits, fatty acid (FA) profile, and caeca microbiome. A total of 552 one-d-old male Ross 308 broilers, with equal initial weights (48.89 ± 0.18 g; P = 0.597), were allocated to three dietary treatments with 8 replicate pens per group (23 birds/pen). All birds received the same commercial basal diet, formulated to be isoenergetic and with the same amino acid profile, differing only in the source of the supplemented oil: 100% soybean oil group (CON), 50% soybean oil + 50% HI larvae oil group (MIX), or 100% HI larvae oil group (HIO). Growth performance parameters were recorded at the end of each feeding phase (14, 28, and 42 d). At slaughter (42 d), 10 breasts (pectoralis-major muscle) and thighs (extensor-iliotibialis muscle) samples per group were collected for meat quality assessment, and caecal content samples were obtained from 8 birds/group for microbiome analysis. Growth performance metrics showed an improvement in feed conversion ratio during the starter phase for HI larvae oil-fed groups (1.54 vs. 1.45 vs. 1.46 for CON, MIX, and HIO, respectively; P < 0.001) and comparable performance across the trial. Meat quality traits remained within commercially acceptable ranges, with minimal effects observed, apart from variations in breast fillet redness and thigh protein oxidation. FA analysis indicated higher levels of saturated FAs in the HI groups, with a concurrent reduction in omega (n)-6 levels and a more balanced n-6 to n-3 ratio (16.47 vs. 15.18 vs. 11.60 for CON, MIX, and HIO, respectively; P < 0.001). The caecal microbiome revealed stable diversity across groups, with only minor shifts in relative abundance. Overall, the findings showed that HI larvae oil is an effective alternative to conventional vegetable lipid sources in poultry nutrition, with added potential to enhance growth performance during the early growth stages.},
}
@article {pmid41969555,
year = {2026},
author = {Attard, TM and St Peter, SD and Kats, A and Lagemann, DR and Lawson, CE and Roy, BC and Yusuf, K and Harvey, L and Bhanja, P and Chugh, RM and Saha, S and Washburn, MP and Umar, S},
title = {Molecular and regional characterization of colorectal polyps: insights from proteomics, phosphoproteomics, and immune profiling.},
journal = {Translational gastroenterology and hepatology},
volume = {11},
number = {},
pages = {44},
pmid = {41969555},
issn = {2415-1289},
abstract = {BACKGROUND: Familial adenomatous polyposis (FAP) is an inherited predisposition to colorectal cancer and characterized by profuse colorectal adenomas starting from the second decade of life. Regional (left vs. right) differences in the colonic microbiologic and immunologic microenvironment may impact adenoma evolution but are poorly understood. We aimed to characterize regional molecular, microbial, DNA damage, and immune differences in pediatric FAP polyps to test the hypothesis that polyps in pediatric FAP exhibit distinct regional and molecular features that contribute to differential growth and genomic instability.<br><br>METHODS: Colonic polyps and adjacent non-polyp mucosa were harvested from pediatric FAP patients undergoing colonoscopy. Tandem mass tag-based proteomic and phosphoproteomic profiling was performed and were followed by functional assays including colony formation, spheroid growth, and patient-derived organoid culture. &#x3b3;H2AX staining was used to quantify induction of DNA double-strand breaks (DSBs) in HCT116 colon cancer cells cultured in Fusobacterium nucleatum conditioned media (FnCM). Immunohistochemistry and immunofluorescence were used to assess ATR, CDK4, &#x3b3;H2AX, and oxidative damage (8-OxoG). Immune profiling was performed by flow cytometry, focusing on CD103[+] tissue-resident memory T cells (TRMs).<br><br>RESULTS: Right-sided polyps exhibited increased ATR and CDK4 expression compared with left-sided lesions and adjacent mucosa. FnCM exposure induced a marked increase in &#x3b3;H2AX staining in HCT116 cells, consistent with our in vivo findings of elevated DSB burden in proximal versus distal FAP polyps. Biofilm enrichment and higher microbial staining were observed in right-sided lesions, whereas distal polyps were enriched with CD103[+] TRM populations. Pharmacologic inhibition of ATR or CDK4 significantly suppressed both colony formation and spheroid growth. Organoids derived from proximal colon polyps exhibited accelerated growth and crypt budding, with higher expression of stemness markers (CD44, CD133, Lgr5, BMI-1) compared with distal polyps.<br><br>CONCLUSIONS: Integrated proteomic, phosphoproteomic, and immune-microbiome profiling reveals regional heterogeneity of adenomas in pediatric FAP. Right compared to left sided polyps harbor greater DNA damage, elevated ATR/CDK4 kinase activity, reduced immune surveillance, and increased stem-like growth. These findings identify ATR and CDK4 as potential therapeutic targets and suggest that regional microenvironmental differences can impact chemoprevention strategies in pediatric FAP.},
}
@article {pmid41969565,
year = {2026},
author = {Kavagutti, VS and Beavogui, A and Wiart, N and Wincker, P and Oliveira, PH},
title = {Defensomes, counter-defensomes, and the remodeling of microbial communities.},
journal = {PNAS nexus},
volume = {5},
number = {4},
pages = {pgag073},
pmid = {41969565},
issn = {2752-6542},
abstract = {Bacteria and mobile genetic elements (MGEs) have coevolved for billions of years in an enduring evolutionary arms race, leading to the emergence and diversification of a vast arsenal of defense and counter-defense systems. In the last recent years, high-throughput screening methods and genome-resolved metagenomics have markedly enhanced our understanding of the diversity and abundance of immune systems across cultured and uncultured microorganisms. This fueled subsequent interest in better understanding the dynamic tri-kingdom interplay between bacteria, bacteriophages, and eukaryotic cells, and led to renewed efforts to improve alternative antibacterial phage-based therapies. Here, we discuss the evolutionary and ecological dynamics underlying the bacteria-MGE arms race, recent findings on bacterial defensomes, MGE counter-defensomes, holodefensomes, and their key role in the development of microbiome-targeted therapies. To this end, we argue why and how highly conserved anti-MGE defense systems should be prioritized as promising targets for the development of next-generation bacterial inhibitors with broad biomedical relevance, supported by a comprehensive analysis of their distribution and diversity across bacteria.},
}
@article {pmid41969649,
year = {2026},
author = {Ryan, LK and Duran-Pinedo, AE and Irelan, DW and Mulcahy, B and Galeas-Pena, M and Glover, SC and Frias-Lopez, J and Diamond, G},
title = {Vitamin D deficiency in mice modulates oral microbiome stability over time and leads to changes in host inflammatory gene expression pathways.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1775097},
pmid = {41969649},
issn = {2235-2988},
mesh = {Animals ; *Vitamin D Deficiency/microbiology/complications ; Mice, Inbred C57BL ; Mice ; *Microbiota ; Disease Models, Animal ; *Inflammation ; *Mouth/microbiology ; Male ; Vitamin D ; },
abstract = {INTRODUCTION: We previously showed that vitamin D deficiency leads to gingival inflammation and alveolar bone loss in mice, and that topical vitamin D3 administration prevents that bone loss and inflammation and fosters a health-associated oral microbiota in a murine ligature model of periodontal disease. To understand the relationship between vitamin D, the oral microbiome, and host factors, we performed taxonomic profiling of the oral microbiome from C57Bl/6 mice fed either a vitamin D-deficient diet or a standard diet.<br><br>METHODS: This was a 13-week study, with a group crossover period at week 7. Oral microbiomes were sampled weekly. At the end of the 13 weeks, single-cell analysis was performed on the gingival and buccal tissues.<br><br>RESULTS: During the first 6 weeks, the vitamin D3-deficient group 1 showed higher diversity at the start of the experiments but was more volatile in alpha-diversity values, with a notable dip in diversity at week 8. Group 2 showed lower initial diversity but was more stable by mid-study and remained relatively higher during the period where group 1 diversity crashes (weeks 6-8). The most striking feature occurs around weeks 6-8, coinciding with the change in vitamin D diet, group 1 plummets while group 2 either remained stable or rose.<br><br>DISCUSSION: This showed that elimination of vitamin D3 in the diet altered the diversification of bacterial species in favor of an oral microbiome associated with inflammation and bone loss. This persistent dysbiosis contrasts with the transcriptomic changes, which showed mice on a vitamin D deficient diet displayed an overall enrichment of gene sets involved in epithelial development, suggesting that re-introduction of vitamin D into the diet may help improve mucosal barrier health in the face of persistent microbiome dysbiosis.},
}
@article {pmid41969652,
year = {2026},
author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X},
title = {Correction: Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1826950},
doi = {10.3389/fcimb.2026.1826950},
pmid = {41969652},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1726935.].},
}
@article {pmid41969654,
year = {2026},
author = {Kubba, R and Kejriwal, S and Razzouk, J and Evans, JR},
title = {Megasphaera in the gut microbiome and cancer: from Megasphaera elsdenii dysbiosis to Megasphaera sp. XA511 in tumor microenvironments.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1766220},
pmid = {41969654},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Tumor Microenvironment ; *Dysbiosis/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Neoplasms/microbiology ; Lung Neoplasms/microbiology ; },
abstract = {Growing evidence suggests that the gut microbiome and specific gut microbes influence carcinogenesis both within the gastrointestinal tract and in distant organs through immune, metabolic, and inflammatory pathways. Megasphaera elsdenii, a gram-negative-staining, strictly anaerobic member of the Veillonellaceae family, has been implicated in disruption of colonic epithelial homeostasis and may exert systemic effects beyond the intestine. While much attention has focused on the gut-brain axis, this mini-review synthesizes current evidence linking intestinal dysbiosis, microbial metabolite signaling, and immune crosstalk along the gut-lung axis. By integrating findings from studies on microbial translocation, mucosal immunity, and metabolite-mediated inflammation, we present a hypothesis-generating model in which M. elsdenii-driven gut dysbiosis may shape lung cancer pathogenesis through short-chain fatty acid-dependent immunometabolic signaling and hypothesized lymphatic and outer membrane vesicle-mediated pathways, recognizing that existing lung data derive solely from non-causal, genus-level 16S rRNA surveys. We further distinguish viable colonization from detection of immunogenic DNA and vesicular debris in distal tissues and discuss the context-dependent roles of the genus, contrasting the systemic pathogenicity of M. elsdenii in the gut-lung axis with the divergent, protective metabolic profile of a distinct gut-derived strain, Megasphaera sp. XA511, in pancreatic tumor microenvironments. This framework highlights Megasphaera as an understudied but potentially actionable modulator of cancer immunobiology.},
}
@article {pmid41969655,
year = {2026},
author = {Sohrabi, A and Sadeghi, F and Zagai, U and Andreasson, A and Vieth, M and Agréus, L and Talley, NJ and Ye, W},
title = {Duodenal microbiota profiling and its effects on gastrointestinal tract dysfunction.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1761015},
pmid = {41969655},
issn = {2235-2988},
mesh = {Humans ; Middle Aged ; Female ; *Duodenum/microbiology/pathology ; Male ; Cross-Sectional Studies ; Adult ; RNA, Ribosomal, 16S/genetics ; Aged ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Diseases/microbiology ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; Young Adult ; Biodiversity ; *Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: Duodenal microbiota has been proposed to be associated with gastrointestinal dysfunction, but population-based data are sparse. Profiling duodenal microbiota using 16S rRNA approach would appear to be a powerful tool for better understanding its role in gastrointestinal manifestations.<br><br>METHODS: In a population-based cross-sectional study, 265 adult subjects chosen randomly underwent symptom assessment, upper endoscopy, and gastroduodenal biopsies, with collection of duodenal brushing specimens. The 16S rRNA gene (V3-V4 region) sequencing was conducted using Illumina[&#xa9;] MiSeq platform. The microbiome taxonomy was constructed and classified to identify the microbiota composition. The diversity and composition were compared among subjects categorized based on gastrointestinal dysfunction, histopathological features, and demographic characteristics.<br><br>RESULTS: The five most abundant genera in individuals with a normal duodenum were Streptococcus (33%), Veillonella (12%), Prevotella (11%), Rothia (5%), and Actinomyces (5%). Alpha diversity metrics showed that there were no significant differences among the participants with different demographic or histopathological features. However, the beta diversity of the duodenal microbiota differed significantly between current smokers and non-smokers, and across education level, BMI, as well as age groups. Furthermore, alteration of duodenal microbiota diversity was strongly associated with the presence of non-H. pylori gastritis or the co-occurrence of gastroesophageal reflux and functional dyspepsia based on Adonis R&#xb2; (PERMANOVA) test (P < 0.05). Differential abundance of duodenal microbiota composition analysis at genus level illustrated that known pathogens and commensal bacteria, such as Sphingomonas, Lactobacillus, Streptococcus, Sphingomonas, Neisseria, Veillonella, Staphylococcus, Haemophilus, Gemellacea, and Intrasporangiaceae, were related to different histopathological manifestations.<br><br>CONCLUSION: Alterations of duodenal microbiota signatures are linked to smoking, aging, BMI, education and gastroduodenal disorders. Further mechanistic studies are warranted to further explore the potential effects of duodenal microbiota on gastrointestinal health.},
}
@article {pmid41969757,
year = {2026},
author = {Anderson, SM and Cing, Z and Drewes, JL and White, JR and Southward, T and Beauregard, H and Ferri, JT and Wanyiri, JW and Roslani, A and Vadivelu, J and Tang, SN and Queen, J and Sears, CL},
title = {Clostridioides difficile Detection in a Human CRC Cohort.},
journal = {Open forum infectious diseases},
volume = {13},
number = {4},
pages = {ofag169},
pmid = {41969757},
issn = {2328-8957},
abstract = {BACKGROUND: The role of the gut microbiome and specific enteric bacteria in influencing the development of colorectal cancer (CRC) remains incompletely understood. Recently, it was shown that human CRC-derived strains of Clostridioides difficile were capable of inducing colonic tumorigenesis in a susceptible mouse model. We hypothesized that C. difficile contributes to the pathogenesis of human CRC and would be enriched in CRC tumors compared to paired normal tissues from the same individual.<br><br>METHODS: We analyzed matched tumor/normal tissue samples from a cohort of 108 individuals presenting to a tertiary care hospital in Kuala Lumpur, Malaysia, for CRC resection between 2013 and 2014. We assessed the prevalence of C. difficile detection using 16S rRNA amplicon sequencing with high-resolution taxonomic assignment as well as culture and PCR.<br><br>RESULTS: We found that detection of C. difficile was prevalent (38% of individuals), but of low abundance (tumor median relative abundance 0.01%, paired normal 0.006% [P = .4]). Detection of C. difficile was more prevalent in individuals with biofilm-positive tumor tissues than biofilm-negative (ie, 81% of C. difficile-positive individuals were biofilm-positive vs 63% of C. difficile-negative individuals [P = .04]). Additionally, in exploratory analyses, we describe patterns of taxonomic and inferred functional pathway differences between C. difficile-positive and C. difficile-negative groups.<br><br>CONCLUSIONS: These findings suggest that C. difficile is frequently present in low abundance in the tumor microbiome with a potentially significant impact on community composition and function.},
}
@article {pmid41969917,
year = {2026},
author = {Osuji, IE and Akanmu, AO and Babalola, OO},
title = {Leveraging Microbe-Rhizosphere Interactions in Organic Farming Systems: A Route to Sustainable Soybean Production.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {7},
number = {2},
pages = {e70147},
pmid = {41969917},
issn = {2575-6265},
abstract = {Soybean (Glycine max L.) is a major legume crop of global agricultural significance, and its yield is heavily dependent on the rhizospheric microbes. Conventional farming systems can enhance yields in the short term but often at the expense of soil health and biodiversity. Organic farming systems, by contrast, avoid the use of synthetic inputs and depend on microbial processes to achieve yield. This review aggregates peer-reviewed literature on organic soybean farming systems, drawing from a body of work that has characterized the diversity, composition, and functions of rhizospheric microbes in these systems. Organic amendments such as compost, manure, and biochar enhance the abundance of microbial communities in the rhizosphere of organic soybean crops, buffer soil pH, and improve soil structure. Organic soils have greater microbial biomass and functional activity than conventional soils, with increased populations of bacteria such as Bradyrhizobium, arbuscular mycorrhizal fungi, Trichoderma, Streptomyces, and phosphate-solubilizing bacteria. The rhizospheric microbes are responsible for processes such as nitrogen fixation, phosphorus acquisition, organic matter decomposition, and induced systemic resistance (ISR). Measures of soil health, such as microbial biomass, enzyme activity, respiration rates, and soil organic matter (SOM) content, all demonstrate that organic farming systems have greater ecological value than conventional systems. Organic soybean production systems foster distinct rhizosphere microbial assemblages that confer measurable functional benefits to the agroecosystem. Future research is required in microbiome engineering, biostimulant design for specific applications, biomarkers for monitoring changes in soil microbiology, and precision organic farming systems. This review demonstrates that microbe-rhizosphere interactions are a key factor to consider in the development of sustainable agricultural practices for soybean production.},
}
@article {pmid41970196,
year = {2026},
author = {Agache, I and Li, S and Zheng, Y and Gao, Y},
title = {Asthma endotypes and theratypes.},
journal = {Chinese medical journal pulmonary and critical care medicine},
volume = {4},
number = {1},
pages = {19-38},
pmid = {41970196},
issn = {2772-5588},
abstract = {The model of asthma as a single entity has now been replaced by a much more complex biological network of distinct and interrelating inflammatory and tissue driven pathways. Individual disease manifestations (phenotypes), pathogenetic pathways (endotypes) and response to therapy (theratypes) are discussed here in the context of current stratified management of asthma in the clinic based on biomarkers measured at the point-of-care. As the current classification criteria result in significant overlaps among phenotypes, endotypes and theratypes, this paper further describes the advantage of combining precision immunology, imaging and the digital biomarkers in an unbiased approach offered by machine learning. The new European Academy of Allergy and Clinical Immunology (EAACI) nomenclature for hypersensitivity reaction is detailed as a basis for the stratified asthma management with a special focus on tissue-driven mechanisms (type V asthma), metabolic/microbiome/epigenetic/neurogenic mechanisms (type VI asthma) and direct cellular activation (type VII asthma).},
}
@article {pmid41970284,
year = {2026},
author = {de Kreek, KA and Gols, R and de Zeeuw, JM and van Dam, I and Nijhof, R and Noordijk, BS and Dicke, M and Kloth, KJ},
title = {Caterpillar-induced plant-soil feedback affects resistance in wild and cultivated cabbage.},
journal = {Plant and soil},
volume = {520},
number = {2},
pages = {1721-1740},
pmid = {41970284},
issn = {0032-079X},
abstract = {BACKGROUND AND AIMS: Aboveground insect herbivory can change the plant rhizosphere and modulate the composition of the soil microbiome. However, it is unclear to what extent these changes in the rhizosphere affect plant resistance to above-ground herbivorous insects, and how these plant-soil feedback (PSF) mechanisms are shaped. Here, we investigated whether herbivore-induced changes in the rhizosphere increase resistance against caterpillars in cabbage, Brassica oleracea, and how intraspecific variation of the host plant, herbivory intensity, and soil type affect PSF outcomes.<br><br>METHODS: PSF experiments with rhizosphere-soil transfer were performed for a wild and cultivated B. oleracea, with different densities of the caterpillar Mamestra brassicae, and different soil types.<br><br>RESULTS: We found that caterpillar-induced soil conditioning affected the performance of M. brassicae feeding on the shoot, depending on both intraspecific variation of the host plant and the intensity and duration of herbivory. On wild cabbage, caterpillar-induced PSF positively affected plant resistance to M. brassicae, which needed more than two weeks to become detectable. In contrast, in cultivated cabbage, caterpillar-induced PSF had a neutral to negative effect on plant resistance and did not differ between soil types. The observed negative PSF effect was associated with downregulation of genes involved in jasmonic acid biosynthesis and downstream signalling.<br><br>CONCLUSION: Overall, we found that natural variation within one plant species can, depending on intensity and duration of herbivory, result in opposite PSF effects with consequences for jasmonic acid-mediated defences.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-026-08355-4.},
}
@article {pmid41970365,
year = {2026},
author = {Bradshaw, AJ and Poo, S and Malter, TE and Strasbaugh, RM and Bodner, B and Hincher, MR and Devan-Song, A and Tabima, JF},
title = {Characterization of a Core Fungal Community and Captivity-Induced Gut "Mycobiome" Change in Fowler's Toad (Anaxyrus fowleri).},
journal = {Ecology and evolution},
volume = {16},
number = {4},
pages = {e73430},
pmid = {41970365},
issn = {2045-7758},
abstract = {Amphibious animals, such as frogs, are found at the intersection of aquatic and terrestrial ecosystems. They may serve as keystone and sentinel species and play key roles in nutrient cycling and food webs. In recent decades, amphibians have experienced drastic population declines due to habitat loss, climate change, and disease. These declines have prompted investments in ex situ conservation and captive breeding programs, which aim to reduce extinction risk by creating assurance colonies and reintroducing individuals once threats are mitigated. A critical component of these programs is proper husbandry, which ensures the health and longevity of captive populations and their ability to produce offspring that can be reintroduced into the wild. The artificial environment in captivity can profoundly impact animal behavior and health, particularly in relation to diet and nutrition. Diet not only provides nutrients and energy but also shapes the host's gut microbial community, which in turn impacts digestive health. Complex microbial communities, collectively known as the microbiome, are characterized by a high diversity of prokaryotes, microscopic fungi, and viruses. The diet-associated microbiome is increasingly studied for its role in captive animal health and behavior, although research has focused more on bacteria than fungal communities, or the "mycobiome". Here, we investigated the core mycobiome using metabarcoding of fungal communities in 15 wild-caught Anaxyrus fowleri (Fowler's Toad), documenting shifts as toads transitioned from wild to captive settings. We identified a core set of fungal taxa and observed distinct changes in non-core fungi associated with dietary differences associated with captivity. The non-core mycobiome exhibited an ecological guild functional shift of the saprotrophic dominance relative to wild individuals, indicating large losses in both mycobiome diversity and functionality. These findings highlight the dynamic nature of the amphibian mycobiome and the dramatic impact captivity can have on microbial composition, providing a framework for understanding the role of the amphibian mycobiome in future conservation efforts.},
}
@article {pmid41970731,
year = {2026},
author = {Kishore, MM and Jeyaraman, M and Jeyaraman, N and Nallakumarasamy, A and Bharadwaj, S},
title = {Implications of Gut Microbiome in Fibromyalgia: A Scoping Review.},
journal = {Journal of orthopaedic case reports},
volume = {16},
number = {4},
pages = {420-425},
pmid = {41970731},
issn = {2250-0685},
abstract = {INTRODUCTION: Fibromyalgia (FM) is a chronic pain syndrome marked by widespread musculoskeletal pain, fatigue, sleep disturbances, and cognitive dysfunction. Despite extensive research, its pathophysiology remains unclear. Emerging evidence implicates the gut microbiome (GMB) in FM through mechanisms involving pain modulation, immune dysregulation, and neuroinflammation. This review explores the role of gut dysbiosis in FM pathogenesis, focusing on microbial alterations, immune interactions, intestinal permeability, and neurochemical pathways.<br><br>MATERIALS AND METHODS: A systematic search of PubMed, Scopus, and Web of Science was conducted to identify studies published in the last two decades examining the relationship between GMB and FM. Inclusion criteria encompassed original research, systematic reviews, and meta-analyses addressing microbial dysbiosis, immune modulation, and neurochemical alterations in FM. Studies focused solely on treatment interventions were excluded. A narrative synthesis approach was used to integrate findings and highlight mechanistic insights.<br><br>RESULTS: FM patients exhibit significant gut microbial dysbiosis, including reduced butyrate-producing bacteria and increased pro-inflammatory species. These alterations are associated with compromised intestinal barrier integrity, systemic immune activation, and elevated pro-inflammatory cytokines. Neurochemical disruptions include serotonin deficiency, gamma-aminobutyric acid/glutamate imbalance, and reduced short-chain fatty acids, contributing to central sensitization and neuroinflammation. Dysregulation of the gut-brain axis and microbial metabolite pathways further exacerbate FM symptoms.<br><br>CONCLUSION: GMB dysbiosis plays a pivotal role in FM pathogenesis through immune activation, intestinal permeability changes, and neurochemical modulation. Understanding these mechanisms may inform future research into microbiome-based biomarkers and therapeutic strategies. While treatment implications are beyond the scope of this review, the findings underscore the potential of targeting microbial pathways in FM management.},
}
@article {pmid41970986,
year = {2026},
author = {Soto, EK and Wagner, V and Engl, J and Mederer, M and Cibulkova, V and Piater, J and Schäfer, B and Dunzendorfer, E and Waschina, S and Kaser, S and Aden, K and Trajanoski, Z and Tilg, H and Effenberger, M},
title = {Escherichia-Shigella expansion and metabolite dysregulation in type 3c diabetes: linking microbiome alterations to exocrine pancreatic insufficiency.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1786756},
pmid = {41970986},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Exocrine Pancreatic Insufficiency/microbiology/metabolism ; Male ; Female ; Adult ; Middle Aged ; *Escherichia ; *Diabetes Mellitus, Type 1/microbiology/metabolism ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; },
abstract = {Emerging evidence supports a bidirectional gut-pancreas axis in which microbial dysbiosis, barrier dysfunction, and altered metabolite fluxes contribute to pancreatogenic diabetes (T3cDM). Whether gut microbial changes reflect systemic metabolic disturbances or primarily arise from exocrine pancreatic insufficiency (EPI) remains unclear. We profiled the gut microbiome of 48 outpatients with T3cDM, type 1 diabetes (T1DM), and healthy controls. Genus-level 16S rRNA data were analyzed using cross-validated LASSO logistic regression and patient-specific community metabolic models. T3cDM showed reduced α-diversity and distinct β-diversity compared with T1DM and controls. Key compositional shifts included enrichment of Enterobacteriaceae (notably Escherichia-Shigella) and Streptococcaceae in T3cDM. LASSO models discriminated T3cDM from T1DM (AUC 0.867; accuracy 0.818), highlighting Blautia, Escherichia-Shigella, Streptococcus, Clostridium, and Faecalibacterium as predictors. Metabolic modelling indicated elevated Escherichia-Shigella growth in T3cDM and disease-specific metabolite fluxes. Gut microbial shifts in T3cDM predominantly reflect EPI rather than systemic metabolic disturbances characteristic of T1DM, underscoring the central role of exocrine pancreatic dysfunction in shaping the gut microbiome and its metabolic activity.},
}
@article {pmid41971172,
year = {2026},
author = {Prasert, W and Akrimajirachoote, N and Pattarapanawan, M and Kovitvadhi, A and Phuengjayaem, S and Qin, H and Li, BZ and Soontorngun, N and Lansubsakul, N and Areerat, S and Kotatha, D},
title = {Enhancing the resistant starch content of cassava starch via heat-moisture treatment for application as a prebiotic in chicken feed.},
journal = {Veterinary and animal science},
volume = {32},
number = {},
pages = {100630},
pmid = {41971172},
issn = {2451-943X},
abstract = {This study aimed to increase the resistant starch (RS) content of cassava starch via heat-moisture treatment (HMT) and evaluate its prebiotic potential in chicken feed. The HMT involved autoclaving cassava starch at 20% moisture content and 121°C for 1 h (HMT-20), which yielded a high RS content (20.7%) in the cooked starch. In vitro fermentation with Limosilactobacillus reuteri TBRC291 demonstrated the promising prebiotic potential of cooked HMT-20, comparable to that of commercial fructo-oligosaccharides, as indicated by enhanced bacterial growth, reduced pH, and increased short-chain fatty acid (SCFA) production. A 1% concentration of cooked HMT-20 was identified as optimal for prebiotic use. In the in vivo assessment, chickens were given feed supplemented with 1% cooked HMT-20 (HMT-Feed), displaying no adverse effects on growth performance over 35 days and significantly reducing relative abdominal fat and heart weight while increasing breast weight. Meat from the HMT-Feed group also exhibited increased yellowness and reduced cooking loss. Histological analysis revealed an improved intestinal morphology, including a greater villus height, reduced crypt depth, and higher villus-to-crypt ratio. Additionally, the HMT-Feed group exhibited a lower cecal pH and higher SCFA levels (notably butyric acid). Deep gut microbiota profiling revealed enriched levels of lactic acid- and butyrate-producing bacteria, indicating improved gut health. The HMT-modified product demonstrates potential applicability as a value-added and sustainable feed additive in the poultry industry.},
}
@article {pmid41971184,
year = {2026},
author = {Ono, Y and Ota, H and Ogi, M and Fukushi, Y and Wada, S and Arase, H and Yoshino, O and Yamada, H},
title = {Uterine Endometrial Microbiome and Chronic Endometritis in Relation to Anti-β2-Glycoprotein I (β2GPI)/Human Leukocyte Antigen (HLA)-DR Autoantibodies in Women With Recurrent Implantation Failure and Recurrent Pregnancy Loss: A Cross-Sectional Study.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70049},
pmid = {41971184},
issn = {1445-5781},
abstract = {BACKGROUND: Anti-β2GPI/HLA-DR autoantibodies may be involved in recurrent implantation failure (RIF) and recurrent pregnancy loss (RPL). We examined their association with the endometrial microbiome and chronic endometritis (CE).<br><br>METHODS: In this cross-sectional study, 141 women (54 RIF, 87 RPL) were enrolled. Serum anti-&#x3b2;2GPI/HLA-DR positivity was defined using 99th/95th percentile cut-offs. Endometrial microbiome was assessed by 16S rRNA sequencing, focusing on reproductive-failure-related species (Gardnerella, Prevotella, Atopobium, Dialister, Anaerococcus, Ureaplasma, Mycoplasma). Microbiome and CE were compared by antibody status in RIF and RPL.<br><br>RESULTS: In RIF, antibody-positive women more frequently had Lactobacillus iners (99&#x2030; and 95&#x2030; cut-offs: 71.4% vs. 23.4%, p&#x2009;=&#x2009;0.03; and 70.0% vs. 20.5%, p&#x2009;=&#x2009;0.026) and reproductive-failure-related bacterial species (99&#x2030;: 100% vs. 51.1%, p&#x2009;=&#x2009;0.016; 95&#x2030;: 90.0% vs. 52.3%, p&#x2009;=&#x2009;0.032). In multivariable analysis with 95&#x2030; cut-off, Lactobacillus iners (OR 13.1, p&#x2009;=&#x2009;0.003) and reproductive-failure-related species (OR 9.64, p&#x2009;=&#x2009;0.029) were independently associated with antibody positivity. In RPL, Anaerococcus was more frequent in antibody-positive women. CE frequency did not differ by antibody status in RIF or RPL.<br><br>CONCLUSION: Anti-&#x3b2;2GPI/HLA-DR antibody positivity was associated with endometrial dysbiosis and may serve as a biomarker of abnormal intrauterine environment in reproductive failure.},
}
@article {pmid41971315,
year = {2026},
author = {Cosma, BM and Abeel, T},
title = {A conserved bacterial signature characterizes plant microbiome responses to drought.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768028},
pmid = {41971315},
issn = {1664-302X},
abstract = {INTRODUCTION: Plant-associated microbes contribute to host resilience under stress, yet the extent to which microbial responses to drought generalize across hosts and environments remains unclear.<br><br>METHODS: Here, we performed a meta-analysis of 13 studies including more than 3,000 root and bulk soil samples from 52 plant hosts to identify bacterial taxa consistently affected by drought and link them to inoculation outcomes. Using a standardized processing workflow and differential abundance analysis, we derived a "drought signature" of taxa differentially abundant under water limitation across the endosphere, rhizosphere, and bulk soil.<br><br>RESULTS: The signature is dominated by Gram-positive Actinobacteria enriched under drought, including Kribella, and by Gram-negative taxa depleted under drought, such as Ramilbacter. Comparison with four independent inoculation experiments revealed limited overlap between drought and inoculation responses, with only Nitrospira depleted in both contexts.<br><br>DISCUSSION: Studies reporting improved plant performance under inoculation also exhibited stronger and more extensive microbial shifts, suggesting that the magnitude of community restructuring may be characteristic of successful inoculation outcomes. This work provides the fi rst genus-level meta-analysis of microbial responses under drought and inoculation, across hosts and experimental conditions, and delivers a unifi ed root and soil microbiome dataset.},
}
@article {pmid41971318,
year = {2026},
author = {Jin, L and Bian, X and Zhang, G and Zhu, J and Li, X and Yang, D},
title = {Combined polysaccharides from Angelica sinensis, Crataegus pinnatifida, Prunus persica, and Carthamus tinctorius attenuate cold exposure-induced bone loss by modulating the gut microbiota and fecal metabolites.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768890},
pmid = {41971318},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic cold stress is a significant risk factor for skeletal deterioration; however, effective therapeutic strategies targeting the underlying environmental-metabolic interactions remain unclear. This study investigated the osteoprotective potential of Mixed Polysaccharides (MPs) and elucidated the mediating role of the gut microbiome.<br><br>METHODS: Cold exposure-induced bone loss was established in rats. Fecal microbiota transplantation (FMT), 16S rRNA gene sequencing, and untargeted metabolomics was employed to illustrate the positive effect of MPs on the improvement of cold-exposed bone loss.<br><br>RESULTS: MPs treatment effectively reversed cold-induced trabecular microarchitecture deterioration and bone mass loss. In femoral tissue, MPs rebalanced skeletal turnover by upregulating osteogenic markers (Runx2, Osterix) and suppressing osteoclastogenic factors (TRAP, c-fos), concurrent with a marked reduction in the levels of pro-inflammatory cytokines TNF-&#x3b1; and IL-1&#x3b2; in femur. Furthermore, MPs restored intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Occludin), thereby mitigating the intestinal barrier impairment driven by cold stress. FMT experiments demonstrated that the osteoprotective effects of MPs are microbiota-dependent, as the transplantation of MPs-modulated microbiota recapitulated the bone-preserving and barrier-restoring phenotypes in recipient mice. Multi-omics integration identified that MPs selectively promoted the expansion of Lactobacillus intestinalis and the accumulation of cholylhistidine. Correlation analysis further revealed a strong link between the enrichment of these microbial and metabolic signatures, reduced pro-inflammatory cytokine levels, and improved bone formation.<br><br>CONCLUSION: Our findings indicate that MPs alleviate cold-stress-induced bone loss by remodeling the gut microbiota and metabolic profile, fortifying the intestinal barrier and decreasing pro-inflammatory cytokine.},
}
@article {pmid41971319,
year = {2026},
author = {Zhang, G and Altamimi, M and Shi, J and Lee, Y},
title = {Editorial: The interaction between food ingredients and gut microbiome on health and disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809622},
pmid = {41971319},
issn = {1664-302X},
}
@article {pmid41971320,
year = {2026},
author = {Wu, Y and Deng, L and He, X and Zhou, D and Ling, S and He, M and Wang, Q and Wang, C and Wang, M and Wu, H and Li, L and Li, D and Yun, L},
title = {Intestinal microbiome gone native: gut microbiome shift and resistome diversity in first homecoming giant panda family.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1737792},
pmid = {41971320},
issn = {1664-302X},
abstract = {INTRODUCTION: The world-famous giant pandas (Ailuropoda melanoleuca) often travel abroad for public exhibitions and international scientific cooperations. Previous research has reported alternations in the gut microbiome structure and enrichment of gut antibiotic-resistant genes (ARGs) in human international travelers, the latter of which is harmful to native residents and the environment. The microbiome and ARGs of these animal travelers, however, have not yet been investigated, even though they often interact with local keepers, visitors, and other pandas.<br><br>METHODS: In this study, we have clarified the dynamic microbiome composition and snapshot of ARGs (resistome) of the first panda family returning from overseas. Fecal samples were gathered for high-throughput sequencing for both amplicon and metagenomics sequencing, which were collected on the first day of their quarantine (Admission stage) and 3 days after the quarantine (Release stage). Feces from two native captive pandas were used as controls.<br><br>RESULTS AND DISCUSSION: The predominant Escherichia-Shigella proportion in the mother and father pandas decreased from 79.02 and 47.46% to 57.03 and 33.77%, while the Streptococcus abundance increased from 0.27 and 12.44% to 29.47 and 54.59%. The main genus of child pandas, Weissella, decreased from 45.24 to 0.02% after quarantine, and the Streptococcus ratio increased from 11.89 to 43.82%. Significant richness and bacterial diversities were found in these samples. The main ARG types are multidrug and polymyxin; the latter being an uncommon ARG in native pandas. Consequently, to protect local ecosystems from the introduction of novel ARGs, waste from translocated giant pandas should be managed under strict biosecurity protocols.},
}
@article {pmid41971323,
year = {2026},
author = {David, EM and Parthasarathi, T},
title = {Soil microbial processes shaping seed performance: linking soil microbiomes to sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797362},
pmid = {41971323},
issn = {1664-302X},
abstract = {Soil microorganisms are fundamental to soil sustainability, governing organic matter turnover, nutrient cycling, soil structure formation, and plant health regulation. In the context of accelerating soil degradation, climate change, and expanding agricultural salinization, understanding how soil microbial communities contribute to ecosystem resilience is crucial for sustainable soil management. Although rhizosphere and plant nutrition roles are well recognized, their influence across plant life cycles and generations remains insufficiently integrated. This Review synthesizes recent advances to propose the soil seed microbiome continuum as a unifying concept linking soil microbial processes to seed quality, early plant establishment, and crop stress tolerance under salinity stress. Unlike existing microbiome salinity reviews that predominantly focus on rhizosphere interactions or microbial inoculants under salt stress, this review advances an integrative soil seed continuum framework that connects soil ecological processes, microbial transmission, and seed associated microbiomes with a transgenerational context. We discuss how this ecosystem acts as a dynamic reservoir of beneficial and stress-adapted microorganisms that are selectively recruited by plants, transmitted through plant associated pathways, and ultimately incorporated into developing seeds. Under saline conditions, ecological filtering favors halotolerant microbial taxa that stabilize soil functions, and enhancing plant stress tolerance, with potential transgenerational benefits mediated through seed-associated microbiomes. The evidence from soil microbial ecology, plant microbe interactions, and emerging microbiome-enabled technologies, this review highlights the role of soil microorganisms as biological connectors between soil sustainability and crop performance. We further discuss implications for reduced chemical inputs, yield stability, nature-based restoration, and contributions to the United Nations Sustainable Development Goals. Positioning soil microorganisms within a soil seed continuum offers new perspectives for managing soil biodiversity and functionality, reinforcing their central role in sustainable agriculture and resilient soil ecosystems. This integrative perspective provides a strategic foundation for developing microbiome informed soil management approaches aimed at enhancing long term crop performance under increasing salinization and climate change.},
}
@article {pmid41971325,
year = {2026},
author = {Qi, L and Kang, H and Li, X and Wang, L and Lin, Y and Zhan, M and Zeng, F and Xiao, Z and Liu, X and Chen, Z and Liu, L},
title = {Multi-omics profiling implicates gut microbiota-sphingolipid interplay in the neuroprotective effects of semaglutide on diabetic cognitive impairment.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705784},
pmid = {41971325},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome is a critical regulator of host health, but how it mediates the therapeutic effects of drugs targeting neurodegenerative diseases like diabetic cognitive impairment (DCI) is unclear. Here, we investigated whether the neuroprotective effects of the GLP-1 agonist semaglutide (SE) are linked to its modulation of the gut-brain axis.<br><br>METHODS: We used an integrative multi-omics approach in a mouse model of DCI. We combined fecal shotgun metagenomics and targeted bile acid profiling with cerebral proteomics and metabolomics to characterize the gut-brain crosstalk following a 12-week SE treatment. Animal behavior, neuronal survival and synaptic integrity were assessed to confirm therapeutic efficacy.<br><br>RESULTS: SE treatment reversed cognitive deficits, rescued hippocampal neuronal loss, and restored synaptic integrity in diabetic mice. At the ecosystem level, metagenomics revealed that SE treatment profoundly remodeled the gut microbiota, enhancing microbial &#x3b1;-diversity, enriched beneficial genera (Bacteroides, Barnesiella), and depleted the pro-inflammatory genus Desulfovibrio. This microbial shift was associated with normalized fecal and cerebral bile acid profiles. Mechanistically, our analysis implicated a dysregulated sphingolipid pathway in the DCI brain, characterized by the upregulation of the transporter ATP-binding cassette transporter A2 (ABCA2) and the enzymes sphingosine-1-phosphate phosphatase 1 (SGPP1) and ceramide synthase 2 (CERS2). SE treatment dynamically modulated this pathway: it downregulated ABCA2 in a potentially weight-independent manner and SGPP1 in a weight-dependent fashion, linked to the normalization of cerebral bile acid profiles. In contrast, CERS2, a robust marker of disease severity, was not altered by SE.<br><br>CONCLUSION: Our study uncovers a novel "gut microbiota-bile acid-sphingolipid" axis in DCI and suggests that SE acts via a dual mechanism. It drives a weight-dependent restoration of the gut-brain axis, normalizing microbial and bile acid profiles to regulate SGPP1, while also exerting weight-independent effects, potentially through direct modulation of targets like ABCA2. This work highlights the gut microbiome as a key component in the therapeutic action of SE and reveals the multifaceted nature of its neuroprotective effects.},
}
@article {pmid41971330,
year = {2026},
author = {Shuang, L and Ge, T and Hang, L and Wenjing, L and Jiang, X and Haoyu, H and Shuiming, X},
title = {Disease-induced changes in Panax ginseng phyllosphere fungal community assembly and functional adaptation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1740520},
pmid = {41971330},
issn = {1664-302X},
abstract = {INTRODUCTION: Phyllosphere microorganisms play essential roles in plant health and disease resistance, yet their responses to pathogen infections remain poorly understood. Panax ginseng is susceptible to multiple fungal diseases, which threaten its quality and yield. This study aimed to clarify the underlying disease resistance mechanisms of Panax ginseng by analyzing the phyllosphere fungal communities associated with fungal infections.<br><br>METHODS: Phyllosphere fungal communities of healthy Panax ginseng plants and those with three fungal infections (gray mold, damping-off and root rot) were compared to explore the disease resistance mechanisms related to fungal community changes.<br><br>RESULTS: Results revealed distinct niche differentiation: leaves were dominated by Basidiomycota (82.0%), while stems harbored more Ascomycota (94.2%), including pathogens like Monilinia laxa (35.73%). Fungal infection significantly reduced microbial alpha diversity, altered community structure (PERMANOVA, p = 0.001), and destabilized co-occurrence networks (modularity decreased from 0.8501 to 0.8116). Functional prediction indicated downregulation of key metabolic pathways (e.g., NAD/NADP interconversion, phospholipid biosynthesis). Disease stress induced an enrichment of potentially beneficial taxa (e.g., Rhodotorula) in leaves, indicative of a limited antagonistic response, while the overall community was ultimately dominated and disrupted by pathogens.<br><br>DISCUSSION: Elucidating these compositional shifts of phyllosphere fungal communities advances the understanding of plant-microbe-pathogen interactions and provides a critical theoretical groundwork for development of microbiome-driven early disease diagnosis, resistance breeding, and eco-friendly disease control strategies for Panax ginseng.},
}
@article {pmid41971337,
year = {2026},
author = {Alqaderi, H and Batorsky, R and Azar, G and Malik, MZ and Nizam, R and Altabtbaei, K and Devarajan, S and Ahmad, R and Michaud, DS and Zhao, N and Zavras, A and Al-Mulla, F},
title = {Comparative machine learning analysis of saliva and plaque microbiomes in Kuwaitis with type 1 diabetes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1735375},
pmid = {41971337},
issn = {1664-302X},
abstract = {BACKGROUND: Type 1 diabetes (T1D) is associated with microbial dysbiosis. While most research has focused on the gut microbiome, limited data addresses the role of the oral microbiome in T1D. The oral and gut microbiomes overlap substantially, and the oral cavity may influence gut microbial composition. Saliva and dental plaque represent two distinct oral niches with unique microbial communities, but it remains unclear which is better associated to systemic disease states like T1D. This study compares the performance of salivary and plaque microbiomes in classifying pediatric T1D status.<br><br>METHODS: Paired saliva and plaque samples were collected from 46 children (23 with T1D, 23 healthy controls). Microbial DNA was extracted and sequenced targeting the 16S rRNA gene. Data were processed using QIIME 2 for taxonomic classification and centered log-ratio transformation. Alpha diversity, microbial abundance, and clustering analyses were performed to compare the oral microbiome between T1D and control groups. Random forest classifiers were used to evaluate and compare the predictive accuracy of saliva- and plaque-based models, both with and without clinical metadata.<br><br>RESULTS: Saliva samples exhibited lower alpha diversity than plaque but had significantly higher bacterial load and total microbial abundance. Saliva-based models outperformed plaque-based models, achieving a classification accuracy of 94.2% with or without clinical metadata, compared to 73.3% accuracy for plaque-based models. ROC curve analysis further supported this difference, with saliva models reaching an AUC of approximately 0.94, versus 0.75 for plaque, indicating superior discriminative performance. UMAP clustering revealed more distinct separation of T1D and control groups in salivary profiles than in plaque. Feature importance analysis identified both unique and shared taxa predictive of T1D in each niche. Incorporating clinical and demographic metadata did not enhance model performance, underscoring the robustness and predictive strength of microbiome data alone.<br><br>CONCLUSION: The salivary microbiome is a more effective biospecimen than dental plaque for characterizing T1D-associated microbial profiles in children. It offers superior classification accuracy and greater sensitivity in distinguishing T1D status, supporting saliva's potential as a non-invasive, scalable medium for future microbiome-based monitoring.},
}
@article {pmid41971339,
year = {2026},
author = {Gao, Y and Zhang, J and Sun, L and Wang, K and Tang, X},
title = {Diversity and distribution of the microbiome in the bulbs and rhizosphere soil of Fritillaria thunbergii.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1752283},
pmid = {41971339},
issn = {1664-302X},
abstract = {As global medical resources become increasingly scarce, the demand for medicinal plants continues to rise. The growth and metabolism of medicinal plants are closely linked to rhizosphere and endophytic microorganisms. The rhizosphere soil and internal tissues of plants form stable, nutrient-rich ecosystems largely dominated by microbial communities. However, how the rhizosphere and endophytic microbiomes of Fritillaria thunbergii vary across geographically distinct populations, and what ecological processes shape their assembly and functional potential remain largely unexplored. We hypothesized that distinct environmental selection pressures and spatial isolation would differentially shape the assembly of bacterial and fungal communities in bulb and rhizosphere niches, and that core and unique microbial taxa play pivotal roles in shaping ecological network structure. In this study, metabarcoding was employed to investigate the bacterial and fungal communities in the rhizosphere soil and bulbs of F. thunbergii across four populations in China, with the aim of elucidating the biogeographic patterns, assembly mechanisms, and ecological networks of the plant-associated microbiome. The results indicate that both bacterial and fungal communities exhibited significant differences in diversity and composition across the four populations, shaped jointly by geographic isolation and environmental selection. Only a few taxa displayed both cosmopolitan distributions and high abundance, whereas most communities were distinct among ecotypes. Co-occurrence network analysis revealed that core taxa exerted stronger ecological relevance within bacterial and fungal communities compared to other ecotypes, while unique taxa played more pivotal roles in cross-domain networks. Phylogenetic analyses further uncovered microdiverse clades shaped by environmental selection, which may enhance functional resilience and contribute to the overall biogeographic patterns observed. By elucidating the biogeographic patterns and assembly mechanisms of the F. thunbergii microbiome, the study provides a conceptual framework for understanding plant-microbe interactions in medicinal plants and offers insights for the sustainable utilization of microbial resources in traditional medicine.},
}
@article {pmid41971340,
year = {2026},
author = {Giner-Pérez, L and Felipo, V and Izquierdo-Altarejos, P and Llansola, M and Pérez Martínez, G},
title = {Hyperammonemia reduces the populations of beneficial lactobacilli and bifidobacteria, disrupting the metabolic balance of the gut microbiome in rats.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771709},
pmid = {41971340},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbiome (GM) plays a critical role in metabolic and neurological health and is implicated in hepatic encephalopathy (HE). Chronic hyperammonemia (HA), a major contributor to cognitive and motor impairment in HE, may influence GM structure and function, yet its specific efects in GM remain unclear.<br><br>METHODS: Here, it was investigated how chronic HA alters the GM using a rat model fed an ammonia-enriched diet for 4 weeks. Fecal microbiota profiles obtained by 16S rRNA gene sequencing revealed marked taxonomic shifts in HA rats, with beta-diversity showing clear separation from controls.<br><br>RESULTS: Genera within the Lachnospiraceae family and Alistipes genus were enriched in HA rats, while lactic acid-producing and xylanolytic Firmicutes were reduced. Network analysis identified Alistipes as a central node in the HA microbiome. Predicted metabolic functions were significantly altered, showing negative associations between HA and pathways related to the pyruvate dehydrogenase complex, sucrose and urea degradation, and 4-aminobutyrate (GABA) degradation. Consistent with these predictions, fecal short-chain fatty acid (SCFA) analysis revealed reduced acetic and butyric acid, alongside increased valeric and isobutyric acid levels. The predicted GABA levels increasement by GM would activate GABA receptors in immune cells and would also contribute to peripheral inflammation and, eventually, neuroinflammation.<br><br>CONCLUSIONS: Together, these findings demonstrate that chronic HA reshapes GM composition, disrupts key metabolic pathways, and alters SCFA profiles, providing mechanistic insight into how HA- associated dysbiosis may contribute to the metabolic, immune, and neurological dysfunction characteristic of HE.},
}
@article {pmid41971342,
year = {2026},
author = {Martorell-Múgica, A and Gónzalez-Fernández, C and Greses, S},
title = {Indigenous microbiome as a key strategy for producing green chemicals.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798480},
pmid = {41971342},
issn = {1664-302X},
abstract = {INTRODUCTION: Reactors used for conventional anaerobic fermentation (C-AF) devoted to metabolite production are typically seeded with sludge collected from anaerobic digesters. This inoculum contains methanogens, which are the principal consumers of metabolites involved in biogas production. The use of the indigenous microbial community naturally present in the agroindustrial waste (AGW) was evaluated as an alternative inoculum to take advantage of its naturally scarce methanogenic abundance.<br><br>METHODS: Self-AF (lacking external inoculum) and C-AF were compared in terms of bioconversion yields and metabolite profiles. The effect of pH on community specialization and product distribution was assessed across the pH range naturally occurring during self-acidification.<br><br>RESULTS: Self-AF showed high bioconversion yields to metabolites (65.7 %) when compared to C-AF (58.7 %). Nevertheless, the inherent pH changes that the process suffered from self-acidification also resulted in metabolite profile oscillation. Whereas a pH of 4.5 maximized the lactic acid and ethanol production (13.9 and 11.7 g&#xb7;L[-1], respectively) due to the lactic acid bacteria prevalence, when a pH of 6 was reached, the microbiome specialized in carboxylates production, leading to a concentration of 29.8 g&#xb7;L[-1] in the steady state, with Clostridiales (51.8%) and Bifidobacteriaceae (21.4 %) as key bacteria.<br><br>CONCLUSION: This study demonstrated the feasibility of conducting AF in the absence of external inoculum. Moreover, the wide bacterial metabolisms present in the indigenous microbiome revealed its capability of maximizing product portfolio using self-AF.},
}
@article {pmid41971387,
year = {2026},
author = {Chen, J and Sun, T and Zhang, J and Huang, J and Chen, T and Weng, Y and Xiang, H and Dong, Z and Huang, Z and Cai, X and Liang, C and Zhang, M and Yu, W},
title = {Artificial intelligence-driven personalized dietary recommendations for gastric cancer high-risk populations: a narrative review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1802970},
pmid = {41971387},
issn = {2296-861X},
abstract = {This review summarizes the current applications of artificial intelligence (AI) in providing personalized dietary recommendations, and explores its potential applicability to populations at high risk for gastric cancer. Currently, there are no direct intervention trials for gastric cancer patients. However, evidence from metabolic diseases (like diabetes and obesity) shows that AI-driven dietary interventions could be beneficial. This approach may offer translatable benefits for cancer prevention. First, the paper elaborates on the severe incidence of gastric cancer and the limitations of traditional preventive measures, emphasizing the necessity of developing precise and efficient intervention strategies. Subsequently, it systematically outlines methods for identifying high-risk populations and risk stratification (including pathological basis, biomarkers, and genetic risks), as well as the close relationship between dietary patterns (protective and risky) and gastric cancer risk, with a particular focus on the interaction between diet and the gastric microbiome (especially Helicobacter pylori). The core section analyzes the technical principles of AI-driven personalized nutritional interventions (such as machine learning and deep learning) and their practical effects in improving chronic diseases like blood glucose control and obesity management, while looking forward to the potential of integrating AI with multi-omics data. In addition, the paper extends the discussion to the extended applications of AI in improving screening adherence, assisting endoscopic diagnosis, and clinical decision support systems. Finally, the paper points out current challenges such as technical interpretability, data privacy, population differences, and clinical validation, and proposes prospects for future research directions.},
}
@article {pmid41971531,
year = {2026},
author = {Zhang, W and Han, N and Zhang, T and Qiang, Y and Peng, X and Li, X and Kan, B},
title = {Dynamic change patterns of the human gut microbiota-fluctuation, loss-acquisition, and turnover-and their underlying causes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag046},
pmid = {41971531},
issn = {2730-6151},
abstract = {The temporal dynamics of the gut microbiome are critical to human health, yet their patterns and underlying drivers remain poorly characterized at a monthly resolution and strain level. This knowledge gap limits the development of targeted microbiome interventions. Here, we integrate longitudinal analyses across three human cohorts-a cross-sectional cohort (n = 190), an intensive 52-month time series (n = 7), and a paired 6-month cohort (n = 43)-together with a humanized mouse model under antibiotic perturbation. Using shotgun metagenomics (516 samples), we resolve microbial dynamics at species and strain resolution. We identify three distinct modes of temporal variation: relative abundance fluctuations, species loss-acquisition events, and strain turnover. Strain turnover contributes substantially to the dynamic reservoir of functional genes, including those associated with virulence and antibiotic resistance. These dynamics are influenced by antibiotic exposure and microbial interspecies interactions. Our work provides a month-scale atlas of gut microbiome variation, revealing widespread transient colonization and strain-level plasticity, thereby offering a refined framework for understanding microbiome stability and personalized microbial ecology.},
}
@article {pmid41971550,
year = {2026},
author = {Suarez-Fernandez, M and García-Fernández, C and Ferreira, JJ and Campa, A},
title = {Farming system shapes rhizosphere microbiota and root gene expression in common bean.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1749874},
pmid = {41971550},
issn = {1664-462X},
abstract = {The rhizosphere is a dynamic interface where plant roots and microorganisms interact through the exchange of metabolites and signaling molecules. This study evaluated the impact of organic and conventional farming on the rhizosphere microbiota and root gene expression in common bean by integrating metabarcoding (16S rRNA and ITS) and RNA sequencing (RNA-seq) approaches. Bacterial alpha diversity was higher in the rhizosphere of plants grown under conventional than under the organic system (2961 vs. 1532 Amplicon Sequence Variants (ASVs) observed), whereas fungal alpha diversity was greater in the organic system (372 vs. 321 ASVs observed). The fungi-to-prokaryote ratio was approximately twofold higher in organic systems. Organic farming promoted Funneliformis, Metarhizium, Chitinophaga, and Rhizobium, while conventional farming favored Pirellula, Terrimonas, and Mortierella. Transcriptomic analysis identified 5511 differentially expressed genes (DEGs), of which 1085 showed |log2FC| ≥ 2, mainly upregulated under organic conditions. These genes were enriched in functions related to secondary metabolism, redox homeostasis, hormone signaling, nodulation, and nutrient transport. DEGs involved in the synthesis of root exudate metabolites, including fatty acids, indolic compounds, and organic acids, were also identified, highlighting their potential role in microbial recruitment. Downregulated genes were associated with cell cycle and kinase activity. Correlation analyses linked beneficial fungal taxa with the induction of genes related to plant growth, defense, and symbiosis. This work provides a basis for future studies aimed at identifying key genes involved in root development and plant-microbe interactions, potentially improving breeding programs for cultivar resilience and efficiency.},
}
@article {pmid41971606,
year = {2026},
author = {Zhu, S and Qiao, Y and He, W and Xiao, Y and Song, G and Liu, K and Fang, S},
title = {Multi-Strain Probiotics BLa80, LRa05, and BBr60 Modulate Inflammation, Bile Acids, and Gut Microbiota in Type 2 Diabetes: A Randomized Controlled Trial.},
journal = {Food science &amp; nutrition},
volume = {14},
number = {4},
pages = {e71735},
pmid = {41971606},
issn = {2048-7177},
abstract = {To evaluate the effects of a multi-strain probiotic formula, Bifidobacterium animalis subsp. lactis BLa80, Lacticaseibacillus rhamnosus LRa05, and Bifidobacterium breve BBr60, on inflammation, metabolism, and the gut microbiota in patients with type 2 diabetes mellitus (T2DM). In a randomized, double-blind, placebo-controlled trial, 80 adults with T2DM received either the probiotic or a placebo in addition to standard hypoglycemic therapy for 12 weeks. We assessed inflammatory cytokines, glycemic indices, serum amino acids, bile acids (BAs), short-chain fatty acids (SCFAs), and gut microbiota composition. Compared with the placebo group, the probiotic intervention led to a significant reduction in the levels of IL-17 and TNF-α (p < 0.05), reduced serum concentrations of threonine, isoleucine, and arginine. Additionally, the BA profile was markedly altered, revealing 16 differential metabolites that were associated with pivotal metabolic pathways. SCFA analysis showed higher isobutyric and isovaleric acid after supplementation. The probiotic group also exhibited significant reductions in total glycated hemoglobin (GHb) and fasting plasma glucose (FPG, p < 0.05). Microbiome analyses indicated decreased alpha-diversity and distinct beta-diversity shifts, including increased Gemmatimonadota and reduced Clostridium abundance in the probiotic group. This multi-strain probiotic modulated inflammatory responses, metabolic profiles, including BA metabolism and SCFAs, and gut microbiota composition in T2DM, supporting its potential as an adjunct to metabolic management. Trial Registration: ClinicalTrials.gov identifier: NCT06440486.},
}
@article {pmid41971837,
year = {2026},
author = {Du, S and Lin, D and Zhang, TL and Chu, HY and Zhu, D},
title = {Earthworm gut's potential positive impact on carbon cycle by influencing carbohydrate metabolism and microbial genome size.},
journal = {Fundamental research},
volume = {6},
number = {2},
pages = {837-846},
pmid = {41971837},
issn = {2667-3258},
abstract = {The earthworm microbiome significantly impacts global soil ecosystems. This study explores how earthworm gut eukaryome (fungi and protists) and functional genes respond to land use and climatic factors. Over 150 earthworm-soil sample pairs were collected from arable and forest ecosystems across China. High-throughput and shotgun metagenomic sequencing revealed lower fungal, protistan, and CAZyme gene diversities in the earthworm gut than in the soil (0.77-fold, 0.19-fold, and 0.74-fold compared to the soil, respectively), but higher proportions of parasitic protists (3.78-fold compared to the soil) and carbohydrate metabolism genes involved in glycosyl transfer (1.41-fold compared to the soil). Arable systems showed higher abundances of functional genes associated with carbon fixation, nitrification, phosphorus dissolution, and sulfite reduction compared to forest systems. This study highlights the associations between earthworm gut microeukaryotes and functional genes especially glycosyl transferases involved in carbohydrate biosynthesis. Furthermore, larger microbial genomes were found in the earthworm gut compared to the soil, which may harbor more functional genes involved in cellular processes, carbohydrate binding, and glycosyl transfer. These findings suggest that earthworm gut microeukaryotes may have a positive impact on their average genome sizes and carbohydrate metabolism within the carbon cycle. This study contributes to advancing our understanding of the functionality of microeukaryotes in the earthworm gut, especially for the carbon cycle.},
}
@article {pmid41971848,
year = {2026},
author = {Petersen, AE and Zafeiropoulou, K and Ghiboub, M and van Helsdingen, CPM and Konsten, JLM and Bouvy, ND and Stoot, JHMB and Tanis, PJ and de Jonge, WJ and Derikx, JPM},
title = {Preoperative Gut Microbiome in Patients With Colorectal Cancer: Potential for Fecal Biomarker-Based Recurrence Risk Prediction.},
journal = {JCO oncology advances},
volume = {},
number = {3},
pages = {},
pmid = {41971848},
issn = {2994-9750},
abstract = {PURPOSE: While gut microbiome dysbiosis is known to play a role in colorectal cancer (CRC) initiation and progression, its role in CRC recurrence remains unclear. This study investigates whether the gut microbiome is associated with CRC recurrence.<br><br>PATIENTS AND METHODS: In a prospective observational cohort, preoperative fecal samples from patients with stage I to III CRC undergoing surgical resection were analyzed using 16S rRNA gene sequencing. Alpha diversity and beta diversity were compared between patients with and without recurrence, and differential abundance analyses were conducted to identify bacterial genera associated with recurrence risk.<br><br>RESULTS: Among 294 patients, 61 (21%) patients developed recurrence during a median follow-up of 56 months, with a median time to recurrence of 19 months. Alpha diversity did not differ between groups, but beta diversity analysis revealed significantly distinct microbial clustering in patients with recurrence, particularly those with locoregional recurrence. Differential abundance analysis identified five bacterial genera associated with locoregional recurrence (Acidaminococcus, Alloprevotella, Butyrivibrio, Ruminococcaceae CAG-352, and Lachnospiraceae UCG-003), one with distant recurrence (Megamonas), and two with overall recurrence (Anaeroplasma, Porphyromonas). Stratifying patients into high- and low-abundance subgroups revealed that those with a high relative abundance of Porphyromonas had an increased risk of overall recurrence (hazard ratio, 2.80 [95% CI, 1.54 to 5.10]).<br><br>CONCLUSION: Patients with CRC who develop locoregional recurrence exhibit a distinct preoperative fecal microbial composition compared with those without recurrence. Our findings provide novel insights into the role of the intestinal microenvironment in recurrence and identify Porphyromonas as a potential fecal biomarker for overall recurrence risk.},
}
@article {pmid41971995,
year = {2026},
author = {Zhao, D and Gao, C and Zhu, D and Zheng, X and Sun, J and Liu, C and Chen, L and Shen, L and Wang, X and Zhang, Y},
title = {Gut microbiota-derived cholic acid ameliorates lung inflammation in bronchopulmonary dysplasia through modulation of macrophage function.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115398},
pmid = {41971995},
issn = {2589-0042},
abstract = {This study explores the impact of gut microbiota-derived metabolites on the pathogenesis of bronchopulmonary dysplasia (BPD), focusing on their roles in macrophage plasticity and inflammation. In a prospective nested case-control cohort of 30 infants with BPD and 33 preterm controls, 16S ribosomal RNA (16S rRNA) and mass spectrometry analyses identified seven differential gut bacterial genera, with depleted Streptococcus and enriched Klebsiella in patients with BPD, alongside reduced fecal and serum cholic acid levels. In chorioamnionitis-induced rat models of BPD, cholic acid supplementation alleviated lung inflammation by regulating macrophage migration and polarization. RNA-sequencing and in vitro experiments revealed that cholic acid acts by inhibiting hypoxia-inducible factor-1α (HIF-1α) expression and transcriptional activity, an effect that was abolished by HIF-1α silencing. These findings connect the gut microbiota to BPD, highlighting cholic acid as a key regulator of macrophage function through the HIF-1α pathway in mitigating inflammation and providing new clues for understanding and intervening in BPD.},
}
@article {pmid41972113,
year = {2026},
author = {Ramos, C and Hunter, K and Walton, GE and Whitham, A and Camp, N and Poveda, C and Gibson, GR and Hough, J and Magistro, D},
title = {Associations Between the Gut Microbiota and Physical Activity, Sedentary Behaviour and Physical Function in Community-Dwelling Older Adults.},
journal = {Journal of aging research},
volume = {2026},
number = {},
pages = {8981398},
pmid = {41972113},
issn = {2090-2204},
abstract = {Gut microbiota (GM) plays a crucial role in maintaining health through metabolic, endocrine and immune functions. With ageing, shifts in GM composition, characterised by increased pathogenic and decreased health-promoting bacteria, contribute to dysbiosis, which is linked to several age-related diseases. Given the global trend of increasing sedentary behaviour (SB) and declining physical activity (PA) among older adults, this study aims to explore the relationships between GM and two critical indicators of healthy ageing, movement behaviours and physical function. Cross-sectional study assesses the GM composition, PA levels and physical function of 101 healthy, community-dwelling older adults aged 65-85 years. Participants undertook anthropometric measures and functional tests, wore an accelerometer for 7 days and provided a faecal sample which was analysed using 16s rRNA sequencing. All the results were adjusted for key covariates such as diet, age and activity levels. Key findings include positive associations of Prevotella copri with moderate-to-vigorous PA, physical function and negative associations with SB, while Roseburia species were linked to better mobility and strength measures. Conversely, potentially pathogenic taxa like Bilophila wadsworthia and Eggerthella were negatively associated with PA and handgrip strength, underscoring their possible detrimental roles in muscle function and healthy ageing. This cross-sectional study highlights the associations between GM, PA, physical function and healthy ageing in older adults. These findings emphasise the potential for leveraging GM and PA interactions to develop nonpharmacological strategies for promoting healthy ageing, warranting further research through interventional and longitudinal studies.},
}
@article {pmid41972174,
year = {2026},
author = {Cui, L and Liu, P and Wu, K and Han, X and Peng, G},
title = {Targeting the JAK/STAT pathway in atopic dermatitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1757562},
pmid = {41972174},
issn = {1664-3224},
mesh = {Humans ; *Dermatitis, Atopic/drug therapy/metabolism/immunology/etiology ; *Janus Kinases/metabolism/antagonists &amp; inhibitors ; *STAT Transcription Factors/metabolism/antagonists &amp; inhibitors ; *Signal Transduction/drug effects ; *Janus Kinase Inhibitors/therapeutic use/pharmacology ; Animals ; Molecular Targeted Therapy ; },
abstract = {Atopic dermatitis (AD) is a chronic, inflammatory skin disorder characterized by immune dysregulation, skin barrier dysfunction, and pruritus. Central to its pathogenesis is the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway, which mediates cytokine responses-including interleukin (IL)-4, IL-13, IL-31, and thymic stromal lymphopoietin-that drive T-helper 2-skewed inflammation and epidermal barrier impairment. In recent years, the therapeutic landscape of AD has been transformed by the development of JAK inhibitors, offering both systemic and topical treatment options for patients unresponsive to conventional therapies. This narrative review provides a comprehensive overview of the JAK/STAT pathway's biological role in AD, including its regulation of immune responses and skin inflammation. We summarize current JAK inhibition therapies under clinical use or investigation, compare their efficacy and safety profiles, and examine unresolved controversies surrounding long-term outcomes and adverse effects. Furthermore, we explore future innovations in JAK/STAT research, including precision medicine approaches, third-generation allosteric inhibitors, microbiome-informed strategies, and advanced drug delivery technologies. Collectively, understanding and refining JAK/STAT-targeted therapy hold great promise for individualized, safe, and effective management of AD.},
}
@article {pmid41972361,
year = {2026},
author = {Engin, ED and Engin, AB and Engin, A},
title = {Immune Evasion of Helicobacter pylori and Extra-Gastric Cancer Risk.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70376},
pmid = {41972361},
issn = {1440-1746},
abstract = {Helicobacter pylori (H. pylori) is a group 1 gastric carcinogen that plays a significant role in extra-gastric digestive system cancers. H. pylori disrupts host cell homeostasis through expression of virulence factors leading to immune evasion as well as persistent gastric mucosal colonization. H. pylori infection has been shown to play a role in extra-gastric cancers such as, hepatocellular cancer, cholangiocarcinoma, colorectal, pancreatic, and esophageal cancers. H. pylori are highly heterogeneous bacterium, and different strains may carry different virulence factors, which varies across geographic regions. Intercellular communication via exosomes derived from H. pylori-infected cells, and the H. pylori-related gut microbiota dysbiosis leads to extra-gastric cancer development through the "microbiota-epigenetic-cancer regulatory axis" in epigenomic reprogrammed host. Because of the regional and social variabilities, studies have conflicting results concerning the effect of the mutual interactions between the virulence factors of H. pylori, host, and host's microbiota on the development of extra-gastric cancer. Consistently, a significant increase in kynurenine production from tryptophan via indoleamine-2,3-dioxygenase activity of gut microbiome suppresses host's immune response by activating the aryl hydrocarbon receptor in H. pylori seropositive patients. Immune suppression in extra-gastric digestive system cancer development preserves the tumor cells from immune attack and promotes tumor growth.},
}
@article {pmid41972428,
year = {2026},
author = {Wang, YF and Wang, YN and Lin, D and Xu, JY and Qi, FY and Cui, HL and Lu, HJ and Qiao, M and Topp, E and Zhu, D and Rillig, MC and Zhu, YG},
title = {Diversity of Pharmaceuticals Enhances Antibiotic Resistance in the Invertebrate Gut via Biofilm-Mediated Mechanisms.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18849},
doi = {10.1002/advs.202518849},
pmid = {41972428},
issn = {2198-3844},
support = {42307169//National Natural Science Foundation of China/ ; 42577136//National Natural Science Foundation of China/ ; U25A20803//National Natural Science Foundation of China/ ; 2023J02031//Fujian Provincial Natural Science Foundation of China/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; },
abstract = {The environmental accumulation of non-antibiotic pharmaceuticals is an emerging driver of antibiotic resistance. While individual compounds are known to shape the soil resistome, and contaminant diversity also plays a role, the impact of pharmaceutical diversity on the gut resistome of soil invertebrates remains unclear. Here, we combined metagenomics and metaproteomics to examine the collembolan gut and soil resistome across a gradient of pharmaceutical diversity under diurnal warming. Increasing pharmaceutical diversity at a constant total concentration significantly enriched antibiotic resistance genes (ARGs) in the gut microbiome, with no comparable effect in surrounding soils. This enrichment was mainly driven by multidrug resistance associated with efflux activity and biofilm-related processes, accompanied by increases in ARG-carrying taxa such as Gordonia and Ochrobactrum. Notably, Ochrobactrum encoded biofilm-related aryl polyene pathways. In vitro experiments confirmed that biofilm formation promotes resistance through coordinated cellular responses. Metaproteomic data indicated that Ochrobactrum initiates early biofilm formation by recruiting extracellular matrix producers such as Bacillus and Pseudomonas. Diurnal warming modulated these responses, indicating an interaction between chemical diversity and climate stress. These findings identify pharmaceutical diversity as an independent driver of ARG enrichment in host-associated microbiomes and establish chemical complexity as a key factor in assessing the ecological risks of pharmaceutical pollution.},
}
@article {pmid41972576,
year = {2026},
author = {Ma, R and Liu, Y and Wang, R and Li, S and Yang, Q and Chen, Y and Ren, J and Luo, Y and Xiang, Y and Luo, X},
title = {Polyethylene Microplastics Exert Dose-Dependent Effects on the Growth, Physiology, and Rhizosphere Microbiome of Persicaria capitata.},
journal = {Biology},
volume = {15},
number = {7},
pages = {},
pmid = {41972576},
issn = {2079-7737},
support = {2024YB002 and 2024BSKQ003//Fundamental Research Funds for the Guizhou Education University Scientific Research Fund Project/ ; 2024142234020, 2024142234044, 2024142230467//Innovation and Entrepreneurship Training Program for College Students of Guizhou Education University/ ; QKHJC MS&#x3014;2025&#x3015;079//Guizhou Provincial Basic Research Program (Natural Science) General Program/ ; },
abstract = {Microplastic pollution has become a major environmental challenge for terrestrial ecosystems; however, the mechanisms by which it affects the growth of medicinal plants and their rhizosphere microecology remain unclear. This study selected the important medicinal herb P. capitata as the research subject. A pot experiment was conducted to investigate the effects of different concentrations (0%, 1%, 4%, and 8% w/w) of polyethylene microplastics (PE-MPs) on its growth performance, physiological responses, and rhizosphere bacterial communities. The main findings are as follows: (1) PE-MPs exhibited a hormetic effect on the biomass of P. capitata. A low concentration (1%) slightly promoted total biomass (44.78 g) compared to the control (40.94 g), whereas higher concentrations caused significant inhibition. Total biomass decreased by 28.5% and 53.5% under the 4% and 8% treatments, respectively, indicating that the transition from stimulation to inhibition occurred between the 1% and 4% PE-MPs. (2) Chlorophyll a was more sensitive to stress, with its content significantly increasing under the 1% treatment but declining at higher concentrations. (3) Regarding the antioxidant system, POD activity was significantly inhibited at low and medium concentrations, while MDA content increased significantly only under the 8% treatment (by 72%). SOD and CAT showed no significant changes, indicating that POD and MDA were more sensitive indicators of oxidative damage. (4) PE-MPs significantly reduced rhizosphere bacterial community richness (Chao1 index), and the loss of microbial diversity was highly coupled with the decline in plant biomass and the exacerbation of oxidative damage. In conclusion, this study confirms a threshold effect in the toxicity of PE-MPs to P. capitata, with the transition from hormetic stimulation to toxic inhibition occurring between 1% and 4% (w/w). Furthermore, rhizosphere microecological imbalance is identified as a key indirect mechanism underlying phytotoxicity. These findings provide a new theoretical basis for understanding the potential impacts of microplastic pollution on medicinal plants and agroecosystems.},
}
@article {pmid41972590,
year = {2026},
author = {Suo, L and Bian, K and Tang, J and Li, F and Sun, K and Yang, C},
title = {Nasopharyngeal Bacterial-Fungal Dysbiosis in Respiratory-Diseased Endangered Forest Musk Deer (Moschus berezovskii).},
journal = {Biology},
volume = {15},
number = {7},
pages = {},
pmid = {41972590},
issn = {2079-7737},
support = {2024K-08; 2025k-26//Science and Technology Projects of Shaanxi Academy of Science/ ; 2025NC-YBXM-120//Shaanxi Key Research and Development Program/ ; },
abstract = {BACKGROUND: The nasopharyngeal microbiome is crucial for respiratory health in mammals, yet it remains poorly characterized in the endangered forest musk deer (Moschus berezovskii), particularly in the context of disease.<br><br>METHODS: We compared the bacterial (16S rRNA) and fungal (ITS2) communities in the nasopharynx of healthy (n = 6) and clinically diseased (n = 6) individuals.<br><br>RESULTS: Although alpha diversity did not differ significantly, beta diversity (PCoA) analysis revealed distinct bacterial (PERMANOVA, R[2] = 0.165, p = 0.014) and fungal (R[2] = 0.577, p = 0.003) community structures between groups. The diseased group exhibited a significant increase in the bacterial phylum Proteobacteria (70.97% vs. 46.27%), primarily driven by the genera Bibersteinia and Pseudomonas. Fungal communities in the diseased group were dominated by a higher relative abundance of Ascomycota and Basidiomycota, with significant enrichment of Wallemia and Aspergillus. LEfSe analysis identified Pseudomonas and multiple fungal taxa (e.g., Wallemia, Aspergillus) as biomarkers for the diseased group. PICRUSt2 prediction indicated enrichment of pathways related to carotenoid biosynthesis and sphingolipid metabolism in the diseased state, while FUNGuild analysis suggested a higher abundance of animal/plant pathogen-related fungi.<br><br>CONCLUSIONS: Symptomatic respiratory infections in forest musk deer are associated with significant dysbiosis of the nasopharyngeal microbiome, characterized by the marked enrichment of potential bacterial opportunists (e.g., Pseudomonas) and specific fungal taxa (e.g., Wallemia, Aspergillus), alongside distinct functional shifts in the microbiome. These findings provide the first integrated bacterial-fungal profile of the nasopharyngeal microbiome in this endangered species, and highlight potential microbial biomarkers associated with respiratory disease.},
}
@article {pmid41972685,
year = {2026},
author = {Andrzejczak, K and Kucharczyk, E and Sternak, A and Busłowicz, T and Ponikowska, M},
title = {Gut Dysbiosis and the Molecular Landscape of the Gut-Skin Axis: Comparative Insights and Therapeutic Implications for Atopic Dermatitis and Psoriasis.},
journal = {Cells},
volume = {15},
number = {7},
pages = {},
pmid = {41972685},
issn = {2073-4409},
mesh = {Humans ; *Dysbiosis/microbiology ; *Dermatitis, Atopic/microbiology/therapy/immunology ; *Gastrointestinal Microbiome ; *Psoriasis/microbiology/therapy/immunology ; *Skin/pathology/microbiology/immunology ; Animals ; },
abstract = {Chronic inflammatory skin diseases, including atopic dermatitis (AD) and psoriasis, are systemic immune-mediated disorders driven by dysregulated immune responses. The gut-skin axis is a bidirectional network linking intestinal microorganisms, their metabolites, and host immunity. It connects microbiome composition and function with systemic inflammation and cutaneous pathology, shaping disease-specific mechanisms such as Th2/IL-4/IL-13-mediated barrier dysfunction in AD and Th17/IL-23/IL-17-driven hyperproliferation in psoriasis. Microbiota-derived metabolites, including short-chain fatty acids, tryptophan-derived aryl hydrocarbon receptor ligands, and bile acid-dependent FXR/TGR5 signaling, modulate immune homeostasis and epithelial integrity. Gut dysbiosis, impaired metabolite production, and barrier dysfunction disrupt regulatory networks, amplifying inflammation. Microbiota-targeted interventions, including probiotics, synbiotics, postbiotics, and precision nutrition, may serve as adjunctive therapies, although further well-controlled clinical studies are needed. Integrating multi-omics, metabolomics, and functional microbial profiling, alongside investigations of the gut mycobiome and virome, will be critical to identify predictive biomarkers and optimize therapeutic strategies. These concepts remain mechanistically compelling but largely theoretical, requiring validation in longitudinal and interventional studies.},
}
@article {pmid41972755,
year = {2026},
author = {Langenfeld, K and Arts, P and Monahan, A and Criswell, A and Wigginton, KR and Duhaime, MB},
title = {Novel machine learning-based approach to identify viral biomarkers of human respiratory emissions from oral and nasal metagenomes.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0011326},
doi = {10.1128/msphere.00113-26},
pmid = {41972755},
issn = {2379-5042},
abstract = {Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental sampling of respiratory viral pathogens is often challenging because of frequent non-detect measurements. Non-detect measurements do not differentiate between samples containing low or no pathogens from samples that simply lack respiratory expulsions altogether. This ambiguity can be resolved by scanning samples for a biomarker of human respiratory emissions. To do so, reliable biomarkers for environmental monitoring need to be identified. Ideal biomarkers are prevalent across individuals, abundant, and unique to the human respiratory tract. Here, we present a new machine learning-based approach to query for suitable biomarker candidates from publicly available metagenomes and apply it to identify viral biomarkers of healthy oral and nasal microbiomes. Twelve viral biomarker candidates were selected from 1,232 curated viral operational taxonomic units. The viral biomarker candidates had as much as 63% prevalence across respiratory metagenomes, and prevalence was further increased to 77%-81% by combining two or three biomarkers. Real-time PCR confirmed that these viral biomarkers were prevalent and abundant in nasal swabs and saliva samples. Notably, top candidate biomarkers remained stable and detectable through multiple lab purification steps, increasing confidence in their viral origins and demonstrating their suitability for environmental monitoring. These findings demonstrate that existing metagenomes can be used to identify effective biomarker candidates for environmental sampling.IMPORTANCEDeveloping non-pharmaceutical interventions to reduce virus transmission indoors relies on robust environmental monitoring methods. Monitoring viral pathogens is challenging because of frequent non-detect measurements that introduce uncertainty. For instance, a non-detect measurement could indicate either the absence of the pathogen or simply the lack of human respiratory activity and, thus, exposure. To aid in distinguishing these scenarios, this study identifies viruses from the human respiratory tract using publicly available sequencing data that can be incorporated into environmental monitoring as biomarkers of human respiratory activity. These viral biomarkers will improve indoor monitoring to help enact interventions to mitigate virus transmission. Furthermore, our approach to identify biomarkers from existing metagenomes can be adapted for future biomarker identification in any system.},
}
@article {pmid41973033,
year = {2026},
author = {Unlu, O and Chen, T and Yakar, N and Guney, Z and Paster, B and Carreras, I and Dedeoglu, A and Kantarci, A},
title = {Aging and periodontitis increase brain dissemination of oral bacteria.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70118},
pmid = {41973033},
issn = {1943-3670},
support = {RF1AG062496//National Institute for Health Research/ ; 2219-1059B192202291//Scientific and Technological Research Council of Turkey/ ; 2214/A-1059B142200465//Scientific and Technological Research Council of Turkey/ ; 2219-1059B192202848//Scientific and Technological Research Council of Turkey/ ; },
abstract = {BACKGROUND: The microbiome is a dynamic system that changes throughout life. Studies have revealed the relationship between periodontal disease and the oral microbiota; however, the impact of periodontal disease on the expression of senescence markers and on the inflammaging of the oral and systemic microbiome remains unclear. We hypothesized that aging increases the periodontitis-induced changes in the oral and systemic microbiome and is accompanied by an altered inflammatory response.<br><br>METHODS: Experimental periodontitis was induced in 18-month-old (old) and 8-month-old (young) C57BL/6 mice by placing ligatures around the second maxillary molars. Bone morphometric analyses were conducted to assess bone loss. Senescence- and inflammatory-related gene expression in the gingiva was measured by quantitative polymerase chain reaction (qPCR). Serum inflammatory markers were evaluated via immunoassay. Oral, brain, and gut microbial content were analyzed using next-generation sequencing.<br><br>RESULTS: Maxillary bone loss was significantly higher in the old mice with periodontal disease than in young mice. Senescence and inflammatory markers were higher in old mice than in young ones, and periodontitis increased their expression. The alpha diversity of the oral and brain microbial communities differed significantly between old and young mice. Treponema denticola, Fusobacterium nucleatum, Porphyromonas gingivalis, P. pasteri, and Prevotella nigrescens were only detected in the brains of old animals with periodontitis.<br><br>CONCLUSION: Periodontopathogens and oral commensals are either only found in the brains of old animals with periodontal disease or are more prevalent in the brains of old animals, suggesting that aging and periodontitis may contribute to the dissemination of oral bacteria to the brain.<br><br>PLAIN LANGUAGE SUMMARY: Aging may increase the periodontitis-induced changes in the oral and systemic microbiome, which an altered inflammatory response may accompany. Experimental periodontitis was created in old and young mouse models. Bone loss, senescence, and inflammatory gene expression and serum inflammatory markers were assessed in each model, and oral, brain, and gut microbial content was analyzed. Senescence and inflammatory markers were higher in old mice than in young ones, and periodontitis increased their expression. Our results suggested that aging and periodontitis may contribute to the dissemination of oral bacteria to the brain.},
}
@article {pmid41973043,
year = {2026},
author = {Hoff, CO and Heeke, S and Mitani, Y and de Sousa, LG and Siqueira, JM and Li, K and Bonini, F and Bell, D and Marques-Piubelli, ML and Lin, SY and Wargo, JA and El-Naggar, AK and McGrail, DJ and Ferrarotto, R},
title = {Axitinib plus Avelumab in Recurrent/Metastatic Adenoid Cystic Carcinoma: Biomarker Analysis and Updated Results of the Phase II Trial.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-25-4599},
pmid = {41973043},
issn = {1557-3265},
abstract = {PURPOSE: The phase II axitinib plus avelumab trial in recurrent/metastatic adenoid cystic carcinoma (ACC) demonstrated favorable response rates and progression-free survival (PFS), leading to its inclusion in NCCN guidelines as the first immunotherapy-based option for ACC. We sought to identify biomarkers predictive of clinical benefit from axitinib plus avelumab.<br><br>EXPERIMENTAL METHODS: Twenty-eight patients with ACC enrolled. Pre-treatment tumors underwent whole exome sequencing, transcriptome profiling, imaging mass cytometry, and tumor, oral rinse and stool microbiome characterization using 16s rRNA gene sequencing. Associations with PFS were assessed using Cox proportional hazards model, incorporating ACC subtype (ACC-I vs. ACC-II) as a covariate.<br><br>RESULTS: ACC comprises two proteogenomically distinct subtypes: aggressive, NOTCH1-activated ACC-I and more indolent ACC-II. Here, median PFS was 1.8 months for ACC-I versus 11.4 months for ACC-II (HR, 0.14; P<0.0001), representing the first demonstration of subtype-specific clinical trial outcomes in ACC. Clinical benefit was not associated with PD-L1 expression, tumor mutational burden, or recurrent genomic mutations. Instead, improved PFS correlated with the presence of intratumoral Escherichia and gut Bifidobacterium and Akkermansia. Transcriptomic profiling identified a 167-gene immune-enriched signature predictive of PFS benefit with axitinib plus avelumab. This signature also predicted benefit from ipilimumab plus nivolumab, but not from regorafenib monotherapy, suggesting its specificity for immunotherapy-based combinations.<br><br>CONCLUSIONS: Clinical trial outcomes with axitinib plus avelumab differ significantly by ACC subtype. Furthermore, the identified 167-gene immune-related signature predicts clinical benefit to immunotherapy-based combinations in ACC. These findings provide a framework for future biomarker-driven trial design and patient stratification strategies for this rare malignancy.},
}
@article {pmid41973071,
year = {2026},
author = {Liu, H and Bo, T and Li, J and Zhang, Y and Zhou, H},
title = {Comparative Analysis of Gut Microbiota Among Captive Waterbird Species: Effects of Diet and Environmental Factors.},
journal = {Veterinary medicine and science},
volume = {12},
number = {3},
pages = {e70865},
pmid = {41973071},
issn = {2053-1095},
support = {5242016//Natural Science Foundation of Beijing Municipality/ ; 32200381//National Natural Science Foundation of China for Youth/ ; 5242016//Beijing Natural Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diet/veterinary ; *Birds/microbiology ; Animals, Zoo/microbiology ; Feces/microbiology ; Lakes ; Species Specificity ; Geese/microbiology ; },
abstract = {The gut microbiota of avian species is influenced by a diverse array of factors, encompassing host genetics, environmental conditions, physiological states, dietary patterns and age, among others. With the advent of high-throughput sequencing technology, research into avian gut microbiota has gained momentum. The artificial lake within the zoo serves as a unique nexus between the natural and captive environments. Despite this, our understanding of the gut microbiota of waterbirds residing in such an artificial habitats remains limited. In this study, we focused on three distinct species of waterbird kept in the artificial lake and traditional enclosures. We used high-throughput sequencing technology to determine the faecal microbiome of 25 waterbirds from three species, including bar-headed goose (Anser indicus), ruddy shelduck (Tadorna ferruginea) and black-necked crane (Grus nigricollis). Our objective was to elucidate the composition and community structure of their gut microbiota, while exploring the nexus between dietary habits and gut microbiota. Our findings revealed that the dietary patterns and gut microbiota of ruddy shelducks and bar-headed geese exhibited similar traits. On the other hand, black-necked cranes, whose food primarily consists of fish and meat, possessed a gut microbiota optimized for the digestion of protein and fat. Notably, artificial lakes may support higher microbial diversity compared to cage feeding. The results underscore the significance of diet as the primary determinant of gut microbiota variation among the captive waterbird. This study provides implications for promoting the healthy growth and well-being of wild waterbird in captivity.},
}
@article {pmid41973243,
year = {2026},
author = {Charaabi, K and Hamden, H and Fadhel, S and Tanfouri, N and Bouzenbila, S and Djobbi, W and Cherif, A and Msaad Guerfali, M},
title = {Probiotic Modulation of Gut Microbiota Enhances Immunity and Nutrition in SIT Ceratitis Capitata Sterile Males.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02754-x},
pmid = {41973243},
issn = {1432-184X},
}
@article {pmid41973268,
year = {2026},
author = {Ramadan, M and Hassan, EK and Abdalla, S and Ahmed, AAA and Azab, M and Ibrahim, KA and Amin, IA and Ali, ME and Alharbi, AE and Salah, M},
title = {Oral-gut microbiome dysbiosis in obese smokers reveals compartment-specific shifts.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02048-y},
pmid = {41973268},
issn = {2191-0855},
}
@article {pmid41973308,
year = {2026},
author = {Aydin, F and Çek, &#x15e;},
title = {Mineral-microbiota interactions in aquaculture: implications for fish gut health and nutrition.},
journal = {Veterinary research communications},
volume = {50},
number = {4},
pages = {},
pmid = {41973308},
issn = {1573-7446},
}
@article {pmid41973542,
year = {2026},
author = {Muurmann, AT and Rasmussen, JA and Limborg, MT and Gilbert, MTP and Bahrndorff, S},
title = {Functional gut microbiomes enhance performance in house fly larvae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0001126},
doi = {10.1128/aem.00011-26},
pmid = {41973542},
issn = {1098-5336},
abstract = {UNLABELLED: In a world with an increase in human population, food consumption, and the generation of organic waste, insects are emerging as a promising tool to convert organic waste material into human food or animal feed. The insect microbiome is known to play a key role in the degradation of organic substrates, but little is known about the metabolic potential of the microbiome of industrially reared fly larvae. We investigated the microbial composition and metabolic potential of the house fly (Musca domestica) larva gut microbiome from larvae grown on three different waste and by-product-based substrates. We found that bacteria associated with the larval gut were enriched for functions related to microbial stress mechanisms, indicating strong selection of the gut microbiome by house fly larvae. In addition, the gut microbiome of larvae reared on sludge-based substrate had higher diversity when weighting for rare species and a higher coverage of "carbohydrate transport and metabolism" genes compared to brewery by-product-based substrate. A positive correlation between coverage of "pyridoxal-P synthesis" and larval survival and substrate conversion efficiency suggests that microbial synthesis of vitamin B6 could enhance larval performance. Additionally, a negative correlation between coverage of the "Entner-Doudoroff pathway" and "homoprotocatechuate degradation" and substrate conversion indicates microbial competition for sugars and aromatic amino acids. Together, these results reveal how the host selects on gut microbiomes with metabolic potential that is optimized toward the conversion of substrates that may be ultimately valuable for commercial insect production.<br><br>IMPORTANCE: Fly larvae are expected to play an important role in future food and feed production through the conversion of low-value biomass into high-quality protein. The gut microorganisms of fly larvae are expected to play an important role in bioconversion and could potentially be manipulated to improve biomass conversion. In this study, the importance of the gut bacteria of house fly larvae for bioconversion was investigated by metagenomic sequencing, which provided information on the bacterial abundance and potential functional roles in the larval gut. The results reveal that the functional potential of gut bacteria is affected by larval feed and correlates with larval performance, highlighting the importance of the gut microbiome for efficient biomass conversion.},
}
@article {pmid41973609,
year = {2026},
author = {Jalan-Sakrikar, N and Anwar, AA and Ali, A and Nasser-Ghodsi, N and Felzen, A and Huebert, RC and LaRusso, NF and O'Hara, SP},
title = {Cholangiocyte Biology in Primary Sclerosing Cholangitis and Other Cholangiopathies: Pathogenesis, Clinical Insights, and Experimental Tools.},
journal = {Physiological reviews},
volume = {},
number = {},
pages = {},
doi = {10.1152/physrev.00022.2025},
pmid = {41973609},
issn = {1522-1210},
support = {KL2 TR002379/TR/NCATS NIH HHS/United States ; //PSC Partners Seeking a Cure (PSC)/ ; //American Association for the Study of Liver Diseases (AASLD)/ ; DK117861//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; DK57993//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; DK57993//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; K2R Award//MC | Center for Clinical and Translational Science, Mayo Clinic (CCaTS)/ ; },
abstract = {Cholangiocytes are specialized epithelial cells that line the intrahepatic and extrahepatic biliary tree and play a critical role in bile modification, liver homeostasis, and response to injury. Cholangiocytes exhibit notable heterogeneity and plasticity, and their dysfunction is central to a spectrum of diseases targeting the bile ducts, collectively called cholangiopathies. These disorders include genetic, infectious, immune-mediated, and malignant diseases, with Primary Sclerosing Cholangitis (PSC) representing one of the most complex and enigmatic of these disorders. PSC is a progressive, fibro-inflammatory disease of the bile ducts that is closely linked to inflammatory bowel disease, carries a heightened risk of cancer, and lacks any approved therapies. This review explores the biology of cholangiocytes, including their development, functional plasticity, and roles in secretion, absorption, and cellular signaling. We provide a detailed examination of cholangiopathies, particularly PSC, a complex cholangiopathy characterized by a paradoxical state of cholangiocyte senescence and hyperproliferation. We describe how immune cell dysfunction, the gut microbiome, genetic predispositions, and environmental factors converge to mediate PSC pathogenesis. We revisit the foundational technologies that empowered early discoveries and shaped the field as we know it today. We also explore how newer techniques such as organoid cultures, single-cell transcriptomics, epigenomics, and spatialomics have transformed our modern understanding of biliary pathophysiology. Lastly, we provide an overview of existing rodent models of cholangiopathies and discuss their relevance to human disease. PSC remains therapeutically unaddressed, and thus ongoing multidisciplinary efforts are essential to developing targeted interventions. This review serves as a comprehensive resource for researchers and clinicians navigating the rapidly evolving landscape of cholangiocyte-centered liver disease research.},
}
@article {pmid41973723,
year = {2026},
author = {Denison, ER and Hillary, LS and Bolanos, HA and Anagu, HI and Emerson, JB},
title = {DNA Viral Size Fraction Metagenomics for Human Stool Samples.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {229},
pages = {},
doi = {10.3791/70187},
pmid = {41973723},
issn = {1940-087X},
mesh = {Humans ; *Feces/virology ; *Metagenomics/methods ; *DNA, Viral/genetics/isolation &amp; purification/chemistry ; *DNA Viruses/genetics/isolation &amp; purification ; },
abstract = {Understanding the healthy human virosphere (the viral component of the microbiome) requires accurate measurements of viral community composition across a diverse range of viral types. Building on prior experience with soil viral community ecology methods, here we demonstrate a series of laboratory approaches for enriching and extracting DNA from extracellular DNA viruses in human stool samples. A working primary protocol is presented, along with options for deviations at different steps. The general approach involves adding a liquid buffer (default: protein-enhanced phosphate buffered saline, PPBS) to facilitate removal of free viral particles from the stool matrix, centrifugation to separate the liquid fraction containing viral particles, filtration (default: 0.2 µm pore size) to remove most cells, concentration of viral particles (default: ultracentrifugation), removal of free nucleic acids with nucleases prior to virion lysis, and then DNA extraction for sequencing. Alternative techniques, including different buffers, filter sizes, and concentration methods, are also noted. Overall, multiple options for generating high-quality viromic DNA for sequencing are offered. Rather than tailoring the approach to specific equipment and resources, the protocol's flexibility should make it broadly applicable across labs with varying standard molecular biology equipment.},
}
@article {pmid41973868,
year = {2026},
author = {Zhang, X and Yu, C and Zhang, Z and Liu, M and Huang, X and Bai, D and Yang, R and Wang, P and Yang, C},
title = {The Nasal Microbiome in Inflammation and Disease: Bridging Mechanisms to Therapeutics.},
journal = {Annals of the New York Academy of Sciences},
volume = {1558},
number = {1},
pages = {e70258},
doi = {10.1111/nyas.70258},
pmid = {41973868},
issn = {1749-6632},
support = {82160211//National Natural Science Foundation of China/ ; 20252BAC250088//Jiangxi Provincial Nature Science Foundation/ ; },
mesh = {Humans ; *Microbiota/immunology ; *Inflammation/microbiology/immunology/therapy ; Probiotics/therapeutic use ; *Sinusitis/microbiology/immunology/therapy ; Dysbiosis/microbiology/immunology ; *Nasal Mucosa/microbiology/immunology ; Anti-Bacterial Agents/therapeutic use ; Animals ; Rhinitis, Allergic/microbiology/immunology/therapy ; },
abstract = {The nasal microbiome, an integral component of the upper respiratory tract's microecological system, plays a pivotal role in inflammatory diseases such as allergic rhinitis and chronic sinusitis, which affect a substantial population and markedly reduce quality of life. A healthy nasal flora and its metabolites are crucial for maintaining immune homeostasis and mucosal barrier integrity. This review comprehensively discusses the pathological mechanisms, immune interactions, and clinical intervention strategies involving the nasal microbiota in nasal inflammation. It has been shown that dysbiosis of the nasal flora disrupts immune function and compromises the epithelial barrier, thereby initiating and exacerbating a vicious cycle of inflammation. Furthermore, the formation of bacterial biofilms and the emergence of drug resistance contribute to persistent and recurrent symptoms. Regarding treatment, while antibiotics may offer short-term efficacy, they risk aggravating the microbial imbalance. In contrast, therapies including probiotics, novel immunomodulators, and traditional Chinese medicine demonstrate significant therapeutic potential by restoring microbial balance and modulating immune responses. This review synthesizes current research to provide new perspectives for understanding host-microbiome interactions and to guide future clinical treatments and drug development.},
}
@article {pmid41973926,
year = {2026},
author = {Brittain, RSA and Bribiescas, RG and Jasienska, G},
title = {Industrialization increases the estrogen-recycling capacity of the gut microbiome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {16},
pages = {e2523589123},
doi = {10.1073/pnas.2523589123},
pmid = {41973926},
issn = {1091-6490},
support = {2313905//National Science Foundation (NSF)/ ; },
mesh = {Humans ; *Estrogens/metabolism ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Feces/microbiology ; Adult ; *Gastrointestinal Tract/microbiology/metabolism ; Infant ; },
abstract = {Estrogens influence many aspects of human physiology and health, including fertility, growth, metabolic function, and susceptibility to disease. Up to 65% of circulating estrogens are excreted into the gut via bile, but only 10-15% are eliminated in feces, indicating substantial estrogen reabsorption [H. Adlercreutz and P. Järvenpää, J. Steroid Biochem. 17, 639-645 (1982); A. A. Sandberg and W. R. Slaunwhite, J. Clin. Investig. 36, 1266-1278 (1957)]. This estrogen recycling is enabled by the gut estrobolome, a subset of microbes that deconjugate conjugated estrogens in the gastrointestinal tract, facilitating their reabsorption into systemic circulation [C. S. Plottel and M. J. Blaser, Cell Host Microbe 10, 324-335 (2011)]. To date, it is not known if populations differ in this microbial function, and little is known about its determinants. Here we analyze estrobolomes using publicly available gut microbiome data from 24 populations spanning four continents and subsistence modes ranging from hunting and gathering to pastoralism, rural farming, and industrialized agriculture. We show that industrialized populations exhibit up to seven times greater estrogen-recycling capacity and nearly twofold higher estrobolome diversity compared with nonindustrial groups. We further find that formula-fed infants display two- to threefold higher recycling capacity and as much as eleven times greater estrobolome diversity than breastfed counterparts, revealing early-life divergence in microbial estrogen metabolism. By contrast, sex, age, and BMI are not associated with estrobolome characteristics. These findings demonstrate the crucial impact of industrialized lifestyles, including formula feeding, on the microbial capacity to influence systemic estrogen levels, with implications for life history, reproductive biology, and estrogen-associated diseases, including cancer.},
}
@article {pmid41973972,
year = {2026},
author = {Asa'ad, F and Hasuike, A and Yoshida, K and Lira-Junior, R and Chaurasia, A and Giraldo-Osorno, PM and Garaicoa-Pazmino, C},
title = {Impact of OMICS Technologies in Our Understanding of the Pathogenesis of Peri-Implantitis.},
journal = {Clinical and experimental dental research},
volume = {12},
number = {2},
pages = {e70350},
pmid = {41973972},
issn = {2057-4347},
support = {HJSV2023038//Hjalmar Svensson Foundation/ ; },
mesh = {*Peri-Implantitis/genetics/immunology/etiology/metabolism ; Humans ; Proteomics/methods ; *Genomics/methods ; Metabolomics/methods ; Epigenomics ; Transcriptome ; Microbiota ; },
abstract = {OBJECTIVES: To evaluate the contribution of OMICS technologies to the understanding of peri-implantitis pathogenesis from a host immune perspective.<br><br>MATERIALS AND METHODS: A narrative review was conducted based on electronic searches of PubMed, MEDLINE, and Google Scholar up to October 2025, complemented by manual screening of reference lists. Search terms combined "peri-implantitis" with OMICS-related keywords, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, RNA sequencing, single-cell and spatial transcriptomics, multi-omics, and machine learning. Studies were selected based on clinical relevance and their contribution to understanding peri-implantitis pathogenesis from a host immune perspective.<br><br>RESULTS: Among the studies included, most focused on transcriptomic analyses, while fewer investigated genomics, epigenomics, proteomics, or metabolomics. Integration across OMICS layers highlights peri-implantitis as a multilayered host-microbiome molecular ecosystem. Genomic variants affecting metal ion binding, cytoskeletal organization, and cell adhesion may predispose tissues to heightened immune sensitivity. Epigenomic analyses revealed differential DNA methylation of immune-regulatory and signaling genes, linking environmental exposures, such as smoking, to altered host responses. Transcriptomic studies, including bulk, single-cell, and spatial approaches, demonstrated dysregulated immune signaling, pro-inflammatory fibroblast-neutrophil interactions, oxidative stress, and dysregulated tissue remodeling. Proteomic profiling of peri-implant crevicular fluid confirmed elevated neutrophil-derived antimicrobial proteins and inflammatory mediators, reflecting active host defense responses. Metabolomic studies identified disease-specific alterations in amino acids, organic acids, and polyamines, which correlate with pathogenic microbial taxa and modulate immune and tissue responses. Collectively, these findings reveal convergent pathways of immune dysregulation, extracellular matrix disruption, tissue remodeling, and host-microbiome crosstalk as central features of peri-implantitis.<br><br>CONCLUSIONS: OMICS analyses show that peri-implantitis is a complex host-microbiome molecular ecosystem. Integrated molecular insights provide a foundation for biomarker development, predictive diagnostics, and targeted interventions. However, future studies with larger cohorts and functional validation are needed to support clinical translation.},
}
@article {pmid41974263,
year = {2026},
author = {Chen, R and Liu, L and Lin, Y and Yang, B and Wang, J},
title = {Chemotherapy-Induced Gastrointestinal Dysfunction: Mechanisms and Integrative Western-Chinese Medicine Strategies.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108191},
doi = {10.1016/j.phrs.2026.108191},
pmid = {41974263},
issn = {1096-1186},
abstract = {Chemotherapy-induced gastrointestinal dysfunction (CIGD) is a multifactorial clinical syndrome that substantially limits treatment tolerance, continuity, and quality of life in patients with cancer. Although targeted therapy and immunotherapy have expanded therapeutic options, chemotherapy remains a cornerstone of cancer treatment, and its gastrointestinal toxicities continue to pose major clinical challenges. Current evidence indicates that CIGD arises not from isolated lesions, but from interconnected pathological processes involving oxidative stress, mucosal barrier disruption, gut microbiota dysbiosis, immune amplification, and enteric nervous system (ENS) remodeling. In particular, microbiota-immune interactions and ENS-associated neuroimmune alterations may contribute to the persistence and amplification of tissue injury. Existing management strategies are still focused largely on symptom control and often do not adequately address the underlying biological drivers of dysfunction. In this review, we summarize the major mechanistic modules involved in CIGD and discuss a conceptual translational framework for mechanism-informed intervention. This framework includes: (1) targeted approaches aimed at interrupting key pathogenic loops, such as oxidative injury, microbial metabolite-related toxicity, and barrier dysfunction; (2) parameterizable integrative Western and Chinese medicine approaches, in which acupuncture and Chinese herbal formulae are considered as testable adjunctive modules alongside evidence-based supportive care; and (3) stratified management informed by interindividual variation in genetic background, drug metabolism, and microbiome features. On this basis, we further propose a working "niche medicine" framework that views CIGD as dysregulation of multicellular and molecular microenvironments across the gut ecosystem. This perspective may help connect mechanistic research with longitudinal monitoring, patient stratification, and multimodal intervention design, and may support a shift in CIGD management from predominantly symptomatic relief toward mechanism-guided restoration and recovery.},
}
@article {pmid41974411,
year = {2026},
author = {Ahmad, F and Sun, C and Muhammad, A and Shao, Y},
title = {Microplastics and pathogen risk across ecosystems: From biofilm to antimicrobial resistance and host susceptibility.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128128},
doi = {10.1016/j.envpol.2026.128128},
pmid = {41974411},
issn = {1873-6424},
abstract = {Microplastics (MPs) are ubiquitous in terrestrial and aquatic ecosystems, where they rapidly acquire organic coatings and biofilms (the plastisphere) and interact with co-occurring chemical pollutants. However, the conditions under which MPs become ecologically relevant in increasing disease risk remain underexplored. A key controversy is that microbial detection or enrichment on MPs is often treated as evidence of pathogen "vectoring," yet most studies do not quantify viability/infectivity, detachment, or delivered dose to hosts under environmentally realistic conditions. This review synthesizes evidence on MP-pathogen interactions and dispersal across ecosystems and reframes "MPs as vectors" through a vectorial-capacity lens that distinguishes association from transmission relevance and links MP-mediated risk to measurable dose delivery at host-relevant interfaces. Across ecosystems, evidence supports biofilm-driven persistence and enrichment of opportunistic taxa, but direct demonstrations of MP-mediated infection remain limited. We further highlight an unresolved issue, whether MPs confer unique transmission advantages compared with size-matched natural particulates that also sorb microbes and contaminants but are rarely used as comparators. We examine host susceptibility as a risk multiplier: MP exposure can compromise epithelial barriers via oxidative stress, modulate innate immunity, and disrupt microbiome-mediated colonization resistance. Plastisphere biofilms may also function as eco-evolutionary microhabitats that enrich antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), with plausible enhancement of horizontal gene transfer, although field-scale attribution is still scarce. Finally, we outline priorities for standardized evidence grading, comparator-based study designs, and quantitative metrics (loading, viability decay, detachment kinetics) to enable risk attribution and guide monitoring and mitigation.},
}
@article {pmid41974522,
year = {2026},
author = {Druzhinin, VG and Baranova, ED and Demenkov, PS and Matskova, LV and Larionov, AV and Zhivotovskiy, AS and Yuzhalin, AE},
title = {Bacterial effectors disrupt host DNA: Linking sputum microbiome profiles to chromosomal aberrations in leukocytes of lung cancer patients and healthy controls.},
journal = {Mutation research. Genetic toxicology and environmental mutagenesis},
volume = {911},
number = {},
pages = {503928},
doi = {10.1016/j.mrgentox.2026.503928},
pmid = {41974522},
issn = {1879-3592},
mesh = {Humans ; *Sputum/microbiology ; *Lung Neoplasms/genetics/microbiology/pathology ; *Microbiota/genetics ; Male ; Female ; Middle Aged ; *Chromosome Aberrations ; *Leukocytes/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Case-Control Studies ; Aged ; Adult ; },
abstract = {BACKGROUND: Bacterial microbiome of the respiratory tract can influence the development of respiratory diseases, including lung cancer (LC). However, establishing a causal link between certain members of the respiratory microbiota and LC is challenging. This study aimed to analyze the sputum microbiome and its association with chromosome damage in leukocytes of LC patients and healthy controls.<br><br>METHODS: Sputum samples from 150 LC patients and 104 healthy donors were analyzed by 16S rRNA gene sequencing. Chromosomal aberrations (CA) were assessed cytogenetically in lymphocytes. Bioinformatics analyses examined correlations between sputum microbiome profiles and chromosome damage.<br><br>RESULTS: The sputum microbiomes of LC patients and healthy controls did not have significant indicators for the species richness index and the Faith's phylogenetic diversity, whereas the comparison index in LC patients was significantly lower than that of healthy controls. Bacterial community structures (beta diversity) were also similar in patients and controls. We showed higher abundance of Bacillus, Prevotella, Granulicatella and Bergeyella in LC patients' sputum. LC patients exhibited increased aberrant metaphases, as well as all major CA types, compared to healthy subjects. Positive associations between aberrant metaphases and bacteria from Fusobacteria phylum, genera Bacteroidetes, Leptotrichia, Lactobacillus, Macellibacteroides, Mycoplasma, Lachnoanaerobaculum, Bulleidea, and Dialister were found in LC patients. In healthy donors, CA only correlated with Anaerorhabdus and Peptococcus. Streptobacillus and Zhouia positively correlated with the proportion of aberrant metaphases in both LC patients and in healthy individuals.<br><br>CONCLUSIONS: Specific bacterial genera in sputum associate with chromosomal damage in host cells, suggesting possible genotoxic potential of these bacteria.},
}
@article {pmid41974712,
year = {2026},
author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y},
title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71718-z},
pmid = {41974712},
issn = {2041-1723},
support = {R01AI143313//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI143313//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.},
}
@article {pmid41974724,
year = {2026},
author = {Lydon, EC and Deosthale, P and Glascock, A and Phan, HV and Osborne, CM and Leroue, MK and Allen, J and Mick, E and Wagner, BD and DeRisi, JL and Ambroggio, L and Mourani, PM and Langelier, CR},
title = {Host-microbiome archetypes differentiate infection from pathogen carriage in the human lower airway.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71863-5},
pmid = {41974724},
issn = {2041-1723},
support = {R01HL155418//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL124103//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI182308//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {Distinguishing lower respiratory tract infection (LRTI) from incidental pathogen carriage (IPC) is clinically challenging. The immunologic and microbial factors defining the states of LRTI and IPC are poorly understood. Here, we perform host-microbe metatranscriptomic profiling of tracheal aspirates from 326 mechanically ventilated children with clinically adjudicated LRTI (n = 207), IPC (n = 70), or non-infectious respiratory failure (n = 49). In the airway microbiome, LRTI shows reduced alpha diversity and taxonomic richness, while IPC displays greater bacterial abundance, enrichment in respiratory anaerobes, and increased metabolic activity. At the host level, patients with LRTI exhibit a distinct lower airway transcriptional signature of innate and adaptive immune activation compared to those with IPC, who have similar transcriptional profiles to uninfected controls. Mediation analyses suggest the airway microbiome influences the host response to pathogens. An integrated host-microbe metatranscriptomic classifier accurately discriminates LRTI from IPC and controls (AUC = 0.89, 95% confidence interval (CI) 0.85-0.92). The single gene FABP4, encoding a macrophage-associated lipid chaperone and recently described pneumonia biomarker, performs similarly when combined with alpha diversity; FABP4 protein alone achieves an AUC = 0.88 (95% CI 0.82-0.93). Together, our findings reveal distinct ecological and immunologic archetypes defining LRTI and IPC, and support data-driven, biology-informed LRTI diagnostics incorporating host and microbial features.},
}
@article {pmid41975031,
year = {2026},
author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE},
title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10048-8},
pmid = {41975031},
issn = {2399-3642},
support = {DairyBio//Dairy Australia/ ; },
abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.},
}
@article {pmid41961090,
year = {2026},
author = {Cao, Z and Chen, T and Xie, J and Xie, J},
title = {Artificial Intelligence in Functional Polysaccharides for Food Applications: Process Optimization, Structure-Function Decoding, and Rational Design.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c00806},
pmid = {41961090},
issn = {1520-5118},
abstract = {Functional polysaccharides are widely used as food ingredients but are hindered by extreme structural heterogeneity, poorly defined structure-function relationships, and inefficient trial-and-error production workflows. This review provides an integrative synthesis of how AI is reshaping functional polysaccharide research toward food-grade ingredients and formulations. We organize recent advances into a three-stage framework: (1) efficiency amplification, where machine-learning models improve extraction/fermentation optimization and enable rapid analysis when coupled with spectroscopic fingerprints; (2) mechanism-informed hypothesis generation, where deep Deep-QSAR, graph-based learning, and interpretable modeling begin to uncover quantitative links between structural motifs and functional properties, including microbiome-mediated effects relevant to health; and (3) design assistance, in which AI supports precision-guided polysaccharide engineering and formulation for targeted food functionalities. By bridging computational advances with experimental validation, this review provides a cohesive roadmap for polysaccharide discovery and discusses key translational barriers─data scarcity and standardization, model generalizability and interpretability, and regulatory acceptance─highlighting practical strategies for AI-guided polysaccharide discovery and application.},
}
@article {pmid41961102,
year = {2026},
author = {King, AC and Seiler, K and Swanson, K and Ciorba, MA and Alvarado, DM},
title = {IBD risk locus rs1077773 enhances aryl hydrocarbon receptor activity and modulates immune cell function in vitro.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {75},
number = {1},
pages = {},
pmid = {41961102},
issn = {1420-908X},
support = {R01-AI167285/DK/NIDDK NIH HHS/United States ; #648423//Crohn's and Colitis Foundation/ ; #UL1TR002345//Institute of Clinical and Translational Sciences/ ; },
mesh = {Humans ; *Receptors, Aryl Hydrocarbon/genetics ; Polymorphism, Single Nucleotide ; *Inflammatory Bowel Diseases/genetics/immunology ; *Basic Helix-Loop-Helix Proteins/genetics ; Cytochrome P-450 CYP1A1/genetics ; Genetic Predisposition to Disease ; Cytochrome P-450 CYP1B1/genetics ; Organoids ; Male ; Macrophages/immunology ; Female ; },
abstract = {INTRODUCTION: The inflammatory bowel diseases (IBD) Crohn's disease (CD) and ulcerative colitis (UC) are disorders that cause chronic inflammation of the gastrointestinal tract. Both genetic and environmental factors contribute to the pathogenesis of IBD. There are currently >200 known genetic susceptibility loci for the development of IBD. The physiological impact of the majority of these loci remain a gap in our knowledge. One such locus is the single nucleotide polymorphism rs1077773, located ~56 kbp downstream from the aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that is crucial to maintaining intestinal homeostasis. We hypothesized that rs1077773 enhances AHR activity to regulate mucosal immune response and maintain intestinal homeostasis.<br><br>METHODS: All study procedures and reagents were approved by the Washington University Institutional Review Board (#202011003). Patient biopsies were collected at Barnes Jewish Hospital and genotyped using the IBD Genetics Consortium custom GSA SNP chip (Broad Institute) followed by imputation using TopMed Imputation Server at University of Michigan. Patient derived organoids (PDOs; N=3 G/G, N=4 G/A, N=5 A/A) were derived and maintained in 3D culture and supplemented with 50% L-WRN conditioned medium with passage every 3-4 days as previously described. PDOs were treated with AHR agonist 6-Formylindolo[3,2-b]carbazole (FICZ) or vehicle for 48 h. Expression of AHR and its transcriptional targets Cytochrome P450 1A1 (CYP1A1) and CYP1B1 was assessed by RT-qPCR. Blood was collected from pediatric patients undergoing intestinal resection at St. Louis Children's Hospital and was genotyped with custom TaqMan SNP assay (N=3 G/G, N=5 G/A). Peripheral blood monocyte-derived macrophages (MDM&#x3a6;s) were treated with lipopolysaccharide in the presence or absence of AHR ligands FICZ or indole-3-carboxaldehyde for 24 h. Cytokine levels in culture supernatant were measured via using the ProcartaPlex human cytokine, chemokine, and growth factor 45-plex (ThermoFisher) on a Luminex FLEXMAP3D instrument.<br><br>RESULTS: AHR expression was similar across genotypes and treatments. PDOs homozygous for rs1077773 demonstrate enhanced CYP1A1 expression in response to AHR activation. In MDM&#x3a6;s, cytokine secretion was stimulated by LPS treatment and was abrogated by FICZ treatment. MDM&#x3a6;s with rs1077773 alternate allele demonstrated significant reduction in secretion of 12 cytokines and chemokines.<br><br>CONCLUSIONS: This work demonstrates that rs1077773 enhances AHR activity and modulates epithelial and immune cell function in vitro. Further mechanistic understanding of this locus and its correlates could improve our understanding of the molecular mechanisms of IBD susceptibility and may lead to novel personalized therapeutic approaches in IBD.},
}
@article {pmid41961107,
year = {2026},
author = {Rai, SK and Gupta, S and Sarangi, PP},
title = {Metabolite sensing receptors in macrophage reprogramming: from inflammation to resolution.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {75},
number = {1},
pages = {},
pmid = {41961107},
issn = {1420-908X},
support = {MoE-STARS/STARS-2/2023-0939//Ministry of Education, Govt. of India/ ; },
mesh = {Humans ; *Macrophages/immunology/metabolism ; Animals ; *Inflammation/immunology/metabolism ; *Receptors, G-Protein-Coupled/metabolism/immunology ; },
abstract = {BACKGROUND: Macrophages are central to innate immunity, orchestrating both the inflammatory and resolution phases of host defense. Emerging evidence indicates that immunometabolic crosstalk critically dictates macrophage polarization and functions. Disruptions in cellular metabolism can impair these regulatory mechanisms, leading to dysfunctional immune responses associated with various disease pathologies. A key aspect of this regulation involves metabolite-sensing receptors that detect changes in intracellular metabolic intermediates and in extracellular metabolites derived from the diet, host tissues, and the microbiome.<br><br>METHODS: We have conducted a literature review of original research and review articles on metabolite-sensing receptors and their roles in immune cell function, drawn from central databases including PubMed and Google Scholar.<br><br>RESULTS AND CONCLUSION: A major class of extracellular metabolite-sensing receptors is G-protein-coupled receptors (GPCRs), which can directly or indirectly modulate macrophage activation, migration, cytokine production, and metabolic reprogramming. By fine-tuning macrophage-specific functions, metabolite-sensing receptors act as critical regulatory nodes in both inflammation and immune homeostasis, beyond their canonical role in sensing metabolic cues. This review provides a comprehensive overview of the metabolite-sensing receptor interactome, highlighting their central role in macrophage biology and underscoring their potential as therapeutic targets in inflammatory and metabolic diseases.},
}
@article {pmid41961381,
year = {2026},
author = {Low, A and Juang, YR and Ivan, FX and Ang, L and Ooi, LHS and Chan, SWJ and Mac Aogain, M and Jaggi, TK and Chotirmall, SH and Boucher, YF and Yii, ACA and Koh, MS and Lim, DWT and Lee, JWJ and Seow, WJ},
title = {Bacterial taxa associated with lung cancer cases in Southeast Asians: a pilot case-control study.},
journal = {Cellular oncology (Dordrecht, Netherlands)},
volume = {49},
number = {2},
pages = {},
pmid = {41961381},
issn = {2211-3436},
abstract = {PURPOSE: Lung cancer is the leading cause of cancer-related mortality worldwide, yet its underlying mechanisms remain unclear. Disruptions in the respiratory microbiome may promote inflammation and carcinogenesis. This study aimed to comprehensively compare genus-level sputum microbiota between lung cancer patients and healthy controls in a multiethnic Southeast Asian population.<br><br>METHODS: Sputum samples were collected from lung cancer patients across three Singapore hospitals. Socio-demographic data were obtained via questionnaire. We analyzed 16S rRNA amplicon sequences from 70 lung cancer patients and 47 healthy controls from a separate local cohort, using identical sequencing protocols to minimize batch effects. Alpha- and beta-diversity metrics, random forest models, and ANCOM-BC2 were used to identify microbial features associated with lung cancer and host characteristics.<br><br>RESULTS: Lung cancer cases showed significantly reduced genus richness compared to controls. Beta-diversity (Aitchison distance) differed by case-control status, sex, age, and smoking history. ANCOM-BC2 identified Lactobacillus as differentially enriched in cases. However, this enrichment did not pass the pseudo-count test among never-smokers. Further sex-stratified analysis revealed that the Lactobacillus enrichment was driven primarily by male cases. Conversely, [Eubacterium] nodatum group, Mogibacterium, and Campylobacter emerged as robust inverse signatures for lung cancer, with their depletion consistently supported across stratified and unstratified differential abundance analyses, random forest modeling, and Wilcoxon rank-sum tests. However, these findings may still be subjected to residual confounding by exogenous factors, such as medication use, which could not be adequately adjusted for between case-control groups.<br><br>CONCLUSION: This pilot case-control study, conducted in a multiethnic Southeast Asian population, identified distinct respiratory microbiota signatures associated with lung cancer using robust differential abundance and machine-learning methods, providing preliminary evidence for a potential role of the respiratory microbiome to lung carcinogenesis, warranting validation in larger, longitudinal studies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13402-026-01193-7.},
}
@article {pmid41961384,
year = {2026},
author = {Trivedi, A and Roy, S and More, M and Bose, D and Saha, P and Kumar, R and Sarkar, S and Skupsky, J and Tuteja, A and Sullivan, K and Klimas, N and Chatterjee, S},
title = {Spermidine Attenuates Neuroimmune Dysfunction in Gulf War Illness via Modulation of the Gut- Brain Axis.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {41961384},
issn = {1559-1182},
mesh = {Animals ; *Spermidine/pharmacology/therapeutic use ; *Persian Gulf Syndrome/drug therapy/immunology/microbiology/metabolism ; *Brain/drug effects/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; Male ; Receptors, Aryl Hydrocarbon/metabolism ; HMGB1 Protein/metabolism ; Receptor for Advanced Glycation End Products/metabolism ; *Brain-Gut Axis/drug effects ; },
abstract = {Gulf War illness (GWI) affects nearly one-third of US veterans deployed during the 1990-1991 Gulf War (GW) and is characterized by chronic fatigue, neuroinflammation, and gut dysbiosis. Through comprehensive fecal metabolomics sequencing, our lab previously reported the depletion of beneficial metabolites including spermidine in the preclinical GWI mouse model. Spermidine is an endogenously synthesized polyamine known for its anti-inflammatory and mucosal barrier protective effects in various pathological diseases. Given its established role in mitigating intestinal inflammation and maintaining homeostasis, this study investigated the therapeutic potential of spermidine in a persistent (22 weeks) GWI mouse model, with a specific focus on gut-brain axis regulation. Our results demonstrated that spermidine effectively restored both microbial richness and diversity by selectively enriching beneficial bacterial taxa and suppressing growth of opportunistic pathogens, which are otherwise dysregulated following exposure to GW chemicals. Spermidine treatment also improved gut epithelial barrier integrity and reduced epithelial release of high-mobility group box 1 (HMGB1) into systemic circulation. Recent studies on GWI have implicated a critical role of gut-derived damage-associated molecular patterns (DAMPs), particularly HMGB1 in mediating neuroinflammation. Our findings indicate that systemic levels of HMGB1 critically influence the extent of blood-brain barrier (BBB) disruption and subsequent microglial activation. Mechanistically, spermidine activated intestinal aryl hydrocarbon receptor (AhR)/nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) signaling, which played a role in limiting intestinal HMGB1 release and suppressing downstream receptor for advanced glycation end-product (RAGE)-mediated microglial activation in the brain. In vitro results indicate spermidine promoted AhR/Nrf2 nuclear translocation which reduced LPS-induced HMGB1 release from primary intestinal epithelial cells (IECs), effects abrogated by AhR inhibition. Additionally, we observed that HMGB1 directly induces microglial activation via RAGE receptors in immortalized microglial (IMG) cell lines in a dose-dependent manner. These results demonstrate that spermidine decreases neuroinflammation by modulating gut-brain axis pathophysiology associated with GWI. Together, this study demonstrates the therapeutic role of spermidine in ameliorating systemic and neurological disturbances in GWI.},
}
@article {pmid41961453,
year = {2026},
author = {Daly, L and Sullivan, ES and Fouhy, F and Watkins, C and Linaries, D and Power, D and O'Suilleabhain, C and O'Sullivan, A and O'Toole, P and Ross, P and Stanton, C and Ryan, A},
title = {The gut microbiota of hepato-pancreatico-biliary and gastric cancer patients is altered in composition and functionality.},
journal = {Irish journal of medical science},
volume = {},
number = {},
pages = {},
pmid = {41961453},
issn = {1863-4362},
support = {SFI/12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; },
}
@article {pmid41961543,
year = {2026},
author = {Shamabadi, A and Arabzadeh Bahri, R and Arab Bafrani, M and Karimi, H and Asadigandomani, H and Vahidi, H and Akhondzadeh, S},
title = {The gut-brain axis and inflammatory mediators in suicide and mental disorders with high suicide rates: a review of current evidence.},
journal = {Dialogues in clinical neuroscience},
volume = {28},
number = {1},
pages = {145-156},
doi = {10.1080/19585969.2026.2636468},
pmid = {41961543},
issn = {1958-5969},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mental Disorders/metabolism/immunology/microbiology/psychology ; *Suicide/psychology ; *Brain/metabolism/immunology ; *Brain-Gut Axis/physiology ; *Inflammation Mediators/metabolism ; *Inflammation/metabolism ; Animals ; },
abstract = {The interplay between gastrointestinal microbiota and mental disorders has recently been spotlighted. This review investigated discrete evidence suggesting associations between the gastrointestinal microbiome and inflammation with suicide. Fusicatenibavter, Hungatella, Veillonella, and Megasphaera have positive associations, but Clostridium, Butyricicoccus, Desulfovibrio piger, and Parabacteroides merdae have negative associations with suicidality. Additionally, lower species uniformity index, higher intestinal fatty acid binding protein secretion, lower zonulin secretion, higher interleukin-6 in cerebrospinal fluid, and laxative abuse are associated with suicidality. As nearly 90% of suicides occur in patients with mental disorders, the interaction between the gut microbiota and inflammation with these disorders together was also documented. Regarding this, major depressive disorder, psychosis and schizophrenia, generalised anxiety disorder, and substance use disorder were investigated. Bacteroidetes and Firmicutes show prominent changes in most cases. In addition, gut bacterial and non-bacterial microbiome alterations and subsequent dysbiosis may contribute to inflammation, in which cytokines affect microglial activity. Meanwhile, impaired intestinal homeostasis may influence these disorders through the vagus nerve, the hypothalamus-pituitary-adrenal axis, and the kynurenine pathway. Beyond these, direct effects of the gut microbiome on immunity are being hypothesised. In conclusion, the gut microbiota imbalance may influence the nervous system environment from non-inflammatory to inflammatory caused by pro-inflammatory cytokine influx into the brain. Consequently, microbiota imbalances may be associated with mental disorders. Specifically, limited evidence indicated possible links between microbiome alterations and suicide, highlighting the need for further research clarifying these associations and underpinning mechanisms. Other factors, including genetic vulnerability, environmental influences, and neurochemical pathways, should also be considered.},
}
@article {pmid41961656,
year = {2026},
author = {Zhang, Y and Zhang, G},
title = {Causal relationship between gut microbiome, plasma metabolites, inflammation, and aortic stenosis: A multi-omics Mendelian randomization analysis.},
journal = {Medicine},
volume = {105},
number = {15},
pages = {e48238},
doi = {10.1097/MD.0000000000048238},
pmid = {41961656},
issn = {1536-5964},
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Aortic Valve Stenosis/genetics/blood/microbiology ; *Inflammation/blood/genetics ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; Biomarkers/blood ; Metabolomics ; Multiomics ; },
abstract = {As life expectancy increases and the population ages, aortic stenosis (AS) is the most common heart valve disease. Despite rapid improvements in interventional treatment options in recent years, morbidity and mortality from asymptomatic AS remain high. To date, there is no pharmacological therapy to prevent AS. In this study, we used multi-omics to systematically investigate potential causal association between the gut microbiome, human blood metabolites, inflammation and risk of AS, and search for potential biomarker for AS. Single-nucleotide polymorphisms associated with 207 gut microbiota, 1091 blood metabolites and the ratios of 309 metabolites, 731 immune cell phenotypes, 91 circulating inflammatory proteins, as exposures all were selected from recent large genome-wide association study and explored their causal association with AS using Mendelian randomization methods. We used the inverse variance weighted estimation method as the main method and other methods as supplementary methods. Mendelian randomization analysis has shown that 7 gut microbiota, 80 metabolites, 29 immune cells phenotypes, and 6 circulating inflammatory proteins are causally associated with AS. Co-localization analysis showed a significant correlation between 1-stearoyl-2-acryloyl-GPE levels and AS, with a P-value of .981 for posterior probability for hypothesis 4. In addition, metabolic pathway analysis revealed that the valine, leucine, and isoleucine biosynthesis (P = .0312) pathways were associated with AS. Four omics, including 207 gut microbiota, 1091 blood metabolites and the ratios of 309 metabolites, 731 immune cells, and 91 inflammatory proteins were used in this study to explain the causal relationship between multi-omics and AS.},
}
@article {pmid41961851,
year = {2026},
author = {Davey, SD and Forde-Thomas, JE and Hulme, BJ and Lees, K and Costain, AH and Evans, M and Rinaldi, G and Frame, L and Stojanovski, L and Simeons, FRC and Tavendale, A and MacLeod, AK and Pichon, R and Lee, YH and Polak, O and Chalmers, IW and Dankwa, B and Odhiambo, BK and Guimaraes, VH and Hegarty, M and Swain, MT and Aubrey, W and Caldwell, N and MacDonald, AS and Gilbert, IH and Baragaña, B and Read, KD and Hoffmann, KF},
title = {Use of a cytochrome P450 humanized mouse model to refine schistosomiasis drug discovery.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {15},
pages = {e2600197123},
doi = {10.1073/pnas.2600197123},
pmid = {41961851},
issn = {1091-6490},
support = {222153/Z/20/Z//Wellcome/ ; MR/W013568/1//UK Research and Innovation (UKRI)/ ; },
mesh = {Animals ; Mice ; *Cytochrome P-450 Enzyme System/metabolism/genetics ; Humans ; Disease Models, Animal ; Schistosoma mansoni/drug effects ; Praziquantel/pharmacology/therapeutic use ; *Drug Discovery/methods ; *Schistosomiasis mansoni/drug therapy/parasitology ; *Schistosomiasis/drug therapy/parasitology ; Anthelmintics/pharmacology ; Female ; Mice, Transgenic ; *Schistosomicides/pharmacology ; },
abstract = {Control of schistosomiasis, a neglected tropical disease caused by infection with Schistosoma spp., remains reliant on a single chemotherapy, praziquantel (PZQ). This strategy presents a risk to global health should PZQ-resistant schistosomes establish in endemic areas and justifies the search for new drugs. However, species-specific metabolic differences between humans and preclinical models hinder the optimization of next-generation anti-schistosomal therapeutics. Here, to bypass these species-specific limitations, we exploited a humanized mouse model, 8HUM, engineered to express the principal human Phase I cytochrome P450 enzymes (CYP1A1/2, CYP2C9, CYP2D6, CYP3A4/7) as well as the transcription factors constitutive androstane receptor and pregnane X receptor in place of 35 murine orthologs. We characterized Schistosoma mansoni development, immunopathology, hepatic transcriptomic responses, intestinal microbiome changes, and PZQ metabolism as well as PZQ efficacy in 8HUM vs. wild-type (WT) mice. 8HUM mice supported normal S. mansoni maturation, infection-associated microbiome dysbiosis, Th2-dominant immune responses, and characteristic hepatic pathology. PZQ intrinsic clearance in 8HUM hepatic microsomes mirrored human levels and was >10-fold lower than that found for WT microsomes. Oral dosing revealed human-like PZQ exposures of (R)-PZQ and 4OH-PZQ in 8HUM mice at 25 mg/kg bodyweight and >90% reductions in worm burdens at 100 mg/kg bodyweight (equivalent to that seen in WT mice administered PZQ at 400 mg/kg bodyweight). Our results revealed that 8HUM mice recapitulate key features of murine schistosomiasis while exhibiting human-relevant drug metabolism. These findings establish 8HUM as a refined translational platform for anti-schistosomal drug development, improving predictive accuracy and accelerating therapeutic discovery.},
}
@article {pmid41961873,
year = {2026},
author = {Golpasand, S and Ghavi Hossein-Zadeh, N and Ghovvati, S},
title = {Genomic dissection of methane emission traits in cattle: A meta-GWAS and heritability analysis across populations.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0344752},
pmid = {41961873},
issn = {1932-6203},
mesh = {Animals ; Cattle/genetics ; *Methane/metabolism ; *Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; *Quantitative Trait, Heritable ; Genomics ; Quantitative Trait Loci ; },
abstract = {Enteric methane emissions from ruminants represent a significant contributor to agricultural greenhouse gases, necessitating precise genetic tools to guide mitigation strategies. This study aimed to identify genomic regions and estimate heritability parameters associated with methane-related traits in cattle through an integrated meta-analytical framework. The meta-analysis of the genome-wide association studies (meta-GWAS) was carried out with the METAL software, combining SNP level data extracted from published studies. Simultaneously, a distinct random effects meta-analysis of genomic and pedigree-based heritability estimates was performed using Comprehensive Meta-Analysis software. Functional analysis of the post-GWAS, including: Gene Ontology, KEGG, and network-based enrichment analysis, was also performed to describe the biological context of significant genes. The meta-GWAS identified 74 significant SNPs that were significant for the traits of methane, which are related to 113 candidate genes. Functional enrichment analyses revealed pathways related to metabolism, immune response, ion transport, and host-microbiome interactions. The KEGG metabolic pathway emerged as a highly enriched term, encompassing key genes such as: ALDH7A1, CYP51A1, P4HA2, and SHPK, which are involved in amino acid catabolism, lipid processing, and redox regulation functions critical to energy balance and digestive efficiency. Network analysis with Cytoscape has revealed TRPV3, TRPV1, ANK3, PKD2 and SHPK as network hub genes. Heritability meta-analysis indicated that methane production exhibited the moderate genomic (h2 = 0.296) and pedigree-based (h2 = 0.299) heritability estimations, and methane yield was also found to have moderate and high heritability. The findings highlight the potential for methane-related traits as viable targets for genetic selection. This research demonstrates the value of integrating functional genomics and quantitative genetic approaches to enhance understanding of the biological and heritable components of methane emissions, providing a robust foundation for an environmentally sustainable livestock breeding program.},
}
@article {pmid41961886,
year = {2026},
author = {Cosma, BM and Pillay, S and Calderón-Franco, D and Abeel, T},
title = {Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0345919},
pmid = {41961886},
issn = {1932-6203},
mesh = {Humans ; *Metagenomics/methods ; Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; Neural Networks, Computer ; Multiomics ; },
abstract = {Imbalances in the gut microbiome have been linked to conditions such as inflammatory bowel disease, diabetes, and cancer. While metagenomics and amplicon sequencing are commonly used to study the microbiome, they do not capture all layers of microbial functions. Other meta-omics data can provide more insights, but these are more costly and laborious to procure. The growing availability of paired meta-omics data offers an opportunity to develop machine learning models that can infer connections between metagenomics data and other forms of meta-omics data, enabling the prediction of these other forms of meta-omics data from metagenomics. We evaluated several machine learning models for predicting meta-omics features from various meta-omics inputs. Simpler architectures such as elastic net regression and random forests generated reliable predictions of transcript and metabolite abundances, with correlations of up to 0.77 and 0.74, respectively, but predicting protein profiles was more challenging. We also identified a core set of well-predicted features for each meta-omics output type, and showed that multi-output regression neural networks performed similarly when trained using fewer output features. Lastly, our experiments demonstrated that predicted features can be used for the downstream task of inflammatory bowel disease classification, with performance comparable to that of experimental data.},
}
@article {pmid41962053,
year = {2026},
author = {Westcott, RG and Rudzki, EN and Emerson, KJ and Woodley, SK and Kohl, KD},
title = {Exposure to Environmental Microbes Alters Responsiveness of Tadpole Gut Microbiome to Dietary Tannins.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70102},
pmid = {41962053},
issn = {1749-4877},
support = {1945956//National Science Foundation/ ; 2139321//National Science Foundation/ ; },
abstract = {Amphibian larvae consume variable diets in the wild, which can include tannin-rich plant material. Tannins are secondary metabolites that, when consumed, could have complex effects on herbivorous amphibian larvae, including altering their microbiome. Previous studies on the effects of dietary tannic acid on tadpoles were performed using laboratory water, largely devoid of natural microbes. Given that tadpoles acquire much of their gut microbiota from the aquatic environment, we sought to understand the effect of dietary tannins on tadpole size and the gut microbiome when animals were raised in natural pond water, supplying a diverse repertoire of microbes. We raised Green Frog (Lithobates clamitans) tadpoles in autoclaved (microbially depleted) or natural (microbially rich) pond water treatments for 4 weeks. Tadpoles were fed a control diet or a diet containing 2% tannic acid. Tadpoles raised in natural pond water had a greater body mass and length than those raised in autoclaved pond water, but dietary tannins had no effect on body size. Gut bacterial diversity was profiled using 16S rRNA sequencing. The gut microbiome from tadpoles raised in natural pond water was more diverse than that of tadpoles raised in autoclaved pond water. In general, dietary tannins caused a decrease in bacterial diversity and a net reduction in the relative abundance of potentially pathogenic bacterial genera in tadpoles raised in natural pond water but not autoclaved pond water. This study highlights the importance of replicating natural microbial contexts in captive experiments to better investigate biological interactions, such as plant-herbivore and host-microbe interactions.},
}
@article {pmid41962103,
year = {2026},
author = {Paczwa, J and Wu, C and Mulica, J and Siwasan, K and Fuentes, K and Razowska, D},
title = {The gut-brain axis and its role in obesity-induced homeostatic dysregulation.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {3},
pages = {597-604},
doi = {10.36740/WLek/218289},
pmid = {41962103},
issn = {0043-5147},
mesh = {Humans ; *Obesity/physiopathology/metabolism ; *Homeostasis ; *Gastrointestinal Microbiome/physiology ; *Brain/physiopathology/metabolism ; *Gastrointestinal Tract/physiopathology/metabolism ; *Brain-Gut Axis/physiology ; },
abstract = {OBJECTIVE: Aim: The gut-brain axis (GBA) plays a crucial role in maintaining systemic homeostasis through bidirectional communication between the central nervous system and the gastrointestinal tract. This review aims to summarize current evidence regarding the impact of obesity on GBA function and to discuss potential therapeutic strategies targeting this pathway.<br><br>PATIENTS AND METHODS: Materials and Methods: A narrative literature review was conducted using scientific publications indexed in databases including PubMed, ScienceDirect, and the European Journal of Endocrinology. Studies addressing obesity-related alterations in neural signaling, gut microbiota composition, and peptide hormone regulation (e.g., cholecystokinin, peptide YY, ghrelin) were analyzed. Particular attention was given to mechanisms involving dopaminergic reward circuits and emerging therapeutic targets such as ghrelin antagonists, gamma-aminobutyric acid modulators, and melanocortin-4 receptor agonists. Evidence indicates that obesity is associated with significant alterations in gut microbiota composition, vagal signaling, and neuroendocrine regulation of appetite and reward pathways. These changes contribute to dysregulation of nutrient absorption, inflammatory responses, and metabolic homeostasis. Both invasive and non-invasive interventions - including dietary modification, microbiome-targeted therapies, pharmacological agents, and neurostimulation techniques - show potential to modulate GBA signaling and restore physiological balance.<br><br>CONCLUSION: Conclusions: Understanding the complex relationship between obesity and the gut-brain axis may provide novel therapeutic targets for improving metabolic regulation and reducing obesity-related complications. Further clinical and translational studies are required to confirm the long-term effectiveness of GBAoriented interventions.},
}
@article {pmid41962111,
year = {2026},
author = {Sobiech, L and Wójcik, L and Jankowska, N and Turżańska, K},
title = {Periodontitis as a systemic inflammatory disorder - implications for cardiovascular and neurodegenerative diseases.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {3},
pages = {646-650},
doi = {10.36740/WLek/218274},
pmid = {41962111},
issn = {0043-5147},
mesh = {Humans ; *Cardiovascular Diseases/etiology ; *Neurodegenerative Diseases/etiology ; *Periodontitis/complications/microbiology ; *Inflammation/complications ; },
abstract = {OBJECTIVE: Aim: Periodontitis is a chronic inflammatory condition associated with oral microbiome dysbiosis and the dominance of Gram-negative bacteria such as Porphyromonas gingivalis. It is characterized by progressive destruction of the supporting tissues of the tooth, leading to loss of connective tissue attachment, resorption of the alveolar bone, and, consequently to tooth loosening and loss. If left untreated, it leads to recurrent bacteremia and persistent systemic inflammation. The aim of this study is to discuss the mechanisms linking periodontitis to cardiovascular and neurodegenerative diseases.<br><br>PATIENTS AND METHODS: Materials and Methods: A comprehensive literature review was conducted examining clinical studies, systematic reviews, and meta-analyses assessing the impact of periodontal disease on the development of cardiovascular and neurodegenerative diseases.<br><br>CONCLUSION: Conclusions: Chronic activation of the immune response, oxidative stress, and lipid metabolism disorders promote endothelial dysfunction and the progression of atherosclerosis, increasing the risk of cardiovascular events. At the same time, systemic inflammation can affect the permeability of the blood-brain barrier and exacerbate neuroinflammatory processes, promoting &#x3b2;-amyloid accumulation and the progression of Alzheimer's disease. Analysis of the literature indicates the significant, albeit complex, nature of these relationships, emphasizing the importance of prevention and treatment of periodontal disease as part of comprehensive patient care. The key in the approach to periodontal patients is an interdisciplinary perspective, integrating dentistry, cardiology, neurology, and geriatrics.},
}
@article {pmid41962296,
year = {2026},
author = {Wang, Y and Yu, K and Meng, L and Gong, S and Yu, X and Huang, X and Huang, W},
title = {Host proteins and symbiotic bacteria mediate the thermal response differences of the two color phenotypes of Porites lutea to extreme marine heatwaves in Weizhou Island.},
journal = {Marine pollution bulletin},
volume = {229},
number = {},
pages = {119723},
doi = {10.1016/j.marpolbul.2026.119723},
pmid = {41962296},
issn = {1879-3363},
abstract = {Extreme marine heatwaves driven by global warming are the major threat to coral reefs, causing mass coral bleaching and mortality. Color polymorphism is a key coral phenotypic trait, but the mechanisms underlying thermal adaptability differences among color phenotypes remain unclear. This study investigated two Porites lutea phenotypes (green and brown) from Weizhou Island, integrating field surveys, proteomics, and symbiotic microbial community analyses to explore their thermal response differences and molecular mechanisms. Field monitoring during the 2020 marine heatwave revealed a 46% bleaching rate in brown P. lutea, whereas green P. lutea exhibited no bleaching, demonstrating the latter's superior thermal tolerance. Proteomics revealed that green coral hosts maintained thermal adaptability by regulating proteins related to heat shock response, antioxidant defense, and green fluorescent protein (GFP), with GFP expression significantly upregulated by 7.2-fold compared to the brown phenotype. Additionally, the two phenotypes differed in symbiotic bacterial relative abundance: the green P. lutea was dominated by Proteobacteria and Chloroflexi (aiding nitrogen fixation and photosynthesis), while the brown P. lutea was enriched with Thermus and Prosthecochloris (enhancing antioxidant capacity and thermal resistance). No significant differences were found in the community structure or density of Symbiodiniaceae. In conclusion, differential host protein expression and functional complementarity of symbiotic bacteria jointly mediate thermal adaptation differentiation between the two P. lutea phenotypes. This study reveals color phenotypic differentiation as an effective coral survival strategy against environmental stresses, enhancing adaptive potential under future climate change and providing theoretical and technical support for coral reef ecological early warning and restoration under global warming.},
}
@article {pmid41962521,
year = {2026},
author = {Yamada, S and Morine, Y and Ikemoto, T and Saito, Y and Teraoku, H and Miyazaki, K and Shimada, M},
title = {Effect of TU-100 on Colorectal Liver Metastasis in Mouse Model of MASH.},
journal = {The Journal of surgical research},
volume = {322},
number = {},
pages = {10-16},
doi = {10.1016/j.jss.2026.03.073},
pmid = {41962521},
issn = {1095-8673},
abstract = {INTRODUCTION: The incidence of metabolic dysfunction-associated steatohepatitis (MASH) is rapidly increasing, and colorectal liver metastasis (CLM) has been reported to be enhanced in MASH. We previously reported that the herbal medicine Daikenchuto (TU-100) regulates the intestinal microbiome and MASH in a mouse model. This study was performed to examine the effect of TU-100 on CLM using a Western diet (WD)-fed mouse model.<br><br>METHODS: Six-week-old male C57BL/6J mice were used. Mice in the WD group were fed a WD, and TU-100 was administered to mice in the WD+TU-100 group. Splenic injection of MC38 colon cancer cells was performed at 16 wk, and mice were sacrificed 2 wk after splenic injection to assess steatosis, fibrosis, and hepatic mRNA expression.<br><br>RESULTS: The degree of steatosis was significantly reduced in the WD+TU-100 group compared with the WD group (P < 0.05). The maximum tumor diameter was significantly smaller in the WD+TU-100 group than in the WD group (P < 0.05). Hepatic mRNA expression of serum amyloid A1 and tissue inhibitor of matrix metalloproteinases 1 was significantly suppressed in the WD+TU-100 group compared with the WD group (P < 0.05).<br><br>CONCLUSIONS: TU-100 improved hepatic steatosis in an MASH mouse model and suppressed CLM. Suppression of hepatic serum amyloid A1 and tissue inhibitor of matrix metalloproteinases 1 expression may contribute to these effects.},
}
@article {pmid41962594,
year = {2026},
author = {Ott, A and Gül, AZ and Löber, U and Birkner, T and Popova, E and Winter, C and Hadar, R},
title = {Exposure to a High-Fat Diet Compromises Gut Health, Behavior, and HPA Axis Function, with Partial Reversal When Limited to Adolescence.},
journal = {Brain research bulletin},
volume = {},
number = {},
pages = {111883},
doi = {10.1016/j.brainresbull.2026.111883},
pmid = {41962594},
issn = {1873-2747},
abstract = {High-fat diet (HFD) consumption contributes to obesity, yet its impact on females of (pre)reproductive age and the effects of dietary modification after adolescence remain underexplored. This study examined how continuous HFD exposure or an adolescent switch from HFD to a standard diet (SD) shapes the gut microbiome, behavior, neurochemistry, metabolism, and key components of the hypothalamic-pituitary-adrenal (HPA) axis in female rats. Because HPA-axis alterations can occur across generations after HFD exposure, we examined reproductive-tissue HPA-axis components as potential mechanisms of transmission. Females received SD, HFD, or HFD followed by SD after majority of adolescence (postnatal day 60). HFD exposure impaired HPA-axis regulation and switching to SD during adolescence did not prevent persistent dysfunction into adulthood. However, reproductive HPA-axis components remained unaltered. Diet also strongly influenced the microbiome: while HFD disrupted microbial composition in adolescence, switching to SD partially restored it by adulthood. Behavioral and metabolic effects, including increased adiposity and anxiety-like behavior, emerged only with prolonged HFD exposure. Brain neurotransmitter concentrations remained largely unaffected. Overall, dietary history across adolescence and early adulthood shaped long-term HPA-axis function, microbiome composition, and behavioral outcomes. The absence of reproductive HPA-axis alterations suggests it is not a major mediator of maternal HFD-induced intergenerational effects. Persistent HPA-axis dysfunction despite dietary switching indicates limited reversibility, whereas the microbiome showed the greatest adaptive capacity. In contrast, lasting behavioral and metabolic consequences of HFD require continued exposure to adulthood.},
}
@article {pmid41962630,
year = {2026},
author = {Venezia, M and Russo, M and Colomba, P and Zizzo, C and Vinci, M and Marsana, EM and D'Errico, A and Giacalone, I and Duro, G and Moschetti, M},
title = {Epigenetic Modulation of the Gut-Muscle Axis in Pompe Disease: Microbiota Fingerprints to Cellular and Molecular Pathomechanisms.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102364},
doi = {10.1016/j.molmet.2026.102364},
pmid = {41962630},
issn = {2212-8778},
abstract = {Inter-organ cross-talk is increasingly recognised as a fundamental determinant in the pathogenesis of neurodegenerative and neuromuscular disorders, modulating neuroinflammation, protein misfolding, and cellular dysfunction through systemic mediators such as cytokines, adipokines, and growth factors. In neuromuscular diseases, particularly Pompe disease, muscle degeneration is tightly linked to impaired autophagy and chronic inflammation. Recent evidence highlights the gut microbiota as a key regulator of innate and adaptive immune responses, exerting direct effects on skeletal muscle and supporting the existence of a gut-muscle axis. Dysbiosis has been proposed to influence myopathy progression, suggesting that modulation of the intestinal ecosystem may hold therapeutic relevance. Consequently, interventions employing probiotics, prebiotics, and targeted nutritional compounds have emerged as promising strategies to modulate immune activity, attenuate inflammation, and enhance autophagic efficiency, thereby contributing to the restoration of intestinal eubiosis and complementing enzyme replacement therapy.In parallel, epigenetic mechanisms are gaining prominence as additional modulators of pathogenic pathways, with the potential to influence microbiome composition and function. Collectively, these insights position the gut-muscle axis as a central regulatory node in Pompe disease and a compelling target for personalised nutritional and nutraceutical approaches. This review aims to provide a comprehensive examination of the gut-muscle axis and its implications in Pompe disease. Understanding how nutrient-induced changes in microbial gene expression may be harnessed to develop novel, synergistic therapeutic strategies could ultimately improve clinical outcomes and enhance the quality of life of affected individuals.},
}
@article {pmid41962883,
year = {2026},
author = {Li, D and Du, H and Xu, J and Zhang, C and Hou, N},
title = {Bisphenol A-mediated root exudates of ryegrass as potential activators of functional succession in the rhizosphere microorganisms: Mechanistic insights into microbial community assembly and biodegradation.},
journal = {Environmental research},
volume = {300},
number = {},
pages = {124466},
doi = {10.1016/j.envres.2026.124466},
pmid = {41962883},
issn = {1096-0953},
abstract = {The toxic threat of bisphenol A (BPA) pollution to plant growth has drawn increasing attention. Although the plant's inherent repair mechanisms and the regulation of rhizosphere microecological processes hold promise as green remediation strategies, the specific mechanisms by which plants actively modulate rhizosphere metabolites at this critical interface to directionally enhance microbial remediation capacity under BPA stress remain to be further elucidated. Here, during the reclamation process of ryegrass exposed to a BPA concentration of 50 mg kg[-1], the contents of key rhizosphere metabolites (abscisic acid, xanthine, trehalose) in the rhizosphere soil solution significantly increased from 95 ± 12.4 to 201.7 ± 19.1 mg L[-1]. Multi-omics analysis revealed that BPA stress induced the phased accumulation of three key metabolites. From days 0-30, abscisic acid peaked (114.6 ± 11.1 mg L[-1]), coinciding with the upregulation of microbial genes related to cell membrane biosynthesis (slp, lolC) by 1.3-3.8 folds. During days 30-60, xanthine peaked (201.7 ± 19.1 mg L[-1]), corresponding to the highest BPA degradation percentages (62.5 ± 4.2%) and upregulation of TCA cycle-related genes (CS, aco, mdh) by 2.2-4.6 folds. From days 60-90, trehalose accumulation peaked (159.4 ± 19.5 mg L[-1]), alongside stabilized BPA degradation and upregulation of glycolytic pathway genes (ATH1, NTH1, HK) by 2.2-4.6 folds. A structural equation model further demonstrated that these metabolites directly and indirectly influence microbial community function, with abscisic acid, xanthine, trehalose strongly affecting microbial structure and functional gene. This study provides inspiration for the development of technologies related to phytoremediation and root exudates to reduce pollutant in agriculture.},
}
@article {pmid41963036,
year = {2026},
author = {Hou, J and Li, Y and Liu, M and Li, L and Chen, H and An, Y and Xu, H and Yao, Y},
title = {Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105055},
doi = {10.1016/j.fm.2026.105055},
pmid = {41963036},
issn = {1095-9998},
mesh = {*Oryza/microbiology/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Phylogeny ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Seeds/microbiology ; Microbiota ; Metagenome ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; },
abstract = {Rice grains can harbor antibiotic resistance genes (ARGs), yet the relative roles of seed-associated and environmental reservoirs remain unclear. We used shotgun metagenomics on rice tissues (grain, seed, leaf, stem, root) and surrounding matrices (bulk/rhizosphere soil, irrigation water, rainwater, PM10). In total, 1019 ARG subtypes were detected; grains contained 395, the largely overlapping with seeds (290) and environmental samples (322). FEAST source tracking revealed contrasting attribution patterns: seed sources explained nearly half of the grain microbiome (average contribution 49.49%) versus 8.45% from environmental sources, whereas environmental sources contributed more strongly to the grain resistome (20.68%). 747 metagenome-assembled genomes (MAGs) were reconstructed, including 275 ARG-carrying MAGs. Phylogenetic screening identified 39 near-identical (≥99%) ARG linkages across samples, operationally classified by host consistency (same vs different predicted hosts) into 11 putative VGT-like and 28 putative HGT-like patterns. For example, blaGOB-50 in grains and seeds shared near-identical sequences within Elizabethkingia anopheles (VGT-like), while APH(9)-Ic in grains (Burkholderia) matched PM10 (Comamonas), consistent with an HGT-like linkage. In selected cases, ARG-MGE co-localization (e.g., umuC, cca) further supported mobility interpretations. Together, these results indicate seedborne signatures in the grain microbiome but comparatively stronger environmental association for the grain resistome, informing efforts to trace ARG reservoirs in rice systems.},
}
@article {pmid41963048,
year = {2026},
author = {Diaz, M and Wilson, N and Ponsero, AJ and Seecharran, T and Som, N and Al-Khanaq, H and Gutiérrez, AV and Gilmour, M},
title = {Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105075},
doi = {10.1016/j.fm.2026.105075},
pmid = {41963048},
issn = {1095-9998},
mesh = {Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Animals ; Swine ; Food Storage ; *Meat Products/microbiology/analysis ; Cooking ; *Microbiota ; Food Microbiology ; Food Handling ; },
abstract = {Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute to desired product characteristics related to product quality, while also presenting as a spoilage risk. Microorganisms are introduced early during the live brining of raw meat, with the brine representing a long-standing, complex and active culture that influences nitrate generation, preservation, and flavour development. To support quality control and identify early indicators of spoilage, this study investigated taxonomic and functional microbiome changes across production stages, from brining and cooking to cold storage, slicing, and packaging under modified atmosphere. Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate production steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining markedly reduced diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterwards, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation. These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.},
}
@article {pmid41963066,
year = {2026},
author = {Yan, R and Watson, SC and Wei, X and Kovac, J},
title = {Psychrotolerant spoilage bacteria enhanced Campylobacter jejuni culturability on refrigerated chicken meat.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105051},
doi = {10.1016/j.fm.2026.105051},
pmid = {41963066},
issn = {1095-9998},
mesh = {Animals ; *Campylobacter jejuni/growth &amp; development/genetics/isolation &amp; purification/physiology ; Chickens/microbiology ; *Meat/microbiology ; Refrigeration ; Microbial Viability ; Microbiota ; Food Packaging ; Food Microbiology ; *Bacteria/isolation &amp; purification/genetics/classification/growth &amp; development ; Food Storage ; },
abstract = {Campylobacter jejuni is a leading cause of bacterial foodborne illness, with poultry as a major transmission vehicle. The bacterium can enter a viable but non-culturable (VBNC) state, which complicates detection using culture-based methods. While cold and oxidative stress are known VBNC inducers, the role of poultry-associated microbiota in influencing C. jejuni culturability and viability during refrigeration is poorly understood. This study characterized the effect of retail chicken microbiota on C. jejuni over 10 days of cold storage in aerobic and vacuum conditions. We profiled microbiota from chicken breasts in aerobic, modified atmosphere, and vacuum packaging, and from whole chicken under aerobic packaging conditions. Microbiota composition varied with packaging, with Pseudomonas, Brochothrix, and Acinetobacter dominating in aerobic, and Lactococcus and Leuconostoc in vacuum conditions. These genera were isolated and assessed for growth and biofilm formation at 4 °C. Psychrotolerant isolates were whole genome sequenced and used to evaluate their effect on C. jejuni viability and culturability on chicken breast. Three microbiome treatments, including T1 (Pseudomonas, Brochothrix, Acinetobacter), T2 (Lactococcus, Leuconostoc), and T3 (T1 + T2), were co-inoculated with C. jejuni and stored at 4 °C. Viability was assessed by viability qPCR and culturability by plating on Campy Cefex and mCCDA agars. Campy Cefex recovered significantly more (0.74 log10) C. jejuni than mCCDA on day 10 but underestimated viable cell concentration by 2.87 log10. All microbiome treatments improved culturability by > 1 log under aerobic conditions, but not vacuum, highlighting the need to further explore the interactions between non-pathogens and Campylobacter in meat stored aerobically. Microbiome effects on viability were modest and variable. Overall, culture-based methods underestimated C. jejuni viability, underscoring the need for complementary molecular quantification in food safety assessments.},
}
@article {pmid41963103,
year = {2026},
author = {García-García, B and de Oro, LM and Dorado-Rico, MJ and Martín, L},
title = {Biological protection of grapevine pruning wounds: Training system design and mycobiome dynamics.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70804},
pmid = {41963103},
issn = {1526-4998},
support = {//Junta de Extremadura/ ; //European Regional Development Fund/ ; //Instituto Nacional de Investigaci&#xf3;n y Tecnolog&#xed;a Agraria y Alimentaria/ ; //Agencia Estatal de Investigaci&#xf3;n/ ; },
abstract = {BACKGROUND: Grapevine trunk diseases (GTD) lead to progressive vine decline and are a major threat to viticulture sustainability worldwide. GTD can involve multiple fungal species, with Phaeomoniella chlamydospora being one of the most prevalent pathogens. Pruning wounds are the primary entry point for wood-inhabiting fungi. This study assesses the effectiveness of the biological control agent (BCA) Trichoderma atroviride strain SC1 in preventing natural GTD pathogen infections across three vineyard training systems.<br><br>RESULTS: Trichoderma recovery was significantly lowest (48.1%) in the double-cordon training system (V3) and consistently higher (71.9%) in the head/spur system (V1). The treatment reduced GTD infection by 3.75%, and disease control declined markedly 1&#x2009;year after application (61.1%) compared with &#x2264;90&#x2009;days post-treatment (92.6%). The controlled assay including culture-dependent and culture-independent approaches (high-throughput sequencing and quantitative polymerase chain reaction) revealed distinct detection patterns: culture methods favoured fast-growing fungi such as Trichoderma, whereas molecular tools enabled the detection of slower-growing taxa like P. chlamydospora. T. atroviride colonised wood up to 1-2&#x2009;cm from the application point, whereas P. chlamydospora spread up to 5&#x2009;cm. Overall, the pathogen had a stronger impact on wood mycobiome than the BCA, supporting the compatibility of Trichoderma with the resident grapevine microbiome.<br><br>CONCLUSION: These findings provide new insights into the integration of BCAs within vineyard GTD management strategies and contribute to the broader transition towards sustainable viticulture and integrated pest management. &#xa9; 2026 Society of Chemical Industry.},
}
@article {pmid41963512,
year = {2026},
author = {Matoba, R and Iijima, H and Sakamoto, Y and Kawabata, R and Ishiguro, A and Akamaru, Y and Kito, Y and Aizawa, M and Matsuyama, J and Takahashi, M and Makiyama, A and Suzuki, T and Tsuda, M and Yasui, H and Hihara, J and Okuda, H and Kawada, J and Yoshioka, T and Kawakami, H and Eguchi Nakajima, T and Muro, K and Ichikawa, W and Fujii, M and Sunakawa, Y},
title = {Metabolic and functional pathways of gut microbiota in patients with gastric cancer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47830-x},
pmid = {41963512},
issn = {2045-2322},
abstract = {We analysed the differences in bacterial composition between 475 Japanese patients with advanced gastric cancer (median age, 70 years; median BMI 20.0) and 106 healthy individuals using a comprehensive metagenome shotgun analysis. Among the patients with advanced gastric cancer, 71% were male, 37% had relapsed, and 55.5% previously underwent gastrectomy. Bifidobacterium, Anaerostipes, and Parabacteroides were predominant in healthy individuals, whereas Streptococcus, Lactobacillus, and Odoribacter were predominant in patients with advanced gastric cancer. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that butanoate and pyruvate metabolism was enriched in healthy individuals, whereas factors, such as ABC transporters and ribosomes, were enriched in patients with advanced gastric cancer. Cluster analysis broadly classified patients with advanced gastric cancer and healthy individuals into two clusters; however, clustering using pathway data more clearly classified patients with advanced gastric cancer and healthy individuals than clustering using flora analysis. Moreover, healthy individuals showed higher bacterial flora diversity than those with advanced gastric cancer. Although the dataset we used was limited and may be difficult to generalise, we identified some molecular characteristics and functional pathways of the microbial genera within the intestines of patients with advanced gastric cancer.},
}
@article {pmid41963777,
year = {2026},
author = {Rosenbaum, W and Rubio Garcia, M and Löfgren-Burström, A and Larsson, P and Edin, S and Bronnec, V and Palmqvist, R},
title = {Full-length 16S rRNA nanopore sequencing enables species resolution of Fusobacterium associated with colorectal cancer.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2656004},
doi = {10.1080/19490976.2026.2656004},
pmid = {41963777},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Fusobacterium/genetics/classification/isolation &amp; purification ; *Nanopore Sequencing/methods ; *Fusobacterium Infections/microbiology ; DNA, Bacterial/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome ; },
abstract = {Recent studies have revealed that the long-recognized link between the historically defined Fusobacterium nucleatum group and colorectal cancer is largely driven by Fusobacterium animalis. This species, along with two others (Fusobacterium polymorphum and Fusobacterium vincentii), was recently reclassified as distinct from F. nucleatum, highlighting functional divergence within this group. Due to their close genetic relatedness, traditional partial 16S rRNA gene sequencing lacks the resolution to reliably distinguish these species. Nevertheless, accurate species-level identification remains essential in cancer-associated microbiome research. Here, we demonstrate that full-length 16S rRNA sequencing using Oxford Nanopore Technology, combined with a novel custom demultiplexing software, enables robust species-level discrimination within the Fusobacterium genus. Our approach accurately classified clinically relevant Fusobacterium species and recovered their expected proportions from whole cells, DNA mixtures, and clinical CRC specimens. This method provides high-resolution profiling to elucidate species-specific roles of Fusobacterium in colorectal cancer.},
}
@article {pmid41963929,
year = {2026},
author = {Liu, M and Zhou, M and Zhang, J and Chen, C},
title = {Unraveling the relationship between the vaginal microbiome and return to estrus in post-weaning sows.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05467-y},
pmid = {41963929},
issn = {1746-6148},
support = {2022YFA1304204//National Key R&amp;D Program of China/ ; },
abstract = {BACKGROUND: Return to estrus in post-weaning sows has a significant impact on reproduction performance. Changes in sex hormone levels influence the composition of the vaginal microbiota in sows. However, the relationship between return to estrus and the vaginal microbiota in post-weaning sows remains poorly understood.<br><br>RESULTS: In this study, we characterized the vaginal microbiota of 74 Landrace &#xd7; Yorkshire post-weaning sows including 40 normal-return and 34 non-return sows by sequencing the V3-V4 region of the 16&#xa0;S rRNA gene. The results revealed significant differences in both the composition and predicted functional capacities of the vaginal microbiota between normal-return and non-return sows. Non-return sows were characterized by reduced abundances of Clostridium sensu stricto 1, Lactobacillus, and Christensenellaceae R-7 group, and increased abundances of Facklamia and Weissella. Furthermore, the predicted functional pathways of Clostridium acetobutylicum acidogenic fermentation and pyruvate fermentation to butanoate were significantly enriched in normal-return sows. Significant differences were also observed in the co-occurrence networks of the vaginal microbiota between normal and non-return sows, revealing distinct microbial interaction patterns between normal return and non-return sows. A random forest analysis identified several vaginal bacterial taxa that showed high discriminatory capacity between normal and non-return sows (AUC&#x2009;=&#x2009;0.907), including Rikenellaceae RC9 gut group and Christensenellaceae R-7 group that were strongly associated with return to estrus in post-weaning sows.<br><br>CONCLUSIONS: We observed significant differences in the composition and predicted functional capacities of the vaginal microbiota between normal-return and non-return sows, and identified several bacterial taxa associated with return to estrus of weaned sows. These findings enhance our understanding of the relationship between the vaginal microbiota and return to estrus in post-weaning sows and provide a foundation for future mechanistic and interventional studies.},
}
@article {pmid41964025,
year = {2026},
author = {Yoshioka, H and Debeljak, P and Prado, S and Fuji, Y and Ichihashi, Y and Iwata, H},
title = {Interpretable multi-omics machine learning reveals drought-driven shifts in plant-microbe interactions.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00883-x},
pmid = {41964025},
issn = {2524-6372},
support = {JP23KJ0506//Japan Society for the Promotion of Science/ ; JPMJCR16O2//Japan Science and Technology Agency/ ; },
abstract = {BACKGROUND: Plant-microbe interactions in the rhizosphere are central to plant growth, nutrient acquisition, and stress resilience. Although multi-omics approaches enable comprehensive profiling of different biological layers, integrating these data to understand the mechanisms underlying plant-microbe symbiosis, particularly under drought stress, remains a challenge.<br><br>RESULTS: Genomic, metabolomic, and microbiome data from 198 soybean accessions grown under both control and drought conditions were integrated to identify environment-specific predictive features of the plant phenotypes. We compared best linear unbiased prediction (BLUP), genome-wide association study (GWAS), and a nonlinear machine learning model to evaluate their ability to detect informative features. The machine learning models provided flexible variable selection and outperformed linear models in capturing nonlinear dependencies. Model interpretation using SHapley Additive exPlanations (SHAP) indicated that the isoflavone derivative, daidzin, and the drought-tolerant Candidatus Nitrosocosmicus, were major contributors to phenotypic variation, specifically under drought stress. SHAP-based interaction networks indicated cross-omics links, including connections between daidzin, gamma-aminobutyric acid (GABA), and Paenibacillus.<br><br>CONCLUSION: The proposed interpretable machine learning approach for plant phenotype prediction identified multi-omics biomarkers and interactions, providing insights into plant adaptation to drought stress through environment-dependent rhizosphere networks and symbiotic associations.},
}
@article {pmid41964088,
year = {2026},
author = {Krysmann, A and Woolsey, I and da Silva Duarte, V and Kranjec, C and Porcellato, D and Boysen, P},
title = {Bacteria-dependent modulation of immune responses in the bovine udder.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-026-01754-6},
pmid = {41964088},
issn = {1297-9716},
support = {314733//Norges Forskningsr&#xe5;d/ ; },
abstract = {Subclinical mastitis remains difficult to characterize due to the complex interplay between pathogens, local microbiota, and host immune responses. The aim of this study was to investigate how different bacterial species detected in the hindmilk influenced bovine udder immune response and its regulation. Quarter-level hind milk samples were collected from 24 healthy Norwegian Red cows before drying off and through a next full lactation period. Somatic cell populations, cytokines and host-proteome were assessed and combined with the presence of different pathogens. Quarters harboring Staphylococcus aureus and Streptococcus spp. showed significantly elevated somatic cell counts and inflammation associated patterns of somatic cell populations, while those with minor pathogens exhibited lower counts, particularly fewer granulocytes. Cytokines profiling revealed suppressed levels of IFN-γ, IL-10 and TNF-α in the presence of Staphylococcus chromogenes in contrast to the intensive inflammatory activity associated with S. aureus. Weighted gene co-expression network analysis of the host proteome identified two modules of proteins that were negatively correlated with increasing somatic cells count and several modules with strong positive correlation with the SCC. At protein level, we detected 67 proteins differentially expressed based on the pathogen present in the hindmilk. Of these, 19 were linked to immune system functions such as TLR2 and lactoferrin. Our study provides insights into host response in bovine mastitis and reveals a notable lack of interaction between S. chromogenes and the host body compared to an intense immune response in the presence of other pathogens such as S. aureus.},
}
@article {pmid41964093,
year = {2026},
author = {Wang, Q and Duan, C and Dai, H and Lv, D and Shi, Z and Joshi, N and Gierus, M and Zhu, W and Hao, L and Cheng, Y},
title = {Phytosterols improve feed efficiency in yaks by enriching rumen Succiniclasticum.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00562-9},
pmid = {41964093},
issn = {2524-4671},
support = {2024-ZJ-905//Qinghai Provincial Natural Science Fund for Distinguished Young Scholars/ ; 2022YFD1302103//National Key Research and Development Program of China/ ; 2025KTST04//Qinghai University Research Ability Enhancement Project/ ; 2025, L.Z.H.//Qinghai University Graduate Supervisor Innovation Team/ ; QHKLYC-GDCXCY-2024-071//Leading talent of "Kunlun Talents High-level Innovation and Entrepreneurial Talents" in Qinghai Province/ ; },
abstract = {BACKGROUND: Yaks are important livestock species on the Qinghai-Tibet Plateau (QTP), but their productivity is constrained by the harsh alpine environment and the seasonal scarcity of forage resources. Improving feed efficiency has become the key to the sustainable development of Plateau Yak breeding industry. Phytosterols have shown a good application prospect in ruminant feed efficiency improvement, but the impact on yaks is not clear. This study explored the effects of dietary phytosterols supplementation on growth performance, nutrient digestibility, rumen microbial community structure and metabolic function of yaks fed in a barn.<br><br>RESULTS: Twenty-eight 1.5-year-old male yaks (137.10&#x2009;&#xb1;&#x2009;8.70&#xa0;kg) were randomly divided into two groups after 28 days of pre feeding period: the control group (Con, n&#x2009;=&#x2009;14) was fed with basic diet, and the experimental group (PS, n&#x2009;=&#x2009;14) was added with 200&#xa0;mg/kg phytosterols in concentrate. The formal test period was 60 days. Compared with Con group, PS group significantly increased average daily gain (P&#x2009;=&#x2009;0.001), apparent digestibility of crude protein (P&#x2009;=&#x2009;0.036) and neutral detergent fiber (P&#x2009;=&#x2009;0.006), and reduced feed conversion rate (P&#x2009;=&#x2009;0.002). The rumen fermentation mode of PS group changed, the proportion of propionate increased significantly (P&#x2009;=&#x2009;0.001), while the proportion of acetate (P&#x2009;=&#x2009;0.006), acetate to propionate ratio (P&#x2009;=&#x2009;0.001) and lactate (P&#x2009;=&#x2009;0.035) concentration decreased significantly. Phytosterols significantly changed the structure of rumen microbial community and significantly increased the copy number of rumen bacteria (P&#x2009;<&#x2009;0.05). Metatranscriptomic analysis showed that PS group significantly increased the relative abundance of key bacteria, including Succiniclasticum, Faecalibacterium, Ruminococcus, Butyrivibrio, and Alistipes (P&#x2009;<&#x2009;0.05). Microbial co-occurrence network analysis revealed that the number of edges, average degree and modular index of microbial community structure network in PS group increased. Rumen function analysis showed that glycolysis / gluconeogenesis and propionate metabolism were significantly enhanced in PS group (P&#x2009;<&#x2009;0.05), and the expression of key enzymes such as hexokinase and fumarate hydratase were significantly enhanced (P&#x2009;<&#x2009;0.05). Metabolomic analysis revealed that phosphoenolpyruvic acid, fumarate and methylmalonyl-CoA were significantly accumulated in the rumen of PS group (P&#x2009;<&#x2009;0.05). Pathway analysis showed that the pathway impact value of propionate metabolism and glycolysis / gluconeogenesis was greater than 0.1.<br><br>CONCLUSIONS: Phytosterols (200&#xa0;mg/kg of concentrate) can effectively improve the feed efficiency of yaks by regulating the structure and function of rumen microorganisms and altering the fermentation patterns.},
}
@article {pmid41964098,
year = {2026},
author = {de Medeiros, MC and Fontaine, S and Danella, E and Hillman, E and Schmidt, TM and Furgal, A and Wellik, DM and Inohara, N and Núñez, G and Li, G and Chen, GY and D'Silva, NJ},
title = {Loss of salivary agglutinin induces changes in the salivary microbiome and accelerates development of oral cancer.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02337-5},
pmid = {41964098},
issn = {2049-2618},
support = {CA250214/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND: Salivary agglutinin, also known as deleted in malignant brain tumors 1 (DMBT1), is an anti-microbial protein. DMBT1 is low in saliva from patients with oral squamous cell carcinoma (OSCC) and dramatically increases after treatment, with accompanying microbial changes. While this suggests an association between DMBT1 suppression and changes in the oral microbiota, causation has not been established. DMBT1 is also a tumor suppressor protein; its loss promotes OSCC progression, but its role in OSCC development is unknown. In this study, OSCC development was investigated in a murine carcinogen model that simulates human OSCC. Microbiota were standardized between Dmbt1 knockout (Dmbt1[-/-]) and wild-type (Dmbt1[+/+]) mice via interbreeding and co-housing. Saliva was collected at baseline and at 4, 8, 12, 16, and 22 weeks post-carcinogen initiation (stopped at 16 weeks). Tongues were harvested at week 22 for histopathology, and the salivary microbiome was profiled by 16S rRNA sequencing. Microbial diversity metrics and conditional dependence networks assessed community structure, while longitudinal patterns were analyzed using a locally sparse varying coefficient mixed model and functional principal component analysis (fPCA).<br><br>RESULTS: Despite microbiota standardization, Dmbt1[-/-] and Dmbt1[+/+] displayed differences in microbiome composition based on &#x3b2;-diversity metrics. At endpoint, carcinogen-treated Dmbt1[-/-] showed higher OSCC prevalence and more aggressive invasion than Dmbt1[+/+]. Several OTUs, including those from Lachnospiraceae, Sphingomonas, Carnobacteriaceae, and Candidatus Saccharibacteria families, demonstrated differential abundance patterns over time, either genotype-specific, diagnosis-specific, or both. Notably, Sphingomonas and Lachnospiraceae exhibited time-dependent abundance differences in mice that developed OSCC. fPCA identified taxa with abundance trajectories that were different between OSCC and precancer and genotype specific.<br><br>CONCLUSIONS: Thus, DMBT1 shapes salivary microbiota composition and protects against OSCC development. Dynamic, genotype-specific microbial shifts during carcinogenesis underscore the complex interplay between the oral microbiota and cancer progression. Video Abstract.},
}
@article {pmid41964141,
year = {2026},
author = {Durham, SH and McAllister, AK and Chahine, EB},
title = {Gepotidacin for the Treatment of Uncomplicated Urogenital Gonorrhea.},
journal = {The Annals of pharmacotherapy},
volume = {},
number = {},
pages = {10600280261435593},
doi = {10.1177/10600280261435593},
pmid = {41964141},
issn = {1542-6270},
abstract = {OBJECTIVE: To review the efficacy and safety of gepotidacin for the treatment of uncomplicated urogenital gonorrhea (uUGG).<br><br>DATA SOURCES: A literature search of PubMed and Google Scholar (January 2010 to January 2026) was conducted using the terms gepotidacin and GSK2140944. Additional sources included conference abstracts, the manufacturer's website, and prescribing information.<br><br>Relevant English-language studies evaluating the efficacy and safety of gepotidacin for uUGG were included.<br><br>DATA SYNTHESIS: Gepotidacin is a first-in-class triazaacenaphthylene antibiotic with a novel mechanism of action and potent activity against Neisseria gonorrhoeae. In the phase 3 EAGLE-1 trial, gepotidacin demonstrated noninferiority to ceftriaxone plus azithromycin for uUGG treatment. It was generally well tolerated, with gastrointestinal adverse effects most commonly reported. Gepotidacin is administered as 3000 mg orally every 12 hours for 2 doses and is approved for adults and pediatric patients aged &#x2265;12 years weighing &#x2265;45 kg with limited or no alternative treatment options. Administration with food is recommended to reduce gastrointestinal adverse effects.Relevance to Patient Care and Clinical Practice in Comparison to Existing Drugs:Gepotidacin provides a new 2-dose oral option for uUGG treatment. Compared with ceftriaxone, the current drug of choice, oral administration may improve convenience and access. Similar to cefixime and zoliflodacin, its oral formulation may facilitate treatment while potentially reducing microbiome disruption compared with ceftriaxone.<br><br>CONCLUSIONS: Gepotidacin is a promising oral antibiotic with a novel mechanism of action and demonstrated efficacy for uUGG treatment.},
}
@article {pmid41964374,
year = {2026},
author = {Mustafa, AM},
title = {Commentary on oral microbiota analysis in HPV-infected individuals: considerations for future research.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-2},
doi = {10.1080/17460913.2026.2656108},
pmid = {41964374},
issn = {1746-0921},
}
@article {pmid41964509,
year = {2026},
author = {Chen, Z and Zhu, P and Kong, D and Luo, L and Yu, X and Liu, G},
title = {Decoding the genetic mechanism of heterosis in rice: insights from multi-omics and systems approaches.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcag010},
pmid = {41964509},
issn = {1095-8290},
support = {23015821200//Project for Demonstration and Industrialization of Water-Saving and Drought-Resistant Rice in Hainan/ ; //Qinghe Program/ ; //Shanghai Agrobiological Gene Center/ ; },
abstract = {Heterosis, or hybrid vigour, describes the superior growth, yield and adaptability of F1 hybrids from genetically diverse parents and is vital for global food security. Although widely applied for over a century, its molecular basis remains unresolved. Classical hypotheses, including dominance, overdominance and epistasis, serve as theoretical frameworks to explain this complex phenomenon. Recent progress in genomics and multi-omics technologies has deepened our understanding, but genome-level insights alone are insufficient to fully account for hybrid performance. This review synthesizes current advances in elucidating the genetic architecture and regulatory mechanisms underlying heterosis in rice. It emphasizes key genetic loci, the integration of high-throughput omics data, and insights gained from structural variation and plant-microbiome interactions. By integrating diverse omics layers through classical genetic frameworks, the field is moving towards a more comprehensive model of heterosis. These advances offer new strategies for molecular design breeding in rice and point to future directions for enhancing the utilization of heterosis in crop improvement.},
}
@article {pmid41964565,
year = {2026},
author = {Valentine, YA and Duff, AF and Bailey, MT and Pyter, LM},
title = {A systematic assessment of the short- and long-term effects of commonly used breast cancer chemotherapeutics on the gut microbiome‒blood‒brain axis of female mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655149},
doi = {10.1080/19490976.2026.2655149},
pmid = {41964565},
issn = {1949-0984},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Breast Neoplasms/drug therapy/microbiology ; Cyclophosphamide/adverse effects ; *Antineoplastic Agents/adverse effects/therapeutic use ; Cisplatin/adverse effects ; *Brain/drug effects/metabolism ; Doxorubicin/adverse effects ; Paclitaxel/adverse effects ; Bacteria/classification/genetics/drug effects/isolation &amp; purification ; },
abstract = {Chemotherapy affects over 300,000 U.S. breast cancer patients, which disrupts the gut microbiome and induces gut inflammation-an effect hypothesized to drive gastrointestinal side effects (e.g., diarrhea, vomiting) experienced by 50%-80% of patients. Preclinical studies have found causal links amongst chemotherapy-induced gut microbiome disruption, systemic inflammation, and brain-mediated side effects. Therefore, the gut microbiome represents a therapeutic target to attenuate chemotherapy side effects. Because clinical populations are administered multiple chemotherapeutics in combination, a comprehensive understanding of which treatments disrupt the gut microbiome‒blood‒brain axis is lacking. Here, translationally-relevant regimens of four commonly used breast cancer chemotherapies (paclitaxel, cyclophosphamide, cisplatin, and doxorubicin) were given to adult female C57BL/6 mice, and inflammatory, metabolomics and/or bacteriome outcomes were measured in the gut, gut contents, blood, and brain tissues, along with a fatigue and anxiety-like behavioral assessment. Many inter-chemotherapy differences were observed but notable findings include prolonged circulation and central proinflammatory signals by paclitaxel and sustained disruption of the gut microbiome by cisplatin. In contrast, cyclophosphamide and doxorubicin modestly disrupted the gut microbiome‒blood‒brain axis. Taken together, this study systematically identified that paclitaxel and cisplatin most robustly disrupted the gut microbiome‒blood‒brain axis, suggesting that those treated with these drugs may benefit the most from gut-targeted interventions for associated side effects.},
}
@article {pmid41964647,
year = {2026},
author = {Khanna, S and Bloom, PP},
title = {Difficile to treat: advanced management strategies in difficult to treat clostridioides difficile infections.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2026.2659725},
pmid = {41964647},
issn = {1744-8336},
abstract = {INTRODUCTION: Clostridioides difficile infection (CDI) remains a leading cause of healthcare-associated infectious diarrhea, with a major burden driven by recurrences and severe or even fulminant disease in vulnerable hosts. The therapeutic landscape has shifted toward fidaxomicin-based antibiotic regimens, and microbiota restoration strategies including standardized microbiota-based products.<br><br>AREAS COVERED: Recent international guidelines, outcome studies and pivotal trials focused on difficult-to-treat phenotypes: refractory or fulminant CDI, multiply recurrent CDI, and CDI in high-risk populations (immunocompromised, inflammatory bowel disease, critical illness) were reviewed. A PubMed search was supplemented by hand-searching additional references, guideline and regulatory documents. Evidence is summarized for optimized antibiotic regimens, bezlotoxumab, conventional fecal microbiota transplantation (FMT), FDA-approved microbiota-based products, and salvage strategies including intracolonic therapy and surgery.<br><br>EXPERT OPINION: Advanced CDI management is moving from repeated antibiotic cycling toward individualized recurrence prevention and microbiota restoration strategies. Implementation requires diagnostic stewardship, earlier recognition of recurrences, clear pathways for microbiota-based therapy access, and multidisciplinary care for fulminant infection. Over the next five years, standardized microbiota therapeutics and better risk tools should shift care toward earlier, more durable recurrence prevention.},
}
@article {pmid41964677,
year = {2026},
author = {Moomthong, S and Woraruthai, T and Tirapanampai, C and Rungjroenchaiwat, S and Kruasuwan, W and Uthaipaisanwong, P and Kusonmano, K and Jenjaroenpun, P and Wongsurawat, T and Wongnate, T},
title = {A novel Azospirillum vistecanum strain from methane digestate promotes plant growth via indole-3-acetic acid biosynthesis.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13808-y},
pmid = {41964677},
issn = {1432-0614},
abstract = {The urgent need for sustainable agricultural inputs has accelerated the search for microbial alternatives to synthetic agrochemicals. In this study, we report the isolation and comprehensive characterization of a novel strain, Azospirillum vistecanum VT-I1, obtained from a methane-enriched digestate system. This strain demonstrated exceptional plant growth-promoting potential through the biosynthesis of indole-3-acetic acid (IAA), a key phytohormone. Genome sequencing and annotation revealed the presence of genes associated with the indole-3-pyruvate (IPyA) pathway, aro9, ipdC, and aldA, with no detectable IAA-degrading gene clusters, supporting a high net auxin yield. Under optimized culture conditions, VT-I1 produced up to 1.206 mM of IAA, significantly surpassing the levels observed in A. brasilense. Functional assays confirmed the bioactivity of this microbial IAA, which enhanced root development in Exacum affine and improved seed germination in Andrographis paniculata. Collectively, these results establish A. vistecanum VT-I1 as a promising candidate for next-generation biofertilizers, offering a scalable, eco-friendly alternative to chemically synthesized auxins. This work expands our understanding of auxin biosynthesis in rhizobacteria and provides a strong foundation for future field applications and microbiome-based crop enhancement strategies. KEY POINTS: • A novel Azospirillum vistecanum was isolated from methane digestate. • The strain produces high levels of indole-3 acetic acid via the IPyA pathway. • Microbial IAA enhances root growth and seed germination in model plants.},
}
@article {pmid41964722,
year = {2026},
author = {Liedtke, J and Rodenburg, F and Du, C and Zhang, L and Raaijmakers, JM and van Wezel, GP and Briegel, A},
title = {Morphological plasticity of endophytic Chitinophaga pinensis.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {41964722},
issn = {1572-9699},
mesh = {*Endophytes/genetics/cytology/physiology ; Microbiota ; },
abstract = {Environmental changes, whether due to climate change or human influences, compromise the resilience of plants to biotic and abiotic stresses, such as pathogens, drought and heat. Plant microbiota are known to promote plant resilience. To be able to harness the power of the plant microbiome we need to identify microbiota with health-promoting properties. Recent studies have demonstrated that the bacterium Chitinophaga pinensis enhances plant health and increases resistance to fungal infections. Here, we show that C. pinensis exhibits an unusually high morphological plasticity, switching between a filamentous and a spherical cell state, each of which is characterized by a distinct transcriptional profile. Despite these transcriptional differences, spherical cells remained metabolically active and replicating, while lacking structural characteristics typically associated with dormant states. Furthermore, the spherical cell morphology of C. pinensis facilitates hitchhiking behaviour and motility via surfactin cheating, potentially influencing its dispersal and interactions within the plant microbiome. To investigate the structural dynamics and transcriptional adaptation of this plant endophyte, we applied a combination of microscopy and culture-based techniques. Taken together, our study provides new insights into the morphological flexibility and transcriptional regulation of the plant-beneficial C. pinensis.},
}
@article {pmid41964817,
year = {2026},
author = {Longo, S and Rinaldi, TG and Fernández-Real, JM and Federici, M},
title = {Dysregulation of the Gut-Adipose Tissue-Liver Axis: a Possible Mechanism Behind the Relationship Between Metabolic Dysfunction-Associated Steatotic Liver Disease and Type 2 Diabetes.},
journal = {Current diabetes reports},
volume = {26},
number = {1},
pages = {},
pmid = {41964817},
issn = {1539-0829},
mesh = {Humans ; *Diabetes Mellitus, Type 2/metabolism/complications ; *Adipose Tissue/metabolism ; *Liver/metabolism ; Gastrointestinal Microbiome/physiology ; *Metabolic Syndrome/metabolism/complications ; *Fatty Liver/metabolism ; Insulin Resistance ; Animals ; },
abstract = {PURPOSE OF REVIEW: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a hepatic manifestation of metabolic syndrome, frequently occurring alongside type 2 diabetes (T2D), and it can present in varied phenotypes. This review provides a critical analysis of gut-adipose tissue-liver axis (GALA) dysregulation in MASLD pathogenesis, contextualizing the discussion within both established and emerging paradigms. The review elucidates how GALA dysregulation shapes the interplay between MASLD and T2D, emphasizing inter-organ crosstalk among the gut, liver, and adipose tissue, and highlighting the role of microbial metabolites, notably bile acids. The review further summarizes recent advances in stratifying MASLD into distinct clusters, examining intricate associations with cardiometabolic comorbidities, and critically evaluates novel therapeutic approaches targeting GALA modulation.<br><br>RECENT FINDINGS: MASLD can show heterogeneous phenotypes. It significantly increases the risk of developing new-onset T2D, and both conditions often coexist due to their shared pathophysiological basis in insulin resistance. The gut microbiota influences immune function and modulates host metabolism by regulating glucose tolerance and insulin sensitivity through a specific crosstalk between the gut, liver, and adipose tissue. The dysregulation of the GALA may be a mechanism underlying the interplay between MASLD and T2D, influencing IR and metabolic syndrome. A thorough investigation of GALA's role in the physiopathogenesis of MASLD and T2D highlights its potential to distinguish specific MASLD clusters and to identify personalized therapeutic strategies.},
}
@article {pmid41965068,
year = {2026},
author = {Wu, H and Hu, L and Pu, J and Yang, L and Han, F and Wang, Y and Tu, A and Gao, R and Lin, K and Liang, Y and Wu, Z and Pan, S and Song, J and Tang, J and Wang, X},
title = {Oral Microbiome Dysbiosis in Primary Sjögren's Syndrome: A Systematic Review and Meta-Analysis.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keag178},
pmid = {41965068},
issn = {1462-0332},
abstract = {OBJECTIVES: Dry mouth symptoms in patients with primary Sjögren's syndrome (pSS) may be associated with oral microbiome dysbiosis, which plays a critical role in the pathogenesis of pSS and potentially contributes to disease progression. This study systematically reviews and meta-analyzes the latest research on the relationship between the oral microbiome and pSS to identify potential diagnostic biomarkers.<br><br>METHODS: A systematic search was conducted across nine international databases (PubMed, Cochrane Library, Embase, Web of Science, Scopus, VIP, CNKI, Wanfang, and SinoMed) up to October 1, 2024, using a combination of Medical Subject Headings (MeSH) and free-text terms: "oral microbiome" OR "oral flora" AND "Sj&#xf6;gren's Syndrome" OR "pSS." Only studies analyzing the oral microbiota of pSS patients were included. A random-effects meta-analysis was performed for quantitative synthesis. And use a funnel chart to assess the publication bias of the included articles. The conclusions are tempered by the moderate risk of bias in some included studies, substantial heterogeneity (partly attributed to methodological), and the limited number of studies for certain subgroup analyses, which may affect the precision of the pooled estimates.<br><br>RESULTS: A total of 833 studies were identified, 21 of which were included, with 16S rRNA sequencing being the most commonly used technique. QIIME (Quantitative Insights Into Microbial Ecology) is a mainstream bioinformatics analysis tool. Of the 21 studies (1094 participants) included, 19 provided data on &#x3b1; diversity. Overall, declines in the &#x3b1; diversity index were common in pSS (Chao1: SMD = -0.79, [95% CI = -1.381, -0.21], p&#xff1c;0.001; Shannon index: SMD = -0.16, [95%CI = -0.53, -0.21], p=0.400; Simpson index: SMD = -0.14, [95% CI = -0.79, -1.06]), p=0.770. Ten of these studies provided data on &#x3b2; diversity, suggesting a clear difference between the pSS group and the healthy control group. Firmicutes (mainly including Streptococcus spp., Velon spp., etc.) showed a significant enrichment trend in pSS patients, and the relative relative abundance of Proteobacteria (Haemophilus), Actinomycetes and Spiromycetes decreased in pSS patients.<br><br>CONCLUSION: pSS patients demonstrate reduced oral microbiome diversity compared to HCs&#xff08;Healthy controls&#xff09;. Enrichment of Veillonella, Streptococcus, and Prevotella may correlate with pSS pathogenesis, whereas Haemophilus parainfluenzae might serve as a protective taxon. Oral dysbiosis appears to be a distinctive feature of pSS compared to systemic lupus erythematosus (SLE). Further mechanistic studies are needed to explore causal relationships and therapeutic targets.},
}
@article {pmid41965123,
year = {2026},
author = {Machida, E and Takamizawa, Y and Takayanagi, D and Cho, H and Shida, D and Yamada, M and Asami, Y and Ono, H and Takeuchi, M and Hamamoto, R and Rikiyama, T and Suzuki, K and Kanemitsu, Y and Kohno, T and Takashima, A and Sekine, S and Shiraishi, K},
title = {Microbiomic and immunogenic biomarkers of adjuvant chemotherapy efficacy in stage III colorectal cancer.},
journal = {JNCI cancer spectrum},
volume = {},
number = {},
pages = {},
doi = {10.1093/jncics/pkag036},
pmid = {41965123},
issn = {2515-5091},
abstract = {BACKGROUND: The standard treatment for stage III colorectal cancer (CRC) is surgery, followed by adjuvant chemotherapy (AC). However, the efficacy of AC is limited and approximately 30% of patients experience recurrence. Therefore, easily assessable molecular biomarkers that can predict the response to AC are needed. Here, we aimed to identify predictive biomarkers of the response to AC using tumor transcriptomic data.<br><br>METHODS: Tumor specimens from 253 patients who underwent surgery for stage III CRC between 1997 and 2019 were analyzed using RNA sequencing. Transcriptional subtyping and analyses of gut microbiome, immune cell fractions, and T-cell receptors (TCRs) were performed to identify factors associated with recurrence-free survival (RFS) in patients treated with or without AC.<br><br>RESULTS: Among 253 patients, 118 (46.6%) received AC. Twenty phyla and 799 species were identified in the microbiomes, among which Fusobacteria were identified in 247 patients (97.6%). Multivariable Cox proportional hazards regression analysis of patients who received AC showed that intratumoral Fusobacterium abundance (hazard ratio [HR], 3.95; 95% confidence interval [CI], 1.05 to 14.8; P&#x2009;=&#x2009;0.042) and TCR &#x3b1; and &#x3b4; (TRAD) diversity (HR, 0.41; 95% CI, 0.20 to 0.87; P&#x2009;=&#x2009;0.020) were independently associated with RFS.<br><br>CONCLUSION: Fusobacterium abundance and TRAD diversity were associated with the response to AC, suggesting that these factors could serve as biomarkers for personalized treatment in stage III CRC.},
}
@article {pmid41965517,
year = {2026},
author = {Han, J and Zhou, X and Guo, M and Zhang, C and Liu, C and Cai, L and Zhao, H},
title = {Intestinal dysbiosis associates with silica-induced pulmonary fibrosis in mice via arginine and tryptophan pathways.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05023-6},
pmid = {41965517},
issn = {1471-2180},
support = {2025QN03136//Natural Science Foundation of Inner Mongolia/ ; 2025MS03093//Natural Science Foundation of Inner Mongolia/ ; 62231013//National Natural Science Foundation of China/ ; 62261043//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a life-threatening interstitial lung disease with a lack of effective therapeutic approaches. Silicosis is a subtype of PF that is specifically caused by the inhalation of crystalline silica particles. In recent years, the gut-lung axis has been shown to be involved in the occurrence and progression of various respiratory diseases. However, the involvement and specific mechanism of action of the gut microbiome in silica-induced PF remain to be elucidated. Therefore, we established a silica-induced PF murine model using an inhalation exposure system, and combined gut metagenomic and untargeted metabolomics data to correlate microbial and metabolic changes with profibrotic cytokine levels.<br><br>RESULTS: In mice exposed to silica dust for 64 days and 128 days, Akkermansia muciniphila and Staphylococcus lentus were significantly enriched, whereas the abundance of Lactobacillus murinus was notably reduced. Relevant network analysis revealed that these gut microbiota changes were highly correlated with metabolic disorders of tryptophan and arginine. Moreover, changes in the gut microbiome composition corresponded with the fluctuations in the levels of profibrotic cytokines, including transforming growth factor-beta, tumor necrosis factor-alpha, fibroblast growth factor, and hydroxyproline.<br><br>CONCLUSION: We successfully established a murine model of PF induced by silica inhalation. Our results suggest that Lactobacillus murinus, Akkermansia muciniphila, and Staphylococcus lentus are key microorganisms involved in the development of silica-induced PF, while the arginine and tryptophan metabolic pathways serve as key regulatory pathways in the gut-lung axis contributing to disease development.},
}
@article {pmid41965741,
year = {2026},
author = {Khangarot, R and Kumari, V and Mishra, R and Singh, A},
title = {Artificial intelligence in microbiology: implications for metagenomics, diagnostics, and AMR surveillance.},
journal = {Biomedical engineering online},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12938-026-01568-9},
pmid = {41965741},
issn = {1475-925X},
abstract = {Artificial intelligence (AI) is now a key player in modern microbiology, as it enables high-resolution analyses of genomic, metagenomic, and clinical data for the monitoring of infectious disease and antimicrobial resistance (AMR). Considerable advancements in deep learning, transformer-based sequence models, graph neural networks, and multimodal architectures have greatly improved microbial classification accuracy, antibiotic resistance gene (ARG) detection, and resistance prediction. Taking metagenomic sequencing into consideration, these advancements have contributed to the development of sensitive, scalable, and non-invasive methods to profile microbiomes, determine novel resistance, and monitor AMR trends at the population level. This review summarizes recent advances in AI-aided microbiology, with a particular emphasis on AMR surveillance. Specific topics include deep learning frameworks for ARG annotation, emerging approaches to identifying new resistance genes, and multimodal applications (genomic and clinical metadata) aimed at improving phenotype prediction. The role of metagenome-assembled genomes (MAGs) to enhance AMR surveillance efforts is noted, along with their noted limitations relative to isolate genomes. The discussion includes the examination of explainable AI (XAI) techniques including SHAP, attention mechanism approaches, and gradient-based attribution approaches, with the aim of increasing transparency and clinical explainability. We also cover potential applications including AI-enabled non-invasive fecal microbiome diagnostics, laboratory automation, and environmental surveillance. While there has been significant progress, unresolved issues exist relating to dataset variations, liability of models to datasets, interpretability, and regulatory approval. Overcoming these barriers, however, will require standardized frameworks for these workflows, privacy-preserving federated learning methods, and interpretable AI frameworks for clinical and public health tools. AI could fundamentally change AMR surveillance by allowing for earlier resistance detection, advanced risk assessment recommendation, and improved monitoring strategies globally.},
}
@article {pmid41965779,
year = {2026},
author = {Marawan, AE and Elmetwally, OA and Abass, SA and Marwan, MM and El-Sokkary, MMA and Eissa, LA},
title = {Microbiome/transforming growth factor-β axis as a diagnostic and therapeutic target for MASLD in Egyptian patients.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00826-4},
pmid = {41965779},
issn = {1757-4749},
}
@article {pmid41965787,
year = {2026},
author = {Khan, A and Choi, B and Kang, S and Weng, DY and Ying, K and McElroy, JP and Kamel, S and Reisinger, SA and Wewers, MD and Shields, PG and Song, MA},
title = {Lung microbiome predictors of epigenetic aging and potential associations with smoking and electronic cigarette use.},
journal = {Clinical epigenetics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13148-026-02126-9},
pmid = {41965787},
issn = {1868-7083},
support = {RS- 202300245056//Ministry of Education/ ; (P30 CA016058)//National Cancer Institute of the National Institutes of Health (NIH)/ ; (P50CA180908)//The Food and Drug Administration Center for Tobacco Products (CTP)/ ; (UM1TR004548)//The Clinical and Translational Science Award (CTSA)/ ; (UL1TR001070)//The National Center for Advancing Translational Sciences/ ; },
abstract = {BACKGROUND: The lungs harbor diverse microbial communities that may influence pulmonary health, potentially through lung aging. While accelerated lung aging can increase susceptibility to pulmonary diseases, no studies have yet linked the lung microbiome to biological aging in disease-free individuals.<br><br>MATERIALS AND METHODS: We assessed well-studied methylation-based biological aging (mAge) markers (Horvath, GrimAge, PhenoAge, and telomere-length) in the lungs of healthy smokers (SM), electronic cigarette (EC) users, and never-smokers (NS) (n&#x2009;=&#x2009;26, 21-30&#xa0;years). We used metatranscriptome profiling to detect live bacteria. Using XGBoost, we performed feature selection on 1016 bacterial species to predict faster or slower lung mAge, and the selected bacterial species were used as explanatory variables in a logistic regression model. Linear regression analyses examined the associations between identified bacterial species and urinary metabolites of exposure to smoking and EC use, including volatile organic compounds (VOCs) and polycyclic aromatic hydrocarbons (PAHs).<br><br>RESULTS: The logistic regression models identified bacterial species that classified individuals with faster or slower lung aging based on each mAge estimate (accuracy 77%-85%; AUC 0.78-0.91). Two species strongly predictive of GrimAge, Alistipes finegoldii and Arachidicoccus sp.BS20 were significantly less present in SM compared to NS. Arachidicoccus sp.BS20 was significantly associated with nicotine-intake-adjusted metabolites of several VOCs and PAHs in SM and EC users.<br><br>CONCLUSION: For the first time, our study suggests potential associations of the microbiome with biological aging in the lungs of healthy individuals. In addition, the findings indicate that exposure to smoking and EC may be linked to shifts in particular microbial profiles associated with biological aging of the lungs. These results support the need for larger studies to better understand the direction and possible mechanisms of these relationships, and to further explore the lung microbiome as a potential target for interventions aimed at mitigating pulmonary aging and disease risk.},
}
@article {pmid41965848,
year = {2026},
author = {El-Badry, AA and Al-Quorain, AA and Hosin, N and van der Giezen, M and Seyoum, Y},
title = {Bacterial and fungal biomarkers in irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD): trans-kingdom interactions, Blastocystis carriage, and enterotype-succinotype stratification.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00819-3},
pmid = {41965848},
issn = {1757-4749},
}
@article {pmid41965860,
year = {2026},
author = {Navazesh, S and Ter Horst, A and Wen, W and Brown, CT and Ji, P},
title = {Dietary iron and metal-based growth differentially modulate growth and gut microbiome of weaned piglets.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00561-w},
pmid = {41965860},
issn = {2524-4671},
support = {NNFSA210073688//Novo Nordisk Fonden/ ; },
}
@article {pmid41965866,
year = {2026},
author = {Lyu, Y and Su, C and Sun, K and Wang, Y and Zhang, L and Pu, J and Wu, C and Thomas, D and Che, L},
title = {Post-transport recovery trajectory of the canine gut microbiome and metabolome.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41965866},
issn = {1674-9782},
abstract = {BACKGROUND: Transportation induces a multisystem stress response in companion animals, yet the integrated recovery dynamics across physiological, microbial, and metabolic domains remain poorly characterized. This study comprehensively tracked the 7-day recovery trajectory in dogs following road transport by analyzing clinical parameters, fecal microbiome and metabolome.<br><br>RESULTS: Time-dependent changes were observed across domains, with differing temporal patterns. Fecal consistency improved rapidly, while behavioral scores exhibited a decrease followed by stabilization. Microbial alpha diversity initially decreased, with significant community restructuring persisting throughout recovery, culminating in a new stable state distinct from the arrival (D0) state. This shift was characterized by early enrichment of Fusobacterium and Clostridium sensu stricto 1, followed by late dominance of Erysipelatoclostridium, contrasting with the initial post-transport (D0) community dominated by Prevotella 9, Lactobacillus, Phascolarctobacterium, Anaerobiospirillum, Parabacteroides, and Prevotellaceae GA6A1 group. Metabolomic profiling confirmed a sustained metabolic shift, involving pathways in the biosynthesis of steroid and unsaturated fatty acids and the metabolism of butanoate and several amino acids. Strong cross-domain correlations linked specific microbial genera and metabolites with behavioral improvement, underscoring gut-brain axis involvement.<br><br>CONCLUSION: By D7, several measures remained distinct from the arrival (D0) state, indicating persistent multi-system differences during the first week after transport. These findings elucidate the complex, coordinated adaptation to transport stress, highlighting ongoing clinical, microbial, and metabolic differences by D7 and providing a framework for interventions aimed at enhancing welfare and resilience in transported companion animals.},
}
@article {pmid41966291,
year = {2026},
author = {Ashango, ZA and Seyum, EG and Nwogha, JS},
title = {Integrating metagenomics into legume breeding: A breeder-centered roadmap from core microbiomes to precision inoculation.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105941},
doi = {10.1016/j.meegid.2026.105941},
pmid = {41966291},
issn = {1567-7257},
abstract = {Metagenomics, culture-independent profiling of genetic material recovered from environmental samples, provides a powerful route to characterize microbial communities associated with legumes and to translate their functional potential into breeding targets that enhance resilience and productivity. Across analyses of rhizosphere, endosphere, and seed microbiomes, repeated studies consistently identify a conserved set of microbial functions linked to nutrient cycling, responses to abiotic and biotic stress, and biological control of pathogens, thereby offering mechanistic support that community-level functional capacities can shape host outcomes, including seedling vigor, nutrient-use efficiency, and stress tolerance. To move from descriptive discovery to actionable breeding, three complementary translational strategies have emerged: (i) synthetic microbial communities (SynComs) engineered to deliver targeted metabolic functions while enabling rigorous assessment of community stability and functional consistency; (ii) predictive model systems that integrate metagenomic features with phenotypic measurements to prioritize candidate taxa or functions for subsequent validation; and (iii) precision inoculation approaches that deploy validated microbes or consortia in agronomic settings to test whether metagenome-inferred functions confer robust performance under field-relevant conditions. A critical appraisal of metagenomic, multi-omics, and translational studies indicates that functional-phenotypic mappings are promising, yet substantial barriers continue to constrain reproducibility and scalability, including heterogeneity in sampling and experimental design, biases introduced by DNA extraction and sequencing, variability across bioinformatics workflows and reference databases, and overarching biosafety and regulatory constraints that can obscure true biological signals and weaken the reliability of functional inferences intended to guide selection decisions. To mainstream metagenomics in conventional legume breeding, we propose a breeders' roadmap centered on coordinated standardization and decision-ready analytics, encompassing standardized metagenomics-compatible sampling and sequencing platforms, harmonized computational frameworks and metabolic inference tools to ensure comparable functional calls, high-throughput phenotyping protocols aligned to microbiome-sensitive host traits, and selection frameworks that explicitly incorporate microbiome-oriented decision rules rather than treating microbial signals as ancillary. Finally, integrating machine learning with multi-omics datasets alongside precision delivery systems offers a practical route to generate actionable holobiont-level selection indices, and, when coupled with clearly defined translational pipelines and methodological standardization, metagenomics can broaden breeding gains beyond those achievable using host genomics alone, enabling more reliable, function-driven microbiome-assisted improvement of legume performance.},
}
@article {pmid41966331,
year = {2026},
author = {Southey, NL and Zhu, R and Holscher, HD},
title = {Machine Learning and Artificial Intelligence in Nutrition Research: Analytical Methods, Applications, and Key Considerations.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101528},
doi = {10.1016/j.tjnut.2026.101528},
pmid = {41966331},
issn = {1541-6100},
abstract = {Nutrition research is increasingly utilizing artificial intelligence (AI) and machine learning to address analytical challenges posed by high-dimensional data and to enable personalized recommendations and health predictions. This review provides an overview of machine learning techniques and their application in nutrition research. The article is structured according to the steps of a typical analysis pipeline. First, we outline data quality control, preprocessing, and classical statistical tests for detecting group differences, assessing covariate associations, and prescreening input features. Next, dimension reduction and visualization methods such as principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP) are presented to simplify high-dimensional data and reveal nutrition indicators. Supervised learning approaches that support classification and outcome prediction are then reviewed, followed by unsupervised learning methods for clustering unlabeled observations. Integrative tools combining approaches such as canonical correlation analysis (CCA) and supervised multiblock methods are discussed for their suitability in multi-omics and multimodal studies. A comparison of commonly used supervised approaches is presented, including random forest, gradient boosting regression, penalized regression methods, least absolute shrinkage and selection operator (LASSO), support vector machines (SVM), and k-nearest neighbors (k-NN). Deep learning techniques, including convolutional neural networks (CNNs), recurrent neural networks (RNNs), long short-term memory (LSTM) models, natural language processing (NLP), and large language models (LLMs), are highlighted for analyzing unstructured, sequential, and text-based data. To ensure the reproducibility and generalizability of findings, we discuss strategies for model validation, including cross-validation, external replication, and permutation testing. We also discuss practical considerations for implementing advanced analytic approaches in nutrition research, such as interpretability, sample size constraints, and overfitting, to guide responsible implementation. Collectively, this review provides a framework for understanding and thoughtfully applying machine learning approaches to nutrition research.},
}
@article {pmid41966334,
year = {2026},
author = {M, P and Rajendiran, U and Wahab, MT and Venkatachalam, I},
title = {Interventions Targeting Gut Colonization by Multidrug-Resistant Organisms in Healthcare Settings: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2026.03.035},
pmid = {41966334},
issn = {1532-2939},
abstract = {BACKGROUND: Gut colonization with multidrug-resistant organisms (MDRO) increases risks of infection, transmission and mortality in healthcare settings. Although decolonization strategies have been attempted to reduce the impact of gut MDRO, no consensus exists on their effectiveness. Our study evaluates the effectiveness of these strategies.<br><br>METHODS: We searched PubMed, EMBASE, CENTRAL, CINAHL and Web of Science for randomized controlled trials (RCTs) published from Jan 2005 to Dec 2024. Eligible studies included patients in healthcare settings, with baseline MDRO colonization confirmed by rectal swab or stool sample. The primary outcome was reduction in colonization rates in the short term (<28 days) and long term (&#x2265;28 days). Two reviewers independently screened studies, extracted data and assessed bias using the Cochrane RoB2 tool. A random-effects model was used for meta-analysis.<br><br>PROSPERO: CRD42025625291.<br><br>RESULTS: Of 900 studies screened, 14 RCTs were included. Interventions included probiotics (n=7), oral non-absorbable antibiotics (n=6), and fecal microbiota transplantation (FMT) with antibiotics (n=1). No significant effect was observed for short-term (RR=1.18; 95% CI 0.81-1.71; p=0.39) and long-term decolonization (RR=1.12; 95% CI 0.95-1.32; p=0.16). Post-hoc subgroup analyses showed no significant differences across immune status, target organisms, intervention types and timing of outcome assessment. Risk of bias was low in four studies, with seven having some concerns and three at high risk. Certainty of evidence was low.<br><br>CONCLUSION: Current evidence does not support routine use of interventions for gut MDRO decolonization. Well-powered RCTs focused on pathogen-specific interventions and clinically meaningful endpoints are needed to evaluate promising strategies for sustained decolonization (e.g. FMT) and emerging strategies (e.g. bacteriophages).},
}
@article {pmid41966472,
year = {2026},
author = {Merkhan, K and Chaudhry, AS},
title = {Phytogenic feed additives mitigate in vitro methanogenesis and alter microbial community and functional pathways in the dairy cow rumen.},
journal = {Anaerobe},
volume = {98},
number = {},
pages = {103046},
doi = {10.1016/j.anaerobe.2026.103046},
pmid = {41966472},
issn = {1095-8274},
abstract = {OBJECTIVES: Using phytogenic feed additives (PFA) could be a promising strategy for mitigating enteric methane (CH4) emissions from ruminants. This study aimed to evaluate the efficacy of specific phytogenic additives on rumen fermentation, methanogenesis, microbial community, and functional pathways.<br><br>METHODS: This 2 x 4 x 3 factorial study was conducted using an in vitro rumen fermentation system for a period of 72&#xa0;h. Treatments included two silage-to-concentrate ratios (60:40 and 40:60), four PFA (great burnet leaves, GBL; oregano leaves, OL; cumin seeds, CS; and garlic bulbs, GB), and three inclusion levels (0, 10, and 20&#xa0;g&#xa0;kg[-1] DM) for each PFA.<br><br>RESULTS: The GB addition proved the most potent anti-methanogenic additive, reducing CH4 by up to 32.8% at 20&#xa0;g&#xa0;kg[-1] DM, followed by GBL with a 28.5% reduction at 10&#xa0;g&#xa0;kg[-1] DM, without impairing total volatile fatty acid production. Methane suppression was associated with a lower acetate-to-propionate ratio, decreased abundance of methanogenic archaea (particularly Methanobrevibacter), and reduced expression of the key methanogenesis gene mcrA and fmdB. While GB exhibited a strong anti-protozoal effect, OL effectively reduced ruminal ammonia concentrations. Additionally, metagenomic analysis identified Porcincola was among the core and most abundant genera in our bovine rumen dataset.<br><br>CONCLUSION: Optimising the inclusion of specific phytogenic additives can selectively manipulate the rumen microbiome, concurrently reduce methane production and influence nitrogen metabolism. Further research is warranted to evaluate potential synergistic interactions among these additives to enhance fermentation efficiency of ruminant diets.},
}
@article {pmid41966488,
year = {2026},
author = {Sucheta, and Basha, NS and Yadav, K and Khan, L and Siddiqui, AA and Dubey, A and Pradhan, M and Minz, S and Sahu, KK},
title = {Plant exosomes as multifunctional platforms for metabolic targeting and drug delivery in cancer therapy.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {117956},
doi = {10.1016/j.bcp.2026.117956},
pmid = {41966488},
issn = {1873-2968},
abstract = {Plant-based extracellular vesicles (Ph-EXs) represent an innovative new approach for targeting cancer, as they combine natural anti-cancer activity with an advanced ability to deliver drugs. Ph-EXs have direct killing activity against cancer cells through different mechanisms, including the initiation of apoptotic pathways, inhibition of cell growth signals, alteration of the metabolism of cancer cells, and overcoming the effects of drug resistance. Ph-EXs have the ability to alter immune cells' programming, modify cancer-associated fibroblasts, and change the composition of the microbiome, impacting the tumor microenvironment as well as contributing to tumor formation. Additionally, Ph-EXs can cross biological barriers (specifically across the blood-brain barrier) and, due to their lower costs in comparison with other anti-cancer drug delivery methods, present a feasible alternative to synthetics. Ph-EXs have been developed with many engineering efforts, including novel ways to load therapeutic agents onto exosomes as well as surface functionalization. There are several challenges associated with translating Ph-EXs into the clinical setting; these include: potential variability in effect depending on the botanicals they were extracted from, standardization of extraction and characterization methods, and regulatory obstacles for clinical implementation. This review identifies critical knowledge gaps and proposes priority research directions to advance Ph-EX-based platforms toward clinical use.},
}
@article {pmid41966656,
year = {2026},
author = {Gavi, F and Bracco, M and Testori, N and Rossi, F and Fettucciari, D and Panio, E and Assumma, S and Russo, P and Gandi, C and Foschi, N and Ragonese, M and Turri, F and Bientinesi, R and Palermo, G and Ciccarese, C and Iacovelli, R and Kröner, PT and Gasbarrini, A and Sighinolfi, MC and Rocco, B},
title = {Gut microbiome impact on systemic therapy outcomes in metastatic renal cell carcinoma: a systematic review.},
journal = {World journal of urology},
volume = {44},
number = {1},
pages = {},
pmid = {41966656},
issn = {1433-8726},
}
@article {pmid41966784,
year = {2026},
author = {Haider, S and Munyaneza, V and Zhang, W and Ren, L and Song, H and Ahmad, IA and Mehran, M and Liu, S and Xu, F and Kant, S and Yang, J and Yang, C and Ding, G},
title = {Plant-microbe interactions under drought stress: Unlocking new pathways for sustainable agricultural resilience.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128516},
doi = {10.1016/j.micres.2026.128516},
pmid = {41966784},
issn = {1618-0623},
abstract = {Drought stress is among the most significant abiotic constraints on agricultural productivity, a challenge that is intensifying under climate change. Translating the microbial mechanisms under drought into a holistic and systemic strategy remains largely unexplored. This review addresses this gap by advancing the plant-microbiome holobiont framework, which integrates such mechanisms into a unified approach to enhance drought tolerance. The framework constitutes four interrelated pillars which include (1) microbes induced modulation of host physiology and molecular responses through nutrient cycling, phytohormone regulation, osmotic adjustment, biofilm formation, and priming of systemic stress resistance, (2) Root exudates as signal-rich mediators that dynamically shape rhizosphere microbial communities and facilitate the recruitment and activity of drought-adaptive microbes and (3) the evaluation of emerging technological interventions to manipulate the plant-microbe dialogue. These interventions include genetic engineering which enables targeted modification of root exudation patterns and stress-responsive genes to enhance beneficial microbial recruitment, SynComs combining functionally complementary microbes to improve water-use efficiency and nutrient uptake, and mGWAS studies to identify plant genetic loci influencing microbiome composition and interactions, supporting the breeding of cultivars that preferentially associate with beneficial microbes under drought conditions. While (4) modulation of carbon pool, nutrient uptake and resistance priming upon leveraging microbial functions. Explicitly integrating these pillars, framework offers a practical roadmap for transitioning from mechanistic knowledge to targeted advancement of resilient agroecosystems. Harnessing the plant-microbiome holobiont through this integrated approach offers an innovative and sustainable pathway to sustain crop productivity and soil health in increasingly water-limited environments.},
}
@article {pmid41966829,
year = {2026},
author = {Tóth, AG and Paholcsek, M and Solymosi, N and Stágel, A and Gömbös, P and Posta, K and Lakatos, I and Nagy, S&#xc1; and Ferenczi, S and Szőke, Z},
title = {Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer.},
journal = {STAR protocols},
volume = {7},
number = {2},
pages = {104498},
doi = {10.1016/j.xpro.2026.104498},
pmid = {41966829},
issn = {2666-1667},
abstract = {Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies. For complete details on the use and execution of this protocol, please refer to Tóth et al.[1].},
}
@article {pmid41966990,
year = {2026},
author = {Maseng, MG and Hansen, SH and Grännö, O and Bang, C and Lund, C and Huppertz-Hauss, G and Perminow, G and Valeur, J and Bengtson, MB and Opheim, R and Boyar, R and Frigstad, SO and Aabrekk, TB and Detlie, TE and Kristensen, VA and Strande, V and Hovde, &#xd8; and Asak, &#xd8; and Franke, A and Halfvarsson, J and Høivik, ML and Hov, JR},
title = {Disentangling the gut microbiome and inflammation in inflammatory bowel diseases: longitudinal observations from the IBSEN III study.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag051},
pmid = {41966990},
issn = {1536-4844},
support = {//Takeda Pharmaceuticals, Pfizer, Ferring Pharmaceuticals, Tillotts Pharma, Foundation Dam, and the Norwegian South-Eastern Health Authorities/ ; 90569 to J.H.//NordForsk/ ; 2019-01185 to JH//Vinnova/ ; 2988039 to MLH//Research Council of Norway/ ; No: 2020066//Regional Health Authorities South-Eastern Norway/ ; //DFG Excellence Cluster 2167 "Precision Medicine in Chronic Inflammation" (PMI) and the DFG Research Unit 5042 "miTarget"/ ; no: 327634//Research Council of Norway/ ; },
abstract = {BACKGROUND AND AIM: Despite the well-established involvement of the gut microbiome in inflammatory bowel disease (IBD), less is known about how the gut microbiome changes over time and how it varies with clinical disease activity and fecal calprotectin (f-calprotectin). To address this gap, we utilized samples from the population-based inception cohort of the Inflammatory Bowel Disease in South-Eastern Norway III (IBSEN III) study.<br><br>METHODS: Data and stool samples from study participants with IBD and symptomatic controls were collected at diagnosis and after 3, 6, and 12&#x2009;months. Microbiome profiling of stool samples was performed targeting the V3-V4 region of the 16S rRNA gene, and a consensus-based approach of mixed models was employed for the longitudinal microbiome analysis.<br><br>RESULTS: We included 1251 samples from 744 patients with ulcerative colitis, 618 samples from 356 patients with Crohn' s disease and 266 samples from 164 symptomatic non-IBD controls. In the IBD population, we observed that levels of f-calprotectin decreased over time, as did the patient-reported disease activity (P&#x2009;<&#x2009;.001). Distinct changes in the gut microbiome of IBD patients were observed throughout the first year, such as increased alpha diversity (P&#x2009;<&#x2009;.001) and significant taxonomic changes.Notably, there was no covariation between the changes in alpha diversity and f-calprotectin or symptom score.<br><br>CONCLUSION: The gut microbiome during the first year after IBD diagnosis showed changes that paralleled inflammation and clinical disease activity, albeit without covariation, suggesting that there may be a disease-driving impact of gut microbiome independent of inflammation and inflammation-driven symptoms.},
}
@article {pmid41967083,
year = {2026},
author = {Pum, K and Lou, E and Goffredo, P and Jahansouz, C and Subramanian, S and Prakash, A},
title = {Immunotherapy with Guts: A review of microbial therapeutic adjuncts for immunotherapy in solid tumors.},
journal = {The oncologist},
volume = {},
number = {},
pages = {},
doi = {10.1093/oncolo/oyag131},
pmid = {41967083},
issn = {1549-490X},
abstract = {BACKGROUND: Immunotherapy has transformed the management of some solid tumor types, but its impact has been limited to the subset of cancer patients who have 'hot' or immunogenic tumors. Numerous studies are based on strategies for turning 'cold', or immune-unresponsive, tumors into a 'hot' state. The gut microbiome has emerged as a potential co-therapy for standard immune checkpoint inhibitors (ICIs) to achieve this goal. Recent approaches have primarily focused on the use of probiotics, microbial consortia, or fecal microbiota transplantations in combination with anti-PD-1 and anti-CTLA-4 antibodies.<br><br>METHODS: This review highlights the current status of microbiome modulation and its potential impact on clinical practice. Probiotics, such as CMB588, and microbial consortia have been selected following successful preclinical studies. These taxa may initiate T cell infiltration and are commonly found in the microbial profiles of individuals who have previously responded to immunotherapy.<br><br>RESULTS: Several trials with these therapies have had success and noted minimal safety concerns compared to monotherapy treatments. Fecal microbiota transplantation (FMT), originally used to treat Clostridium difficile infections, has also demonstrated promising results in increasing immune checkpoint inhibitor (ICI) efficacy across various cancer types and is being utilized in multiple ongoing trials.<br><br>CONCLUSION: These therapeutics form the foundation for exciting possibilities in immunotherapy and improving patient outcomes.},
}
@article {pmid41967141,
year = {2026},
author = {Vasiliki, G and Konstantina, F and Olga, B and Georgios, T and Helen, G and Chistina, V},
title = {GC-MS method development and validation for the determination of Short Chain Fatty Acids in human feces.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {277},
number = {},
pages = {117488},
doi = {10.1016/j.jpba.2026.117488},
pmid = {41967141},
issn = {1873-264X},
abstract = {Short Chain Fatty Acids (SCFAs), the end products of microbial fermentation of dietary fibers, appear to be key mediators of the beneficial effects elicited by the gut microbiome and have been shown to exert multiple effects on metabolism. In this study, we developed and validated a sensitive, accurate, and reproducible GC-MS method for the simultaneous quantification of SCFAs (Acetic acid (C2), propionic acid (C3), butyric acid (C4), isobutyric acid and isovaleric acid) in human feces. Sample preparation was simplified while maintaining robustness, following systematic evaluation of homogenization, extraction solvents, and acidification conditions. The optimized method demonstrated high analytical performance, with limits of detection ranging from 0.01 to 0.52 μmol/g and good precision and accuracy in accordance with FDA and EMA bioanalytical guidelines Stability studies revealed that SCFAs remain stable in acidified fecal samples for up to 10 days without cold-chain requirements, while -80 °C storage was optimal for long-term preservation and 4 °C suitable for short-term handling. The applicability of the method was confirmed through analysis of samples collected from healthy volunteers. Overall, the developed approach provides a practical, high-throughput, and scalable tool for SCFA analysis, supporting applications in clinical research, metabolomics, and large-scale microbiome studies.},
}
@article {pmid41967167,
year = {2026},
author = {Okoye, CO and Okoye, KC and Ezenwanne, BC and Olalowo, OO and Andong, FA and Echude, D and Chukwudozie, KI and Emencheta, SC and Ezeonyejiaku, CD and Ikele, CB},
title = {Microbiome and multi-omics insights into sustainable aquaculture: A triennial systematic review.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {59},
number = {},
pages = {101830},
doi = {10.1016/j.cbd.2026.101830},
pmid = {41967167},
issn = {1878-0407},
abstract = {Aquaculture is the fastest-growing food production sector, yet intensive practices drive disease outbreaks, antibiotic resistance, and environmental degradation, threatening long-term sustainability. The aquaculture microbiome, encompassing host-associated and environmental microbial communities, regulates nutrient cycling, pathogen suppression, immunity, and overall system resilience. This triennial systematic review (2023-2025), conducted according to PRISMA guidelines, synthesized 19 highly relevant peer-reviewed studies that applied multi-omics approaches (metagenomics, transcriptomics, metabolomics, SNP genotyping, and their integration) to aquaculture microbiomes across shrimp, finfish, and hybrid species. The studies collectively revealed diverse host-microbe-metabolite interactions underpinning growth, immunity, and disease resistance, with representative examples including microbial-metabolite-host signaling axes and microbiome-mediated immune modulation, as seen in Salinivibrio-AMP-mTOR axis, EHP-resistant shrimp via metabolic reprogramming and stable microbiota, and Bacillus-mediated diglyceride production. Beneficial taxa such as Cetobacterium and Salinivibrio, heritable microbiome traits, and sustainable interventions including insect-meal feeds, phytogenic additives, and organic copper consistently improved growth, immunity, and microbial stability while reducing dysbiosis under stress. Environmental stressors and pathogens induced reproducible shifts in microbial diversity, functional pathways, and host metabolism. These findings demonstrate that multi-omics integration is transforming aquaculture into a precision discipline, enabling microbiome-informed selective breeding, targeted probiotics, and environmentally sound nutrition. To translate these insights into practice, future research must emphasize functional validation, machine learning-driven predictive models, and ecosystem-level assessments to achieve resilient, antibiotic-reduced, and sustainable aquaculture systems.},
}
@article {pmid41967481,
year = {2026},
author = {Liu, Q and Cheng, L and Zhang, E and Ling, L and Tan, W and Liang, S and Shu, C and Ma, Q and Zhao, S and Wei, J and Wang, Y and Nian, H and Cheng, Y and Lian, T},
title = {Cross-niche metabolite-microbiome interactions orchestrate systemic soybean resistance to Fusarium root rot.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag080},
pmid = {41967481},
issn = {1751-7370},
abstract = {Fusarium root rot, predominantly caused by Fusarium falciforme, poses a significant threat to soybean productivity globally. Microbiome-based strategies offer sustainable alternatives, but the mechanisms underlying multi-niche interactions remain elusive. Here, we found that a tolerant soybean cultivar (GXD2) coordinates spatially resolved metabolite signals to recruit beneficial microbes across the rhizosphere, root endosphere, and leaf endosphere. Specifically, formononetin and maltol selectively enrich Bacillus and Massilia in the rhizosphere; arctigenin and isovanillic acid recruit Bacillus and Streptomyces to the root endosphere; and flavonoids such as diosmetin attract Penicillium and Aspergillus to the leaf endosphere. Leveraging these interactions, we constructed different types of synthetic communities (SynComs) via top-down (host-selected taxa) and bottom-up (antagonist-based) strategies. Both SynComs suppressed root rot in susceptible cultivars, with foliar application of top-down SynComs significantly enhancing shoot growth. Transcriptomics revealed distinct modes of actions, that top-down SynComs activated mitogen-activated protein kinase (MAPK)-linked terpenoid and flavonoid pathways, whereas bottom-up SynComs primarily modulated host carbon-nitrogen allocation, effectively limiting pathogen resources. Our findings unveil a "metabolite-mediated, multi-niche collaborative defense" model, presenting a robust framework for microbiome-based disease management and paving the way toward sustainable crop protection strategies.},
}
@article {pmid41967489,
year = {2026},
author = {Toju, H and Suzuki, K and Sánchez-Pinillos, M and Shima, G and Kageyama, T and Hayashi, I and Noguchi, M and Fujita, H and Goto, Y and Nakaoka, S and Ushio, M and Ichihashi, Y and Fricke, WF and Mizumoto, K and Takayasu, L and Suda, W and Takayasu, M and Yamamichi, M and Weckwerth, W},
title = {Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag085},
pmid = {41967489},
issn = {1751-7370},
abstract = {Microbiomes are increasingly recognized as key to addressing global challenges in health and sustainability, as they can provide emergent biological functions unattainable with single microbial species. However, microbial communities occasionally undergo abrupt shifts in species composition despite their intrinsic steadiness, making it difficult to maintain highly functional microbiome states. Here, we outline emerging statistical frameworks that integrate ecological stability theory with empirical analyses of microbiome structure and function. Approaches inspired by the concept of "stability landscapes" now enable inference of how the relationship between community structure and assembly potential changes along environmental gradients. Such empirical analyses offer bird's-eye perspectives for maintaining or restoring community states with desirable microbiome functions. Moreover, identifying the attractors of microbiome dynamics facilitates forecasting of abrupt transitions into dysfunctional states (i.e., dysbiosis). Bridging classic ecological theory and empirical microbiome analyses will deepen our understanding of the principles governing species-rich community assembly, expanding the scope of microbiome-based solutions across medical, industrial, agricultural, and environmental sciences.},
}
@article {pmid41967501,
year = {2026},
author = {Deschamps, C and Tronel, A and Bailly, E and Tanfede, MRS and Gilibert, S and Denis, S and Soranzo, T and Van De Wiele, T and Marinelli, L and Blanquet-Diot, S},
title = {Small intestinal microbiome, the underrated maestro of SIMO disease.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag016},
pmid = {41967501},
issn = {1574-6976},
abstract = {Small intestinal microbial overgrowth (SIMO) results from a breakdown in the delicate equilibrium between luminal environment, gut motility, and microbial ecology. Despite extensive research, these factors have largely been investigated as separate entities, with limited integrative insights into their interplay. This review is the first comprehensive synthesis of physicochemical, mechanical, and microbial parameters shaping SIMO pathogenesis. By reviewing both clinical and experimental data, we reveal how alterations in pH, transit time, digestive secretion dynamics, bile acid composition and impaired intestinal absorption collectively reshape microbial load, diversity, and metabolic output, establishing a self-perpetuating loop of dysfunction. We further discuss the limitations of current diagnostic tools and the transformative potential of emerging approaches, from sampling capsules enabling molecular analyses, to in vitro models simulating human small intestinal ecosystem. This integrative perspective shifts the paradigm from a microbe-centered to an ecosystem-based understanding of SIMO, outlining key challenges and opportunities for personalized diagnostics, mechanistic research, and microbiota-targeted next-generation therapeutics including pre-, pro-, postbiotics and faecal transplantation.},
}
@article {pmid41967563,
year = {2026},
author = {Álvarez-Luquín, DD and González-Fernández, RR and Ichikawa-Escamilla, E and Torres-Velasco, ME and Martínez-Martínez, E and Arce-Sillas, A and Juárez-Vaquera, VH and Miranda-Narvaez, CL and Hernández, M and Adalid-Peralta, L},
title = {Models of neuroprotection in Parkinson's disease: Exploring cellular, molecular, and microenvironmental targets.},
journal = {Experimental neurology},
volume = {},
number = {},
pages = {115764},
doi = {10.1016/j.expneurol.2026.115764},
pmid = {41967563},
issn = {1090-2430},
abstract = {Parkinson's disease (PD), the second most common neurodegenerative disorder in the world, is characterized by the chronic and progressive death of dopaminergic neurons. Several intraneuronal mechanisms, as well as microenvironmental factors, are involved in neurodegeneration. Currently, the care for PD patients is focused on controlling motor symptoms. Designing interventions that help stop neurodegeneration remains a major challenge in PD management. This review analyzes various neuroprotective approaches that could promote neuronal survival. We explore innovative strategies, such as gene therapy, the use of exosomes, microbiome modulation, and vagus nerve stimulation. The study emphasizes that these interventions could prevent cellular damage and potentially restore neuronal function. Furthermore, the study emphasizes the importance of understanding the underlying molecular mechanisms in order to develop combined therapies. The research considers critical factors, such as suppressing neuroinflammation and the role of sex hormones in neuron survival. Thus, this review focuses on the molecular mechanisms of neuroprotective strategies under investigation to aid in developing new therapeutic interventions.},
}
@article {pmid41967658,
year = {2026},
author = {Ganamurali, N and Sabarathinam, S and Narasimhan, MK and S, ES},
title = {Nitrogen-Containing Steroidal Alkaloids and the Gut Microbiome: A Steroid-Xenobiotic Axis Perspective for Drug Discovery and Therapeutic Modulation.},
journal = {Steroids},
volume = {231-232},
number = {},
pages = {109789},
doi = {10.1016/j.steroids.2026.109789},
pmid = {41967658},
issn = {1878-5867},
abstract = {Drug metabolism has traditionally emphasized hepatic pathways; however, the gut microbiome introduces a parallel system of biochemical modification that profoundly affects drug efficacy, safety, and variability. This review integrates the emerging steroid-xenobiotic-microbiome axis, emphasizing nitrogen-containing steroidal alkaloids (NSAs) as pivotal modulators. These compounds, combining a hydrophobic steroidal scaffold with nitrogen-based polarity, exhibit unique bioactivities through microbial biotransformation. Gut microbes enzymatically modify steroids and xenobiotics via reduction, deconjugation, and oxidation, shaping pharmacokinetics and receptor signaling. Conversely, steroidal scaffolds regulate microbial enzyme expression, forming reciprocal metabolic feedback. Case studies on digoxin, solanine, and veratramine illustrate this interplay. Understanding how nitrogen incorporation governs structure activity relationships and microbial interactions offers a new avenues for precision pharmacology, biomarker discovery, and rational drug design. This integrated perspective bridges medicinal chemistry, microbiome science, and steroid pharmacology to develop next generation therapeutics guided by host-microbe metabolic crosstalk.},
}
@article {pmid41967847,
year = {2026},
author = {Roy, A and Lu, J and Satten, GA and Zhao, N},
title = {DTH: A nonparametric test for homogeneity of multivariate dispersions.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag178},
pmid = {41967847},
issn = {1367-4811},
abstract = {MOTIVATION: Testing for differences in within-group dispersion is a fundamental problem in multivariate data analysis, with direct implications for interpreting group structure and validating statistical assumptions of other analysis such as ANOVA. Existing methods typically construct test statistics either based on the distance of each observation from the group center or on the mean of pairwise dissimilarities among observations within a group. Both approaches can fail when the mean within-group distance is similar across groups but the distributions of the within-group distances differ. This issue is particularly relevant in high-dimensional microbiome data, where outliers and overdispersion can distort the performance of mean-dissimilarity-based tests.<br><br>RESULTS: We introduce the non-parametric Distance-based Test for Homogeneity (DTH), which measures dispersion of a group by computing within-group dissimilarity. Difference in dispersion across groups is tested by comparing the distributions of the within-group dissimilarity across different groups. A combination of Kolmogorov-Smirnov and Wasserstein distances are used to construct the difference between the distributions. For more than two groups, pairwise group tests are combined using a permutation-based p-value. Through simulations, we show that our method has higher power than existing tests for homogeneity in certain situations and comparable power in others. For continuous covariates, we offer an heuristic extension of DTH that showed good performance in simulations.<br><br>The DTH package, along with the code for reproducing all simulations, analyses, and an accompanying vignette, is available at https://github.com/asmita112358/DTH.},
}
@article {pmid41968003,
year = {2026},
author = {Kalia, S and Nath, P and Anand, AC and Mallick, B and Praharaj, D and Panigrahi, SC and Sahu, SK and Giri, S and Acharya, SK},
title = {Response to letter to the editor regarding methodological refinement and microbiome-centric endpoints.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pan.2026.04.013},
pmid = {41968003},
issn = {1424-3911},
}
@article {pmid41968347,
year = {2026},
author = {Wang, Y and Ko, K and Kim, E and Kačániová, M and Lee, Y and Zhang, G},
title = {Dietary inulin modulates pork quality and systemic health via gut microbiome and metabolome changes in finishing pigs.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00566-5},
pmid = {41968347},
issn = {2524-4671},
support = {2019YFE0107700, NRF-2019K1A3A1A20081146//National Key R&amp;D Program of China-Korea cooperative project/ ; WRS2023075//the key project for foreign experts of Shandong Province/ ; SDAIT-23-05//the Forage Industrial Innovation Team Project/ ; 2022TZXD0018//the Key R&amp;D Program of Shandong Province/ ; NRF-2020R1A2C2004144, RS-2024-00334577//the National Research Foundation Grant of Korea/ ; RS-2024-00410255//Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education/ ; },
}
@article {pmid41968366,
year = {2026},
author = {Pang, F and Solanki, MK and Dong, D and Li, F and Wang, Z},
title = {Rhizobacteria-Mediated Plant Resilience to Abiotic Stresses: Drought, Salinity, and Heat.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70532},
pmid = {41968366},
issn = {1365-3040},
support = {2023GXNSFAA026182//Guangxi Natural Science Foundation (CN)/ ; 2022GXNSFDA035074//Guangxi Natural Science Foundation (CN)/ ; 32101836//National Natural Science Foundation of China/ ; },
abstract = {The frequent occurrence of drought, salinity and heat disasters due to global climate change has become a problem that cannot be ignored and seriously restricts food security and sustainable agricultural development. The role of rhizobacteria in the response of plants to abiotic stress has an important guiding significance in improving plant growth. This paper summarizes the response of plant rhizosphere microbial communities to abiotic stress, analyzes the mechanism by which rhizosphere-related bacteria assist plants to resist abiotic stress, and expounds on the interaction between soil physical and chemical properties, the plant root metabolome, and the rhizosphere microbiome under abiotic stress. This review systematically summarizes the core roles and mechanisms of rhizobacteria in plants' defense against abiotic stress. Stress reshapes the rhizosphere microecology, with drought enriching Firmicutes and Actinobacteria, salt stress increasing Bacteroidetes abundance, and heat stress expanding the dominance of thermotolerant bacteria. Microbial diversity and network structure undergo adaptive reorganization. Streptomyces and Bacillus, as the twin stars aiding plants in enhancing stress resistance, provide medium- to long-term protection through rich secondary metabolites and mycelial networks, while Bacillus achieves acute responses via rapid spore germination, signal induction, and nutrient competition. Rhizobacteria improve soil nutrient availability by regulating carbon, nitrogen, and phosphorus cycles, secreting organic acids and enzymes, and induce plant osmotic adjustment, antioxidant, and anti-ethylene signaling networks through extracellular polysaccharides, volatile organic compounds, plant hormones, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase pathways, thereby systematically enhancing the host's water use efficiency and membrane stability. Future research should integrate multi-omics and field validation to precisely construct rhizosphere bacterial communities, providing theoretical basis and technical routes for green agriculture.},
}
@article {pmid41968380,
year = {2026},
author = {Azargun, R and Azargoon, M and Asefy, Z and Yekani, M and Tarhriz, V and Yeganeh, F and Memar, MY and Eyvazi, S},
title = {Bacterial Infections Role in Gynecological Cancers Development: Narrative Review.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {9},
number = {4},
pages = {e70499},
doi = {10.1002/cnr2.70499},
pmid = {41968380},
issn = {2573-8348},
mesh = {Humans ; Female ; *Genital Neoplasms, Female/microbiology/pathology/etiology ; Microbiota/immunology ; *Bacterial Infections/complications/microbiology ; },
abstract = {BACKGROUND: Gynecological cancers are among the most common cancers in women that affect female reproductive organs. The most common gynecological cancers are ovarian, cervical, uterine/endometrial, vaginal, and vulvar cancer. Women's reproductive organs have a dynamic and relative microbial balance. The disruption in the balance of the microbiome could result in numerous gynecological diseases, as well as, gynecological cancers. In this study, we aimed to review new findings on the role of different bacterial infections in various types of gynecological cancers.<br><br>RECENT FINDINGS: The role of bacterial infection, as an external factor, has been established in several cancers. However, the ways in which bacteria can promote the development of cancer are not fully understood. It seems that inflammation induced by bacterial infections could promote carcinogenesis. In addition, bacterial toxins and effector proteins play important roles in the progression of cancer. In this review, we attempt to present the different bacterial infections, which have been linked to gynecological cancers development. According to different researches, Chlamydia, Mycoplasma, and Bacteroides spp. are the most common bacterial infections associated with gynecological cancers.<br><br>CONCLUSION: Evaluation of microbiome in reproductive organs of the patients with gynecological cancer and studies on prevention and control of the infections in the patients could be useful in verification of pathogenesis of the diseases and also founding suitable therapeutic interventions.},
}
@article {pmid41968400,
year = {2026},
author = {Mahnert, A and Dreer, M and Perier, &#xdc; and Melcher, M and Duller, S and Lehnen, A and Goessler, T and Brunner, D and Graier, T and Wolf, P and Ponce-Toledo, RI and Hodgskiss, LH and Kerou, M and Moissl-Eichinger, C and Schleper, C},
title = {Cultivation and Molecular Profiling Reveal Ammonia-Oxidizing Archaea as Skin Commensals.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag078},
pmid = {41968400},
issn = {1751-7370},
abstract = {Ammonia-oxidizing archaea (AOA) have repeatedly been detected with molecular methods on human skin, yet their persistence, physiological traits, and adaptations remain poorly understood. This is mostly owed to a lack of cultured representatives of AOA taxa from healthy human skin. Using a customized enrichment scheme, we cultivated two autotrophic strains, Candidatus Nitrosocosmicus epidermidis and Ca. Nitrosocosmicus unguis, from human skin samples. Genomic analyses revealed specific adaptations for skin colonization, including genomic islands, and expanded gene families linked to interactions with host proteins, and signaling pathways, distinguishing these AOA from their soil-dwelling relatives. Profiling of more than 700 samples from 8 body sites in cross-sectional, and longitudinal cohorts consistently validated the detection of Nitrosocosmicus species with up to 100% prevalence in a longitudinal cohort, and particularly in sebaceous areas. Co-occurrence patterns with specific bacterial taxa reinforce their role as stable components of the skin microbiome. Our results establish Nitrosocosmicus species as common skin commensals, that are evolutionarily capable of transitioning from soil to human skin. They likely play a critical role in the skin ecosystem by recovering nitrogen from the sebum through utilisation of urea and ammonia. This sheds new light on the role of archaeal species in maintaining the nitrogen balance in the human skin microbiome which might be of importance maintaining a healthy skin.},
}
@article {pmid41968561,
year = {2026},
author = {Nayan, S and Baghel Chauhan, S and Singh, I and Jain, C},
title = {Unravelling the Regulatory Paradox of Probiotics: Challenges in Standardization, Clinical Validation, and Global Acceptance.},
journal = {Recent advances in food, nutrition &amp; agriculture},
volume = {},
number = {},
pages = {},
doi = {10.2174/012772574X441445251207215223},
pmid = {41968561},
issn = {2772-5758},
abstract = {Age-specific probiotic-drug hybrid formulations represent an emerging class of therapeutics that combine live microorganisms with pharmaceutical agents to enhance clinical efficacy, minimize adverse effects, and maintain gut microbiome homeostasis across different age groups. Despite their potential, these hybrids face significant regulatory challenges due to their dual identity as both biologics and drugs, creating ambiguity in classification, evaluation, and approval. Global regulatory agencies, including the U.S. Food and Drug Administration (FDA), European Medicines Agency (EMA), and Central Drugs Standard Control Organization (CDSCO), lack harmonized guidelines for such formulations, resulting in fragmented standards and delayed market entry. This study provides a comprehensive review of existing regulatory frameworks to identify gaps in safety assessment, clinical validation, manufacturing, and postmarket surveillance of probiotic-drug hybrids. A comparative decision matrix is developed to map and contrast the FDA, EMA, and CDSCO approval pathways, highlighting differences in evidentiary and procedural requirements. Building on this analysis, an age-stratified regulatory roadmap is proposed to account for physiological, metabolic, and microbiome-related variations among pediatric, adult, and geriatric populations. The roadmap emphasizes adaptive trial designs, long-term safety monitoring, and age-appropriate dosage and labeling requirements. By integrating scientific, clinical, and regulatory perspectives, this paper provides a structured foundation for harmonizing international approval processes and guiding future policy development. The findings aim to support regulatory convergence, enhance safety assurance, and facilitate the ethical and efficient advancement of probiotic-drug hybrid formulations in global healthcare.},
}
@article {pmid41968607,
year = {2026},
author = {Ma, J and Ruan, J and Yi, J and Zhang, S and Ma, Y and Chen, R and Wang, H and Luo, L and Fang, B and Wu, W and Yang, Q and Sun, D},
title = {Delivery System Based on Akkermansia Muciniphila Loaded Salidroside for the Treatment of Osteoporosis in Zebrafish Model.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e04437},
doi = {10.1002/adhm.202504437},
pmid = {41968607},
issn = {2192-2659},
support = {//Scientific Research Cultivation Project of the College of Life and Environmental Sciences/ ; SHPY2025010//Wenzhou University/ ; 2025ZY01039//Central Government Funds for Guiding Local Scientific and Technological Development/ ; JFLKYXM202303AZ-204//JinFeng Laboratory of Chongqing/ ; },
abstract = {Glucocorticoid-induced osteoporosis (GIOP) is a frequent cost of dexamethasone (Dex) therapy; salidroside (SAL) shows promise but suffers from rapid clearance and poor oral bioavailability. We present an oral, living co-therapy in which viable Akkermansia muciniphila is vacuum-loaded with intracellular SAL and protected by a pH-responsive Eudragit L100 enteric coat (SAL@AKK@EL100). This construct effectively retains probiotic activity, shields the cargo through gastric transit, and shows prolonged intracellular retention with gradual release. In Dex-challenged zebrafish, SAL@AKK@EL100 reversed behavioral dysregulation and improved skeletal mineralization, outperforming SAL or AKK alone. Integrative RNA-seq/16S analysis revealed that SAL@AKK@EL100 treatment was associated with modulation of pathways related to tight junctions, ECM-receptor interaction, actin cytoskeleton, glutathione metabolism, and unsaturated fatty acid biosynthesis, alongside remodeling of the gut microbiota. SAL@AKK@EL100 establishes a modular, microbiome-anchored platform that couples probiotic viability with drug gradual release for promising oral management of GIOP.},
}
@article {pmid41968668,
year = {2026},
author = {Saha, S and Mondal, S and Chatterjee, O and Devroy, P and Sur, D and Bala, A},
title = {Bromocriptine Attenuated Ulcerative Colitis and Colonic Inflammation by Inhibiting IL-1β, Likely through NF-κB Down-regulation: Integrated Network Pharmacology and in vivo Experimental Validation.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128418229260223013818},
pmid = {41968668},
issn = {1873-4286},
abstract = {INTRODUCTION: Gastrointestinal dopamine (DA) plays a crucial role in maintaining gut homeostasis. In patients with ulcerative colitis (UC), a decrease in DA levels due to changes in the gut microbiome can activate immune cells in the colon's mucosal layer, leading to the secretion of various inflammatory mediators and ultimately causing damage to the colonic mucosa. In the present study, we initially analysed integrated network pharmacology and investigated the protective effect of bromocriptine (BRO), a dopamine D2 receptor (D2R) agonist, on acetic acid (AA)-induced UC in rats.<br><br>METHODS: Wistar rats were randomly divided into six groups (N=6/group). The intrarectal administration of AA induced UC. Treatment groups (III-IV) received three doses (2, 5, and 10 mg/kg) of BRO once daily for seven days. Group VI animals were administered mesalamine. On the eighth day, the animals were sacrificed to evaluate the lesion scores, ulcer indices, histopathological findings, nitric oxide (NO) levels, and myeloperoxidase (MPO). Finally, tissue levels of interleukin (IL-1&#x3b2;) and nuclear factor kappa B (NF-&#x3ba;B) were measured using ELISA.<br><br>RESULTS: BRO treatment effectively improved the disease severity index (DAI), colonic lesion score, and ulcer index in rats with AA-induced UC. Histopathological studies revealed that treatment with BRO limited mucosal damage and neutrophil extravasation in colonic tissue. Moreover, biochemical assessments of MPO and NO showed a significant decrease in the levels of both inflammatory mediators following treatment with BRO. Additionally, the results indicated a reduction in the expression of IL-1&#x3b2; and NF-&#x3ba;B in colonic tissue, further supporting the amelioration of colonic inflammation caused by BRO.<br><br>DISCUSSION: The present research demonstrated that BRO exerts a protective effect by influencing the expression of IL-1&#x3b2; and NF-&#x3ba;B in rats with AA-induced UC, thus restricting the activity of immune cells in the colonic mucosa.<br><br>CONCLUSION: Findings of this research suggest that BRO may be a promising therapeutic agent for the management of UC.},
}
@article {pmid41968748,
year = {2026},
author = {Hilpert, K},
title = {Peptidomics: A New Dimension in Microbiome Research.},
journal = {Protein and peptide letters},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298665436241260327111926},
pmid = {41968748},
issn = {1875-5305},
abstract = {The human gut microbiome is now recognised as a major determinant of health, with roles extending beyond digestion to influence neurodegeneration, metabolism, immunity, and pharmacological responses. Clinical studies link microbial imbalances to Alzheimer's disease, Parkinson's disease, depression, and cardiovascular disorders, yet the underlying mechanisms remain only partly understood. Methodological advances have progressively deepened our insight. DNA-based sequencing (metagenomics) catalogues microbial genes but reveals only potential functions. RNA-based sequencing (metatranscriptomics) highlights active gene expression, but instability of transcripts and poor correlation with protein activity limit its predictive value. Metabolomics measures small-molecule end products, providing direct evidence of microbial biochemistry and identifying disease-linked metabolites such as urolithin A, trimethylamine N-oxide, and equol. These approaches together have transformed microbiome science, but they remain incomplete. A critical and underutilised dimension is peptidomics: the systematic analysis of endogenous peptides in the gut and circulation. Enabled by peptide-enriching, protease-inhibiting workflows and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), peptidomics directly captures unstable signaling peptides and proteolytic fragments that are often invisible to conventional proteomics. Coupled with emerging gut-specific peptide databases, such as MetaPep, and Artificial Intelligence (AI) assisted de novo sequencing and spectral prediction for non-human peptides, this provides a concrete technical route to reading out the functional peptide layer of the microbiome. Peptidomics can capture functional signals of host-microbiome interaction, reveal context-specific biomarkers, and provide mechanistic insight into disease. Recent studies demonstrate that peptide-level resolution uncovers microbial contributions to gut inflammation, modulates the gut-brain axis, and enables peptide-based disease stratification in conditions such as inflammatory bowel disease. However, despite these promising examples, peptidomics remains largely absent from mainstream microbiome research, which needs to be changed. Integrating peptidomics with existing genomic, transcriptomic, and metabolomic approaches will generate a more complete and functional picture of the microbiome. This shift will accelerate biomarker discovery, refine diagnostics, and expand the search for peptide-based therapeutics, positioning peptidomics as an essential next step in microbiome science.},
}
@article {pmid41968757,
year = {2026},
author = {Wu, M and Zhang, Y and Yu, J},
title = {How the gut microbiome affects the immunotherapy response in hepatocellular carcinoma.},
journal = {Cancer biology &amp; medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0761},
pmid = {41968757},
issn = {2095-3941},
support = {2023ZD0500200//Non-communicable Chronic Diseases-National Science and Technology Major Project/ ; 3133344//Strategic Seed Funding Collaboration Research Scheme CUHK/ ; 3135509//Strategic Impact Enhancement Fund CUHK/ ; 3134277//Impact Case for RAE CUHK/ ; },
abstract = {Hepatocellular carcinoma (HCC) remains a major global health challenge with limited long-term survival despite advances in surgical, locoregional, and systemic treatments. Although immune checkpoint blockade (ICB) has reshaped HCC therapy, only a subset of patients achieves durable responses, reflecting substantial heterogeneity in tumor biology and immune microenvironments. Dysbiosis, involving the loss of beneficial bacteria, like Lactobacillus reuteri and Akkermansia muciniphila, and the expansion of pathogens, such as Klebsiella pneumoniae and Catenibacterium mitsuokai, drives HCC by promoting microbial translocation and chronic inflammation. This process is mediated by microbiota-derived metabolites. Pro-carcinogenic agents, like deoxycholic acid (DCA) and quinolinic acid, induce inflammation and activate oncogenic pathways, while protective short-chain fatty acids (SCFAs), like acetate and butyrate, modulate T-cell and ILC3 responses to influence antitumor immunity. Tryptophan catabolites, acting via the aryl hydrocarbon receptor (AhR), further fine tune immune and barrier functions. In addition, emerging data implicate intratumoral microbiota as active modulators of immune suppression and metastatic behavior. These mechanistic insights have accelerated the development of microbiome-targeted interventions, such as probiotics, prebiotics, engineered bacterial strains, and fecal microbiota transplantation, to enhance ICB responsiveness. This review synthesizes current advances linking the gut microbiome to HCC immunobiology and highlights emerging therapeutic strategies aimed at optimizing immunotherapy through precise microbial modulation.},
}
@article {pmid41969116,
year = {2026},
author = {Shakirov, R and Pankratova, Y and Shakurov, A and Senina, A and Boulygina, E and Grigoryeva, T and Yarullina, D and Karpukhin, O},
title = {Comparative characteristics of the microbiota of diverticula in complicated diverticulitis.},
journal = {The new microbiologica},
volume = {49},
number = {1},
pages = {65-70},
pmid = {41969116},
issn = {1121-7138},
mesh = {Humans ; *Diverticulitis/microbiology/complications ; Male ; *Gastrointestinal Microbiome ; *Bacteria/classification/isolation &amp; purification/genetics ; Middle Aged ; *Diverticulum/microbiology/complications ; Aged ; RNA, Ribosomal, 16S/genetics ; Female ; },
abstract = {We present a comparison of the mucosal microbiota within different diverticula in a patient with diverticular disease (DD) complicated by diverticulitis and pelvic abscess. The conventional culture method and the 16S rRNA-based sequencing approach were employed to characterize the microbiota of perforated diverticulum (PD) and adjacent visually intact diverticulum (ID) from the same surgically resected colonic segment. Compared to PD, the microbiota of ID demonstrated depletion in butyrate-producing genera and increased abundances of Proteobacteria, Enterobacteriaceae, and Bacteroides. The predominantly pro-inflammatory character of the microbiota in ID suggests its probable pathological role in the progression of DD towards more complicated forms, up to inflammatory destruction (perforation) of the diverticulum wall. The insights of this study pave the way for the development of forthcoming clinical trials focusing on microbiota-related therapies, including the use of antibiotics, probiotics, and fecal microbiota transplantation (FMT), to potentially treat or manage DD and its complications.},
}
@article {pmid40796214,
year = {2026},
author = {Kopylov, U and Verstockt, B and Marigorta, UM and Noviello, D and Bossuyt, P and Mookhoek, A and Sinonquel, P and El-Hussuna, A and Sahnan, K and Baumgart, DC and Noor, NM and Allocca, M and Carter, D and Ensari, A and Iacucci, M and Pellino, G and Soriano, A and de Laffolie, J and Daperno, M and Raine, T and Cleynen, I and Sebastian, S},
title = {Results of the Ninth Scientific Workshop of the European Crohn's and Colitis Organisation (ECCO): Artificial Intelligence in medical management and precision medicine.},
journal = {Journal of Crohn's &amp; colitis},
volume = {20},
number = {4},
pages = {},
doi = {10.1093/ecco-jcc/jjaf134},
pmid = {40796214},
issn = {1876-4479},
mesh = {Humans ; *Artificial Intelligence ; *Precision Medicine/methods ; *Inflammatory Bowel Diseases/therapy/diagnosis ; Natural Language Processing ; Wearable Electronic Devices ; *Crohn Disease/therapy ; Telemedicine ; },
abstract = {BACKGROUND AND AIMS: Artificial intelligence (AI) is increasingly being applied in various fields of medicine, including inflammatory bowel diseases (IBD). This systematic review, conducted as part of the ECCO 9th Scientific Workshop on AI in IBD, explores AI applications in multiomics precision medicine, large language models (LLMs) for textual tasks, and utilization of wearable and remote care technologies.<br><br>METHODS: A comprehensive systematic analysis of the literature was undertaken, emphasizing three topics: multiomics predictive models in IBD; natural language processing (NLP) and LLMs for clinical practice, research and patient communication; and the role of remote monitoring and wearable devices.<br><br>RESULTS: Key areas of promise include the implementation of NLP and LLMs for case identification and differentiation, tracking disease activity, pharmacovigilance, quality assurance, and patient support. Multiomic approaches, integrating genomics, transcriptomics, proteomics, metabolomics, and metagenomics, show potential for developing more accurate diagnostic and risk prediction models and improving treatment response prediction and detection of actionable drug targets for future therapeutics. Wearables and remote monitoring technologies can transform IBD management from episodic assessments to continuous, less biased tracking of patient-reported outcomes and physiological biomarkers.<br><br>CONCLUSIONS: While AI and multiomics approaches hold substantial promise for advancing IBD management and research, further refinement is necessary to ensure content validity and address safety concerns, thereby allowing integration of AI into clinical workflows and safeguarding of data privacy. Future research should prioritize the integration of diverse omic data, conduct of longitudinal studies, and validation in large and diverse cohorts.},
}
@article {pmid41779268,
year = {2026},
author = {Trujillo-López, MA and Muñoz-Olivos, C and Garduño-Vargas, M&#xc1; and Sánchez-López, JM and Martínez-Ortiz, VM and Pérez-Armendáriz, B and El-Kassis, EG and Bautista-Rodriguez, E},
title = {Bacillus mojavensis postbiotics: transcriptomic and anticancer effects in colon cancer cells.},
journal = {AMB Express},
volume = {16},
number = {1},
pages = {},
pmid = {41779268},
issn = {2191-0855},
support = {CBF-2025-I-3072//SECIHTI/ ; },
abstract = {UNLABELLED: Probiotics have been shown to exert antiproliferative effects on colon cancer cells. While these effects are often attributed to microbiome regulation, they may also result from bioactive metabolites produced by probiotic bacteria. In the present study, we investigated the impact of a cell-free extract, hereafter referred to as a postbiotic, derived from Bacillus mojavensis, a strain isolated from aguamiel (a traditional Mexican beverage). The antiproliferative activity was evaluated in SW480 human colon cancer cells using MTT and crystal violet assays, while antimigratory effects were assessed through a wound-healing assay. In addition, the ability of the postbiotic to counteract inflammatory proliferation was evaluated in SW480 cells treated with lipopolysaccharide (LPS). Biosafety was tested using peripheral blood mononuclear cells (PBMCs) from healthy donors. Results demonstrated that treatment with 25–50 µg/mL of B. mojavensis postbiotic reduced SW480 cell viability by 75.15% and 79.3%, respectively, and significantly inhibited cell migration after 24 h. Moreover, the postbiotic decreased LPS-induced proliferation without exerting any cytotoxic effect on PBMCs, underscoring its selectivity toward malignant cells. To elucidate the underlying mechanisms, transcriptomic profiling was performed, revealing extensive modulation of oncogenes and tumor suppressors, with enrichment of PI3K–Akt, MAPK, apoptosis, and cytokine receptor pathways. In conclusion, postbiotics from B. mojavensis isolated from aguamiel exhibit selective anticancer activity by inhibiting proliferation, migration, and inflammation-induced growth in colorectal cancer cells. Transcriptomic findings further support these effects.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13568-026-02018-4.},
}
@article {pmid41957950,
year = {2026},
author = {van der Heijden, M and Clubb, JHA and Erawijantari, PP and Ronkainen, A and Arias, V and Jirovec, E and Kudling, T and Pakola, SA and Ojala, N and Haybout, L and Basnet, S and Grönberg-Vähä-Koskela, S and Karoliina Raatikainen, S and Hemminki, O and Kanerva, A and Quixabeira, DCA and Cervera-Carrascon, V and Manuel Dos Santos, J and Lahti, L and Hemminki, A},
title = {Alistipes and Eggerthella shape the response to oncolytic adenovirus therapy in mice and humans through short-chain fatty acid metabolism.},
journal = {Oncoimmunology},
volume = {15},
number = {1},
pages = {2656514},
doi = {10.1080/2162402X.2026.2656514},
pmid = {41957950},
issn = {2162-402X},
mesh = {*Oncolytic Virotherapy/methods ; Humans ; Animals ; Mice ; *Adenoviridae/genetics ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; *Oncolytic Viruses ; Feces/microbiology ; Female ; *Neoplasms/therapy/microbiology ; Male ; },
abstract = {Accumulating evidence implicates the microbiome as an important determinant of clinical outcomes in cancer therapies; however, the role of the microbiome in oncolytic virus therapy remains largely unexplored. We investigated the gut microbiome of cancer patients following treatment with the oncolytic adenovirus igrelimogene litadenorepvec (Ad5/3-E2F-d24-hTNF-IRES-hIL2; TILT-123). Baseline fecal samples from phase I clinical trials (NCT04695327 and NCT05271318) were analyzed using shotgun metagenomic sequencing and compared to treatment outcomes. A higher relative abundance of Alistipes was observed in patients with treatment benefit, while elevated Eggerthella was observed with reduced benefit. These associations were validated in a preclinical mouse model where administration of Alistipes shahii improved the efficacy of adenovirus therapy. In addition, enrichment analysis in patient samples showed a positive correlation between higher relative abundance of Alistipes and elevated short-chain fatty acids in both feces and serum, which in turn revealed higher circulating neutrophil counts. Finally, in a case study, we observed that adenovirus treatment resulted in increased Alistipes relative abundance and reduced Eggerthella relative abundance, indicating that adenovirus therapy may beneficially modulate the microbiome. Overall, our findings reveal a novel association between Alistipes, Eggerthella, and the therapeutic response to oncolytic adenovirus therapy, highlighting their potential as biomarkers or targets for microbiome-based interventions such as pre-, pro-, or postbiotics.},
}
@article {pmid41958318,
year = {2026},
author = {Lee, CZ and Worsley, SF and Burke, T and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS},
title = {Social Structure and Interactions Differentially Shape Aerotolerant and Anaerobic Gut Microbiomes in a Cooperative Breeding Species.},
journal = {Molecular ecology},
volume = {35},
number = {7},
pages = {e70304},
pmid = {41958318},
issn = {1365-294X},
support = {BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13631/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/S010939/1//Natural Environment Research Council/ ; ECF-2023-433//Leverhulme Trust/ ; erc-stg-948219 EPYC/ERC_/European Research Council/International ; BBX011089/1//Earlham Institute ISP Decoding Biodiversity/ ; BBS/E/ER/230002A//Earlham Institute ISP Decoding Biodiversity/ ; BBS/E/ER/230002B//Earlham Institute ISP Decoding Biodiversity/ ; ALWOP.531//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 854.11.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 823.01.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //Rosalind Franklin Institute/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Songbirds/microbiology ; *Cooperative Behavior ; Breeding ; Anaerobiosis ; Female ; Male ; Social Behavior ; Seychelles ; },
abstract = {Social transmission of microbes has profound impacts on disease epidemiology and host health. However, how social factors influence gut microbiome (GM) transmission in wild populations is not well understood. Here, we use a wild population of the Seychelles warbler, a facultative cooperatively breeding passerine, to determine whether cooperative breeding behaviour influences the GM. Specifically, we hypothesise that close social interactions as part of cooperative breeding should encourage the sharing of anaerobic microbes, which may be less likely to transmit indirectly through the environment. We found that GM composition was more similar within versus between social groups, and this effect was driven by sharing both aerotolerant and anaerobic bacterial genera. As predicted, the similarity of anaerobic, but not aerotolerant, GM communities between pairs of individuals within a group was positively correlated with the strength of their social interactions (defined by their cooperative breeding status). Specifically, anaerobic GM composition was more similar between pairs of individuals that cooperate at the nest (dominant breeders and dominant-helper pairs) than for non-cooperative pairs (involving non-helping subordinate individuals). This is likely because breeders and helpers directly interact while caring for offspring at a nest. This work reveals how cooperative social interactions lead to microbial transmission and thus contribute to shaping specific components of a host's gut microbiome.},
}
@article {pmid41958322,
year = {2026},
author = {Yang, D and Bao, C and Xia, Y and Ling, Y and Zhang, F and Ji, R and Zhong, J and Zhang, T and Tian, H and Xu, X and Sun, B},
title = {Insights Into Variations in the Gut Virome of Tibetan Macaques (Macaca thibetana) Across Wild, Captive, and Semi-Provisioned Environments.},
journal = {American journal of primatology},
volume = {88},
number = {4},
pages = {e70148},
doi = {10.1002/ajp.70148},
pmid = {41958322},
issn = {1098-2345},
support = {32171488//National Natural Science Foundation of China/ ; 32300400//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Macaca/virology/microbiology ; *Virome ; Tibet ; Male ; Animals, Zoo/virology ; Female ; },
abstract = {Viruses are integral components of the mammalian gut ecosystem, playing crucial roles in regulating the gut microbiome and maintaining host health. However, the impact of human activity on the gut virome of mammals remains poorly understood. This study investigated the gut viromes of Tibetan macaques (Macaca thibetana), a primate species endemic to China, under three distinct human-influenced environments (wild, semi-provisioned, and captive) using metagenomic sequencing. Our results revealed that semi-provisioned macaques supported the highest viral diversity, while captive and wild groups exhibited lower diversity, with distinct functional shifts among groups. Furthermore, the co-variation and highly coupled KEGG functional profiles between viral and bacterial communities suggest they function as an integrated synergistic network, where changes in one directly impact the metabolic output of the other. Co-occurrence network analysis further demonstrated that the virus-bacterium interaction network in the captive group was the most fragile, with a structure indicative of a high risk of micro-ecosystem imbalance. Microbial system imbalance is characterized by alterations in both community composition and function, resulting in diminished resilience and stability, which may ultimately compromise host intestinal health. Our results demonstrate that captivity and provisioning drive divergence in the Tibetan macaque gut virome. The fragile, skewed networks in captive individuals highlight a potential cost to microbial health, which may underlie broader health and adaptation risks such as heightened pathogen susceptibility and diminished capacity to cope with environmental perturbations. Thus, monitoring the virome offers a novel early-warning system, informing strategies to enhance welfare and conservation outcomes.},
}
@article {pmid41958469,
year = {2026},
author = {Voigt, RM and Chaudhary, A and Naqib, A and Engen, PA and Adnan, D and Dhana, K and Green, SJ and Villanueva, M and Agarwal, P and Barnes, LL and Sacks, F and Keshavarzian, A},
title = {Weight loss and metabolic improvements dominate the microbiome response in the MIND diet intervention: a randomized controlled trial.},
journal = {Alzheimer's &amp; dementia (New York, N. Y.)},
volume = {12},
number = {2},
pages = {e70239},
pmid = {41958469},
issn = {2352-8737},
abstract = {INTRODUCTION: Observational studies link the MIND diet to reduced risk of Alzheimer's disease (AD) and slower cognitive decline. However, a recent randomized controlled trial found no differential cognitive benefit of the MIND diet over a control diet in the context of shared caloric restriction. Given that both groups achieved significant weight loss and metabolic improvements, this study aimed to disentangle the impact of the MIND diet and host metabolic improvements on the intestinal microbiome.<br><br>METHODS: A subset of participants (n = 213) from the MIND trial were analyzed in this study. Clinical data and stool samples were collected at baseline, Year 1, Year 2, and Year 3, and longitudinal changes in microbiome composition were assessed via shotgun metagenomics.<br><br>RESULTS: Both groups exhibited significant, transient microbiome remodeling at Year 1 (the period of most active weight loss). The control group demonstrated a broad range of altered metabolic pathways, whereas the MIND diet group showed only one, suggesting a functional buffering effect of the MIND diet. Prospective modeling independent of diet group revealed that a poorer cognitive trajectory was significantly associated with increased inositol degradation (PWY-7237) and purine nucleotide salvage (PWY66-409); conversely, a better cognitive trajectory was associated with increased degradation of deoxy sugars (FUC-RHAMCAT-PWY).<br><br>DISCUSSION: Caloric restriction, weight loss, and host metabolic improvement are the dominant factors shaping the intestinal microbiome, overshadowing diet-specific taxonomic shifts. The MIND diet appeared to provide a modest stabilizing effect on the microbial functional profile against perturbations during active weight loss; however, these dietary associations did not persist in covariate-adjusted models, suggesting that host metabolic improvements remained the primary driver of functional shifts.},
}
@article {pmid41958528,
year = {2026},
author = {Li, L and Lv, F and Du, C and Yang, L and Pa, C and Dai, Y},
title = {Artificial intelligence-driven gastrointestinal functional assessment: multimodal imaging, digital biomarkers, and real-time monitoring.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1778235},
pmid = {41958528},
issn = {1664-042X},
abstract = {Gastrointestinal (GI) functional disorders and chronic inflammatory diseases impose a substantial health burden, yet their assessment remains challenging because symptoms reflect dynamic interactions among motility, visceral sensation, immune-microbiome regulation, and brain-gut signaling. Artificial intelligence (AI) is rapidly reshaping GI functional medicine by enabling scalable, quantitative interpretation of complex data generated from multimodal imaging, physiological sensing, and real-world patient monitoring. This review synthesizes advances across three tightly connected pillars that map onto a physiology-informed "assessment-to-action" loop: (i) AI-assisted multimodal GI imaging for quantitative phenotyping and integrated diagnosis; (ii) AI-enabled discovery and validation of digital biomarkers that capture dynamic GI function in naturalistic settings; and (iii) real-time monitoring platforms that support early warning, longitudinal assessment, and adaptive management. We summarize representative applications in functional GI disorders, inflammatory bowel disease (IBD), and GI oncology, highlighting methodological themes including multimodal fusion, temporal modeling, uncertainty estimation, and explainable AI. We then discuss barriers to translation-standardization and interoperability, external validation under dataset shift, privacy and governance, and workflow integration-and outline practical directions for building clinically trustworthy AI systems for GI functional assessment. Collectively, physiology-centered AI approaches have the potential to transform GI care from episodic testing to longitudinal, mechanism-aware monitoring and personalized intervention.},
}
@article {pmid41958652,
year = {2026},
author = {Nurgaziyev, M and Kozhakhmetov, S and Issilbayeva, A and Jarmukhanov, Z and Nurgaziyeva, A and Sergazy, S and Kuantkhan, M and Chulenbayeva, L and Kushugulova, A},
title = {Gut microbiome differences by serostatus in rheumatoid arthritis: a systematic review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1722255},
pmid = {41958652},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/blood ; *Gastrointestinal Microbiome/immunology ; Anti-Citrullinated Protein Antibodies/blood/immunology ; Rheumatoid Factor/blood/immunology ; },
abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a heterogeneous autoimmune disease in which serological status, defined by rheumatoid factor (RF) and anti-citrullinated protein antibodies (ACPA), influences disease course. Alterations of the gut microbiome have been implicated in RA, but differences between seropositive and seronegative patients, and between seropositive RA and healthy controls, have not been systematically reviewed.<br><br>METHODS: PubMed, Scopus, Web of Science, and the Cochrane Library were searched to July 2025 for observational studies of adult RA patients reporting RF and/or ACPA status with gut microbiome analysis. Two reviewers independently screened, extracted data, and assessed quality using the Newcastle-Ottawa Scale (NOS).<br><br>RESULTS: Eight studies published between 2016 and 2024 met the inclusion criteria. Six investigated both RF and ACPA, while two focused primarily on ACPA. In seropositive RA, higher abundances of Collinsella and Blautia and lower levels of Faecalibacterium were consistently reported. Several studies demonstrated reduced &#x3b1;-diversity in seropositive patients compared with seronegative RA or healthy controls, particularly in preclinical or early disease, while established RA showed no consistent differences. Findings for &#x3b2;-diversity were heterogeneous, with some cohorts reporting significant associations with serostatus, whereas others found no clear separation.<br><br>CONCLUSIONS: Seropositive RA, especially ACPA-positive, is frequently associated with reduced microbial diversity and distinct compositional shifts compared with seronegative RA and healthy controls. Larger standardized studies are required to validate these associations and assess their biomarker potential.<br><br>https://www.crd.york.ac.uk/prospero/, identifier CRD420251140715.},
}
@article {pmid41958661,
year = {2026},
author = {Wuyi, W and Tao, P},
title = {Microbe-driven immune suppression in colorectal cancer: the Fusobacterium nucleatum playbook.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1795703},
pmid = {41958661},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/immunology/microbiology/therapy ; *Fusobacterium nucleatum/immunology ; Tumor Microenvironment/immunology ; Animals ; *Fusobacterium Infections/immunology/microbiology ; },
abstract = {Fusobacterium nucleatum, a key oral-pathobiont in colorectal cancer (CRC), has evolved from a presumed "passenger" to an active "co-conspirator" in tumorigenesis. This review systematically delineates its core role as an "architect of the immune microenvironment," whereby it remodels T-cell immune responses through precise mechanisms to establish an immunosuppressive tumor microenvironment. Specifically, F. nucleatum employs virulence factors such as Fap2 and FadA for specific colonization, and achieves immune evasion by inhibiting NK and T-cell function and recruiting myeloid-derived suppressor cells (MDSCs). Post-colonization, it further fine-tunes T-cell subsets: driving Th17 polarization to create a pro-inflammatory milieu while suppressing the infiltration and function of CD8[+] T cells and promoting their exhaustion. Intriguingly, it upregulates programmed death-ligand 1 (PD-L1) expression, which may conversely enhance tumor sensitivity to anti-PD-1/PD-L1 immunotherapy. Moreover, it collaborates with other microbes via quorum sensing and the oral-gut axis to construct a procarcinogenic ecosystem. Based on these mechanisms, F. nucleatum exhibits substantial clinical translational potential. Its load serves as an effective non-invasive diagnostic biomarker and a prognostic predictor, and may help predict responses to immune checkpoint inhibitors. Therapeutically, strategies targeting the eradication or inhibition of F. nucleatum-including antibiotics, specific phages, virulence factor inhibitors, and combination immunotherapy-represent highly promising novel directions. Despite existing challenges, future efforts to deepen mechanistic understanding, develop precision intervention tools, and establish integrated patient stratification systems hold the potential to revolutionize CRC prevention, diagnosis, and combination therapy by targeting F. nucleatum.},
}
@article {pmid41958678,
year = {2026},
author = {Li, J and Shen, J and Lu, D and Ding, E and Wei, L},
title = {Gut microbe Terrisporobacter promotes papillary thyroid carcinoma progression by upregulating the NTRK1 oncogene and fostering an immunosuppressive tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1740257},
pmid = {41958678},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Thyroid Cancer, Papillary/immunology/pathology/genetics/microbiology ; *Gastrointestinal Microbiome/immunology ; *Thyroid Neoplasms/immunology/pathology/microbiology/genetics ; *Receptor, trkA/genetics/metabolism ; Disease Progression ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Up-Regulation ; },
abstract = {Growing evidence suggests a link between the gut microbiome and papillary thyroid carcinoma (PTC), but the causal relationships and the impact on the tumor immune microenvironment (TME) are poorly understood. This study aimed to elucidate the causal role of specific gut microbes in PTC and uncover the underlying immunological and molecular mechanisms. We employed a multi-stage design, beginning with a two-sample Mendelian randomization (MR) analysis using large-scale GWAS data to infer causality. Findings were then validated in 450 PTC patients from The Cancer Genome Atlas (TCGA) by analyzing correlations between microbial abundance, gene expression, immune cell infiltration, and survival. Finally, the core mechanism was confirmed through extensive in vitro experiments with PTC cell lines. Our MR analysis identified a causal association between a genetically predicted higher abundance of the genus Terrisporobacter and an increased risk of PTC (Odds Ratio [OR] = 2.06, 95% Confidence Interval [CI]: 1.34-3.16). In the TCGA cohort, higher intratumoral signals of Terrisporobacter was significantly correlated with an immunosuppressive TME, characterized by increased infiltration of M2 macrophages (ρ = 0.25, p < 0.001) and decreased CD8+ T cells (ρ = -0.19, p = 0.008). Mechanistically, Terrisporobacter abundance was also strongly associated with the upregulation of the oncogene NTRK1 (ρ = 0.35, p < 0.001), which independently predicted poorer overall survival (Hazard Ratio [HR] = 2.15, p = 0.004). In vitro experiments confirmed that supernatant from Terrisporobacter culture not only upregulated NTRK1 expression and promoted PTC cell proliferation but also enhanced invasion and induced cell de-differentiation. Importantly, pharmacological inhibition of TRK signaling reversed the bacteria-induced aggressive phenotype. Our integrated analysis provides robust, multi-layered evidence for a causal role of Terrisporobacter in promoting PTC progression. We define a novel gut-thyroid axis where Terrisporobacter contributes to PTC development by upregulating the NTRK1 oncogene and shaping a pro-tumorigenic, immunosuppressive microenvironment. These findings reveal a new dimension of host-microbe interaction in thyroid cancer and highlight the TME as a key downstream target of microbial influence.},
}
@article {pmid41958966,
year = {2022},
author = {Silverman, JD and Roche, K and Holmes, ZC and David, LA and Mukherjee, S},
title = {Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes.},
journal = {Journal of machine learning research : JMLR},
volume = {23},
number = {},
pages = {},
pmid = {41958966},
issn = {1532-4435},
support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; T32 GM007171/GM/NIGMS NIH HHS/United States ; },
abstract = {Bayesian multinomial logistic-normal (MLN) models are popular for the analysis of sequence count data (e.g., microbiome or gene expression data) due to their ability to model multivariate count data with complex covariance structure. However, existing implementations of MLN models are limited to small datasets due to the non-conjugacy of the multinomial and logistic-normal distributions. Motivated by the need to develop efficient inference for Bayesian MLN models, we develop two key ideas. First, we develop the class of Marginally Latent Matrix-T Process (Marginally LTP) models. We demonstrate that many popular MLN models, including those with latent linear, non-linear, and dynamic linear structure are special cases of this class. Second, we develop an efficient inference scheme for Marginally LTP models with specific accelerations for the MLN subclass. Through application to MLN models, we demonstrate that our inference scheme are both highly accurate and often 4-5 orders of magnitude faster than MCMC.},
}
@article {pmid41959050,
year = {2026},
author = {Wilson, J and Amir Hamzah, AS and Jordan, C and Hayward, JA and Kullin, B and Manhanzva, MT and Tyssen, D and Mehou-Loko, C and Abrahams, AG and Radzey, N and Harryparsad, R and Meyer, B and Hearps, AC and Ziemann, M and Humphries, H and Mkhize, P and Bekker, LG and Passmore, JS and Jaspan, HB and Sheppard, AE and Tachedjian, G and Masson, L},
title = {Characterisation of vaginal Lactobacillus isolates from South African women towards the development of a biotherapeutic to optimise the vaginal microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.26.714511},
pmid = {41959050},
issn = {2692-8205},
abstract = {UNLABELLED: HIV remains among the world's most serious healthcare challenges, with adolescent girls and young women in sub-Saharan Africa at particularly high risk of infection. Bacterial vaginosis (BV) is a key risk factor for HIV acquisition, however current treatment strategies are limited. Optimal vaginal Lactobacillus spp. protect against BV and HIV, largely through immunoregulatory and antimicrobial activities mediated in part by lactic acid. Towards the development of a Lactobacillus -containing live biotherapeutic for African women, we sampled 181 vaginal Lactobacillus isolates from 25 BV-negative South African women. Fifty isolates were selected for evaluation of inflammatory responses using vaginal epithelial cells, D- and L-lactate and lactic acid production and culture acidification. Aside from a single Lactobacillus salivarius strain, L. crispatus isolates acidified the culture media the most and produced the most D- and L-lactic acid. Inflammatory cytokine responses to Lactobacillus strains were variable, with L. crispatus eliciting the lowest levels of cytokine production. When all properties were evaluated collectively, L. crispatus strains exhibited the most desirable biotherapeutic characteristics. Whole genome sequence analysis of ten L. crispatus isolates showed that the majority were more closely related to one another than to isolates from other geographical regions. This supports the need for live biotherapeutics to be tailored for the population of intended use. No antimicrobial resistance elements were detected, while putative bacteriocins and intact prophage sequences were identified in all isolates. L. crispatus isolates displayed characteristics essential for optimal live biotherapeutic performance, however additional analysis is required to determine the functionality of identified putative prophages.<br><br>IMPORTANCE: HIV is a leading cause of morbidity and mortality in sub-Saharan Africa, where adolescent girls and young women are three times more likely to acquire HIV than their male counterparts. A key risk factor for HIV is bacterial vaginosis (BV), a condition characterised by the loss of beneficial Lactobacillus species and increased abundance of non-optimal, inflammatory bacteria. Although BV affects approximately 25% of women in sub-Saharan Africa, effective therapeutics are lacking. Live biotherapeutics containing optimal Lactobacillus spp. represent a promising strategy to improve BV treatment outcomes and reduce HIV infection risk. We isolated 181 vaginal Lactobacillus spp. from 25 BV-negative South African women and characterized 50 selected isolates. This led to the identification of live biotherapeutic candidates for African women with distinct genomes compared to isolates from other geographical regions. This study contributes to current knowledge of the characteristics that should be considered when screening novel isolates for this purpose.},
}
@article {pmid41959053,
year = {2026},
author = {Midani, FS and Lee, DH and Moon, Y and Seale, M and Horvath, TD and Ardis, AK and Cantú, J and Coles, E and Pizzini, JD and Zhu, D and Dooling, SW and Ahern, GJ and Ardis, CK and Beckford, A and Ruggiero, NM and Shin, J and Joos, R and Stanton, C and Ross, RP and Dai, DLY and Mandhane, PJ and Petersen, C and Turvey, SE and Kiely, ME and Murray, DM and Costa-Mattioli, M and Tolias, KF and Britton, RA and Danhof, HA},
title = {Infant gut microbiomes contribute to metabolic states that impact brain function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.09.710596},
pmid = {41959053},
issn = {2692-8205},
abstract = {Alterations in the gut microbiome are associated with neurodevelopmental disorders, but causal mechanisms and therapeutic strategies remain undefined. Here, we demonstrate that human infant microbiomes isolated during the first six months of life drive behavioral impairments in mice and that microbiota-based interventions restore mice to normal behavior. Early-life microbiomes from twelve infants who later exhibited cognitive deficits at 2 years old (low-scoring) transferred adverse metabolic, brain, and behavioral phenotypes to mice, in contrast to microbiomes from twenty-three cognitively typical or high-scoring infants. Deficits in mice were rescued by fecal microbiota transplant from high-scoring infants or a rationally designed consortium that promoted amino acid levels. We confirmed lower fecal amino acid concentrations in low-scoring infants and replicated the association between early-life microbiome composition and cognitive outcomes in a second geographically independent infant cohort. Altogether, we discovered an early-life microbiome-mediated metabolic state causally linked to cognitive deficits and amenable to microbial intervention.},
}
@article {pmid41959059,
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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.20.624577},
pmid = {41959059},
issn = {2692-8205},
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 vectors 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 = 5.5 &#xb1; 1.3% and 4.5 &#xb1; 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 {pmid41959063,
year = {2026},
author = {Moscalu, A and Babygirijia, R and Mathew, T and Chaudhari, SN and Zhang, D and Zhou, L and Sheu, EG and Harris, DA},
title = {Sleeve gastrectomy protects lean mice from future obesity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.09.710623},
pmid = {41959063},
issn = {2692-8205},
abstract = {BACKGROUND: Obesity and metabolic disease drive premature aging and reduced lifespan. While metabolic interventions like calorie restriction, protein restriction, and time restricted feeding have been shown to improved lifespan, they are either not effective or sustainable for most humans. Bariatric surgery is the most efficacious metabolic intervention available and is associated with increased lifespan. However, whether its longevity benefits derive solely from weight reduction or reflect surgery-specific metabolic reprogramming remains unknown.<br><br>METHODS: We employed a lean mouse model of sleeve gastrectomy (SG) in which young, lean male C57BL/6J mice underwent SG or sham operation while maintained on low-fat chow, then were challenged with high-fat diet (HFD) in midlife. We assessed glucose metabolism, body composition, energy expenditure, hepatic histology, adipose tissue inflammation, and cecal microbiome composition.<br><br>RESULTS: Despite identical weight and food intake on low-fat chow, SG mice demonstrated improved glucose tolerance and insulin sensitivity prior to HFD challenge. Upon HFD exposure, SG animals exhibited enhanced metabolic flexibility with greater capacity for fat oxidation, increased energy expenditure, attenuated weight gain, and reduced adiposity compared to sham controls. SG further reduced hepatic lipid accumulation and attenuated visceral adipose tissue inflammation, marked by decreased pro-inflammatory cytokine expression and reduced macrophage infiltration. These metabolic benefits occurred independently of caloric intake. Cecal microbiome profiling revealed surgery-specific remodeling characterized by Lactobacillus enrichment and reductions in Verrucomicrobia and Clostridia - a pattern distinct from caloric restriction and consistent with prior SG studies.<br><br>CONCLUSIONS: Early-life SG confers durable, weight-loss-independent protection against midlife metabolic deterioration. Gut microbiome remodeling, particularly enrichment of Lactobacillus species, represents a candidate mediating mechanism and a potential therapeutic target for aging and metabolic disease.},
}
@article {pmid41959121,
year = {2026},
author = {Solomon, Z and Eno, M and Thompson, SC and Rager, SL and Jin, JC and Zeng, MY and Keerthy, D and Worgall, S and Johnson, EL and Heras, A},
title = {Increased S. epidermidis in the airway-gut microbiome of infants with bronchopulmonary dysplasia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.03.715941},
pmid = {41959121},
issn = {2692-8205},
abstract = {RATIONALE: Bronchopulmonary dysplasia (BPD), the lung disease associated with premature birth, is a significant health problem, often with long-term respiratory consequences. Recent research has highlighted the potential role of the lung and gut microbiome in the development and progression of BPD, yet it is unclear what aspects of the microbiome may contribute to BPD susceptibility.<br><br>OBJECTIVES: To comprehensively characterize the lung and gut microbiomes of preterm infants and identify shared microbial taxa that are associated with BPD development.<br><br>METHODS: Tracheal aspirate and stool samples were collected from 39 premature infants over the first month of life. To assess the taxonomic microbial composition of the lung and gut, samples were analyzed using shotgun metagenomic sequencing. BPD classification was determined using the National Institute of Child Health and Human Development severity-based definition at 36 weeks postmenstrual age.<br><br>MEASUREMENTS AND MAIN RESULTS: Microbial communities of the lung and gut were significantly different between infants who went on to develop BPD and those who did not, with an enrichment of skin-associated microbial genera such as Staphylococcus, Corynebacterium, and Cutibacterium in infants who developed BPD. Specifically, Staphylococcus epidermidis was enriched in premature infants who developed BPD and was the most prominent species shared between lung and gut communities. Temporal changes in gut microbial communities co-occurred with feeding practices and antibiotic exposure, suggesting an influence of external factors on microbiome composition.<br><br>CONCLUSIONS: Our findings provide evidence that certain microbial colonization patterns among premature infants are closely associated with the pathogenesis and progression of BPD.},
}
@article {pmid41959202,
year = {2026},
author = {Yang, Y and Nettifee, J and Azcarate-Peril, MA and Muñana, KR and Callahan, B},
title = {Gut Microbiome Alterations in Canine Idiopathic Epilepsy: A Pairwise Case-Control Study.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.02.716098},
pmid = {41959202},
issn = {2692-8205},
abstract = {BACKGROUND: Idiopathic epilepsy (IE) is the most common chronic nervous system disorder of dogs, and its cause is poorly understood. Emerging evidence suggests that microbiome alterations can occur with IE via the microbiota-gut-brain axis. Therefore, we analyzed the fecal microbiomes of 98 dogs (49 IE, 49 control) in a pairwise case-control observational study using 16S rRNA gene sequencing.<br><br>RESULTS: Although the microbial community was mostly similar between groups, IE was associated with a modest but significant shift in Weighted-Unifrac distance (P = 0.042). We used six differential abundance (DA) methods to identify differentially abundant amplicon sequencing variants (ASVs) between IE and control groups. Notably, one Collinsella ASV was found to be significantly more abundant in IE dogs by all six methods. The gut microbial compositions varied drastically across households (accounting for about 69% of the total variation), but did not have significant differences between sex, age, or breed. Phenobarbital administration in IE dogs had a significant effect on seizure control, and was not associated with changes in the microbiome.<br><br>CONCLUSION: Our findings suggest a relationship between gut microbiomes and IE. However, the specific mechanism needs to be further investigated.},
}
@article {pmid41959210,
year = {2026},
author = {Muller, E and Baum, S and Borenstein, E},
title = {MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.27.714614},
pmid = {41959210},
issn = {2692-8205},
abstract = {MOTIVATION: A central goal in human gut microbiome research is to identify disease-associated functional shifts, an objective increasingly pursued through metagenomic and metabolomic assays. However, common differential abundance analyses of genes or metabolites often yield long and difficult-to-interpret feature lists. Aggregating features into predefined pathways can improve interpretability but relies on fixed pathway boundaries that may not reflect context-specific functional changes. Moreover, even when paired metagenomic-metabolomic data are available, they are often analyzed separately or linked only through simple statistical associations.<br><br>RESULTS: We introduce MAAMOUL, a knowledge-based computational framework that integrates metagenomic and metabolomic data to identify disease-associated, data-driven microbial metabolic modules. Leveraging prior knowledge of bacterial metabolism, MAAMOUL maps disease-association scores onto a global microbiome-wide metabolic network and identifies custom modules enriched for altered genes and metabolites. Applying MAAMOUL to inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) datasets revealed significant disease-associated modules not detected by conventional pathway-level analysis. In IBD, modules reflected disrupted sulfur and aromatic amino acid metabolism and enhanced microbial nucleotide salvage, whereas in IBS they linked purine and nicotinate/nicotinamide metabolism. These results demonstrate that network-guided multi-omic integration can uncover coherent functional shifts in the gut microbiome overlooked by single-omic or purely statistical approaches.<br><br>AVAILABILITY: MAAMOUL is available as an R package at https://github.com/borenstein-lab/MAAMOUL .},
}
@article {pmid41959214,
year = {2026},
author = {Skupa, SA and Hernandez, JB and Smith, AL and Drengler, EM and Seth, AK and Rai, SN and Clayton, JB and D'Angelo, CR and El-Gamal, D},
title = {Impact of high-fat Western diet on chronic lymphocytic leukemia disease progression and gut microbiome profile in Eμ-TCL1 mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.30.715124},
pmid = {41959214},
issn = {2692-8205},
abstract = {BACKGROUND: The composition and function of the gut microbiome have been shown to contribute to both health and disease. One of the most powerful modulators of microbial composition and function is diet.<br><br>MATERIALS &amp; METHODS: Using the E&#x3bc;-TCL1 murine model of B-cell chronic lymphocytic leukemia (CLL), we assigned male and female mice to a high-fat, high-carbohydrate Western diet (HF) or standard chow (CH) diet.<br><br>RESULTS: Mice consuming a HF diet had significantly shorter survival than those consuming a CH diet, irrespective of sex, with female mice exhibiting particularly poor outcomes. We also observed a significant increase in splenic involvement by CLL in the HF diet-fed mice at time of sacrifice. Mice receiving the HF diet demonstrated immediate and profound effects on the gut microbiome, marked by reduced alpha diversity and significantly different community composition as measured by beta diversity. Notably, there was a sustained increase in Akkermansia muciniphila and Bacteroidetes thetaiotaomicron in HF diet-fed mice, coupled with a corresponding increase in microbiome functional pathways related to arginine and histidine biosynthesis, chitin degradation, and nucleotide biosynthesis.<br><br>DISCUSSION: Collectively our data provides evidence of the profound and sustained impact of a high-fat Western diet upon the gut microbiome community and CLL pathogenesis in the E&#x3bc;-TCL1 murine model of CLL.},
}
@article {pmid41959235,
year = {2026},
author = {Zhang, YJ and Tanofsky-Kraff, M and Reyes, MM and Zeve, D and Ehrmann, KJ and Lee, J and Schaan, AP and Prado, A and Ma, XC and Parker, MN and Brady, SM and Saint-Denis, E and Sharma, K and Frintu, B and Richmond, C and Desai, N and Yeliseyev, V and Bry, L and Avila-Pacheco, J and Clish, CB and Quealy, M and Clardy, J and Breault, DT and Ding, Y and Wang, X and Jost, M and Poyet, M and Groussin, M and Yanovski, JA and Lencer, WI and Alm, EJ},
title = {Blautia wexlerae Transforms Dietary Fatty Acids to Activate Enteroendocrine Signaling and Improve Metabolic Health in Mice and Humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.13.709143},
pmid = {41959235},
issn = {2692-8205},
abstract = {Metabolites produced by the gut microbiome influence host metabolic health, but how this occurs remains incompletely defined. Here, we report that a common human gut commensal, Blautia wexlerae , converts dietary fats into bioactive metabolites that induce gut hormone production to affect glucose metabolism and suppress appetite. We found that colonization with Blautia wexlerae correlated with healthier eating behaviors in humans. Blautia wexlerae encodes a unique acyl transferase and is capable of producing acyl amines from nutrient substrates. These Blautia acyl amines stimulated human enteroendocrine cells to secrete GLP-1 and other gut peptide hormones more potently than endogenously produced acyl amines. When fed to mice, acyl amines improved glycemic control and decreased appetite. In humans, higher stool levels of Blautia DNA encoding acyl amine synthesis genes correlated with leanness and decreased dietary fat intake. These results define a mechanism of action for how Blautia wexlerae affects host metabolic control.},
}
@article {pmid41959264,
year = {2026},
author = {Rigas, YE and Shane, J and Treat, B and Shanks, RMQ and Leger, AJS},
title = {C. mastitidis requires the protein Sortase F to colonize the eye.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.12.711320},
pmid = {41959264},
issn = {2692-8205},
abstract = {The ocular surface is a mucosal tissue that is constantly exposed to environmental antigens and potential pathogens. Human microbiomes play a critical role in the balance of surveillance and inflammation at sites of colonization. Historically, the investigation of the ocular microbiome has been difficult due to its paucibacterial nature and the inhospitable environment of the ocular surface. Despite this, Corynebacterium mastitidis (C. mast) developed a unique ability to colonize the eye and elicit a protective immune response characterized by induction of IL-17 from γδ T cells and protection from corneal infection. Therefore, we sought to understand the unique bacterial machinery that C. mast utilizes to colonize the eye and how it affects the induction of an eye-specific immune signature. Using a C. mast transposon mutant library, we identified a mutant that completely lacked an ability to form biofilm, colonize the eye, and induce in vivo immunity. Whole genome sequencing revealed a disruption in the sortase F gene, which anchors proteins to the cell wall of C. mast , governing biofilm formation and tethering of adhesins to the cell surface. Additionally, we show that mutation in individual C. mast adhesins does not affect ocular colonization or immune induction. By understanding the molecular mechanism of ocular microbial colonization, this work advances our understanding of how bacteria colonize and induce immune responses on the eye, providing a foundation for developing novel therapeutic strategies against ocular infections.},
}
@article {pmid41959277,
year = {2026},
author = {Bodkhe, RL and Blank, RB and Trepka, KR and Orellana, DA and Scher, JU and Turnbaugh, PJ and Nayak, RR},
title = {Multi-cohort Analysis Reveals Microbiome Signatures Associated with Drug Response in New-Onset Rheumatoid Arthritis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.30.715090},
pmid = {41959277},
issn = {2692-8205},
abstract = {The human gut microbiome influences treatment outcomes, but whether microbiome signatures of drug response generalize across cohorts remains unclear. Here, we perform a multi-cohort analysis (3 cohorts, N=100 patients) to determine whether cross-cohort microbial signatures are associated with methotrexate (MTX) response in new-onset rheumatoid arthritis (RA) patients. Pre-treatment gut microbiome community structure and function differed by future MTX response status, with MTX-nonresponders (MTX-NR) showing Bacteroides caccae depletion and Ruminococcus bromii enrichment. Multiple microbial functions were depleted in MTX-NR, including nucleotide metabolism, one-carbon pool by folate, and histidine metabolism. Notably, candidate MTX-degrading genes were enriched in MTX-NR. Microbiome functional profiles outperformed clinical metrics in predicting future MTX response. These results show that consistent microbiome signatures are associated with MTX response across different RA cohorts and pave the way for microbiome-based precision medicine in newly diagnosed RA patients.},
}
@article {pmid41959294,
year = {2026},
author = {Binion, B and Ahmad, S and Wang, T and Tang, E and Barnick, B and Olukoya, D and Mbuvi, P and Dutta, D and Erdman, JW and Gaskins, HR and Yang, G and Irudayaraj, J and Ridlon, JM},
title = {The Urinary Tract commensal Peptoniphilus spp. Encodes a Novel 17β-Hydroxysteroid Dehydrogenase.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.29.714803},
pmid = {41959294},
issn = {2692-8205},
abstract = {UNLABELLED: Microbial steroid metabolism represents an underappreciated extension of the vertebrate endocrine system, with growing evidence that host-associated microbes contribute to the diversity and bioavailability of sex steroids within human tissues. Emerging studies have linked microbial androgen metabolism to urinary microbiome composition and to resistance to androgen deprivation therapy (ADT) in prostate cancer. While microbial pathways capable of converting steroid precursors such as cortisol to androgens, via the steroid-17,20-desmolase pathway, such as DesG-mediated interconversion of androstenedione to testosterone have been reported, the diversity of enzymes mediating downstream androgen interconversion remains incompletely defined. Here, we investigate the androgen-forming capabilities of anaerobic bacteria from the male genitourinary microbiome, focusing on NADPH-dependent 17β-hydroxysteroid dehydrogenases (17β-HSDHs) that catalyze interconversion of androstenedione and testosterone. We isolated androgen-forming bacterial strains from human male urine and identified a previously uncharacterized 17β-HSDH encoded by Peptoniphilus obesi , demonstrated that this enzyme catalyzes the NADPH-dependent reduction of androstenedione to testosterone and the reverse oxidation reaction. Sequence similarity searches further identified a homologous 17β-HSDH in Anaerococcus , which was synthesized and functionally validated, revealing conserved activity despite low sequence identity to the previously characterized urinary tract enzyme DesG. The enzymes were found to have broad substrate specificity for C19 and C18 17keto- and 17β-hydroxysteroids. Together, these findings expand the known diversity of microbial 17β-HSDHs and identify previously unrecognized androgen-forming activities within the genitourinary microbiome.<br><br>IMPORTANCE: Microbial steroid-transforming pathways may provide a mechanism by which commensal anaerobes contribute to androgen availability in the genitourinary tract. By identifying novel 17&#x3b2;-hydroxysteroid dehydrogenases from Peptoniphilus and Anaerococcus , genera repeatedly associated with prostate cancer, this study provides mechanistic insight into how microbial steroid metabolism may influence hormone-driven disease.},
}
@article {pmid41959308,
year = {2026},
author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.11.711154},
pmid = {41959308},
issn = {2692-8205},
abstract = {UNLABELLED: Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.<br><br>IMPORTANCE: Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.},
}
@article {pmid41959458,
year = {2026},
author = {Kvitne, KE and Zuffa, S and Charron-Lamoureux, V and Patan, A and Agongo, J and Cai, J and Deleray, V and El Abiead, Y and Xing, S and Zemlin, J and Thomas, S and Nelson, MR and Gant, A and Ghadishah, A and Lam, A and Ho, B and Momper, JD and Suhandynata, RT and Bertrand, K and Knight, R and Chambers, C and Dorrestein, PC and Tsunoda, SM},
title = {Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.31.715750},
pmid = {41959458},
issn = {2692-8205},
abstract = {Infant antibiotic treatment is associated with increased risk of developing non-communicable diseases, potentially through disruption of the gut microbiome. However, the impact of indirect antibiotic exposure via human milk remains largely unexplored. Here, we investigate a cohort (n =80) of antibiotic-treated breastfeeding mother-infant dyads and untreated matching controls using integrative multi-omics analyses of fecal, milk, and skin samples (n =1,455). Maternal antibiotic treatment was associated with different infant fecal microbiome and metabolome profiles, including lower abundance of Bacteroides , Lactobacillus , and Bifidobacterium , and higher levels of antimicrobial resistance gene reads. Further, fecal metabolic alterations associated with indirect antibiotic exposure were exacerbated by formula milk supplementation. In a subset of infants (n =61), indirect exposure was associated with higher body mass index (BMI). These findings suggest that maternal antibiotic treatment during lactation may influence the early-life infant gut microbiome with potential long-term implications.},
}
@article {pmid41959463,
year = {2026},
author = {Noecker, C and Guo, L and Daté, C and Rai, N and Daramy, F and Ramirez Hernandez, LA and Kyaw, TS and Trepka, KR and Gupta, CL and Ha, CWY and Babdor, J and Spitzer, MH and Turnbaugh, PJ},
title = {A widespread gut bacterial lineage distinguished by redox metabolism and phage defense.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.31.715625},
pmid = {41959463},
issn = {2692-8205},
abstract = {UNLABELLED: Genomic variation within gut microbial species can have consequences for host health and disease. However, for low abundance species, these variations can be difficult to capture by both culture-dependent and -independent approaches. Here, we focus on the prevalent but low abundance gut Actinomycetota Eggerthella lenta . We developed a selective media for sensitive and specific isolation of E. lenta from human stool. Genomes from 87 new E. lenta isolates were combined with prior high-quality assemblies, shedding light on within-species functional diversity. Phylogenetic analysis revealed a broadly distributed subclade, which we refer to as E. lenta Group B. This lineage was differentiated by its metabolic potential and bacteriophage defense, though mobile elements were shared broadly across the species. Notably, Group B was positively associated with intestinal inflammation in subjects with inflammatory bowel disease. Overall, these results emphasize the importance of bacterial population structure in host-microbiome interactions and provide a framework to study low-abundance gut taxa.<br><br>HIGHLIGHTS: Selective media enables E. lenta isolation and reveals high prevalence in humans Discovery of a distinctive lineage within E. lenta undergoing genome reduction E. lenta Group B has altered metabolism, phage defense, and disease associations A widespread conjugative plasmid could enable improved genetics.},
}
@article {pmid41959466,
year = {2026},
author = {Sapoval, N and Treangen, TJ and Nakhleh, L},
title = {Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.10.710879},
pmid = {41959466},
issn = {2692-8205},
abstract = {MOTIVATION: Measures of microbial diversity that can be derived directly from metagenomic sequencing data offer a valuable summary view of the underlying complex systems. Prior work has shown that both taxonomic composition and abundances that are captured by standard diversity measures (e.g., Shannon entropy), and structural variation within the metagenome due to gene duplications, losses and horizontal transfers (HGT), can correlate with the host's health. However, there are no diversity measures available that simultaneously account for the genome architecture and taxonomic composition within the sample. Thus, in this work we propose the spectral energy of a graph sheaf Laplacian as such a measure, and justify its applicability through a simulation study and analysis of biological data.<br><br>RESULTS: First, we describe a theoretical framework that allows us to combine the features of genome graphs with the taxonomic data. Then, we explore the sensitivity of the proposed diversity measure to genome rearrangements and HGT events in a simulation study. Finally, we explore applicability of our proposed measure to characterization of diversity of human gut metagenomes. We find our proposed measure to offer better discrimination between healthy controls and inflammatory bowel disease (IBD) patients' samples (n = 403) in the cohorts analyzed.<br><br>https://github.com/nsapoval/bd-gsl.},
}
@article {pmid41959531,
year = {2026},
author = {Orlov, M and Karr, M and Hara, N and Needell, J and Aherne, CM and Matsuda, JL and Palmer, BE and Lozupone, C and Clark, SE and Janssen, WJ and Evans, CM},
title = {Amoxicillin induces gut dysbiosis leading to long term suppression of type-17 immune tone in the lungs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.05.709937},
pmid = {41959531},
issn = {2692-8205},
abstract = {T-helper (Th)-17 lymphocytes are central mediators of adaptive type 17 immunity. Decreased type-17 signaling increases severity of infections in humans and mice. However, detrimental effects of excessive type 17 responses in autoimmune and other inflammatory diseases highlight a need for type-17 immune calibration to support beneficial host defense requirements. Mechanisms of type 17 calibration are poorly understood. A gut-lung axis has been proposed to coordinate homeostatic protection and acute host defense. Factors that acutely alter the gut microbiome are heterogeneous and include acute intestinal infections, non-infectious colitis, and medical treatments such as antibiotics. How changes in the gut microbiome affect lung immune tone during homeostasis and acute pulmonary infections are also poorly understood. Prior studies have shown that antibiotics reduce expression of IL-17-mediated host defense in the gut. Since gut microbial homeostasis influences Th17 cell numbers in both the intestine and remote tissues, we postulated that antibiotic treatment would result in gut dysbiosis and weakened type-17 host defense in the lungs. We found that amoxicillin induces significant dysbiosis that is long-lasting and that there is a long-term decrease in type-17 tone in the lungs. We also found that in mice lacking the gut mucin, Muc2, Th17 cells increased in the lungs following inflammatory challenge. These findings suggest that antibiotic-induced dysbiosis can decrease lung immune defenses for long periods of time after cessation of antibiotic treatment.},
}
@article {pmid41959535,
year = {2026},
author = {Xue, J and Allaband, C and Zuffa, S and Zhou, D and Poulsen, O and Meadows, J and McDonald, D and Ambre, M and Ackermann, G and Birmingham, A and Cao, J and Mohanty, I and Dorrestein, PC and Knight, R and Haddad, GG},
title = {Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.31.715631},
pmid = {41959535},
issn = {2692-8205},
abstract = {Intermittent hypoxia and hypercapnia (IHC), a hallmark of obstructive sleep apnea (OSA), accelerates atherosclerosis, yet the underlying mechanisms remain unclear. The gut microbiota and metabolites, specifically bile acids, change with IHC and thus the bile acid receptor farnesoid X receptor (FXR) might mediate IHC-induced atherosclerosis. In this study, ApoE [-/-] and ApoE [-/-] FXR [-/-] mice were exposed to IHC or room air and fed with a high-fat, high-cholesterol diet for 10 weeks. Markers of atherosclerosis, fecal microbiome, and metabolome were then examined via Sudan IV staining, absolute abundance shotgun metagenomics, and untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS). IHC markedly increased aortic atherosclerosis in ApoE [-/-] mice, an increase that was abolished by FXR deficiency. In addition, IHC reshaped gut microbial composition, promoting enrichment of bile acid-modifying taxa and increasing levels of microbial hydroxysteroid dehydrogenase (hsdh). The bile acid pool was also remodeled and associated with aortic atherosclerosis via FXR-dependent metabolic signals in ApoE [-/-] mice. Knockout of FXR disrupted microbiome shift under IHC and uncoupled microbial bile acid metabolism from vascular lesion development, thereby protecting against aortic atherosclerosis. These findings show that FXR has a central role in linking IHC, microbial bile acid metabolism, and cardiovascular pathology.},
}
@article {pmid41959551,
year = {2026},
author = {Lv, W and Hu, H and Huang, Y and Yang, J and Li, Y and He, J and Wang, K and Liu, Y and Wang, Q},
title = {Microbial mechanisms and therapeutic interventions in the periodontitis-inflammatory bowel disease axis: a comprehensive review.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2656084},
pmid = {41959551},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis and inflammatory bowel disease (IBD) are chronic inflammatory conditions of the oral and gastrointestinal tracts that exhibit bidirectional microbial and immunological crosstalk.<br><br>OBJECTIVE: Aimed at elucidating the bidirectional crosstalk between periodontitis and IBD at both microbiological and immunological levels and evaluate related therapeutic interventions, this review comprehensively summarizes recent evidence on their interaction via the oral-gut-bone axis, focusing on microbial ecology, host responses, and innovative therapies.<br><br>DESIGN: Distinct yet overlapping dysbiotic signatures are observed in both diseases, with periodontal pathogens such as Porphyromonas gingivalis and Fusobacterium nucleatum capable of translocating to the gut and perturbing intestinal homeostasis, while gut inflammation reciprocally reshapes the oral microbiome. Mechanistic links include a spectrum of convergent pathways: (i) microbial metabolites-short-chain fatty acids, choline metabolites, indole derivatives, polyamines, and bile acids-that modulate barrier integrity and immune responses; (ii) shared immune cells and inflammatory mediators driving mucosal damage at both sites; (iii) bacterial extracellular vesicles (BEVs) and lysine lactylation (Kla)-mediated signaling; and (iv) oxidative stress, iron metabolism dysregulation, and ferroptosis contributing to tissue destruction.<br><br>RESULTS: Therapeutic strategies targeting this axis encompass bidirectional interventions: periodontal and IBD treatments that mutually influence oral and gut health, natural anti-inflammatory and antimicrobial compounds, probiotics and prebiotics, oral and fecal microbiota transplantation, and emerging bacteriophage therapy. Critically, the clinical translation of collaborative dentistry-gastroenterology management is highlighted as a promising avenue for integrated care.<br><br>CONCLUSIONS: By integrating findings across microbial ecology, host response, and therapeutic innovation, this review provides a comprehensive framework for understanding and targeting the periodontitis-IBD axis.},
}
@article {pmid41959571,
year = {2026},
author = {Tang, Y and Dang, M and Xie, W and Chen, X and Zhang, E and Wang, Z},
title = {Spatial heterogeneity of the microbiota in Cypripedium franchetii and Its correlation with organ-specific metabolomes.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1751651},
pmid = {41959571},
issn = {1664-462X},
abstract = {INTRODUCTION: Cypripedium franchetii, a plant of ornamental and medicinal value, is designated as a Grade II Protected Species in China. The C. franchetii population inhabiting the fragile ecosystem at Galongla Pass exhibits unclear patterns in microbial composition across rhizosphere soil, root, stem, and leaf tissues, as well as metabolite distribution and plant tissue-specific microbe-metabolite relationships.<br><br>METHODS: This study focused on C. franchetii, a plant growing in the fragile ecosystem of Galongla Pass in Tibet. We employed an integrated approach combining high-throughput amplicon sequencing (targeting bacterial 16S rRNA genes and fungal ITS regions) and untargeted metabolomics (LC-MS/MS) to systematically analyze the microbial community structure and metabolite distribution in its rhizosphere soil and root, stem, and leaf tissues. We further explored the associations between endophytic microorganisms and metabolites within plant tissues.<br><br>RESULTS: The results revealed significant differences in microbial composition across plant compartments: distinct variations were observed between rhizosphere soil and plant tissues, while stem and leaf microbial communities exhibited greater similarity. At the phylum level, Pseudomonadota dominated among bacteria, while Basidiomycota and Ascomycota were the predominant fungal phyla. At the genus level, dominant taxa showed tissue specificity: Cronobacter and Lactobacillus were dominant bacterial genera in roots, whereas Acinetobacter dominated in stems, and Acinetobacter and Agrobacterium were prominent in leaves. For fungi, Tulasnella was the dominant genus in rhizosphere soil and roots, while Dioszegia prevailed in stems and leaves. Metabolite analysis indicated significant differences in metabolic profiles among tissues, with stem and leaf metabolite compositions being relatively similar. Correlation analysis further revealed statistically significant correlations between differential microorganisms and differential metabolites in roots and stems, identifying 31 microbial genera significantly correlated with 48 high-abundance metabolites.<br><br>DISCUSSION: This study systematically unveils the tissue-specific microecological and metabolic characteristics of C. franchetii during its post-flowering nutrient accumulation phase. Key findings include: microbial community assembly involves cooperative mechanisms between core conserved taxa (e.g., Tulasnella) and habitat-specific taxa; microbial diversity exhibits a gradient decline from the rhizosphere into plant tissues accompanied by functional group succession; and extensive yet specific potential interaction networks (based on statistical covariation) exist between microorganisms and host metabolites, indicating potential microbial involvement in regulating plant secondary metabolism. These findings not only provide guidance for the conservation of C. franchetii (requiring consideration of both core symbiotic and habitat-specific taxa) and constructing synthetic microbial communities during artificial propagation, but also offer a new theoretical basis for the targeted regulation of medicinal active ingredient synthesis through the microbiome.},
}
@article {pmid41959663,
year = {2026},
author = {Fognani, A and Rotondo, R and Savo Sardaro, ML and de Iure, A and Gaglione, M and Casali, M and Leonardi, L and Radicati, FG and Vacca, L and Guescini, M and Zeppa, SD and Gatta, L and Stocchi, F and Picconi, B and De Pandis, MF},
title = {Effects of combined Mediterranean diet and physical activity intervention on the gut microbiome and disease progression in individuals with Parkinson's disease: study protocol for a multicenter, randomized controlled pilot study (PRIME study).},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1743490},
pmid = {41959663},
issn = {1663-4365},
abstract = {BACKGROUND AND AIMS: Parkinson's disease (PD) is a neurodegenerative disorder for which no disease-modifying therapy currently exists, making it crucial to investigate alternative strategies that may slow its progression. The PRIME study will investigate the effects of combined dietary and physical activity interventions- performed in rehabilitative settings with health professional supervision and evaluation, versus single interventions on the gut microbiome in PD. The aim is to identify microbiome profiles - comparing traditional 16s rRNA gene sequencing with the third-generation method - as potential non-invasive, stage specific biomarkers of PD. In addition, the study will assess whether the combined intervention affects disease progression, symptoms, cognitive abilities, and quality of life.<br><br>METHODS: Eighty participants with PD will be randomized into four arms: a Mediterranean-diet intervention group; a structured physical-activity group; a combination group receiving both dietary and exercise interventions; a control group receiving standard care only.<br><br>CONCLUSION: By integrating microbiome characterization with the evaluation of these interventions, the study aims to explore whether intervention-induced changes in the microbiota are associated with clinical improvement in PD, thus paving the way for the design of future non-pharmacological protocols to slow disease progression, mitigate symptom severity, and promote diagnosis.<br><br>CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT07097103.},
}
@article {pmid41959668,
year = {2026},
author = {Chung, HA and Fralish, Z and Tu, T and Reker, D},
title = {Profiling biological effects of microbiome metabolites via machine learning.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115282},
pmid = {41959668},
issn = {2589-0042},
abstract = {Human microbiome-derived metabolites are key mediators of host physiology. However, their biological effects remain largely uncharacterized due to limitations of current low-throughput and untargeted experimental approaches that are time intensive and costly. This has hindered the systematic biological characterization of microbiome metabolites. To address this gap and accelerate the identification of biological effects of microbiome metabolites, we developed and experimentally validated a machine learning platform trained on publicly available drug development data to rapidly predict a wide array of chemical and biological properties of microbiome metabolites. Prospective experimental validation confirmed the accuracy of our models and uncovered previously unknown effects of several metabolites. For example, we identified previously unknown interleukin 8 secretion stimulation by the metabolites spermine and spermidine, which have been regarded anti-inflammatory thus far. Our findings demonstrate the potential power of machine learning to accelerate the functional annotations of microbiome-derived metabolites, paving the way for biomarker and therapeutic discovery.},
}
@article {pmid41959672,
year = {2026},
author = {Jia, C and Zhang, B and Gan, B and Zhao, Y and Lin, X and Chen, J and Zhao, J},
title = {Divergent dynamics in whole-body regeneration and larval development of sponge Haliclona simulans: cytobiology, microbiome, and transcriptomics.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115344},
pmid = {41959672},
issn = {2589-0042},
abstract = {Sponges are capable of rebuilding functional individuals from cell aggregates (primmorphs), a process termed whole-body regeneration that morphologically parallels larval development. To systematically compare these processes, we established an in vitro primmorph regeneration model in Haliclona simulans and performed multi-level analyses across planktonic, settled, and metamorphic stages. Although both processes formed similar structures (e.g., the aquiferous system), planktonic primmorphs exhibited a reduced stem cell proportion (archeocyte/choanocyte), along with the increase of seemingly dedifferentiating cells and vacuolar cells. Microbiome diverged: while sharing core symbionts (e.g., AqS1), primmorphs enriched Tenacibaculum and Vibrio species during remodeling process. Transcriptomics revealed distinct signatures: regeneration upregulated genes potentially related to DNA repair and dedifferentiation but downregulated stem cell markers. Our integrative study indicates that regeneration and development constitute distinct processes, achieving similar functional outcomes via divergent cellular, microbial, and molecular profiles that provides a foundational framework for future mechanistic studies of regeneration.},
}
@article {pmid41959673,
year = {2026},
author = {Ko, CY and Zhang, L and Lin, Y and Zeng, Y},
title = {Gut microbial metabolites, barrier dysfunction, and endotoxemia in men obstructive sleep apnea-associated hypertension.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115291},
pmid = {41959673},
issn = {2589-0042},
abstract = {Obstructive sleep apnea (OSA) is frequently accompanied by hypertension, yet gut-related mechanisms remain unclear. We profiled fecal and plasma short-chain fatty acids, markers of intestinal barrier injury and endotoxemia, immune phenotypes, and the fecal microbiome in men classified as non-OSA, OSA, OSA with prehypertension, or OSA with hypertension, and reassessed a subset after three months of continuous positive airway pressure. OSA with hypertension was characterized by reduced fecal acetate and butyrate, elevated intestinal permeability and endotoxin markers, and a higher proportion of Th17 cells. Lipopolysaccharide tracked with blood pressure severity and showed inverse associations with fecal butyrate and positive associations with plasma propionate. Short-term CPAP exposure was accompanied by improved sleep metrics, reduced barrier injury and endotoxemia, increased microbial diversity, and altered systemic SCFA patterns. These findings support a gut barrier-endotoxin framework linking sleep-disordered breathing with hypertensive risk.},
}
@article {pmid41960322,
year = {2026},
author = {Hu, F and Wang, F and Tessier, AJ and Glenn, A and Liu, Y and Guasch-Ferré, M and Tobias, D and Eliassen, AH and Manson, J and Clish, C and Lee, KH and Shai, I and Qi, Q and Burk, R and Liang, L and Sun, Q and Kaplan, R and Willett, W and Wang, D},
title = {Epidemiological and Multi-Omics Investigation of Phytosterol Intake and Type 2 Diabetes Risk.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9222420/v1},
pmid = {41960322},
issn = {2693-5015},
abstract = {Objectives Limited evidence exists on the association between dietary phytosterol intake and the risk of type 2 diabetes (T2D). We aimed to investigate this association and identify the underlying plasma metabolic, metabolomic, and gut microbial features. Methods We followed 204,633 participants (79% women) from three large US prospective cohorts for up to 36 years. Validated food-frequency questionnaires were used to estimate dietary intake of total phytosterol and three subtypes: β-sitosterol, campesterol, and stigmasterol. We applied Cox proportional hazards models to evaluate their associations with T2D risk. In a subset of 39,879 participants with plasma metabolic biomarkers and 9,528 participants with plasma metabolomics data, we examined the association between phytosterol intake and metabolic biomarkers related to insulinemia, glycemia, lipids, and inflammation, as well as T2D-related metabolomic profiles. Additionally, we explored the gut microbial species and enzymes involved in these associations in a subset of 465 participants with gut microbiome data. Results During follow-up, we documented 20,708 incident T2D cases. After adjustment for covariates, higher intake of total phytosterol was associated with a lower T2D risk (HR comparing extreme quintiles = 0.87, 95% CI: 0.82, 0.92; P trend<0.001). Similar associations were observed for β-sitosterol (HR=0.86, 95% CI: 0.81, 0.91; P trend<0.001) and campestrol (HR=0.89, 95% CI: 0.84, 0.94; P trend<0.001), but not for stigmasterol.β-sitosterol and campestrol were also associated with favorable plasma metabolic profiles, such as lower levels of C-reactive protein, leptin, and C-peptide, as well as beneficial T2D-relevant metabolomic profiles. Moreover, we identified several gut microbial species, and their enzymes involved in these associations. For example, Faecalibacterium prausnitzii and its β-sitosterol-degrading enzyme 3-oxosteroid 1-dehydrogenase (EC1.3.99.4) were associated with higher β-sitosterol intake and a metabolomic profile indicative of lower T2D risk. Conclusions A higher intake of phytosterols, particularly β-sitosterol and campesterol, was associated with a lower risk of T2D, with consistent findings across epidemiological and multi-omics analyses. These findings support the role of a healthy plant-based dietary pattern rich in phytosterol-containing foods such as whole grains, nuts, seeds, fruits, vegetables, and vegetable oils in lowering T2D risk.},
}
@article {pmid41960429,
year = {2026},
author = {Freund, L and Topacio, TM and Miao, Y and Porter, WC and Swenson, M and Maltz, M and Botthoff, J and Aronson, EL},
title = {Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1691133},
pmid = {41960429},
issn = {1664-302X},
abstract = {INTRODUCTION: The aeolian dust microbiome is composed of uniquely adapted microorganisms that can withstand the harsh conditions of the atmosphere. Specific microbial taxa and survival strategies have been observed in dust microbiomes from around the world, yet the environmental processes that select for microbial composition and function are poorly understood.<br><br>METHODS: Here we explore the taxonomic and functional diversity of the aeolian dust microbiome from sites around the Salton Sea, a hypersaline lake in Southern California, and how dust sources and weather influenced the microbiome. Dust samples were collected from four locations around the Salton Sea in the summer and fall of 2020 and 2021, and 16S (V3-V4) rRNA amplicon sequencing and shotgun metagenomic sequencing was used to characterize the aeolian dust microbiome.<br><br>RESULTS: We observed significant differences in microbial composition between sites, and we were able to identify 13 microbial genera that were members of the core dust microbiome across samples. We also found that genes involved in sporulation, UV-radiation resistance, thermal resistance, osmotic stress resistance, quorum sensing, and antibiotic resistance were shared across the aeolian dust metagenomes. Lastly, local wind conditions and estimated dust source surface categories were significant predictors of the microbial adaptations we found in the aeolian dust metagenomes.<br><br>DISCUSSION: Our results demonstrate the ability of airborne dust microorganisms to readily adapt to their harsh environment and highlight the survival mechanisms that allow them to disperse across broad distances, thus posing a potential health risk to exposed communities.},
}
@article {pmid41960430,
year = {2026},
author = {Khelfaoui, I and Wang, W and Shehata, AI and Meskher, H and El Basuini, MF and Mohamed, AMA and Abouelenein, MF and Degha, HE and Alhoshy, M and Teiba, II and Mahmoud, O and Mahmoud, SS},
title = {STROBE-causal machine learning for the human microbiome: systematic review on methodological innovations and validation frameworks.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705116},
pmid = {41960430},
issn = {1664-302X},
abstract = {The reproducibility crisis in causal microbiome research necessitates robust validation frameworks. Current studies often face inconsistent validation methods, limited interpretability, and a lack of standardized reporting, creating a gap in reliable causal inference. This systematic review evaluates over 60 peer-reviewed studies published between 2015 and 2024 to: (1) establish benchmarking standards leveraging synthetic data and biological plausibility assessments; (2) compare advanced causal machine learning (ML) methodologies, including Double/Debiased ML, Deep Instrumental Variables (Deep IV), and Directed Acyclic Graphs (DAGs), in their application to microbiome-host systems; and (3) propose the STROBE-CML (Strengthening the Reporting of Observational Studies in Epidemiology-Causal Machine Learning) guidelines to standardize reporting practices. We emphasize critical innovations such as federated validation pipelines and time-series causal discovery frameworks that address these gaps by facilitating scalable, privacy-preserving, and reproducible inference across heterogeneous cohorts. A decision support tool is introduced to guide researchers in selecting appropriate causal ML approaches based on data structure, research question, and computational constraints. By synthesizing methodological advances with rigorous validation paradigms, this review provides a roadmap for generating reliable, biologically interpretable, and clinically translatable causal claims in microbiome science.},
}
@article {pmid41960682,
year = {2026},
author = {Luo, T and Xue, M and Du, Y and Chen, H and Sun, Y and Sun, H},
title = {The Mechanism of Gut Microbiota in Breast Cancer Based on the Bulk Transcriptome, Mendelian Randomization Analysis and Single Cell RNA Sequencing.},
journal = {MicrobiologyOpen},
volume = {15},
number = {2},
pages = {e70284},
pmid = {41960682},
issn = {2045-8827},
support = {JCYJ20240813160621028//Shenzhen Science and Technology Program/ ; FTWS075//Futian Healthcare Research Project/ ; //Foundation of Key Clinical Specialty Construction Project in Futian District, Shenzhen City/ ; },
mesh = {Humans ; *Breast Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Female ; Mendelian Randomization Analysis ; *Transcriptome ; Single-Cell Analysis ; Genome-Wide Association Study ; Biomarkers, Tumor/genetics ; Sequence Analysis, RNA ; },
abstract = {Breast cancer (BC) is the leading cause of cancer death in women. Bidirectional regulation between BC and gut microbiota (GM) is established, but GM's mechanistic role in BC pathogenesis remains unclear. Public BC/control samples and GM genome-wide association study data underwent Mendelian randomization to identify GM-BC associations and GMRGs. DEGs between BC and controls were analyzed. Candidate genes were derived from intersecting DEGs and GMRGs. Machine learning identified biomarkers, validated by expression analysis. GSEA, immune infiltration, drug screening with molecular docking, and scRNA-seq were performed. Intersecting 3455 DEGs with GMRGs yielded eight candidates; MCM6 and NR3C1 were validated as biomarkers, enriched in DNA replication pathways. Immune infiltration showed 13 differential immune cells, with macrophages notably influencing biomarkers. Etoposide exhibited strong binding to biomarkers via docking. scRNA-seq identified epithelial cells as key, with stage-dependent biomarker expression. This study redefines BC as a microbiome-regulated network, identifying the MCM6/NR3C1 biomarker pair for early diagnosis and microbiome-targeted interventions.},
}
@article {pmid41960738,
year = {2026},
author = {Cheng, J},
title = {The Microbiome-Gut-Liver Axis Drives Post-Kasai Fibrosis in Biliary Atresia: From Mechanism to Precision Intervention.},
journal = {Hepatology research : the official journal of the Japan Society of Hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/hepr.70184},
pmid = {41960738},
issn = {1386-6346},
abstract = {Biliary atresia (BA) remains the most devastating fibro-inflammatory cholangiopathy of infancy. Even after successful Kasai portoenterostomy (KPE), progressive liver fibrosis ultimately dictates long-term outcomes. The "microbiome-gut-liver axis" has fundamentally reshaped our understanding of liver disease pathogenesis, yet critical questions persist regarding how Kasai surgery reconfigures this axis and whether these changes actively contribute to fibrogenesis. This review traces a mechanistic cascade from anatomical remodeling through dysbiosis, metabolic disruption, immune dysregulation, and ultimately liver fibrosis. We examine how Kasai surgery physically reprograms the gut ecosystem through altered biliary-enteric continuity and bile acid circulation; how microbial metabolites-particularly secondary bile acids and short-chain fatty acids-orchestrate hepatic stellate cell behavior and shape the hepatic immune milieu; and how bacterial translocation sustains inflammation through Toll-like receptor signaling. Recent evidence challenging the primacy of TLR4 in long-term progression instead implicates TLR7 as a potential driver, while acknowledging its complex, context-dependent role that may involve both pro-fibrotic and counter-regulatory functions. Building on this foundation, we critically assess emerging intervention strategies-including probiotics, postbiotics, phage therapy, and personalized approaches-weighing translational potential against current evidence gaps and safety considerations. We propose that post-Kasai alterations in the bile acid pool may drive fibrogenesis through synergistic engagement of FXR and TLR pathways (including TLR4 and TLR7), and outline a stratified, dynamic intervention framework for precision microbiome management grounded in multi-omics integration and longitudinal cohort studies. By synthesizing current knowledge while identifying key uncertainties, this review aims to inform both mechanistic investigation and the development of microbiome-targeted adjunctive therapies for BA.},
}
@article {pmid41960919,
year = {2026},
author = {van Leeuwen, PT and Gadaleta, P and Brul, S and Seppen, J and Wortel, MT},
title = {Environmentally mediated interactions predict community assembly and invasion success in a gut microbiota synthetic community.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0011326},
doi = {10.1128/msystems.00113-26},
pmid = {41960919},
issn = {2379-5077},
abstract = {The gut microbiome plays a crucial role in host homeostasis, with implications for nutrition, immune development, metabolism, and protection against pathogens. Disturbance of the microbiome by microbial invasion can be negative or positive: invasions of opportunistic pathogens can cause disease while dysbiotic states need invasions to recover. However, the complexity of the microbiome challenges our understanding of what factors determine the ability of microbes to invade. In this study, we measure interactions between members of a synthetic community of prominent gut bacteria using supernatant assays, which quantify the growth of one species in the cell-free culture medium of another. We measure relative abundances of co-cultures of up to four species to validate a generalized Lotka-Volterra model parameterized with these supernatant assays. We predict differential invasion outcomes of the opportunistic pathogens Escherichia coli and Bacteroides ovatus based on their monoculture growth profiles and interactions with other species, and we experimentally confirm model predictions of invasion success. The predictive value of our model indicates that environmentally mediated interactions, e.g., through soluble chemicals, primarily determine co-culture abundances and invasion success. Furthermore, model analyses show that negative interactions within the resident community and neutral to positive interactions with the invading species promote invasion success, but the interactions toward the invading species dominate. Our validated approach opens the way for testing of interactions of human gut microbiome species, thereby developing interventions to avoid pathogenic overgrowth and therapies to enhance health-benefitting invasions.IMPORTANCEThe stability of the human gut microbiome is crucial for host health, with opportunistic pathogen invasions causing diseases and healthy strain replacements needed for recovery. The microbiota's complexity complicates the understanding of invasion outcomes. This study uses a 10-species synthetic community of common gut microbiota to predict stable communities and invasion success. We grow cells in the growth medium of other species with the cells removed to parameterize a computational model, accurately predicting community composition up to four species and invasion success of Escherichia coli and Bacteroides ovatus. Our findings show that interactions through soluble compounds in the environment dictate co-culture growth and invasions. Furthermore, model analysis shows that interactions within the resident community and toward the invader are both important, but the latter dominate. These results pave the way for larger-scale studies to characterize gut microbiome interactions and properties that resist invasions, potentially benefiting health through improved probiotics and fecal microbiota transplants.},
}
@article {pmid41954789,
year = {2026},
author = {Schultz, J and García-Martínez, PM and Altalhi, S and Kontis, N and Dos Santos, A and Rosado, AS},
title = {Extreme Arabian environments and their microbiomes: new frontiers for astrobiology and biosignature discovery.},
journal = {Extremophiles : life under extreme conditions},
volume = {30},
number = {1},
pages = {},
pmid = {41954789},
issn = {1433-4909},
abstract = {Astrobiology assesses the habitability of planetary bodies and the potential for extraterrestrial life. Analog environments on Earth serve as sites for studying extreme environments that resemble extraterrestrial conditions, aiding in validating life-detection methods, mission instrumentation, and biosignature preservation. These environments function as a source of model microorganisms and communities that define the habitability and biochemistry of such extraterrestrial environments. Well-known analog environments include the Atacama Desert (Chile) for space mission validation, the McMurdo Dry Valleys (Antarctica) for Mars analog studies, and Rio Tinto (Spain) for extreme acidic environments. Although significant research has been conducted on these sites, various alternative environments may also offer valuable opportunities for astrobiological studies. Saudi Arabia encompasses a variety of pristine (or with minimal anthropic influence) extreme environments with conditions analogous to extraterrestrial settings (e.g., deserts and salt flats as analogs to Mars, and terrestrial and marine volcanic fields as analogs to icy moons), yet their potential remains largely unexplored. Recent studies have identified a volcanic crater with sodium phosphates and chlorates that mimics Enceladus’s ocean chemistry, and researchers have cultured Halalkalibacterium halodurans strains with adaptations to survive these conditions, offering valuable biological models. Additionally, complex metabolic landscapes with implications for icy moon habitability have been observed in Red Sea systems, which could be employed as valuable natural laboratories in astrobiological research. Furthermore, these findings underscore the potential of the Saudi Arabian extremophilic microbiome for space-related research. This review explores the microbial diversity of extreme environments in Saudi Arabia, emphasizing their potential as new terrestrial analogs to Mars and icy moons and the role of their microbiomes as terrestrial proxies for extraterrestrial life.},
}
@article {pmid41957864,
year = {2026},
author = {Mawarda, PC and Speksnijder, A and Krijger, D and Berkhout, J and Hoogenboom, A and Duijker, DA and Khoiri, AN and Kraaijeveld, K and Stech, M and Wittink, F},
title = {Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00886-8},
pmid = {41957864},
issn = {2524-6372},
support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.<br><br>RESULTS: Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.<br><br>CONCLUSIONS: Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.},
}
@article {pmid41957947,
year = {2025},
author = {Cashin, PH and Artursson, S and Sköldberg, F and Melhus, &#xc5;},
title = {Association of the gut microbiome to colorectal anastomotic leakage: systematic review.},
journal = {BJS open},
volume = {10},
number = {2},
pages = {},
doi = {10.1093/bjsopen/zrag005},
pmid = {41957947},
issn = {2474-9842},
support = {24-0824//Cancerfonden/ ; },
mesh = {*Anastomotic Leak/microbiology/etiology ; Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/surgery/microbiology ; Animals ; },
abstract = {BACKGROUND: Research into the gut microbiome and its possible association with anastomotic leakage after colorectal surgery has increased recently with the growing availability of sequencing techniques. There is a lack of systematic reviews addressing specifically microbiomic differences between patients with anastomotic leakage and patients with a successful anastomotic healing. The objective was to systematically review the current research on the microbiome and its effect on the risk of anastomotic leakage in colorectal cancer.<br><br>METHODS: Pubmed/Medline, Cochrane, and Google scholar were searched on 14th February 2025, to identify relevant publications with the following inclusion criteria: colorectal surgery, microbiome sequencing data, anastomotic leakage as endpoint, and comparative groups. Exclusion criteria were studies conducted exclusively on animals, non-peer-reviewed studies, review articles, and unavailable full text. Alpha/beta diversity and microbiomic functional analyses were the focus of the results.<br><br>RESULTS: From 112 studies, 11 studies including 551 patients were included: 143 patients with anastomotic leakage and 408 as controls. Alpha diversity differences were found in 7 of 11 studies-1 of 4 with preoperative sampling versus 6 of 7 studies with intra/postoperative sampling (P = 0.044). Beta diversity differences were found in 5 of 11 studies. Three studies reported on functional analyses, with one study demonstrating an association between methanogenesis and anastomotic leakage. Bacterial abundance was inconsistent across the studies. Three studies involving rodent models indicated a causal effect of the clinical microbiome.<br><br>CONCLUSION: Evidence implicates the gut microbiome as a factor associated with anastomotic leakage in colorectal cancer surgery, with three studies suggesting a causal relationship. There is a shortage of studies evaluating cross-species functional profiling. Optimal sampling should be performed during surgery.},
}
@article {pmid41678296,
year = {2026},
author = {Tamrakar, K and Chavez, ES and Miller, PW and Hale, B and DuVall, J and Williams, N and Brown, E and Mangan, S and Wijeratne, AJ},
title = {Integrated Multi-Omics Analysis Provides Insights into the Rhizosphere Microbial Dynamics in Soybean-Fusarium virguliforme Interaction.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {MPMI09250121FI},
doi = {10.1094/MPMI-09-25-0121-FI},
pmid = {41678296},
issn = {0894-0282},
abstract = {Sudden death syndrome (SDS) is a major disease that affects soybean (Glycine max) production, primarily caused by the soilborne fungus Fusarium virguliforme in North America. Understanding the interactions among soybeans, F. virguliforme, and microorganisms in the soil near the vicinity of roots can provide microbial candidates for SDS management. The objective of this study was to elucidate the role of rhizosphere microbial composition and activity, both in the presence and absence of F. virguliforme, across two commercial soybean cultivars with differing susceptibility to SDS. Bacterial and fungal community dynamics were assessed using full-length 16S rRNA and internal transcribed spacer 1 (ITS1) sequencing, respectively. Microbial activity was further evaluated with an optimized metatranscriptome workflow. Our analysis revealed that SDS-tolerant soybeans recruit microbes with growth-promoting and biocontrol potential, such as members of the genera Bacillus, Pseudomonas, Trichoderma, Mortierella, and Talaromyces, when exposed to F. virguliforme. This distinct microbial recruitment strategy in response to F. virguliforme could provide the ability for soybeans to survive under pathogen stress. In contrast, pathogen inoculation reduced the abundance and activity of the nitrogen-fixing Bradyrhizobium spp. These findings suggest that selective recruitment of beneficial microbes likely contributes to SDS tolerance, whereas pathogen pressure compromises symbiotic nitrogen fixation. The results highlight candidate taxa and interactions for developing synthetic microbial communities to support SDS management. The information generated from this study will be useful for assembling a combined synthetic microbial community and testing. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}
@article {pmid41776697,
year = {2026},
author = {Shi, X and Chen, F and Dai, M and Tang, Y and Wang, J and Lin, Y and Shi, M and Lan, T and Liu, H and Jin, X and Xiao, L and Kristiansen, K and Li, X},
title = {Comprehensive catalog of gut microbial genomes in Asian elephants: insights from shotgun metagenomics.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41776697},
issn = {2524-4671},
abstract = {BACKGROUND: The gut microbiota plays a crucial role in metabolism, immune regulation, and ecological adaptation of mammals. Although significant advancements have been made in shotgun metagenomic sequencing and the emergence of algorithms for generation of metagenome-assembled genomes (MAGs), a comprehensive investigation of the gut microbiota at the species level of wild mammals, among these the Asian elephant (Elephas maximus), is still lacking.<br><br>RESULTS: Here, based on a total of 82 fresh fecal samples collected from Asian elephants residing in distinct regions of the Yunnan Province, we established a comprehensive genome catalog containing 1421 species-level genome bins (SGBs) and a gene catalog comprising 44,596,628 non-redundant genes covering the gut microbiota composition of representative Asian elephant populations. At the species level, 1368 bacteria and 53 archaea were identified, and more than 93% of the SGBs remained unclassified, indicating that there are a large number of potential new species in the Asian elephant gut microbiota. At the functional level, carbohydrate hydrolases, biosynthetic gene clusters, and metabolic pathways dominated the gut microbiome of Asian elephants. Lifestyle and migration affected the composition and functional potential of the gut microbiota of Asian elephants. A northward migration was accompanied by an increase in gut microbiota diversity, an increase in the abundance of the phylum Bacteroidota, and a decrease in the presence of potentially pathogenic genera. In contrast, a southward migration of elephant herds was accompanied by exposure to unfavorable environments, with changes in gut microbiota including increased xenobiotic degradation and metabolic capacity.<br><br>CONCLUSIONS: We constructed comprehensive catalogs of gut microbial genes and genomes representative for Asian elephant populations, providing a valuable data resource for future research. Our study elucidates migration and lifestyle may modulate the composition and functionality of the gut microbiota in Asian elephants, offering critical insights for monitoring their health and enhancing conservation strategies for wild populations.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00533-0.},
}
@article {pmid41950813,
year = {2026},
author = {Jacobson, R and Soundararajan, R and Maurin, M and Bulard, B and Mishra, S and Kain, V and Halade, G and Yadav, H and Yeatman, T},
title = {Intratumoral microbiome varies by site of metastatic spread in colorectal cancer.},
journal = {Surgery},
volume = {194},
number = {},
pages = {110167},
doi = {10.1016/j.surg.2026.110167},
pmid = {41950813},
issn = {1532-7361},
}
@article {pmid41950983,
year = {2026},
author = {Šigutová, H and Geislerová, P and Šigut, M and Pyszko, P},
title = {Trace amounts of insecticide, herbicide, and their combination disrupt the bacterial and fungal microbiome of a nontarget aquatic invertebrate.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {398},
number = {},
pages = {128065},
doi = {10.1016/j.envpol.2026.128065},
pmid = {41950983},
issn = {1873-6424},
abstract = {The ubiquitous contamination of freshwater by pesticides contributes substantially to the ongoing diversity crisis. The animal microbiome affects a range of important functions, including host immunity and resilience to pesticide stress. Therefore, understanding how pesticides impact the microbiome of nontarget organisms is critical; however, this topic remains understudied in freshwater invertebrates. We investigated the effect of sublethal concentrations of pesticides on the host-associated microbiomes of larval Sympetrum vulgatum (Odonata: Libellulidae). Fifth-instar larvae reared in the laboratory and collected in the field were experimentally exposed to the herbicide metazachlor, the insecticide etofenprox, and their combination, and their bacterial and fungal microbiomes were profiled using 16S and ITS2 rRNA gene metabarcoding. Exposure to pesticides, particularly the insecticide, reduced bacterial richness, altered microbial community composition, reduced the complexity of co-occurrence networks, and neutral model deviations were more consistent with increased deterministic structuring. Simultaneously, our results suggested a loss of potentially beneficial taxa and an increase in pathogens, but also xenobiotic-degrading bacteria. The herbicide-insecticide mixture did not cause more profound effects than the insecticide alone, although it modified community assembly patterns. We found a shared set of prevalent genera persisting across treatments, alongside smaller treatment-associated subsets. Using a prevalence-based definition (detected in ≥3 samples per treatment), 91 bacterial and 22 fungal genera were shared across all treatments. The potentially contrasting responses of bacteria and fungi and the lab-reared and field-collected larvae to pesticides highlight the need to integrate the fungal component into microbiome research and suggest the importance of the naturally assembled microbiomes for host resilience.},
}
@article {pmid41950992,
year = {2026},
author = {Liu, K and Chen, Y and Zhao, M and Yang, D and Hu, Q and Cao, Y and Guo, X and Liu, Z},
title = {Integrative microbiome-transcriptome analysis reveals immune activation linked to gut dysbiosis in Vespa magnifica.},
journal = {Journal of invertebrate pathology},
volume = {217},
number = {},
pages = {108618},
doi = {10.1016/j.jip.2026.108618},
pmid = {41950992},
issn = {1096-0805},
abstract = {The gut microbiota plays a central role in the health of social wasps, contributing to nutrition, immunity, and environmental adaptation. However, its role in disease occurrence and host responses in the hornet Vespa magnifica remains poorly understood. Here, we investigated the gut microbial composition and host transcriptomic responses in diseased and healthy V. magnifica from Yunnan, China. High-throughput 16S rRNA gene sequencing revealed that diseased individuals exhibited significantly reduced microbial richness and diversity, characterized by depletion of beneficial taxa such as Lactobacillus (Lb.), Leuconostoc (Leu.), and Bifidobacterium (B.), alongside increased abundance of potential pathobionts including Lactococcus (Lc.) and Yokenella (Y.). Transcriptomic analysis identified 32 differentially expressed genes (DEGs), some of which were enriched for immune signaling pathways. Key immune-related genes, including peptidoglycan recognition proteins (PGRPs) and defensins (DEF), were strongly upregulated, indicating activation of host immune recognition and effector responses. Mantel correlation analysis further revealed significant associations between the top 30 differentially abundant bacterial genera and host immune genes, highlighting microbiota-host interactions in disease development. Collectively, these findings demonstrate that gut dysbiosis is associated with microbial imbalance and immune activation in V. magnifica, providing new insights into its gut health and potential strategies for disease management in hornet farming.},
}
@article {pmid41951111,
year = {2026},
author = {Fässler, D and Wittfeld, K and Frenzel, S and der Auwera, SV and Merhjerd, A and Gholizadeh, M and Simm, S and Kaderali, L and Franck, M and Rühlemann, M and Bang, C and Franke, A and Friedrich, N and Nauck, M and Lerch, MM and Weiss, FU and Völker, U and Bülow, R and Völzke, H and Peuker, K and Zeißig, S and Grabe, HJ and Frost, F and Hertel, J},
title = {Bilophila wadsworthia is linked to basal ganglia atrophy in the general population.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106587},
doi = {10.1016/j.bbi.2026.106587},
pmid = {41951111},
issn = {1090-2139},
abstract = {Bilophila wadsworthia, a sulfite-reducing bacterium stimulated by bile acids and enriched under high-fat diets, has been linked to several neurological disorders involving disturbances of motor function and basal ganglia circuitry. However, its potential association with alterations of brain structure remains unclear. Here, we investigated relationships between Bilophila (wadsworthia) abundance and basal ganglia volumes in two independent population-based cohorts combining gut microbiome profiling and brain MRI. Genus-level Bilophila abundance was assessed using 16S rRNA gene sequencing and complemented by species-level analyses of B. wadsworthia using whole-genome shotgun sequencing. Higher abundance of Bilophila (wadsworthia) was consistently associated with reduced volumes of basal ganglia regions, particularly the globus pallidus and nucleus accumbens. These associations were largely specific to basal ganglia regions when compared across a broad set of cortical thickness and other volumetric brain measures. Additionally, Bilophila (wadsworthia) was linked to elevated liver enzymes, elevated triglycerides, and pro-inflammatory states, confirming prior evidence from animal models while revealing novel associations in the general population. Constraint-based community modeling revealed that B. wadsworthia-enriched microbiomes exhibit increased functional redundancy for bile acid and sulfur metabolism and may modulate trimethylamine (TMA/TMAO) pathways. Together, these findings link variation in B. wadsworthia abundance to structural differences within basal ganglia regions and to unfavorable metabolic and inflammatory profiles in the general population, suggesting a potential role of this microbial species in gut-brain axis alterations relevant to neurodegenerative disease progression.},
}
@article {pmid41951277,
year = {2026},
author = {Bajer, L and Polakovicova, P and Heczkova, M and Holm, K and Hole, MJ and Hlavaty, M and Bohdanecka, A and Drastich, P and Tichanek, F and Meyer-Myklestad, MH and Medhus, AW and Reikvam, DH and Jørgensen, KK and Brezina, J and Macinga, P and Wohl, P and Fabian, O and Hov, JR and Cahova, M},
title = {Geography-independent mucosal microbiota alterations in primary sclerosing cholangitis persist after liver transplantation.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {4},
pages = {101716},
pmid = {41951277},
issn = {2589-5559},
abstract = {BACKGROUND &amp; AIMS: Primary sclerosing cholangitis (PSC)-associated alterations of fecal gut microbiota have already been described, but data on the mucosal microbiota are still limited. We aimed to further define disease-specific mucosal microbial patterns independent of geography and assess the relationship to liver transplantation (LTx), gut inflammation (inflammatory bowel disease), and PSC recurrence (rPSC).<br><br>METHODS: We performed 16S ribosomal RNA gene (V3-V4) sequencing of ileocolonic biopsies from 115 patients with PSC (pre-LTx), 159 liver-transplanted patients (post_LTx, recurrence occurred in 38), and 96 healthy controls (HC) from Norway and the Czech Republic.<br><br>RESULTS: Alpha diversity was lower in all PSC groups compared with HC. Elastic net models discriminated pre_LTx (AUC ileum 0.97; colon 0.93; p <0.001) and post_LTx PSC patients (AUC ileum 0.97; colon 0.97; p <0.001) from HC, and distinguished pre_LTx from post_LTx (AUC ileum 0.83; colon 0.83; p <0.001). The shared, cohort-independent PSC microbiota was dominated by Enterococcus, Pseudomonas, Veillonella, Klebsiella, and Streptococcus, while several common commensals were underrepresented. A microbial dysbiosis index calculated from PSC-associated genera correlated negatively with alpha diversity and serum albumin, while a positive correlation was observed with markers of cholestatic disease (ALP, GGT) and liver fibrosis (APRI). There were no associations with the presence of inflammatory bowel disease or fecal calprotectin. Differences between post-LTx patients with and without recurrence were limited, but several genera deregulated in pre-LTx PSC (Klebsiella, Bilophila, Coprococcus, Odoribacter) showed similar trends in rPSC.<br><br>CONCLUSIONS: Our findings in two European countries revealed a distinct mucosal microbiota composition associated with PSC that persists after LTx. These microbial patterns correlate with the severity of liver injury in PSC but not with markers of intestinal inflammation.<br><br>IMPACT AND IMPLICATIONS: This study provides an extensive evaluation of mucosa-associated microbiota in primary sclerosing cholangitis (PSC) before and after liver transplantation across two European cohorts. The persistence of PSC-related dysbiosis after transplantation highlights the importance of the gut-liver axis in PSC and supports further investigation into microbiota-driven mechanisms. Together with the strong association between microbiota composition and markers of cholestasis and fibrosis, this suggests potential clinical utility as an indicator of disease activity or even as a target for prevention or therapy.},
}
@article {pmid41951350,
year = {2026},
author = {Shokoohi, E and Masoko, P},
title = {Soil Biodiversity of Eucalyptus saligna: Insights Into Bacterial and Nematode Communities.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70341},
pmid = {41951350},
issn = {1758-2229},
support = {RNA-2022//University of Limpopo/ ; },
mesh = {*Eucalyptus/parasitology/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Animals ; *Nematoda/classification/genetics/isolation &amp; purification ; Soil/chemistry/parasitology ; RNA, Ribosomal, 16S/genetics ; South Africa ; Phylogeny ; Rhizosphere ; },
abstract = {Soil microorganisms and nematodes are key regulators of soil function, yet their co-occurrence in Eucalyptus rhizospheres remains poorly understood. In this exploratory study, we characterised bacterial and nematode communities associated with Eucalyptus saligna soils in Limpopo, South Africa, using high-throughput 16S rRNA gene sequencing and nematode surveys. Bacterial assemblages were dominated by Proteobacteria (42%), Acidobacteria (28%), Actinobacteria (12%) and Planctomycetes (9%). Eleven bacterial genera occurred across all sites, with Rhizobiales (prominence value, PV = 315,350) and Xanthobacteraceae (PV = 292,930) emerging as the most prominent taxa. Nematode surveys identified 19 genera, including plant-parasitic such as Meloidogyne (PV = 5759.1) and abundant free-living such as Tylolaimorphus (PV = 4150.0) and Acrobeloides (PV = 2900.0). Principal component analysis showed that bacterial communities were associated with soil pH, salinity and nitrogen forms, whereas nematode assemblages were associated with phosphate and sand content, together explaining 83%-90% of total variance. Network analysis indicated that all sampling sites functioned as central hubs (degree = 19-23; eigenvector centrality = 0.90-1.0), integrating nematode-bacteria associations. Key connector taxa included Acrobeloides, Wilsonema and Aphelenchoides, as well as bacteria such as Rhizobiales and Acidothermus. These findings provide a baseline framework for understanding belowground biodiversity and co-occurrence patterns in Eucalyptus plantation soils.},
}
@article {pmid41951359,
year = {2026},
author = {Zhang, J and Hu, J and Tang, X and Ruan, Y and Hao, F and Zhang, W and Trakman, G and Hamilton, AL and Lin, W and Sun, Y and Ching, JYL and Teh, JJ and Kang, S and Wilson-O' Brien, A and Stanley, A and Zhang, L and Sung, JJY and Yu, J and Miao, Y and Chan, FKL and Morrison, M and Kamm, M and Ng, SC},
title = {Quantifying artificial sweeteners and emulsifiers in Crohn's disease and its relationship with disease activity: the ENIGMA study - a novel and targeted approach.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-333999},
pmid = {41951359},
issn = {1468-3288},
abstract = {BACKGROUND: Food additives have been linked to increased Crohn's disease (CD) risk and activity, but their human quantification has not been explored.<br><br>OBJECTIVE: We aimed to measure artificial sweeteners and emulsifier polysorbate-80 (P-80) in patients with CD and assess their associations with disease activity.<br><br>DESIGN: 1461 biosamples from 487 subjects (245&#x2009;CD and 242 controls) across Australia, Hong Kong and Chinese Mainland were analysed for aspartame, sucralose, saccharin and P-80 levels in stool, urine and serum. CD activity was assessed using Crohn's Disease Activity Index and faecal calprotectin. A generalised linear model (GLM) with P-80 and sweeteners distinguished active CD from inactive CD.<br><br>RESULTS: Patients with CD had higher sweetener levels compared with controls across cohorts (all p<0.0001). P-80 underwent predominantly hydrolytic and oxidoreductive degradation in CD and controls, respectively, while its native form was undetectable. CD-associated P-80 metabolites positively correlated with urinary sweeteners in patients with CD. In vitro, CD-associated P-80 metabolites increased gut permeability, enabling translocation of sweeteners across the epithelium. Sweeteners and specific CD-associated P-80 metabolites were higher in active CD. The GLM built using sweeteners and P-80 metabolites distinguished active CD from inactive CD, achieving an area under the curve (AUC) of 0.86 in the discovery cohort and average AUC of 0.94 in two independent validation cohorts from Australia and Chinese Mainland.<br><br>CONCLUSION: This is the first human study to demonstrate distinct P-80 metabolism in patients with CD compared with controls. Dietary sweeteners and P-80 metabolites showed significant correlations with disease activity, suggesting their potential utility as non-invasive biomarkers for CD activity assessment.},
}
@article {pmid41951494,
year = {2026},
author = {Li, C and Braaten, K and Moser, AB and Fallatah, W and Lorentson, M and Huguenin, S and Torrey, A and Terluk, MR and Durose, W and Nolan, E and Staley, C and Subramanian, S and Lund, TC and Kartha, RV},
title = {Nervonic acid supplementation mitigates disease severity biomarkers in adrenoleukodystrophy.},
journal = {Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics},
volume = {},
number = {},
pages = {e00890},
doi = {10.1016/j.neurot.2026.e00890},
pmid = {41951494},
issn = {1878-7479},
abstract = {X-linked adrenoleukodystrophy (ALD) is a severe neurometabolic disorder caused by mutations in the ABCD1 gene, leading to impaired peroxisomal β-oxidation of very long-chain fatty acids (VLCFAs). The accumulation of saturated VLCFAs, predominantly C26:0, in plasma and across all tissues, contributes to adrenal dysfunction and progressive neurodegeneration. No approved therapy addresses the diverse spectrum of ALD manifestations, underscoring the urgent need for safe, accessible, and preventive treatments. Nervonic acid (NA), a monounsaturated fatty acid, is potentially beneficial for ALD through its neuroprotective effects. Here, we report the safety and therapeutic efficacy of NA in a 4-week dietary intervention study using a mouse model of ALD. NA treatment significantly decreased plasma C26:0-lysophosphatidylcholine, a diagnostic and disease-severity biomarker of ALD, by about 60% as early as one week after intervention. After 4-week treatment, NA markedly reduced free C26:0 and total saturated VLCFA levels in plasma and tissues. Moreover, we observed approximately 56% reduction in brain C26:0-lysophosphatidylcholine levels in NA-fed mice, an effect not reported with other drug intervention. Through comparative microbiome analysis, we show for the first time distinct baseline differences between ALD and wild-type mice, with dietary fatty acid supplementation preventing further dysbiosis. No adverse effects on body weight or food intake were observed throughout the study. Overall, this is the first report demonstrating that an oral dietary fatty acid can ameliorate the hallmark biochemical abnormalities of ALD in plasma and brain, highlighting its potential as a safe and effective therapy, particularly for presymptomatic individuals carrying this genetic defect.},
}
@article {pmid41951635,
year = {2026},
author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S},
title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07154-x},
pmid = {41951635},
issn = {2052-4463},
abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.},
}
@article {pmid41951653,
year = {2026},
author = {He, L and Yuan, D and Li, Q and Zhang, X and Niu, K and Li, X and Ou, Y and Du, H and Yuan, J and Duan, Y and Niu, H},
title = {Fecal virome transplantation attenuates arthritis in mice by remodeling gut ecology, systemic tryptophan metabolism, and innate immune responses.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00980-2},
pmid = {41951653},
issn = {2055-5008},
support = {2024VPPC-S02//the Open Project of the Key Laboratory of Viral Pathogenesis and Infection Prevention and Control (Jinan University), Ministry of Education/ ; 2025A1515012786//the Natural Science Foundation of Guangdong Province/ ; 2022YFF0710702 and 2022YFF0710701//the National Key &amp;D Programs of China/ ; 202201020381//the Guangzhou Joint Fund for Key Laboratory/ ; YXJC2022004//the Medical Joint Fund of Jinan University/ ; },
abstract = {Rheumatoid arthritis (RA) is an autoimmune disorder characterized by chronic joint inflammation and systemic immune dysregulation. Emerging evidence suggests that the gut microbiome plays an important role in immune modulation in RA, yet the role of the gut virome remains poorly understood. Here, using the K/BxN serum-transfer arthritis model, we systematically evaluated the potential role of fecal virome transplantation (FVT) in modulating gut ecology and innate inflammatory responses. Arthritic mice exhibited marked alterations in gut virome composition compared with healthy controls. Administration of purified virus-like particles (VLPs) from healthy donors correlated with reductions in paw swelling, histopathological inflammation, bone erosion, circulating proinflammatory cytokines, and myeloid cell infiltration in inflamed tissues. In parallel, 16S rRNA sequencing showed that FVT remodeled the gut bacterial community toward a composition more similar to that of healthy controls. Targeted serum metabolomics revealed increased levels of microbiota-derived tryptophan metabolites, including indole-3-lactic acid and related indole derivatives, suggesting a link between gut microbial remodeling and systemic immunometabolic regulation. Collectively, these findings indicate that FVT may attenuate inflammatory arthritis by remodeling gut microbial ecology, potentially involving virome-bacteriome interactions and immunometabolic pathways.},
}
@article {pmid41951862,
year = {2026},
author = {Ocejo, A and Kotecha, RR and Voss, MH},
title = {From diversity to function: microbiome precision in RCC.},
journal = {Nature reviews. Urology},
volume = {},
number = {},
pages = {},
pmid = {41951862},
issn = {1759-4820},
}
@article {pmid41952069,
year = {2026},
author = {Klimesova, B and Ruane, NM and Domingo-Bretón, R and Moroni, F and Naya-Català, F and Pérez-Sánchez, J and O'Dwyer, K and Lyashevska, O and Rodger, H and Talbot, A},
title = {Sea Lice (Lepeophtheirus salmonis) Harbour Putative Fish Pathogens: Insights From Illumina and Nanopore Sequencing.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70182},
doi = {10.1111/jfd.70182},
pmid = {41952069},
issn = {1365-2761},
support = {CS/21/005//Marine Institute, Marine Reseach Programme Irish Government/ ; 871108//European Union's Horizon 2020 Research and Innovation Programme/ ; CIAPOS/2024/092//Generalitat Valenciana/ ; FSE+//European Union, Eyropean Social Fun Plus/ ; MMT24-IATS-01-01//NextGeneration EU MOMENTUM-CSIC Postdoctoral Research Contract/ ; },
abstract = {Ectoparasites that penetrate host skin can act as biological or mechanical vectors for pathogens and, in some cases, serve as reservoirs. Crustacean ectoparasites of fish are potential vectors of pathogens, which is especially relevant for obligate pathogens (e.g., Aeromonas salmonicida) with limited seawater survival. Sea lice (Lepeophtheirus salmonis), affecting Atlantic salmon, cause dermal damage and can facilitate secondary infections, resulting in economic losses. While the physical impact of sea lice is well known, their role in pathogen transmission is less clear. The gut bacterial microbiome of lice collected over four months from a salmon farm in Ireland was analysed using Illumina MiSeq and Oxford Nanopore Technologies (ONT) PromethION sequencing for comparison. Illumina and Nanopore sequencing identified 15 and 24 genera of known fish pathogens, respectively. Moreover, Nanopore data revealed up to 15 putative pathogenic species, including Tenacibaculum maritimum, T. dicentrarchi and Vibrio anguillarum, causative agents of tenacibaculosis and vibriosis. The results of this study provide a gut bacterial microbiome characterisation of L. salmonis in a commercial aquaculture setting and demonstrate the potential of sea lice to act as pathogen vectors or reservoirs. These findings have important implications for pathogen surveillance, management, and prevention strategies in salmon aquaculture.},
}
@article {pmid41952172,
year = {2026},
author = {Zhang, J and Jiang, C and Zhou, X and Gao, P and Wong, S and Snyder, M and Shen, X},
title = {Cross-body site microbial interactions influence the human plasma metabolome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02405-w},
pmid = {41952172},
issn = {2049-2618},
support = {#025402-00001//Ministry of Education - Singapore/ ; },
abstract = {BACKGROUND: The human microbiome profoundly influences the host plasma metabolome and health, but most studies have focused on the gut microbiome in isolation. A comprehensive assessment of how microbiomes from multiple body sites jointly shape host metabolism has been lacking.<br><br>RESULTS: Using data from three independent human cohorts (n&#x2009;=&#x2009;435), we systematically analyzed the selective and joint influences of microbiomes from multiple body sites on the human plasma metabolome (814 annotated metabolites). Microbiomes from all body sites contributed to plasma metabolome variation, collectively explaining 30.13% of the inter-individual variation. The gut microbiome showed the largest contribution (18.44%), followed by oral (14.70%), skin (11.5%), and nasal (5.88%) microbiomes. Microbial composition did not necessarily predict metabolic function for example, despite distinct compositions, oral and gut microbiomes exhibited similar associations with circulating metabolites. Machine learning and mediation analyses revealed widespread cooperative and synergistic microbial interactions across body sites, particularly along the oral-gut axis. Over half of the metabolites were jointly influenced by multiple body-site microbiomes. This axis showed cross-site microbial crosstalk and sequential metabolic processing, regulating metabolites such as indole derivatives and carboxylic acids. The oral-gut microbiome-metabolome axis was further amplified in insulin resistance (IR), linking enhanced microbial cooperation to metabolic dysregulation.<br><br>CONCLUSION: Our findings reveal the systemic and interactive nature of microbiome-metabolome relationships and highlight the need to integrate spatially distributed microbial ecosystems to fully understand host metabolic regulation and disease mechanisms. Video Abstract.},
}
@article {pmid41952630,
year = {2026},
author = {Wim, T and Mehraveh, S and Katalina, L and Cheah, CW and Pisha, P and Ana, C and Andy, T and Naiera, Z and Wannes, VH},
title = {Not a miracle, not a myth: The role of probiotics in periodontal health.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.70039},
pmid = {41952630},
issn = {1600-0757},
support = {C3/24/081//KU Leuven/ ; },
abstract = {BACKGROUND: As the understanding of periodontal disease has evolved, therapeutic strategies have increasingly shifted from pathogen eradication toward ecological modulation of the oral microbiome. Within this paradigm, probiotics have emerged as potential adjuncts for maintaining periodontal health by promoting microbial balance and modulating host responses.<br><br>OBJECTIVE: To summarize the historical development, definitions, and mechanisms of probiotics and to critically evaluate the current clinical evidence supporting their use in periodontal therapy.<br><br>METHODS: This narrative review examines the conceptual framework of probiotics in oral health, distinguishing them from related approaches including prebiotics, postbiotics, and synbiotics. Literature from randomized controlled trials and meta-analyses was reviewed to assess the clinical effectiveness of probiotic interventions in periodontal therapy and to explore their proposed mechanisms of action.<br><br>RESULTS: Probiotic effects are highly strain-specific and involve multiple mechanisms, including production of antimicrobial compounds, competition for ecological niches, inhibition of biofilm formation and quorum sensing, strengthening of epithelial barrier integrity, and modulation of host immune and inflammatory responses. Evidence from randomized controlled trials and meta-analyses, particularly those evaluating Limosilactobacillus reuteri strains, suggests that probiotics used as adjuncts to nonsurgical periodontal therapy can significantly improve clinical parameters such as probing pocket depth, clinical attachment level, and bleeding on probing. However, substantial heterogeneity in study design, probiotic strains, delivery systems, and follow-up periods limits the comparability and generalizability of findings.<br><br>CONCLUSIONS: Probiotics represent a biologically plausible and ecologically oriented adjunct in periodontal therapy. While current evidence indicates beneficial clinical effects, further standardized and long-term clinical trials incorporating advanced microbiome analyses (e.g., next-generation sequencing) are needed to clarify mechanisms, optimize formulations, and support personalized probiotic strategies in periodontal care.},
}
@article {pmid41952964,
year = {2026},
author = {Peñalba, F and Guisande, A and Lamberti, L and Rusiñol, C and Irastorza, M and Konik, F and Iglesias, C and Mendive, P and Garrido, G and Parada, A and Riera, N},
title = {Gut microbiota and its association with gastrointestinal symptoms and pharmacological treatments in a sibling-matched cohort with autism spectrum disorder.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1777385},
pmid = {41952964},
issn = {2813-4338},
abstract = {Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder marked by difficulties in communication, social interaction, and restricted, repetitive behaviors. The gut microbiota has emerged as a key factor in the gut-brain axis relevant to ASD. We conducted a cross-sectional study comparing the gut bacterial composition of children with ASD (n=29) and their neurotypical siblings (NT, n=29). To minimize environmental and lifestyle confounders, all pairs were 4 to 10 years old and cohabiting in the same household in Uruguay. We used full-length 16S rRNA gene (V1-V9) sequencing with the latest R10.4.1 Oxford Nanopore Technologies chemistry, enabling high-resolution microbial characterization. While overall β-diversity did not differ significantly between the ASD and NT groups, we identified specific taxonomic shifts. The ASD group was enriched in taxa like Sellimonas, while the NT group showed enrichment of genera like Faecalibacterium and Coprococcus. Furthermore, we found GI symptoms to be significantly more prevalent in the ASD group and some bacterial genera associated with GI symptomatology. In addition, we explored the association of pharmacological treatments. Antipsychotic use was associated with reduced Akkermansia abundance, whereas melatonin and methylphenidate use were associated with the enrichment of Negativibacillus. This study provides novel insights into the gut microbiome of Uruguayan children with ASD, delineating the influence of GI symptoms and pharmacological load on microbial diversity and composition.},
}
@article {pmid41953022,
year = {2026},
author = {Han, W and Li, Q and Yuan, G},
title = {The gut microbiome as an actionable drug-sensitivity modulator for immune checkpoint blockade: clinical evidence for FMT, live biotherapeutics, and defined consortia.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1802676},
pmid = {41953022},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology ; *Fecal Microbiota Transplantation/methods ; Animals ; },
abstract = {Immune checkpoint inhibitors (ICIs) deliver durable benefit to only a subset of patients and can be limited by immune-related adverse events (irAEs). The gut microbiome has emerged as an actionable, host-level modulator of ICI drug sensitivity and toxicity. This mini-review links microbial ecology to antigen presentation, T-cell priming and fitness, metabolite signaling, and barrier inflammation, and summarizes interventional evidence across three modalities. Responder-derived fecal microbiota transplantation (FMT) provides the strongest proof-of-concept for re-sensitization in anti-PD-1-refractory melanoma. Microbiome repair can also improve refractory ICI-associated colitis. Early trials of live biotherapeutics and defined consortia support scalability but highlight context dependence and design pitfalls, including antibiotic preconditioning. We discuss practical determinants of reproducibility, including co-medications, diet, engraftment and functional readouts, and conclude with safety, regulatory, and reporting priorities for clinically deployable microbiome engineering.},
}
@article {pmid41953110,
year = {2026},
author = {Craddock, HA and Motro, Y and Winner, KM and Lotem-Michaeli, Y and Segal, E and Godneva, A and Grinstein, D and Moran-Gilad, J},
title = {Metagenomic analysis of antimicrobial resistance genes in domestic canines.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101380},
pmid = {41953110},
issn = {2352-7714},
abstract = {A One Health approach is critical to addressing the spread of antimicrobial resistance (AMR). A key source of AMR in humans is companion animals, particularly canines. Recent investigation has shown that the canine fecal microbiome is rich in antimicrobial resistant genes (ARGs), yet few studies have studied the resistome of working canines. Our objective was to investigate the resistome of canines to elucidate associations between various exposures and demographic factors and ARG carriage. We performed resistome and microbiome analyses on previously-generated metagenomic sequence data from 126 Israeli working canines and 147 global canines. We found that the canine microbiome and resistome varied significantly with country of origin, and the resistome varied significantly with gastrointestinal disease state, canine job type, and microbiome composition. Tetracycline resistant genes were the most dominant across all canines. Extended-spectrum beta lactamase (ESBL) genes were observed in up to 33% of canines. Genes of concern, including potential carbapenemases (blaOXA-181 and blaOXA-347) and colistin resistance genes (mcr-10) were infrequently observed. The Inc family of plasmids, typically associated with ESBL genes, were frequently detected. Altogether our research suggests that canines, including working dogs, are a potential source of ARGs and plasmids which carry ARGs. Importantly, the abundance and identity of these ARGs is associated with various potentially modifiable factors such as microbiome composition. As canines are an important human exposure within the One Health paradigm, future work is necessary to understand the risk and transmission dynamics of ARGs between humans and their companion canines.},
}
@article {pmid41953220,
year = {2025},
author = {El-Saadony, MT and Saad, AM and Sitohy, M and Alkafaas, SS and Dladla, M and Ghosh, S and Mohammed, DM and Ibrahim, EH and Fahmy, MA and Elkelish, A and AbuQamar, SF and El-Tarabily, KA},
title = {Probiotics and human health: biological activities, nutritional aspects, immunomodulatory properties, applications, and future perspectives - a comprehensive review.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1713426},
pmid = {41953220},
issn = {1664-3224},
mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; *Gastrointestinal Microbiome/immunology ; Animals ; Immunomodulation ; },
abstract = {Probiotics, defined as living microorganisms, are widely recognized for their ability to positively influence the gut microbiota, an effect increasingly linked to a wide array of health benefits. They are claimed to treat or prevent conditions ranging from infant colic to cardiovascular disease, respiratory infections, and certain cancers. Since the beginning of the 21st century, consumer demand for probiotic-enriched foods has risen significantly, propelled by these health assertions. The consumption of such products has been associated with the alleviation of disorders, including irritable bowel syndrome, lactose intolerance, gastroenteritis, obesity, chronic diarrhea, allergies, atopic dermatitis, and infectious diseases. Recent advancements in microbiome and microbiota research are fundamentally transforming probiotic science. Cutting-edge studies on novel strains, their mechanisms, and potential applications are expected to revolutionize our understanding of their roles in human nutrition and medicine. Nevertheless, despite extensive research efforts, critical gaps remain regarding strain-specific mechanisms, optimal dosages, long-term safety, and interactions among probiotics, host genetics, and dietary factors. Addressing these gaps necessitates a comprehensive synthesis of current knowledge and emerging trends. This review aims to critically integrate historical foundations, dosage strategies, mechanisms of action, therapeutic applications, and potential risks associated with probiotics. Unlike previous reviews, this review emphasizes next-generation probiotics, live biotherapeutics, and genetically engineered microbes, and their synergistic interactions with dietary bioactives such as polyphenols and fibers. By providing a forward-looking perspective, this work contributes to the rational design of functional foods, targeted therapies, and microbiome-based interventions, thereby informing future advancements in human nutrition and medicine. It critically examines current and emerging trends in probiotic research, while acknowledging potential adverse effects and risks.},
}
@article {pmid41953221,
year = {2025},
author = {Zhao, Z and Wang, X and Bao, Y and Meng, J and Gong, J and Zhang, L and Li, Z and Yao, W and Chuo, Y and Shi, W and Li, J},
title = {Dietary Bazhen San solid-state fermentation product improves laying performance, immunity and intestinal health in laying hens during the late laying period.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1673604},
pmid = {41953221},
issn = {1664-3224},
mesh = {Animals ; *Chickens/immunology ; Female ; *Animal Feed/analysis ; Fermentation ; *Intestines/immunology/microbiology ; Diet ; Dietary Supplements ; Gastrointestinal Microbiome ; *Oviposition ; Eggs ; Cytokines ; Immunoglobulin A/blood ; },
abstract = {The aim of this study was to investigate the effects of solid-state fermentation products of Bazhen San (FB) on the production performance, immunity, and intestinal health of laying hens during the late laying stage. A total of 150 70-week-old laying hens were randomly assigned to five treatment groups, with five replicates per group and six hens per replicate. The control group (CON) was fed a corn-soybean meal-based diet, whereas the other four treatment groups were supplemented with 0.3% FB (LFB), 0.6% FB (MFB), 0.9% FB (HFB), and 0.6% unfermented Bazhen San (BZ), respectively. The results showed that, compared with the CON group, all treatments significantly increased the egg production rate and reduced the feed-to-egg ratio (P < 0.05). Moreover, the effect in the MFB group was significantly greater than that in the BZ group (P < 0.05). In terms of egg quality, the MFB and HFB groups significantly improved yolk color and Haugh units (P < 0.05). Regarding immune function, serum immunoglobulin A (IgA) levels were significantly increased in all treatment groups (P < 0.05), whereas interleukin-1β (IL-1β) and interleukin-6 (IL-6) concentrations were significantly decreased (P < 0.05). The MFB and HFB groups also significantly increased serum immunoglobulin G (IgG) levels (P < 0.05), as well as jejunal and ileal secretory immunoglobulin A (sIgA) levels (P < 0.05). In addition, serum IgG levels in the MFB group were significantly higher than those in the BZ group (P < 0.05). In terms of intestinal health, FB treatment significantly enhanced antioxidant enzyme activity in the jejunum and ileum, reduced malondialdehyde (MDA) content, improved intestinal morphology. The microbiome analysis of the cecum showed that FB improved the abundance of beneficial bacteria in the intestine. Spearman correlation analysis revealed that the relative abundance of Odoribacter and Enterococcus was positively correlated with serum IgA levels and negatively correlated with IL-6 concentration. Therefore, dietary supplementation with FB can improve intestinal health, and systematically improve the immune status of the body, thereby promoting the health of laying hens during the late laying stage and improving production performance, dietary 0.6% to 0.9% FB inclusion is suggested.},
}
@article {pmid41953438,
year = {2026},
author = {Li, H and Yu, Z and Wu, Z and Lin, Y and Liu, T and Liu, Y and Li, Z and Zhang, S and Su, Z and Wang, H},
title = {Quantifying human-environment interactions through Bayesian modeling of species-resolved microbial transfer signatures: an exploratory proof-of-concept study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1781392},
pmid = {41953438},
issn = {1664-302X},
abstract = {BACKGROUND: Microbial trace evidence offers potential for forensic reconstruction of human-environment interactions, but current methods lack standardized quantitative frameworks. While 2bRAD-M (type IIB restriction site-associated DNA markers for microbiomes) sequencing provides species-level resolution from low-biomass samples, its integration with robust statistical models for forensic applications remains unexplored.<br><br>METHODS: We developed an integrated framework combining 2bRAD-M sequencing with a Bayesian hierarchical model to quantify microbial transfer patterns. The model incorporates geospatial parameters, substrate-specific persistence kinetics, and temporal decay functions. We generated 2bRAD-M data from host-associated (skin, saliva; n&#x202f;=&#x202f;12) and environmental samples (personal devices, high-touch surfaces; n&#x202f;=&#x202f;14), integrated with public 16S rRNA data (Qiita studies; n&#x202f;=&#x202f;2,263 samples) for model training.<br><br>KEY FINDINGS: The Bayesian model demonstrated preliminary accuracy in attributing microbial traces to their likely source environment categories (within ~100 meters in preliminary tests) and provided initial estimates for deposition time. Personal devices were found to retain taxa associated with host such as Staphylococcus hominis for extended periods (exceeding 72&#x202f;h in our observations), suggesting persistent microbial transfer.<br><br>CONCLUSION: This proof-of-concept study suggests that integrating 2bRAD-M sequencing with Bayesian modeling could provide a framework for quantitative reconstruction of microbial transfer histories. The approach indicates potential for forensic applications but is not yet validated for casework. Extensive validation with larger, independent datasets is imperative to assess its reliability and admissibility standards.},
}
@article {pmid41953447,
year = {2026},
author = {Wang, X and Hu, W and Li, R and Sun, R and Liong, MT and Yu, Q and Chen, D},
title = {Gi-MAPS: a quantitative engineering framework for AI-guided pediatric gut microbiome ecological interpretation and digital-twin simulation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1739103},
pmid = {41953447},
issn = {1664-302X},
abstract = {BACKGROUND: Quantitative and reproducible microbiome analysis is limited by fragmented workflows lacking standardized anaerobic sampling, absolute quantification methods, and transparent AI inference. Patent-documented engineering integration is required for reliable microbiome analytics at population scale.<br><br>METHODS: Gi-MAPS was designed as an end-to-end analytical system integrating several core patented innovations, including (i) a press-activated anaerobic sample-preservation device that maintains ultra-low residual oxygen to protect obligate anaerobes during transport, (ii) a multiplex qPCR assay enabling simultaneous absolute quantification of key HMO-utilizing Bifidobacterium species in a single reaction, and (iii) a CIT-Net-based digital-twin engine that supports forward simulation of gut microbiota ecological trajectories. These modules are coupled with explainable ensemble artificial intelligence models to form a fully quantitative and simulation-enabled microbiome analysis framework. Each subsystem was validated under granted patents to define engineering performance boundaries and reproducibility specifications.<br><br>RESULTS: System validation demonstrated <0.1% residual oxygen stability for anaerobic preservation, detection sensitivity down to five genomic copies per microliter, AUC&#x202f;>&#x202f;0.97 for ecological maturity estimation, 89% accuracy for disease-risk classification, and 95% concordance for digital-twin forecasting. Execution-layer software copyright modules and filed patents extend automation, visualization, and future application domains.<br><br>CONCLUSION: Gi-MAPS provides a patent-anchored, standardized engineering framework whose key novelties lie in oxygen-controlled anaerobic sampling, absolute microbial quantification via multiplex qPCR, and digital-twin ecological simulation, enabling quantitative, function-aware, and prospective microbiome analysis. It establishes a reproducible foundation enabling large-scale cohort deployment, longitudinal ecological monitoring, digital-twin simulation, and future multi-omics integration.},
}
@article {pmid41953448,
year = {2026},
author = {Bautista, J and López-Cortés, A},
title = {Biohacking the human gut microbiome for precision health and therapeutic innovation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1776983},
pmid = {41953448},
issn = {1664-302X},
abstract = {Biohacking, the self-directed application of biotechnology, digital tools, and lifestyle interventions, has rapidly converged with gut microbiome science to create adaptive, individualized, and minimally invasive precision-health paradigms. This narrative review integrates current evidence on diet-based modulation, microbial therapeutics (probiotics, prebiotics, postbiotics, and fecal microbiota transplantation), and synthetic-biology approaches (engineered strains and phage or synthetic consortia) within a multi-omics and continuous-phenotyping framework. Mechanistically, short-chain fatty acids (SCFAs), bile-acid derivatives, and tryptophan catabolites operate as endocrine-like mediators linking gut microbial ecology with host immunity, metabolism, and neuroendocrine signaling. Pathways mediated by microbial metabolites underpin translational applications that span metabolic optimization, through improved insulin sensitivity, reduced adiposity, and attenuation of inflammation, and neurocognitive enhancement via the microbiome-gut-brain axis. Evidence from oncology further indicates that microbial metabolites and engineered taxa remodel stromal and immune niches, shaping therapeutic response and disease progression. Concurrently, emerging digital infrastructures, wearables, biosensors, metabolic avatars, and AI-driven "health twins," enable real-time, closed-loop modulation of host-microbe dynamics. Persistent challenges include methodological heterogeneity, safety concerns regarding live biotherapeutics and unsupervised fecal microbiota transplantation (FMT), fragmented regulation, and vulnerabilities in cyberbiosecurity and data equity. We propose a translational roadmap emphasizing standardized metadata (STORMS), validated reference frameworks, longitudinal multi-omics for causal inference, strain-level safety genomics, and governance integrating ethical and cybersecurity oversight. Under these conditions, microbiome-focused biohacking may evolve from anecdotal experimentation into a more reproducible and scientifically grounded component of preventive and personalized medicine. This manuscript is presented as a narrative and conceptual review, integrating validated microbiome research with emerging biohacking frameworks while explicitly distinguishing evidence-based findings from exploratory or speculative concepts.},
}
@article {pmid41953516,
year = {2026},
author = {Qu, HQ and Kao, C and Hakonarson, H},
title = {Redefining the role of the thiol-based agent N-acetylcysteine in human health and disease and elucidating potential advantages of its amide derivative.},
journal = {RSC medicinal chemistry},
volume = {},
number = {},
pages = {},
pmid = {41953516},
issn = {2632-8682},
abstract = {N-Acetylcysteine (NAC) is the established antidote for acetaminophen toxicity and an approved mucolytic agent. Beyond these traditional uses, increasing evidence highlights its broader role as a modulator of thiol-redox biology. Rather than functioning as a nonspecific antioxidant, NAC modulates glutathione metabolism, redox-sensitive signaling, immune checkpoints, thiol-based post-translational modifications, ferroptosis susceptibility, and glutamatergic neurotransmission. This review synthesizes mechanistic, preclinical, and clinical evidence across pulmonary, hepatic, neuropsychiatric, metabolic, cardiovascular, and oncologic disorders, emphasizing how variability in baseline redox state, pharmacogenetics, and delivery contributes to heterogeneous outcomes. Strategies to improve pharmacokinetics and tissue targeting include structural derivatives such as N-acetylcysteine amide (NACA), and combination regimens such as NAC with probenecid or GlyNAC. Emerging applications span long COVID, neurodegeneration, psychiatric disorders, microbiome-redox interactions, environmental toxicology, and cancer immunotherapy. NAC and NACA exemplify the evolution of redox-targeted therapeutics. NAC is well established for safety and clinical utility, but its pharmacokinetic and tissue distribution properties constrain broader efficacy. NACA, a lipophilic amide derivative, enhances membrane permeability and cellular uptake, suggesting it may achieve higher tissue exposure at lower doses. Future progress will rely on biomarker-guided, precision approaches that optimize dosing, formulation, and delivery while exploring rational combinations across disease contexts defined by redox biology.},
}
@article {pmid41953552,
year = {2026},
author = {Hwang, JH and Choi, YK},
title = {Herbal and Natural Product Interventions in Animal Models of Antibiotic-Associated Diarrhea and Their Effects on Gut Microbiota: a protocol for systematic review.},
journal = {Journal of pharmacopuncture},
volume = {29},
number = {1},
pages = {42-47},
pmid = {41953552},
issn = {2093-6966},
abstract = {OBJECTIVES: Antibiotic-associated diarrhea (AAD) is a frequent complication of antibiotic use and is commonly used to investigate gut microbiota dysbiosis and potential therapeutic interventions in animals. Herbal medicines and natural product-derived compounds have shown promising effects in restoring microbial balance; however, no systematic review has yet synthesized the preclinical evidence. Therefore, this review aimed to systematically identify, evaluate, and synthesize animal studies examining herbal and natural product interventions for AAD, with a particular focus on gut microbiota restoration and related functional outcomes.<br><br>METHODS: This protocol has been registered in PROSPERO (CRD420251136553). A systematic search was performed in PubMed, Embase, Web of Science, Scopus, CNKI, and other major Korean medical databases from inception to the search date. Controlled preclinical studies that evaluated herbal or natural product interventions for AAD in animal models and reported gut microbiota outcomes were also included. Two reviewers independently screened the studies, extracted the data, and assessed the risk of bias.<br><br>RESULTS: This systematic review was conducted in accordance with the PRISMA guidelines. The findings were synthesized narratively and, where appropriate, organized by intervention type, animal model, and microbiome analytic method.<br><br>CONCLUSION: This review systematically evaluates the effects of herbal and natural products on the gut microbiota in animal models of antibiotic-associated diarrhea. These findings provide foundational preclinical evidence to support microbiome-directed development of herbal, polysaccharide-based, and synbiotic interventions for antibiotic-associated dysbiosis.},
}
@article {pmid41953674,
year = {2026},
author = {Zhou, H and Saha, S and Morrill, S and Kelly, T and Lewis, WG and Lewis, AL},
title = {Gardnerella biofilm formation in vitro is facilitated by braided sutures: implications for cervical cerclage.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1763531},
pmid = {41953674},
issn = {2235-2988},
mesh = {*Biofilms/growth &amp; development ; *Sutures/microbiology/adverse effects ; Female ; Humans ; *Cerclage, Cervical/adverse effects ; Pregnancy ; *Gardnerella/physiology/growth &amp; development ; *Gardnerella vaginalis/physiology/growth &amp; development ; },
abstract = {INTRODUCTION: In pregnant individuals with certain indications, sutures may be placed circumferentially around the uterine cervix to prevent dilation. Compared to monofilament sutures, the use of braided suture materials has been linked with the development of a dysbiotic vaginal microbiome, as well as higher rates of infection-associated pregnancy outcomes such as chorioamnionitis and preterm birth. In bacterial vaginosis (BV) anaerobic bacteria, including pathogens, overgrow, forming biofilms in direct proximity to the host epithelium. Gardnerella is highly represented among bacterial vaginosis-like microbiotas.<br><br>METHODS: To test our working hypothesis that braided sutures may better support the establishment of high biomass bacterial biofilms compared to monofilament sutures, we measured the extent of Gardnerella bacteria biofilm formation on braided and monofilament sutures in the laboratory. Multiple Gardnerella strains were grown in the presence of braided or monofilament suture materials (polyester or polybutylate-coated polyester versus polypropylene or nylon), and the (biofilm) biomass was measured using crystal violet staining.<br><br>RESULTS: Sutures incubated without Gardnerella were included as controls. To compare staining of biofilm biomass between groups, one-way ANOVA was performed and &#x160;id&#xe1;k was used for pairwise comparisons to control for multiple comparisons between groups. Gardnerella formed significantly more biofilm biomass (>10-fold) on braided polyethylene terephthalate (polyester) sutures compared to monofilament (polypropylene or nylon) sutures (p < 0.0001). This feature was applicable to multiple strains across different taxonomic subsets of Gardnerella.<br><br>DISCUSSION: Together with existing literature, these findings suggest that braided sutures might promote the development of dysbiotic BV-like microbiomes after cerclage placement by facilitating Gardnerella biofilm formation.},
}
@article {pmid41953764,
year = {2026},
author = {Ivan, FX and Versi, A and Tiew, PY and Abdel-Aziz, MI and Kermani, NZ and Maitland-Van Der Zee, AH and Howarth, P and Koh, MS and Adcock, IM and Chotirmall, SH and Chung, KF},
title = {Multidrug-resistant Haemophilus influenzae cluster of severe asthma from sputum bacteriome-resistome.},
journal = {ERJ open research},
volume = {12},
number = {2},
pages = {},
pmid = {41953764},
issn = {2312-0541},
abstract = {BACKGROUND: Severe asthma encompasses heterogeneous inflammatory phenotypes and airway bacteriome diversity but the state of its airway resistome remains understudied. We therefore evaluated the link between the airway microbiome and the antibiotic-resistant genes by determining the clusters from a bacteriome-resistome integration from sputum samples of patients with severe asthma.<br><br>METHODS: Induced sputum samples from severe asthma (SA; n=96), mild-moderate asthma (MMA; n=23) and healthy controls (HCs; n=23) in the European U-BIOPRED asthma cohort were metagenomically sequenced. Respiratory bacteriome was evaluated by taxonomical and functional classification. The comprehensive antibiotic resistance database was used to determine airway resistome and Similarity Network Fusion to cluster integratively the bacteriome-resistome.<br><br>RESULTS: More multidrug-resistance genes were present in SA compared with MMA and HCs with the hmrM, encoded in Haemophilus influenzae chromosome, being highest. Two of the three defined clusters were dominated by commensals with resistance genes from different classes but different in &#x3b1;- and &#x3b2;-diversities. The third cluster was dominated by multidrug-resistant H. influenzae, with SA characteristics of increased asthma duration, reduced pulmonary macrophages and decreased lung function. It had the highest signature expression of neutrophil activation, NETosis and of interleukin (IL)-5, IL-6, IL-13, IL-17 and IL-33 signalling pathways. These clusters were reproduced in an Asian-Singapore SA cohort including the multidrug-resistant H. influenzae cluster, but with an additional cluster of multidrug-resistant Pseudomonas aeruginosa.<br><br>CONCLUSION: The demonstration of U-BIOPRED multiresistant H. Influenzae and of Asian-Singapore multiresistant P. aeruginosa clusters highlights the potential importance of antibiotic-resistant genes in driving severe asthma.},
}
@article {pmid41953919,
year = {2026},
author = {Murmu, M and Singh, R and Barage, S and Kumar, AWS},
title = {Exploratory Study of Virulence Factors and Protein-Protein Interaction Networks in Major Oral Pathogens.},
journal = {Contemporary clinical dentistry},
volume = {17},
number = {1},
pages = {16-30},
pmid = {41953919},
issn = {0976-237X},
abstract = {INTRODUCTION: Periodontitis is a prevalent inflammatory disease driven by dysbiotic microbial consortia. Red-complex pathogens (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) and emerging taxa (Filifactor alocis and Aggregatibacter actinomycetemcomitans) are central contributors, yet their virulence mechanisms remain incompletely defined.<br><br>OBJECTIVE: To construct protein-protein interaction (PPI) networks of key periodontopathogens and identify conserved as well as pathogen-specific virulence hubs.<br><br>METHODOLOGY: High-confidence PPI networks were generated for 1136 proteins across the five pathogens. Network topology was analyzed to identify hubs, and enrichment analyses were performed to map functional clusters.<br><br>RESULTS: Hub proteins such as guaA, metG, pheT, lysS, thrA, rplA, purD, and rpsH demonstrated significant interactions with accessory proteins. Conserved hubs, including guaA and ileS, were shared across pathogens and were essential in purine biosynthesis and aminoacyl-tRNA ligation. Pathogen-specific hubs comprised gingipains (P. gingivalis), leukotoxin (A. actinomycetemcomitans), and dentilisin (T. denticola). Functional clustering revealed adhesion, peptidoglycan biosynthesis, and immune modulation pathways.<br><br>CONCLUSION: PPI networks provide system-level mechanistic insights into pathogen virulence, revealing conserved vulnerabilities and species-specific mechanisms.},
}
@article {pmid41954023,
year = {2026},
author = {Anagnostopoulou, L and Ktenopoulos, N and Apostolos, A and Fragoulis, C and Vlachakis, P and Karakasis, P and Sagris, M and Milaras, N and Drakopoulou, M and Synetos, A and Kyriazis, I and Ioannidis, I and Tsioufis, C and Toutouzas, K},
title = {Intersecting Molecular Pathways in Cardiovascular Disease and Diabetes Mellitus: Emerging Roles of Inflammation and Therapeutics.},
journal = {Diabetes/metabolism research and reviews},
volume = {42},
number = {4},
pages = {e70167},
pmid = {41954023},
issn = {1520-7560},
mesh = {Humans ; *Cardiovascular Diseases/metabolism/pathology/etiology ; *Inflammation/metabolism/pathology ; *Hypoglycemic Agents/therapeutic use ; Gastrointestinal Microbiome ; Animals ; *Diabetes Mellitus/metabolism/drug therapy ; },
abstract = {Diabetes mellitus (DM) and cardiovascular diseases (CVD) remain leading contributors to global morbidity and mortality, imposing a substantial burden on healthcare systems worldwide. The pathophysiological mechanisms underlying these conditions are complex and closely interconnected, with chronic low-grade inflammation, oxidative stress, endothelial dysfunction, insulin resistance and dysregulated lipid metabolism serving as pivotal shared pathways. Persistent hyperglycaemia and metabolic imbalance in DM accelerate vascular injury and atherosclerotic progression, thereby significantly increasing cardiovascular risk. Consequently, therapeutic strategies that concurrently target both metabolic and cardiovascular dysfunction may offer meaningful clinical advantages and improved long-term outcomes. In recent years, novel antidiabetic agents such as sodium-glucose co-transporter 2 (SGLT-2) inhibitors and glucagon-like peptide-1 (GLP-1) receptor agonists have demonstrated not only glycaemic control but also substantial cardiovascular protection, including reductions in major adverse cardiovascular events, heart failure hospitalisations and renal disease progression. These pleiotropic effects extend beyond glucose lowering and involve modulation of inflammatory pathways, improvement of endothelial function, attenuation of oxidative stress and favourable haemodynamic changes. Additionally, emerging evidence highlights the role of the gut microbiota as a critical mediator in the bidirectional relationship between DM and CVD. Alterations in microbial composition and diversity, collectively termed dysbiosis, have been associated with systemic inflammation, impaired metabolic homoeostasis, increased intestinal permeability and the production of pro-atherogenic metabolites such as trimethylamine N-oxide. Understanding these microbiome-related mechanisms may open new avenues for preventive and therapeutic interventions targeting the gut-metabolic-cardiovascular axis. This narrative review provides an updated and comprehensive overview of the molecular and cellular mechanisms linking DM and CVD, with particular emphasis on inflammatory signalling, metabolic dysregulation and the emerging influence of the gut microbiome in their shared pathogenesis and therapeutic modulation.},
}
@article {pmid41954158,
year = {2026},
author = {Glass, BH and Aichelman, HE and Grupstra, CGB and Valadez-Ingersoll, M and Swank, A and Guerra, V and Gondola, P and Nagree, A and Schipfer, J and Gilmore, TD and Davies, SW},
title = {Legacy Effects of an Extreme Marine Heatwave on a Stress-Tolerant Coral.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70853},
doi = {10.1111/gcb.70853},
pmid = {41954158},
issn = {1365-2486},
support = {//Boston University/ ; 1937650//National Science Foundation/ ; 2506815//National Science Foundation/ ; },
mesh = {Animals ; *Anthozoa/physiology/microbiology ; Coral Reefs ; Panama ; *Extreme Heat/adverse effects ; *Coral Bleaching ; Symbiosis ; *Hot Temperature ; Stress, Physiological ; },
abstract = {During the 4th Global Coral Bleaching Event (GCBE4; January 2023-September 2025), an extreme marine heatwave occurred on the Bocas del Toro Reef Complex (BTRC) in Panama. We characterized how this heatwave impacted the health and holobiont communities of the stress-tolerant coral Siderastrea siderea at four sites across the BTRC. Tagged colonies at each site (N = 30-53 colonies per site) were visited before, during, and after the heatwave (early May 2022, mid-August 2023, and late April 2024, respectively), and images and DNA samples were collected at each time point. In situ temperature logger data showed that sites reached maxima of 32.1°C-33.9°C in October 2023, resulting in the accumulation of ~12-20 maximum degree-heating weeks (DHWs). Consequently, S. siderea colonies displayed widespread bleaching (i.e., the loss of algal endosymbionts), with an increase from 8.6% to 33% of colonies bleached per site in May 2022 to 33%-70% in August 2023, followed by a decline to 15%-63% by April 2024. Colony-level partial mortality increased significantly between 2022 and 2024 at three of the four sites, and was observed even in colonies that were not bleached in August 2023. Further, many corals hosting Cladocopium spp. algal symbionts in 2022 shifted towards less diverse communities dominated by heat-tolerant Breviolum and Durusdinium spp., and most of these corals continued to host modified symbiont communities for months. The heatwave also reshaped corals' bacterial microbiomes, including increases in α-diversity and abundances of potentially pathogenic taxa (e.g., Vibrionaceae), and these shifts were persistent following the heatwave. Together, these findings demonstrate that GCBE4 had lasting impacts on S. siderea holobiont health across the BTRC, underscoring that extreme heat events can compromise even stress-tolerant coral species and induce legacy effects that will likely affect their future resilience. Rapid action to minimize further ocean warming is thus necessary to safeguard reef ecosystems.},
}
@article {pmid41954174,
year = {2026},
author = {Torregrosa-Chinillach, A and Tsiara, I and Haberek, W and Lin, W and Globisch, D},
title = {Chemical Metabolomics: Chemical Biology Tools for Advanced Metabolism Investigations.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e26122},
doi = {10.1002/anie.202526122},
pmid = {41954174},
issn = {1521-3773},
support = {2020-04707//Swedish Research Council/ ; FO2024-0407//Swedish Brain Foundation/ ; 254898Pj//Swedish Cancer Society/ ; },
abstract = {Human metabolism has been investigated to understand disease onset for the discovery of new selective pharmaceuticals and the development of diagnostics for early disease detection. Metabolomics, as an interdisciplinary research field, has been implemented to investigate the entirety of the complex metabolite profiles predominantly using mass spectrometry. In the past two decades, the development of chemical biology tools for the detailed metabolism investigation has received a boost to advance metabolomics analyses. Especially, the identification of the microbiome and its importance for human physiology were the main motivation for these strategies. These new tools at the intersection of Chemistry and Biology have especially aided to uncover previously unknown metabolites in humans and have slowly elucidated metabolites produced by microbial communities. These Chemical Biology tools, integrated with metabolomics tools and technologies, build the foundation for Chemical Metabolomics investigations, which have led to the discovery of important metabolites that are modulators or readouts for disease development and human homeostasis. This overview article focuses on the recent developments and the diversity of Chemical Biology tools and technologies, particularly methods involving chemoselective probes, in vivo analysis, host-microbiome co-metabolism, and activity metabolomics, in the context of understanding human metabolism at the molecular level.},
}
@article {pmid41954380,
year = {2026},
author = {Hu, J and Chung, R and Odeneal, R and Zhang, SJ},
title = {AANA Journal Course-The Gut-Brain Axis and Chronic Pain: The Emerging Role of Microbiota.},
journal = {AANA journal},
volume = {94},
number = {2},
pages = {141-151},
doi = {10.70278/AANAJ/.0000001078},
pmid = {41954380},
issn = {2162-5239},
mesh = {Humans ; *Chronic Pain/microbiology/physiopathology/nursing ; *Gastrointestinal Microbiome/physiology ; *Nurse Anesthetists/education ; Dysbiosis ; *Brain ; },
abstract = {Chronic pain is a complex and disabling condition that significantly impairs quality of life. It often arises from central sensitization, an amplified response to pain stimuli driven by neuroinflammatory changes in both the peripheral and central nervous systems. Emerging evidence highlights the gut microbiome's crucial role in the process because it modulates inflammation, immune function, and neurotransmitter production via the gut-brain axis. An imbalance in gut flora, known as dysbiosis, can exacerbate neuroinflammation by altering intestinal barrier integrity, facilitating the release of pro-inflammatory mediators, and activating microglia within the central nervous system. These changes contribute to increased pain sensitivity and the progression of chronic pain states. Consequently, strategies promoting a healthy gut microbiome, such as targeted dietary measures and microbiota-focused therapies, represent promising adjuncts to conventional chronic pain management. This journal course evaluates current research on the connection between the gut microbiome and chronic pain, offering a novel perspective on holistic, microbiome-centered interventions for alleviating pain disorders. As certified registered nurse anesthetists increasingly participate in pain management, understanding this emerging approach is vital for improving patient outcomes in chronic pain conditions.},
}
@article {pmid41954396,
year = {2026},
author = {Drankhan, HR and Taylor, KR and Shah, DH and Park, CH and Grieser, AM and Wild, MA},
title = {An experimental infection model for rapid reproduction of treponeme-associated hoof disease in captive elk (Cervus canadensis).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0382225},
doi = {10.1128/spectrum.03822-25},
pmid = {41954396},
issn = {2165-0497},
abstract = {Treponeme-associated hoof disease (TAHD) is an emerging, polybacterial infection that causes painful foot lesions and lameness in free-ranging elk (Cervus canadensis) across the northwestern USA. Although TAHD is associated with multiple Treponema species and other anaerobic bacteria, current understanding of disease etiology is limited and based primarily on cross-sectional analyses of naturally infected elk, in which lesions were examined at single time points using histopathology and 16S rRNA gene sequencing. Our objective was to develop a rapid and reliable experimental infection model to study TAHD pathogenesis in captive elk under controlled conditions. Inoculum consisting of macerated lesion tissue and mixed cultures of Treponema spp. and other anaerobic bacteria derived from TAHD lesions was applied onto abraded interdigital skin on the hind feet of five treatment elk. Inoculated feet were wrapped to expedite lesion development. Over the 7 week study period, all inoculated feet (10/10) developed interdigital erosions consistent with mild to moderate TAHD lesions observed in free-ranging elk. Lesions were observed on the majority of inoculated feet (9/10) after 28 days, coinciding with concurrent 16S rRNA gene amplicon sequencing detection of three putative pathogens of TAHD: Treponema, Fusobacterium, and Mycoplasma. In contrast, mock-inoculated control elk feet did not exhibit pathological or microbiological changes indicative of TAHD. This experimental infection model provides a valuable platform to investigate the complex interactions between the host, pathogens, and environmental factors that influence TAHD susceptibility, lesion progression, and disease transmission.IMPORTANCEOur study details a new approach for consistent and rapid induction of treponeme-associated hoof disease (TAHD) lesions in captive elk. TAHD is an emerging polybacterial disease of conservation concern that causes chronic lameness and debilitation in free-ranging elk across the northwestern USA. We rapidly and reliably reproduced TAHD lesions following challenge with inoculum consisting of macerated lesion tissue and mixed cultures of Treponema spp. and other anaerobic bacteria. This experimental infection model provides a valuable platform for investigation of the complex interactions between the host, pathogens, and environmental factors influencing TAHD susceptibility, lesion progression, and disease transmission in elk.},
}
@article {pmid41954620,
year = {2026},
author = {Gou, YR and Gu, H and Wang, L},
title = {Beyond tumor biology: nursing interventions for psychological and immune health in cancer patients.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {34},
number = {5},
pages = {},
pmid = {41954620},
issn = {1433-7339},
mesh = {Humans ; *Neoplasms/psychology/immunology/nursing/therapy ; *Stress, Psychological/therapy/etiology/nursing ; *Oncology Nursing/methods/organization &amp; administration ; Depression ; Social Support ; Anxiety ; },
abstract = {Cancer care requires an integrative approach that addresses psychological distress, immune dysfunction, and health disparities across global populations. Psychoneuroimmunology research reveals bidirectional links between psychological well-being, neural signaling, immune activity, and clinical outcomes, underscoring the need for nursing‑led holistic interventions. This review synthesizes evidence on the prevalence and impact of anxiety, depression, fear of recurrence, and stress-mediated neuroendocrine pathways that suppress immune surveillance. It examines tumor-associated immune dysregulation, therapy-induced immune imbalance, and inflammation as a mechanistic bridge between emotional and physical health. Nursing-driven strategies including cognitive-behavioral therapy, mindfulness, narrative care, social support, lifestyle counseling, nutrition, microbiome support, physical rehabilitation, and integrative practices demonstrate measurable benefits for resilience, immune stability, and treatment adherence. Emerging technologies such as AI-enabled telehealth expand the reach and personalization of oncology nursing pathways. Persistent barriers workload, training gaps, cultural differences, and limited resources require policy reform, multidisciplinary integration, and capacity-building. Future directions highlight precision nursing models utilizing biomarkers, digital analytics, and survivorship planning to deliver equitable, patient-centered psychological-immune oncology care.},
}
@article {pmid41954752,
year = {2026},
author = {Saha, S and Shah, AS and Wang, P and Burgess, TI and Bayliss, KL},
title = {Seed Potato Bacteria Transfer Across Generations Within the Tuber Flesh.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02758-7},
pmid = {41954752},
issn = {1432-184X},
abstract = {Potato crops are susceptible to pathogens and environmental extremes. Microbiomes support plant health and stress tolerance, and microbes can transfer across generations in vegetatively propagated potatoes. However, the extent and functional relevance of this transfer are poorly understood. This study investigated bacterial transfer across three tuber generations, from seed to granddaughter in two potato cultivars, Nadine and Royal Blue. Bacterial communities in the peel and flesh compartments were sequenced. The granddaughter generation was cultivated in two separate fields to determine the consistency of vertical transfer, and the tare soil bacterial community was a proxy for environmental acquisition. The overall community composition was influenced by generation, compartment, cultivar and field. Horizontal acquisition significantly increased across generations and was the primary source, accounting for more than 98% of the granddaughter tuber bacteria. Peel had a significantly higher number of horizontally acquired ASVs than flesh. Only a small set of seed tuber bacteria ASVs were vertically transferred to the granddaughter tubers. The overall vertical transfer probability was 1.8% across compartments, cultivars, and fields, and it was higher in flesh than in peel. Cultivar-specific probabilities were 1.8% for Nadine and 1.5% for Royal Blue. Field variance was minimal, indicating consistent vertical transfer regardless of where the tubers were grown. Taxa with stable vertical transfer included Streptomycetaceae, Xanthobacteraceae, Devosiaceae, Sphingomonadaceae, and Micrococcaceae. Vertically transferred ASVs were predicted to have functions associated with core metabolic and stress response pathways. This study confirmed consistent vertical transfer of bacteria across potato tuber generations, mainly in the flesh.},
}
@article {pmid41954871,
year = {2026},
author = {Mac Aogáin, M and Gilmour, A and Chalmers, JD and Chotirmall, SH},
title = {Targeting Inflammation in Bronchiectasis.},
journal = {Drugs},
volume = {},
number = {},
pages = {},
pmid = {41954871},
issn = {1179-1950},
support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001636//National Medical Research Council/ ; MOH-001356//National Medical Research Council/ ; MOH-001855//National Medical Research Council/ ; },
abstract = {Bronchiectasis is defined by chronic infection, dysregulated inflammation and impaired mucociliary clearance underpinning progressive structural lung injury. While airway infection remains a clinical hallmark, numerous studies demonstrate that excessive neutrophil-dominated inflammation is a key determinant of disease severity, exacerbation risk and quality of life. Recent developments have transformed our understanding of inflammatory drivers uncovering distinct inflammatory endotypes defined by dominant microbial species, pattern-recognition receptor activation, inflammasome signalling, Th17-associated cytokine networks and failures of mucosal immunity. The emerging roles of viral-bacterial interactions, fungi, pathobionts and the broader microbiome challenge the conventional infection-only paradigm and highlight gaps in current therapeutic strategies. Such developments underpin the rationale behind anti-inflammatory strategies in bronchiectasis, ranging from suppression of neutrophil-driven injury through direct neutrophil elastase or upstream dipeptidyl peptidase-1 (DPP-1) inhibition, to immunomodulatory macrolides, toward therapies aimed at recalibrating epithelial and mucosal homeostasis. While several antibacterial and anti-infective trials have produced mixed results, this is likely to reflect unresolved heterogeneity in microbiome composition and host immune signalling. In contrast, emerging anti-inflammatory strategies show strong positive signals, reinforcing the need for better endotyping and biomarker-guided patient selection. Here we synthesize recent mechanistic and clinical insights to propose a more integrated framework for understanding and ultimately targeting airway inflammation in bronchiectasis.},
}
@article {pmid41954918,
year = {2026},
author = {Specchia, ML and Beccia, F and Cacciuttolo, MG and Petrella, L and Mungo, T and Thiella, S and Lucarelli, A and Zace, D and Di Pietro, ML},
title = {Maternal and child nutrition insecurity, microbiome, and early neurodevelopment: an intricate interplay. Results from a systematic review.},
journal = {European journal of public health},
volume = {36},
number = {2},
pages = {},
pmid = {41954918},
issn = {1464-360X},
mesh = {Humans ; Female ; Infant ; *Child Development/physiology ; *Gastrointestinal Microbiome/physiology ; *Food Insecurity ; *Neurodevelopmental Disorders ; Child ; *Nutritional Status ; Pregnancy ; Child, Preschool ; Infant, Newborn ; },
abstract = {Emerging research suggests nutrition insecurity influences microbiome composition, which in turn affects early neurodevelopment through the gut-brain axis. This systematic review aimed to evaluate evidence on these relationships. A comprehensive search of the scientific literature was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Studies investigating the links between nutrition insecurity in mothers and children, microbiome, and early neurodevelopment were included. Data on maternal characteristics, microbiota composition, neurodevelopmental outcomes, and nutritional status were extracted from eligible studies. The review included 11 studies, primarily cohort studies, conducted in various countries. According to the study findings, gut maternal and infant microbiota composition in early life appear to be closely connected to early neurodevelopment both in terms of cognitive/motor skills and temperament. Nutrition insecurity has a significant influence in shaping these outcomes as it can alter microbiota balance and contribute to gut dysbiosis and delayed neurodevelopmental milestones. Breastfeeding emerges as a crucial factor in modulating the infant microbiome and supporting neurodevelopment. Also, other factors such as pre-pregnancy overweight/obesity and environment seem to influence offspring gut colonization and neurodevelopmental outcomes. This systematic review highlights the intricate interplay between maternal and child nutrition insecurity, microbiota, and early neurodevelopment. These findings underscore the critical need for targeted interventions addressing maternal and child nutrition to mitigate the adverse effects of nutrition insecurity and support optimal early-life neurodevelopment. Future research should focus on longitudinal studies to explore the causal pathways and to develop nutrition-based strategies to prioritize microbiome health in vulnerable and at-risk populations.},
}
@article {pmid41955160,
year = {2026},
author = {Liu, J and Li, K and Zhang, Y and Huang, K and Guan, X},
title = {Predicting gut metabolites from gut microbiome and their interpretability analysis of IBD prediction based on LIME.},
journal = {Integrative biology : quantitative biosciences from nano to macro},
volume = {18},
number = {},
pages = {},
doi = {10.1093/intbio/zyaf023},
pmid = {41955160},
issn = {1757-9708},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/diagnosis ; Dysbiosis/microbiology ; Oxides ; Calcium Compounds ; },
abstract = {The pathophysiology of inflammatory bowel disease (IBD) is influenced by the gut microbiome and gut metabolite, but understanding how IBD is affected remains challenging. It is crucial to understand which features affect IBD in order to effectively diagnose the disease. Traditional technology for measuring metabolite features is time-consuming and costly. The abundance of metabolite features in IBD patients is altered depending to changes in the abundance of gut microbiome. LSTM-VAE is proposed to predict gut metabolite features using gut microbiome of IBD patients. The pathogenesis of IBD is investigated by LSTM-VAE without gut metabolite data. In order to explore IBD is affected by the features, GBDT-LR is used to predict IBD disease using the gut microbiome and the generated gut metabolites. GBDT-LR achieved high-precision prediction, with an accuracy of 0.97 at the genus level and 0.95 at the species level. It is noteworthy that LIME is used to explain the prediction process of GBDT-LR, solving the prediction of the 'black box model'. The cost of measuring intestinal metabolites were reduced in this study and the researches were assisted in the diagnosis and drug research of IBD diseases. Insight Box Dysbiosis of the gut microbiota and the resulting abnormal metabolites were influenced in the IBD, promoting inflammatory responses and damaging intestinal barrier function. LSTM-VAE was proposed to predict changes in gut metabolite features in IBD patients without the need for direct measurement of costly and time-consuming metabolite data. Furthermore, high-precision prediction of IBD based on gut microbiome data was demonstrated and metabolite features were generated in the GBDT-LR, achieving accuracy rates of 0.97 at the genus level and 0.95 at the species level. Additionally, the LIME is employed to interpret the "black box" prediction process of GBDT-LR. The cost of measuring gut metabolites was reduced, but also strong support for the diagnosis and drug development of IBD was provided.},
}
@article {pmid41955174,
year = {2026},
author = {Kowarsky, M and Dalman, M and Moufarrej, MN and Okamoto, J and Xie, Y and Neff, NF and Abdool Karim, SS and Garrett, N and Moore, PL and Camunas-Soler, J and Quake, SR},
title = {Cell-free RNA reveals host and microbial correlates of broadly neutralizing antibody development against HIV.},
journal = {PLoS pathogens},
volume = {22},
number = {4},
pages = {e1014066},
pmid = {41955174},
issn = {1553-7374},
mesh = {Humans ; *HIV Infections/immunology/virology ; *HIV-1/immunology/genetics ; *HIV Antibodies/immunology ; *Broadly Neutralizing Antibodies/immunology ; Male ; Female ; Adult ; *RNA, Viral/genetics/blood ; Middle Aged ; Longitudinal Studies ; Microbiota/immunology ; },
abstract = {A small number of people living with HIV (PLWH) develop broadly neutralizing antibodies (bNAbs) targeting multiple HIV strains. Although several viral and immune factors contribute to bNAb development, the genetic and environmental factors driving this response remain largely unknown. We performed combined cell-free DNA (cfDNA) and cell-free RNA (cfRNA) sequencing in 42 plasma samples from a longitudinal cohort of 14 PLWH (7 who develop bNAbs and 7 matched controls). This approach enabled us to non-invasively monitor the host transcriptome, viral genetic variation, and microbiome composition during HIV infection, and to identify molecular correlates of bNAb development. We find that development of bNAbs is associated with a transcriptomic signature of early immune activation characterized by elevated levels of MHC class I antigen presentation genes. This signature is independent of viral load or CD4 count and declines over time. In addition to host features, we recovered sufficient viral reads to reconstruct HIV consensus sequences, supporting the utility of cfRNA for viral genotyping. Finally, we also identified an enrichment of several microbial taxa in bNAb producers and increased levels of GB virus C (GBV-C), a non-pathogenic lymphotropic virus. Our findings suggest a distinct early immune activation profile in PLWH who develop bNAbs. More broadly, we show that combined cfDNA/cfRNA sequencing can reveal relationships between a protective immunogenic response to HIV infection, the host immune system, and microbiome, highlighting its potential for biomarker discovery in future vaccine and therapeutic studies.},
}
@article {pmid41955218,
year = {2026},
author = {Yaakop, S and Senen, MA and Adila Rosli, NA and Mohammed, MA},
title = {Molecular identification and microbiome profiling of household casebearer, Phereoeca sp. (Lepidoptera: Tineidae) from Malaysia: Potential implications for human skin irritation.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346590},
pmid = {41955218},
issn = {1932-6203},
mesh = {Animals ; Malaysia ; *Microbiota/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; Skin/microbiology ; *Lepidoptera/microbiology/genetics ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; *Moths/microbiology/genetics ; High-Throughput Nucleotide Sequencing ; Electron Transport Complex IV/genetics ; },
abstract = {In Malaysia, anecdotal accounts have linked the household casebearer (Lepidoptera: Tineidae) to skin lesions and localized inflammation; however, scientific evidence is lacking, and the species' taxonomic identity remains unclear. This study aimed to confirm the species identity and examine the bacteria associated with larvae that may be linked to skin irritation. Larvae were collected from three locations in Peninsular Malaysia and preserved. DNA was extracted from the larvae, and species identification was conducted by analyzing the cytochrome c oxidase subunit I (COI) gene through DNA barcoding. To study the bacteria present, the bacterial 16S rRNA gene was amplified and sequenced using Next-generation sequencing technology. The DNA sequences were analyzed to determine the species and profile the bacterial communities. The results identified the specimens as Phereoeca sp., suggesting they may represent an undescribed lineage. Microbiome analysis revealed that Proteobacteria (40.18%) and Actinobacteriota (32.13%) were the dominant bacterial phyla, with Cutibacterium acnes, Enterobacter, and Pseudomonas among the taxa previously associated with skin irritation or opportunistic infections. Several unclassified but potentially relevant taxa were also identified. These findings provide new insights into the microbial ecology and taxonomy of Phereoeca and underscore its potential role in medically significant interactions within human environments.},
}
@article {pmid41955304,
year = {2026},
author = {Yang, JC and Situ, J and Troutman, R and Zhu, R and Black, M and Buri, H and Gutta, A and Tian, F and Kang, A and Aja, E and Zeng, A and Lai, RW and Tan, J and Liang, F and Brahim, C and Murphy, G and Ahdoot, A and Peng, C and Jacobs, JP},
title = {A microbiome quantitative trait locus in SLC39A8 modulates disease severity in synucleinopathy-induced models of Parkinson's disease.},
journal = {Human molecular genetics},
volume = {35},
number = {6},
pages = {},
doi = {10.1093/hmg/ddag024},
pmid = {41955304},
issn = {1460-2083},
mesh = {Animals ; Mice ; *Parkinson Disease/genetics/microbiology/pathology ; Humans ; alpha-Synuclein/genetics/metabolism ; Disease Models, Animal ; *Cation Transport Proteins/genetics ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci/genetics ; *Gastrointestinal Microbiome/genetics ; *Synucleinopathies/genetics/microbiology/pathology ; Male ; Dopaminergic Neurons/pathology/metabolism ; Female ; Genetic Predisposition to Disease ; Mice, Transgenic ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by motor deficits, dopaminergic neuron loss, and α-synuclein (α-syn) aggregation. While rare mutations underlie familial PD, around 85% of cases are idiopathic. Emerging evidence implicates common genetic variants and the gut microbiome in PD risk, but their interaction has not been studied. We previously demonstrated that the PD-protective SLC39A8 variant rs13107325 (human A391T, corresponding to A393T in mouse) is associated with microbial compositional shifts in humans and reshapes the microbiome in SLC39A8 A393T knock-in mice. Here, we test whether this SNP modifies PD phenotypes in two α-synucleinopathy mouse models. In the human α-synuclein overexpression model, A393T carrier mice show reduced motor deficits, consistent with a protective role. However, in the α-synuclein preformed fibril (PFF) injection model, A393T carriers exhibit worsened motor deficits, increased dopaminergic terminal loss, and enhanced α-synuclein pathology spread. SNP- and model-specific microbiome changes correlated with motor outcomes. These included enrichment of Lactobacillus and Lactobacillaceae HT002 genera in A393T carriers with α-synuclein overexpression, and enrichment of Erysipelatoclostridium in PFF-injected A393T carriers. These findings suggest that SLC39A8 A393T-induced microbiome alterations are associated with differential disease outcomes depending on context. Our results are consistent with a model in which susceptibility gene SNPs may influence PD progression via the gut microbiome, though direct causal effects remain to be tested.},
}
@article {pmid41955364,
year = {2026},
author = {Jain, S},
title = {Pesticides may wreak havoc on the gut microbiome.},
journal = {Science (New York, N.Y.)},
volume = {392},
number = {6794},
pages = {134-135},
doi = {10.1126/science.aeh8589},
pmid = {41955364},
issn = {1095-9203},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Pesticides/toxicity/adverse effects ; Animals ; },
abstract = {Disruption of complex intestinal ecosystem could contribute to diabetes and other health issues, scientists say.},
}
@article {pmid41955483,
year = {2026},
author = {Wang, M and Luo, N and Li, Y and Zhai, H and Xi, J and Li, HB and Zhou, D},
title = {Unlocking the Phyllosphere's Role: Selenium Nanoparticles Reprogram Sulfur Metabolism and Enrich Sphingomonas to Reduce Cadmium in Wheat.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12411},
pmid = {41955483},
issn = {1520-5851},
abstract = {Although selenium nanoparticles (SeNPs) can mitigate cadmium (Cd) accumulation in crops, comparative system-level mechanisms among different SeNPs remain unclear, particularly in wheat. Herein, we compare chemically and biologically synthesized SeNPs (CH/BI-SeNPs) to elucidate Cd detoxification via phyllosphere metabolism-microbiome interactions. Results showed that foliar application of both SeNPs significantly reduced Cd accumulation and mitigated cell membrane damage in wheat. CH-SeNPs exhibited the strongest Cd reduction effect, decreasing grain Cd content by 30.9%. Metabolomic profiling revealed a substantial reorganization of sulfur metabolic pathways under CH-SeNPs treatment, characterized by the accumulation of S-adenosylhomocysteine (SAH), decreased homomethionine, and reduced oxidized glutathione (GSSG), indicating a shift in sulfur flux toward enhanced synthesis of reduced thiol compounds. CH-SeNPs activated the glutathione biosynthesis pathway, significantly increasing the activity of γ-glutamylcysteine synthetase and the contents of cysteine and glutathione, thereby promoting Cd chelation, and reducing its translocation to grains. 16S rRNA sequencing further demonstrated that CH-SeNPs significantly enriched Sphingomonas, a genus involved in sulfur cycling, in the phyllosphere, rhizosphere, and rhizosphere soil, suggesting that microbial interactions facilitated sulfur metabolism and contributed to a systemic reduction in Cd bioavailability. Additionally, HPLC-ICP-MS analysis indicated an increased proportion of selenomethionine in grains under CH-SeNPs treatment, enhancing both nutritional value and food safety. This study reveals that SeNPs alleviate Cd stress in wheat via coordinated regulation involving phyllosphere sulfur metabolism and microbial interactions related to sulfur, providing a mechanistic basis for the application of SeNPs in the remediation of heavy metal contamination and nutritional fortification in agriculture.},
}
@article {pmid41955497,
year = {2026},
author = {Zhang, W and Yang, Z and Zhang, Y and Wang, L and Zhang, X and Mao, J and Dai, Y and Yuan, Y and Wang, M and Yang, X and Yu, X and Liu, J and Chen, C},
title = {Multi-Enzyme Mimetic Molybdenum Nitride Nanozymes Reshape Subgingival Microenvironment for Synergistic Periodontitis Therapy via ROS Regulation and Microbiome Remodeling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17770},
doi = {10.1002/advs.202517770},
pmid = {41955497},
issn = {2198-3844},
support = {2024YFA1210004//National Key Research and Development Program of China/ ; T2422006//National Natural Science Foundation of China/ ; T242200557//National Natural Science Foundation of China/ ; 82201017//National Natural Science Foundation of China/ ; 52422213//National Natural Science Foundation of China/ ; 52272212//National Natural Science Foundation of China/ ; F251001//Beijing Natural Science Foundation/ ; 22388101//Basic Science Center Project of the National Natural Science Foundation of China/ ; 2022QNRC001//Young Elite Scientist Sponsorship Program by CAST/ ; //Hundred-Talent Program of Chinese Academy of Sciences/ ; tsqn202211168//Taishan Scholar Project of Shandong Province/ ; ZR2022JQ20//Natural Science Foundation of Shandong Province/ ; },
abstract = {Periodontitis, a chronic inflammatory disease initiated and sustained by plaque microorganisms and host immune response, remains an intractable oral disease and a leading cause of tooth loss worldwide. Traditional mechanical debridement and adjunctive antibiotic or antiseptic therapy often shows limited efficacy due to the complex anatomical structure, concerns regarding antimicrobial resistance, and poor penetration and retention within the subgingival infection niche. To overcome this limitation, we designed a Mo-N coordinated nanozyme exhibiting synergistic mimetic activities of multiple enzymes, including peroxidase (POD)-like, oxidase (OXD)-like, and catalase (CAT)-like activity. Benefiting from Mo-N coordination and multi-enzyme mimetic behavior, Mo5N6 nanozymes dynamically modulate local oxidative reactions within the gingival sulcus, thereby effectively damaging pathogenic bacteria while avoiding excessive oxidative stress. The nanozymes efficiently suppress anaerobic Gram-negative periodontal pathogens sensitive to elevated reactive oxygen species (ROS), facilitating efficient attenuation of pathogenic stimuli. This strategy not only enhances the periodontal microenvironment but also facilitates the restoration of commensal microbiota and regeneration of periodontal tissues, highlighting the therapeutic potential of Mo5N6 nanozymes in periodontitis treatment.},
}
@article {pmid41955508,
year = {2026},
author = {Chatrizeh, M and Tian, J and Rogers, M and Feturi, F and Wu, G and Firek, B and Nikonov, R and Cass, L and Sheppeck, A and Ojha, L and Carroll, A and Henkel, M and Azar, J and Aneja, RK and Campfield, B and Simon, D and Morowitz, MJ},
title = {Plant-based enteral nutrition outperforms ultra-processed formulas in mitigating consequences of antibiotic-induced dysbiosis.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.199827},
pmid = {41955508},
issn = {2379-3708},
abstract = {Malnutrition, gut inflammation, and antibiotic-induced dysbiosis (AID) are well-recognized risk factors for poor clinical outcomes among critically ill patients. We previously showed that commercially available plant-based enteral nutrition (PBEN) preserves a commensal microbiome compared with commonly used artificial enteral nutrition (AEN). In this study, PBEN was superior to AEN in promoting recovery from antibiotic-induced dysbiosis in mice and humans. PBEN effectively mitigated anemia and leukopenia, restored naïve lymphocyte populations, and reduced bone marrow myeloid expansion. Animals randomized to PBEN also exhibited improved responses to infectious challenges following antibiotic exposure. A pilot clinical study validated these findings, demonstrating increased gut commensals, reduced pathogens, and improved leukocyte balance in critically ill children receiving PBEN compared with AEN. Together, these results suggest that PBEN offers a practical dietary approach to mitigate antibiotic-associated complications and potentially improve clinical outcomes among hospitalized patients requiring supplemental nutrition.},
}
@article {pmid41955569,
year = {2026},
author = {Trunfio, M and Gianella, S and Gaitan, N and Porrachia, M and Gomez-Moreno, V and Lapke, B and Navarrete, A and Wells, A and Smith, D and Little, SJ and Chaillon, A},
title = {Minimal Disruption of the Rectal Microbiome in Acute and Early Untreated HIV Infection.},
journal = {Journal of acquired immune deficiency syndromes (1999)},
volume = {},
number = {},
pages = {},
doi = {10.1097/QAI.0000000000003883},
pmid = {41955569},
issn = {1944-7884},
abstract = {BACKGROUND: Alterations in the gut microbiome have been linked to chronic HIV infection, yet less is known about microbiome dynamics during the earliest phases of HIV acquisition. It remains unclear whether microbial changes precede or follow HIV infection, and whether specific taxa could serve as early biomarkers or modulators of disease progression.<br><br>SETTING: The San Diego Primary Infection Resource Consortium (PIRC), a large HIV resource infrastructure program that enrolled predominantly men who have sex with men in Southern California, USA.<br><br>METHODS: We analyzed rectal swabs from 316 participants, 86 without HIV, 100 with acute (&#x2264;30 days post-infection) and 130 with early (31-180 days) untreated HIV infection. 16S rRNA sequencing was used to characterize bacterial communities. Alpha and beta diversity metrics, and taxon-level relative abundance were compared across groups using generalized linear models and MaAsLin3, adjusting for confounders and correcting for false discovery rate (FDR).<br><br>RESULTS: No significant differences in Shannon and Pielou index or beta diversity were observed by HIV status or stage. However, HIV infection was independently associated with a modest reduction in microbial richness (observed species; p=0.039). Enterocloster clostridioformis was significantly depleted among people with HIV (a&#x3b2; -1.31, FDR p<0.001). Among participants with HIV, relative abundance of Akkermansia muciniphila was positively correlated with plasma HIV RNA levels (a&#x3b2; 0.48, FDR p=0.016).<br><br>CONCLUSION: The rectal bacteriome remains largely preserved during the first six months of untreated HIV infection. Subtle taxon-specific changes may reflect early viro-immunological perturbations but suggest limited diagnostic and prognostic utility of microbiome profiling.},
}
@article {pmid41955745,
year = {2026},
author = {Etesami, H and Schaller, J},
title = {The soil silicon filter: A conceptual model of how mycorrhizal fungi and their microbiome may govern biosilicification and plant-silicon availability.},
journal = {Plant physiology and biochemistry : PPB},
volume = {233},
number = {},
pages = {111235},
doi = {10.1016/j.plaphy.2026.111235},
pmid = {41955745},
issn = {1873-2690},
abstract = {Silicon (Si) plays an important role in plant health and ecosystem function, yet the biological pathways controlling its cycling are often too simplified and underlying mechanisms are not clear. While the plant-centric model of Si uptake and phytolith formation is mostly used, it underestimates the complex role of the soil microbiome. This review synthesizes growing evidence on the importance of the mycorrhizosphere-the zone of interaction between roots, mycorrhizal fungi, and bacteria-as a central processing unit in the terrestrial Si cycle. We develop and evaluate the concept of a "microbial silicon filter" as a working hypothesis, where symbiotic partnerships, particularly between mycorrhizal fungi and their associated bacteria, may collectively influence the Si flux. We line out the mechanisms of mycorrhizal-mediated Si transport and review evidence for bacterial biosilicification alongside the more speculative evidence and open questions regarding fungal (particularly mycorrhizal) biosilicification. Furthermore, we examine potential synergistic microbial weathering of minerals that mobilizes Si and how biofilm matrices may enhance its retention within the hyphosphere. By integrating these processes, we present a more integrated, microbiome-inclusive model of the Si cycle that emphasizes the potential interdependencies between plants, mycorrhizal fungi, and bacteria. This perspective has profound implications, potentially influencing plant stress resilience modulated by Si supply and suggesting a possible, though not yet quantified, role in enhancing long-term carbon sequestration through phytolith formation. Finally, we outline future research directions to unravel the underlying mechanisms of this partnership of plants, mycorrhizal fungi, and bacteria and to harness it for sustainable agriculture and ecosystem restoration. A central focus of these recommendations is the critical need for advanced methodologies-particularly stable isotope tracing and nanoscale secondary ion mass spectrometry (NanoSIMS)-to move from correlative evidence to quantitative, mechanistic understanding of the microbial Si filter.},
}
@article {pmid41955806,
year = {2026},
author = {Lee, EY and Lee, DG and Noh, G and Kwon, S and Shin, H and Shin, Y},
title = {Hierarchical alginate-bentonite beads enable instrument-free pre-analytic enrichment of liter-scale wastewater.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142013},
doi = {10.1016/j.jhazmat.2026.142013},
pmid = {41955806},
issn = {1873-3336},
abstract = {Wastewater-based surveillance (WBS) offers a test-independent window into public community health, but its fidelity depends critically on pre-analytic enrichment that must convert liter-scale, inhibitor-rich influent into microliter analytical inputs without compromising low-titer targets. Here we introduce hierarchical alginate-sulfuric acid-activated bentonite beads (Alg@SAB) that recast pre-analytic enrichment as an interfacial mass-transfer problem. A diffusion-optimized macro-mesoporous scaffold, amine-functionalized surfaces (-NH3[+]), and Ba[2+] crosslinks collectively enable dual-mode capture-electrostatic adsorption and Ba[2+]↔M[n+] cation-exchange-to retain free pathogens and pathogen-metal complexes under passive, pump-free operation, while batch-friendly fabrication from commodity precursors delivers reproducibility with per-test consumables of ∼US$0.06. Alg@SAB retains the two-fold-one-cycle linearity in input viral titer-Ct value while extending instrument-free concentration to the liter scale: 1 L inputs remain measurable where a vacuum-membrane kit fails at ≥ 500 mL; at 100 mL Alg@SAB achieves higher apparent recovery (56%, +27% versus kit). Validation used real municipal wastewater rather than synthetic surrogates, ensuring field realism in matrix complexity and inhibitor profiles. A single-tube, pH-dependent reversible crosslinking chemistry releases nucleic acids in situ while maintaining agreement and collapsing handoffs, enabling low-hardware deployment. Method-dependent microbiome profiling on these raw influent wastewater reveals mechanistically consistent selectivity without systematic inflation of alpha diversity, preserving ecological interpretability under real wastewater plant conditions. By integrating scalable materials engineering with practical deployment, Alg@SAB provides a simple and tunable route to decentralized, interpretable WBS, lowering technical barriers for real-time pathogen monitoring in diverse settings.},
}
@article {pmid41955863,
year = {2026},
author = {Temiz, A and Tascilar, K},
title = {Why we need to maintain a critical view on big data and artificial intelligence predictions.},
journal = {Current opinion in immunology},
volume = {100},
number = {},
pages = {102776},
doi = {10.1016/j.coi.2026.102776},
pmid = {41955863},
issn = {1879-0372},
abstract = {Artificial intelligence (AI) and machine learning are widely promoted as transformative tools for medical practice, yet their impact in daily rheumatology remains limited. This review examines the gap between expectations and reality using historical parallels, conceptual considerations, and recent methodological evidence. Experiences with antioxidant supplementation, vitamin D, the microbiome, and the Human Genome Project illustrate a recurring pattern: early studies report large effects that diminish or disappear in larger, higher-quality studies. Meta-epidemiological work and the 'cursed auction' analogy explain why early and small studies systematically overestimate effects. Conceptually, individualized clinical risk remains a group-based construct, constrained by the reference class problem and irreducible uncertainty. Methodologically, many AI models in rheumatology suffer from small and heterogeneous datasets, overfitting, inadequate handling of missing data, poor calibration, and limited external or prospective validation. The failure of COVID-19 prediction models and the neutral trial of the Ada diagnostic assistant in rheumatology illustrate how strong retrospective performance often collapses in real-world use. In contrast, AI performs well in high signal-to-noise domains with abundant, structured data. Overall, AI can generate valuable insights and support narrowly defined tasks, but it cannot yet overcome the fundamental limits of noisy clinical data and group-based risk. Progress in rheumatology will require realistic expectations, large representative datasets, transparent methods, rigorous validation, and a focus on robust, interpretable tools that improve decisions for populations and well-defined patient subgroups rather than precise individual prediction.},
}
@article {pmid41955934,
year = {2026},
author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM},
title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.},
journal = {The Science of the total environment},
volume = {1030},
number = {},
pages = {181776},
doi = {10.1016/j.scitotenv.2026.181776},
pmid = {41955934},
issn = {1879-1026},
abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.<br><br>METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.<br><br>RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.<br><br>CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.},
}
@article {pmid41955946,
year = {2026},
author = {Jiang, S and Li, T and Lu, J and Cai, F and Pang, G and Liu, J and Liu, D and Shen, Q},
title = {From degradation to alleviation: Trichoderma facilitates plants resisting the PBAT stress through secreting a cutinase-like enzyme.},
journal = {Environment international},
volume = {210},
number = {},
pages = {110228},
doi = {10.1016/j.envint.2026.110228},
pmid = {41955946},
issn = {1873-6750},
abstract = {The ecological impacts of biodegradable plastics like poly (butylene adipate-co-terephthalate) (PBAT) demand urgent investigation due to their unresolved risks to soil-plant systems, including physical interference with root development, disruption of indigenous microbial ecology. While PBAT depolymerization is a prerequisite for its removal, the slow and inefficient breakdown of these polymers in soil often results in the persistent accumulation of phytotoxic monomers, creating a bottleneck for biological remediation. In this study, through transcriptomic and phylogenetic analyses, we identified a key secreted hydrolase CUT2, belonging to a distinct clade of cutinase-like polyester hydrolases. Overexpression of cut2 (OEThcut2) significantly enhanced PBAT depolymerization, resulting in 27.0% and 22.4% increases in the release of terephthalic acid (TPA) and butanediolic acid (BTA) compared to the wild-type strain, respectively. The direct catalytic activity of purified CUT2 was confirmed through vitro film weight-loss assays with a degradation rate of 4.3% observed. In pot experiments, integrated multi-omics analysis revealed that the OEThcut2 strain reconfigured the rhizosphere microbial community and activated the aromatic degradation pathways, coinciding with the attenuated accumulation of degradation monomers. Furthermore, the enrichment of carbohydrate-active enzymes (CAZys) and the reduction of monomer burdens which revitalized the tricarboxylic acid cycle (TCA) and normalized redox homeostasis thereby clearing the metabolic bottleneck for intermediate turnover. Complementary monomer-exposure assays established that the reduction of PBAT monomers is critical for alleviating plant oxidative stress and growth inhibition. These findings provide a depolymerization to detoxification framework that links fungal enzymatic activity to rhizosphere metabolic recovery, offering a robust strategy for mitigating biodegradable plastic toxicity in agroecosystem.},
}
@article {pmid41956062,
year = {2026},
author = {Flury, JD and Schwartz, DJ},
title = {Don't keep this endopeptidase on the DL.},
journal = {Cell host &amp; microbe},
volume = {34},
number = {4},
pages = {551-553},
doi = {10.1016/j.chom.2026.03.007},
pmid = {41956062},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant, Premature ; *Sepsis/microbiology/prevention &amp; control ; Infant, Newborn ; *Nod2 Signaling Adaptor Protein/metabolism/genetics ; *Endopeptidases/metabolism ; *Bacteria/enzymology ; },
abstract = {Gut-derived bacterial DL-endopeptidase may confer protection from late onset sepsis (LOS) in preterm infants. In this issue of Cell Host &amp; Microbe, Shen et al. identified delayed gut microbiome development in preterm infants as a risk factor for LOS and proposed a protective regulatory response by NOD2.},
}
@article {pmid41956066,
year = {2026},
author = {Potiron, A and Francken, JC and El Aidy, S},
title = {Rethinking microbiome health through functional dynamics.},
journal = {Cell host &amp; microbe},
volume = {34},
number = {4},
pages = {562-566},
doi = {10.1016/j.chom.2026.03.005},
pmid = {41956066},
issn = {1934-6069},
mesh = {Humans ; *Microbiota/physiology ; *Host Microbial Interactions/physiology ; *Gastrointestinal Microbiome ; Health ; },
abstract = {Translation in microbiome science is limited by static concepts of health that obscure dynamic host-microbe processes. We propose adaptive coherence: the capacity of host-microbiome systems to sustain integrated function through reorganization. This reframes health as emergent and relational, directing measurement toward system adaptability, functional integrity, and network interactions.},
}
@article {pmid41956067,
year = {2026},
author = {Dillen, J and Dricot, CEMK and Croatti, V and Lebeer, S},
title = {The female urogenital microbiome: Ecological insights, therapeutic strategies, and molecular mechanisms.},
journal = {Cell host &amp; microbe},
volume = {34},
number = {4},
pages = {567-587},
doi = {10.1016/j.chom.2026.03.015},
pmid = {41956067},
issn = {1934-6069},
mesh = {Humans ; Female ; *Microbiota/physiology ; *Vagina/microbiology ; Probiotics/therapeutic use ; *Urogenital System/microbiology ; Host Microbial Interactions ; },
abstract = {Microbiome-based interventions for female urogenital health have gained attention, particularly in strategies aimed at restoring lactobacilli dominance to reduce infection and improve reproductive outcomes. These approaches include defined probiotic strains, engineered microbial consortia, and vaginal microbiota transfer. Observational studies have provided ecological insights into the composition and dynamics of the vaginal microbiome; its associations with infections, inflammation, and reproductive complications; and its interplay with urinary and mucosal niches. These data establish a correlative framework linking microbial community structure to health and disease. However, the efficacy of current interventions remains constrained by an incomplete mechanistic understanding of host-microbiome and microbe-microbe interactions. Recent discoveries highlight the role of vaginally derived microbial molecules in modulating host immune responses, stabilizing microbial communities, and influencing disease outcomes. These mechanistic insights provide a basis for the rational design of microbiome-based therapies. This review synthesizes clinical, observational, and mechanistic evidence and outlines research priorities for translation into clinical practice.},
}
@article {pmid41956093,
year = {2026},
author = {Cao, Z and Zuo, W and Wang, L and Dai, L},
title = {Spatial mapping of microbial communities by an integrated automation platform of sequential FISH.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101381},
doi = {10.1016/j.crmeth.2026.101381},
pmid = {41956093},
issn = {2667-2375},
abstract = {Spatial mapping of microbial communities at single-cell resolution is opening up dimensions to understand microbiome organization and function. However, current fluorescence in situ hybridization (FISH) methods for microbiomes are limited by multiplexity and scalability. Here, we present the sequential error-robust FISH spatial mapping platform (SEER-Map) for fully automated imaging of complex microbial communities. We show that an integrated platform of fluidics control and fluorescence microscopy can perform 40 rounds of sequential FISH. We apply SEER-Map to profile complex microbial communities colonized on plant roots and identify distinct spatial patterns and species co-occurrence at the micron-scale. Our work establishes SEER-Map as a high-throughput and scalable platform for high-resolution spatial profiling of microbiomes.},
}
@article {pmid41956108,
year = {2026},
author = {Kadandelu, M and Periya, S and Rekha, PD and Raghu, SV},
title = {Gut-brain axis mediated therapeutic intervention to mitigate the epileptogenesis: insights from Drosophila melanogaster.},
journal = {Reviews in the neurosciences},
volume = {},
number = {},
pages = {},
pmid = {41956108},
issn = {2191-0200},
abstract = {Drug-resistant epilepsy (DRE) is a prominent concern in the management of recurrent seizures. Anti-seizure medications (ASM), surgical intervention, and neurostimulation are a few classical remedial measures of epilepsy. Nevertheless, DRE requires immense investigation, a comprehensive understanding of holistic management, and additional therapeutic effects. Dysbiosis, an imbalance of the gut microbiome, is the foremost concern associated with various neurological disorders. In epilepsy, the gut microbiome plays a pivotal role in its pathophysiology, unveiling new avenues for microbiome-mediated strategies to treat epileptic patients. Furthermore, the differential gut microbial composition in epileptic patients serves as a cornerstone for advanced research to delineate the influence of each bacterial species on epilepsy. Drosophila melanogaster, a simple model organism with an evolutionarily conserved gut microbiome composition, can be efficiently deployed to scrutinize the role of discrete microbes and their influence on the gut-brain axis, impacting neurological disorders. In this review, the role of distinct bacterial species in influencing epileptic conditions and how model organisms like Drosophila can be employed to explore this realm are deliberated as a comprehensive overview.},
}
@article {pmid41956336,
year = {2026},
author = {Huang, S and Ou, Y and Zhuang, W and Huang, J and Wang, B and Li, Z and Huang, H},
title = {Mapping the immune landscape of PCa: From tumor microenvironment to therapeutics.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189586},
doi = {10.1016/j.bbcan.2026.189586},
pmid = {41956336},
issn = {1879-2561},
abstract = {Prostate cancer (PCa) remains a leading cause of cancer-related mortality in men, yet its response to immunotherapy is notably limited compared to other solid tumors. This resistance stems primarily from a highly immunosuppressive tumor microenvironment (TME), characterized by "cold" tumor features such as low mutational burden, scarce cytotoxic T cell infiltration and extensive regulatory cell populations. Building upon the "tumor ecosystem" concept, we integrate emerging insights from single-cell and spatial transcriptomics to decode the spatiotemporal heterogeneity of the PCa ecosystem. We specifically highlight the underappreciated "neural-immune-microbiome" axis-a triangular regulatory network wherein sympathetic nerves suppress T cell motility, intratumoral microbiota drive chronic inflammation, and metabolic reprogramming creates lipid-mediated immune paralysis. We further dissect how cell-type specific remodeling mechanisms, particularly TREM2+ macrophage-mediated metabolic symbiosis, drive the transition from hormone-sensitive to castration-resistant disease. Furthermore, we critically assess how standard of care (ADT, chemotherapy, radiotherapy) and emerging agents (PARPi, HDACi) reprogram the immune landscape with time-dependent, often paradoxical effects. Finally, we propose a roadmap for precision oncology, emphasizing that future success lies in "ecological editing"-biomarker-driven patient stratification and rational combination strategies to overcome the physical and biological barriers of the TME.},
}
@article {pmid41956379,
year = {2026},
author = {Wang, Y and Zhang, S and Cai, J and Shao, R and Zheng, F and Wang, Y and Xu, C and Yang, Y and Li, L},
title = {Reducing cadmium bioavailability in soil by micronutrient sulfates: Insights from duodenal transporter expression and intestinal microbiota in a mouse model.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124460},
doi = {10.1016/j.envres.2026.124460},
pmid = {41956379},
issn = {1096-0953},
abstract = {Micronutrient amendments have the potential to mitigate cadmium (Cd) accumulation in crops; however, their effects on soil Cd bioavailability remain unclear. To address this knowledge gap, mice were fed a diet containing 10% (w/w) amended Cd-contaminated calcareous soil (amendments: MnSO4, ZnSO4, FeSO4, or Na2SO4) for 15 days. Cd bioavailability was then assessed by measuring Cd accumulation in the kidney and liver (primary endpoints), duodenal transporter expression, fecal microbiota composition, and soil properties. The results demonstrated that all micronutrient sulfate treatments increased the acid-extractable fraction of Cd in soil. Concurrently, soil-available Mn and Zn increased by 94.79% and 89.31%, respectively, following their corresponding sulfate amendments, and available sulfur rose by 0.90- to 21.32-fold across all treatments. Compared with the control, Cd concentrations in the kidney and liver of mice treated with Mn, Zn, Fe, or Na sulfates significantly decreased by 25.95-35.36% and 20.75-35.30%, respectively, and Cd relative bioavailability (Cd-RBA) declined by 27.02-34.13% (p < 0.05). Significant negative correlations were observed between Cd-RBA and molar ratios of nMn/nCd, nFe/nCd, and nZn/nCd in the soil and mouse tissues. Further analyses identified a three-part protective mechanism: (1) Intestinal antagonism: downregulation of duodenal ZIP8 expression by Mn, Zn, and Fe treatments (by 66.49-88.30%), thereby limiting Cd uptake; (2) Microbiome restoration: significant reduction of the Firmicutes/Bacteroidota (F/B) ratio compared with the control group, with reductions of 6.02% (Mn), 15.53% (Zn), 51.11% (Fe), and 17.75% (Na); (3) Enterohepatic elimination: enhanced formation of Cd-S complexes and the resulting increase in fecal Cd excretion across all treatments (by 41.03-60.77%). In conclusion, micronutrient sulfate amendments mitigate Cd bioavailability through a concerted mechanism, involving soil chemical modification, luminal complexation, physiological antagonism, modulation of transporter gene expression, and microbiome-mediated enteric elimination.},
}
@article {pmid41956455,
year = {2026},
author = {Ozduran, E and Gezmen-Karadag, M},
title = {Dietary Fiber in Sport: Implications for Performance and Body Composition Optimization.},
journal = {International journal of sport nutrition and exercise metabolism},
volume = {},
number = {},
pages = {1-13},
doi = {10.1123/ijsnem.2025-0170},
pmid = {41956455},
issn = {1543-2742},
abstract = {Although dietary fiber is widely recognized for its health benefits in the general population, including reduced risk of cardiovascular disease and improved metabolic regulation, its role in athletic performance and recovery remains comparatively underexplored. Current sports nutrition guidelines lack specific recommendations for fiber intake, despite evidence linking adequate consumption to gut microbiome stability, immune modulation, and body composition optimization. Athletes face unique physiological demands that influence gastrointestinal tolerance, nutrient absorption, and energy availability, particularly under high training loads. Although excessive fiber intake may lead to gastrointestinal discomfort or reduced caloric intake, moderate and periodized consumption has been associated with enhanced immune function, improved energy metabolism, and preservation of skeletal muscle mass. Recent findings suggest potential benefits in attenuating exercise-induced inflammation and regulating substrate utilization. Nevertheless, observational data indicate that many athletes fail to meet general population intake targets, often due to precompetition dietary restrictions or concerns about digestive comfort. This review critically synthesizes current evidence on the physiological impacts of dietary fiber in athletic populations, focusing on gastrointestinal health, immune function, body composition, and performance outcomes. It further outlines practical, evidence-based strategies to optimize intake according to individual needs and sport-specific demands, including fiber periodization, source selection, and gradual adaptation.},
}
@article {pmid41956649,
year = {2026},
author = {Yan, Z and Song, F and Zhao, J and Zhang, M and Guan, J and Li, C and Li, D and Tian, H},
title = {Association between microbiome dynamics and aroma evolution in fermented Chinese white pears (Pyrus × bretschneideri): An integrated volatilomics and microbiome analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 2},
pages = {118959},
doi = {10.1016/j.foodres.2026.118959},
pmid = {41956649},
issn = {1873-7145},
mesh = {*Odorants/analysis ; *Fermentation ; *Microbiota ; *Volatile Organic Compounds/analysis ; *Pyrus/microbiology/chemistry ; Saccharomyces cerevisiae/metabolism ; *Fermented Foods/microbiology/analysis ; Food Microbiology ; Butylene Glycols/analysis ; *Fruit/microbiology/chemistry ; Bacteria/classification/metabolism ; },
abstract = {The flavor of pear cider exhibits regional features, with insufficient and unstable aroma constituting key quality issues. The role of its characteristic aroma and the contribution of native microorganisms to regional distinctiveness remain under explored. This study compared the brewing characteristics of representative white pears, conducted an in-depth analysis of aroma compound evolution and their relationship with microbial communities throughout fermentation, and successfully screened strains with aroma-enhancing function. Results indicated that "Xuehua" possessed the optimal processing quality. Six characteristic fermentation aroma were identified, including 2,3-butanediol, hexanal, ethyl caprylate, etc. The core microbes gradually converged, including Saccharomyces cerevisiae, Hanseniaspora, Leuconostoc, etc. Alcohol and total acid correlated strongly with fungi, while reducing sugars correlated strongly with bacteria. Except for hexanal, the characteristic aroma showed positive correlations with F:OTU235. Ethyl caproate and ethyl caprylate correlated positively with B:OTU118. Saccharomyces cerevisiae (F:OTU235) and Lactobacillus plantarum (B:OTU118) were screened selectively and contributed to aroma accumulation.},
}
@article {pmid41956809,
year = {2026},
author = {Li, X and Xie, M and Kang, JX and Chen, Y and Han, J and Chen, Y and Chen, Q and Yu, T and Liu, S and Ouyang, Z and Sun, Q and Li, K and Zhang, S and She, J and Yu, J},
title = {Bifidobacterium catenulatum boosts anti-PD-1 efficacy in microsatellite stable colorectal cancer via activating CD8[+] T cells.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336025},
pmid = {41956809},
issn = {1468-3288},
abstract = {BACKGROUND: Certain gut bacteria are associated with improved responses to immunotherapy.<br><br>OBJECTIVE: We aim to identify bacteria that inhibit colorectal cancer (CRC) progression and enhance immunotherapy efficacy.<br><br>DESIGN: The abundance of bacteria in CRC patients was evaluated in our in-house cohorts and validated in published datasets. The effect of candidate bacterium with anti-PD-1 therapy was determined in two syngeneic mouse models of MC38 (microsatellite instability-high) and CT26 (microsatellite stable, MSS), transgenic Apc [min/+] mice and azoxymethane/dextran sulfate sodium (AOM/DSS)-induced CRC tumourigenesis model. Immune landscape changes were identified by multicolour flow cytometry and immunohistochemistry staining. Metabolomic profiling was performed on stool, serum and tumour tissues.<br><br>RESULTS: Bifidobacterium catenulatum was significantly depleted in stool samples of 110 CRC patients compared with 112 healthy controls, which was further validated in 3 published metagenomic datasets comprising 198 CRC patients and 176 normal subjects. Oral administration of B. catenulatum inhibited tumour growths in multiple CRC models including MC38 and CT26 syngeneic models, Apc[min/+] mice&#x2009;and AOM/DSS-induced CRC. Notably, B. catenulatum synergised with anti-PD-1 therapy through enhancing intratumoural CD8[+] T cell infiltration in MSS CRC models of Apc[min/+] mice&#x2009;and CT26 allografts. B. catenulatum-derived acetate was identified as the functional metabolite. Mechanistically, acetate directly bound to MCT-4 in CD8[+] T cells and activated mitogen-activated protein kinase signalling. Pharmacological and genetic MCT4 ablation abolished acetate-mediated CD8[+] T cell activation in vitro.<br><br>CONCLUSION: B. catenulatum suppresses colorectal tumourigenesis through generating acetate, which also improves anti-PD-1 efficacy through activating CD8[+] T cells in MSS CRC. B. catenulatum is a potential adjuvant to improve immunotherapy against CRC.},
}
@article {pmid41956875,
year = {2026},
author = {Ye, M and Song, C},
title = {Microbiome eavesdropping: root-knot nematodes decode rhizosphere volatile dialogues.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2026.03.007},
pmid = {41956875},
issn = {1878-4372},
abstract = {Root-knot nematodes navigate the underground chemical landscape to find their hosts. Building on Wu et al.'s discovery that plant metabolites shape microbial cues guiding nematode behavior, this commentary explores how rhizosphere chemical communication integrates plant, microbial, and parasite interactions within a shared 'information network'.},
}
@article {pmid41957048,
year = {2026},
author = {Wang, X and Song, Y and Zhao, W and Liu, Y and Fu, Y and Zhang, Y and Zhao, Q and Miao, M and Zhao, W and Wang, X and Li, Z},
title = {Cinnamaldehyde mitigates MASLD through SIRT1/FOXO1-induced autophagy and synergistic gut microbiota modulation.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00815-6},
pmid = {41957048},
issn = {2396-8370},
support = {ZYYZDXK-2023005//National Administration of Traditional Chinese Medicine Key Discipline Construction Project of High-Level TCM/ ; 82304831//National Natural Science Foundation of China/ ; 242300421090//Henan Science Fund for Excellent Young Scholars/ ; 2023TQ0109, GZB20230196//China Postdoctoral Science Foundation/ ; 232301420077//Associates Fund of Henan Province science and technology research and development program/ ; 2025HYTP092//Young Talent Support Program of Henan Association for Science and Technology/ ; NA (2024)//Central Plains Science and Technology Innovation Young Top Talent Project/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a global health burden with limited therapeutic options. Cinnamomum cassia, a medicinal-food homologous plant, contains principal bioactive cinnamaldehyde (CA), whose anti-MASLD mechanisms require clarification. ‌This study employed both a high-fat diet (HFD)-induced MASLD model and a free fatty acid (FFA)-stimulated cell model. CA administration attenuated intracellular lipid accumulation in vitro and ameliorated both hepatic steatosis and systemic hyperlipidemia in vivo, while inhibiting hepatic lipid peroxidation. Mechanistically, integrated RNA-seq, network pharmacology, siRNA, immunofluorescence, and transmission electron microscopy analyses identified the SIRT1/FOXO1-autophagy axis as CA's key regulatory pathway. Gut microbiome profiling revealed CA's capacity to ameliorate HFD-induced dysbiosis, particularly enriching Lachnospiraceae_NK4A136. Fecal microbiota transplantation (FMT) and Spearman correlations link serum lipids and hepatic injury factors to gut microbiota, indicating partially microbiota-mediated metabolic modulation by CA. Collectively, CA ameliorates MASLD through coordinated autophagy enhancement and microbial homeostasis restoration, holding promise as a functional food ingredient for ‌metabolic liver disease prevention.},
}
@article {pmid41957179,
year = {2026},
author = {Li, X and Zhao, K and Chen, J and Ni, Z and Li, L and Chen, Y and Shi, W and Zhang, Y and Gao, X and Wang, C and Gu, L and Dong, Y and Shi, J and Liu, Y and Su, L and Xue, YX and Sun, H},
title = {The Cognitive benefits of nitrate in patients with alcohol use disorder: unraveling the oral microbiome ectopic colonization pathway.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {41957179},
issn = {1476-5578},
support = {81971235//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82071498//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82471514//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Our prior research revealed that dietary nitrate (NO3[-]) may mitigate alcohol-induced cognitive impairment through oral microbiota modulation and attenuation of inflammatory responses in mice. While alcohol use disorder (AUD) is known to associate with cognitive decline and gut dysbiosis, the therapeutic potential of nitrate supplementation in ameliorating these effects remains to be elucidated. In this randomized, double-blind, placebo-controlled pilot trial (NCT05963659), 70 AUD patients received either nitrate-rich beetroot juice or placebo for 14 days. Primary outcomes were spatial memory measured by Cambridge Neuropsychological Test Battery. Oral and gut microbiota were analyzed before and after intervention by 16S rRNA sequencing. To establish causality, germ-free (GF) mice were colonized with pre- and post-nitrate intervention saliva samples from AUD patients, followed by microbiota profiling across gastrointestinal regions. The mean difference in Delayed Matching to Sample (all delays) change between the nitrate consumption group and the placebo group after intervention was 9.784 (95%[CI], 1.85-17.72, P = 0.016), as analyzed using a generalized linear mixed model. Nitrate supplementation induced distinct shifts in oral microbiota, while gut microbiota exhibited less pronounced changes. GF mice receiving pre-intervention microbiota exhibited elevated Klebsiella abundance throughout the gut. Mechanistically, nitrate attenuated systemic inflammation, enhanced intestinal barrier integrity, and improved cognitive performance in mice. Dietary nitrate enhances cognitive function in AUD patients, partially mediated by ectopic colonization of oral microbiota. Our findings identify specific oral bacteria (e.g., Klebsiella) as key contributors to alcohol-induced cognitive impairment and suggest promising therapeutic potential for microbiota-targeted interventions in AUD.},
}
@article {pmid41957208,
year = {2026},
author = {Metz, BN and Gallagher, P and Profet, P and Raymann, K and Tarpy, DR},
title = {Impact of Two Common Beekeeper-Applied Chemicals on Honey Bee Queen Fecundity and Gut Microbial Communities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02755-w},
pmid = {41957208},
issn = {1432-184X},
support = {2022-67013-42296//National Institute of Food and Agriculture/ ; 2022-67013-42296//National Institute of Food and Agriculture/ ; },
}
@article {pmid41957267,
year = {2026},
author = {Baruch, EN and Ajami, NJ and Wargo, JA},
title = {Cultivating the microbiome to enhance cancer immunotherapy.},
journal = {Nature reviews. Clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {41957267},
issn = {1759-4782},
}
@article {pmid41957274,
year = {2026},
author = {Kotsiliti, E},
title = {Diet-microbiome associations.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
pmid = {41957274},
issn = {1759-5053},
}
@article {pmid41957291,
year = {2026},
author = {Yang, M and Fang, J and Liao, Q},
title = {Comment on: "Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens"-a call to disentangle clostridium scindens' bile acid metabolism from glucocorticoid modulation in SLE pathogenesis.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {41957291},
issn = {1434-9949},
}
@article {pmid41957416,
year = {2026},
author = {Hunter, AK and Adair, K and Horgan, A and Jordan, J and Stadler, DD and Bohannan, BJM},
title = {Impact of dietary protein quantity on the non-dysbiotic human microbiome: a controlled feeding study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46663-y},
pmid = {41957416},
issn = {2045-2322},
}
@article {pmid41957526,
year = {2026},
author = {Siow, TY and Wong, AM and Fang, JT and Chiu, CH and Yeh, YM and Cheng, ML and Lo, CJ and Lin, SN and Lin, CP and Toh, CH},
title = {Plasma acetic acid mediates the relationship between gut microbiome and various health measures in older adults.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01566-x},
pmid = {41957526},
issn = {2730-664X},
support = {CORPG3J0371//Chang Gung Memorial Hospital (CGMH)/ ; XMRPG3L102//Chang Gung Memorial Hospital (CGMH)/ ; },
abstract = {BACKGROUND: Short-chain fatty acids are believed to mediate microbiome-host interactions. Acetic acid is the most abundant systemic short-chain fatty acid, but knowledge about its physiological functions comes mainly from rodent experiments, with limited human research particularly in the aging population.<br><br>METHODS: In this cross-sectional observational study, we examined the association between the gut microbiota and plasma acetic acid, specifically investigating the mediating effect of plasma acetic acid on the relationship between the gut microbiota and blood lipid profile, body composition, brain gray matter volume, and cognitive performance in older adults. The gut microbiome was profiled using full-length 16S rRNA gene sequencing to enable taxonomic classification.<br><br>RESULTS: Here we show that specific gut microbial co-abundance group is associated with plasma acetic acid levels. Higher plasma levels of acetic acid are associated with lower plasma triglyceride levels, higher high-density lipoprotein cholesterol levels, lower body mass index, lower body fat mass, higher thalamic volume, and higher cognitive performance in certain domains. Additionally, we show that plasma acetic acid mediates the relationship between gut microbiome on these health measures.<br><br>CONCLUSIONS: This study identifies gut microbial group linked to plasma acetic acid and demonstrates its potential mediating role between the gut microbiome, blood lipid profile, brain volume and cognitive function in older adults. These insights pave the way for future research and highlight the potential of acetic acid as an intervention target for metabolic and neurological diseases, contributing to strategies that promote healthy aging.},
}
@article {pmid41957655,
year = {2026},
author = {Sampath, V and Lee, K and Kim, M and Kim, YS and Min, DH and Han, K and Cho, S and Kang, DK and Kim, IH},
title = {Response of gut microbiome and metabolomic profiles to POLYCAN, a β-glucan derived from Aureobasidium pullulans SM-2001 in beagles.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41957655},
issn = {1674-9782},
abstract = {BACKGROUND: The importance of glucan additives has been widely recognized in farm animals. Yet the precise role of POLYCAN, a β-glucan derived from the black yeast Aureobasidium pullulans SM-2001, remains limited in companion animals. Therefore, this study aims to evaluate its effect on performance, nutrient digestibility, hematology, and the gut microbiome and serum metabolites in beagle dogs.<br><br>METHODS: Eight healthy male beagle dogs (8&#xa0;months old; 10.70&#x2009;&#xb1;&#x2009;1.79&#xa0;kg body weight; 3.00&#x2009;&#xb1;&#x2009;0.15 body condition score) were enrolled in a 10-week study comprising two phases: Phase 1 (weeks 0-4) and Phase 2 (weeks 6-10), separated by a 2-week washout period. The dogs were divided into two groups and fed a control (CON), basal diet and CON diet supplemented with 1,000&#xa0;mg/d of POLYCAN. Each of two diets were provided using a cross over design for eight weeks, with four beagles assigned to each treatment. During the washout period, all dogs were fed only the commercial basal diet.<br><br>RESULTS: Throughout the experimental period, POLYCAN supplementation did not affect growth performance, nutrient digestibility, or fecal pH in beagles. However, serum calcium, insulin-like growth factor-1 (IGF-1), growth hormone, and immunoglobulin G (IgG) concentrations were significantly higher (P&#x2009;<&#x2009;0.05) in the POLYCAN-supplemented group. Alpha-diversity indices of microbial richness and evenness, as well as beta-diversity based on Bray-Curtis dissimilarity and unweighted UniFrac distances, showed no significant differences between treatment group. At the phylum level, Actinobacteria and Proteobacteria were more abundant in the POLYCAN group, followed by Fusobacteria and Bacteroidota. At family level, Lachnospiraceae, Ruminococcaceae, Coriobacteriaceae, Lactobacillaceae, Peptostreptococcaceae, and Erysipelotrichaceae exhibited higher relative abundances. Furthermore, the core gut microbiota at genus level was dominated by Micrococcus and Fusobacterium. Untargeted metabolomic analysis also revealed distinct group separation, identifying key metabolites including lumichrome, D-mannitol, and 2'-deoxycytidine. Pathway enrichment analysis indicated alterations in pyrimidine, histidine, and bile acid metabolism with higher metabolite abundance observed in the POLYCAN-treated group.<br><br>CONCLUSION: Overall, our findings validate that adding 1,000&#xa0;mg/d POLYCAN to canines' diet could serve as a functional nutraceutical to enhance their immune and gut health without affecting growth and digestion.},
}
@article {pmid41765966,
year = {2026},
author = {Kroon, MAGM and Wortelboer, K and Davids, M and Swart, EL and van Tellingen, O and Nieuwdorp, M and D'Haens, GRAM and van Laarhoven, HWM and de Boer, NKH and Kemper, EM},
title = {Effect of curcumin on the gut microbiota of patients with ulcerative colitis, Crohn's disease and healthy participants.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41765966},
issn = {2045-2322},
abstract = {UNLABELLED: Curcumin exhibits anti-inflammatory properties, but clinical evidence is limited, in part because of its low systemic bioavailability. Nevertheless, its limited absorption may favor local activity in the gut, where it could influence inflammatory bowel disease via microbiota modulation. This study assesses the impact of curcumin on gut microbiota diversity, as well as clinical and biochemical parameters in patients with ulcerative colitis, and Crohn’s disease in remission and healthy individuals. In a single-center, open-label, single-arm study, 29 male participants aged 18–65 were included. Participants received 3 g of curcumin twice daily for 8 weeks. Blood, urine, and fecal samples were collected at baseline, 4 weeks, and 8 weeks. Clinical and biochemical parameters, along with curcumin plasma, urine, and fecal concentrations, were assessed. Microbiome diversity was analysed using 16 S rRNA amplicon sequencing. The study was registered in the Dutch Clinical Trial Register with ID NL8770. Twenty-nine participants completed the study. Curcumin was well tolerated with stable clinical scores (SSCAI ≤ 2, HBI ≤ 5). Plasma levels were near the lower limit of quantification, while fecal levels were markedly higher. No significant changes in alpha-diversity were found. A temporary shift in beta-diversity appeared at 4 weeks but reversed by week 8. Curcumin caused only transient microbiota changes and slight alterations in taxa abundance, suggesting limited potential for sustained microbiota modulation in IBD management. Clinical trial registration: The study was registered in the Dutch Clinical Trial Register with ID NL8770.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42095-w.},
}
@article {pmid41943414,
year = {2026},
author = {Yan, D and Zuo, P and Lin, M and Li, S},
title = {The Changes of Microbiome Attached on Clear Aligners after Drinking Coca-Cola.},
journal = {Polish journal of microbiology},
volume = {75},
number = {1},
pages = {109-118},
pmid = {41943414},
issn = {2544-4646},
mesh = {Humans ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Male ; Adult ; *Carbonated Beverages/microbiology ; },
abstract = {This study aimed to investigate the changes in the microbiome on the inner surface of clear aligners following the consumption of Coca-Cola. The pH value and bacterial composition on the inner surface of clear aligners were assessed over five wearing cycles in three groups of subjects: those with a normal diet (Group A), those who drank Coca-Cola while wearing the aligners (Group C), and those who drank Coca-Cola after removing the aligners (Group B). Microbial analysis was performed using 16S rRNA gene sequencing and operational taxonomic unit (OTU) abundance profiling. The pH of the fluid inside the aligners significantly decreased immediately after Coca-Cola consumption (0 hour) in Groups B and C (p < 0.05). Group B exhibited the most pronounced decline in pH and alpha diversity at 12 hours, along with the highest beta diversity among the groups (p < 0.05). In Group A, the relative abundances of the phylum Actinobacteria was highest at 0 hour, Bacteroidetes at 12 hours, and class Actinobacteria, Gammaproteobacteria, and species Haemophilus influenzae peaked at 24 hours; conversely, Neisseria subflava showed the lowest abundance compared to Groups B and C (p < 0.05). Compared to Group C, Group B demonstrated higher levels of phylum Fusobacteria at 4 hours and 12 hours, and lower Actinobacteria abundance at 8 hours (p < 0.05). Consumption of Coca-Cola induces unfavorable changes in the microbiome on the inner surface of clear aligners. Notably, drinking Coca-Cola without wearing the aligners resulted in a lower pH and greater microbial imbalance, especially at 12 hours post-consumption.},
}
@article {pmid41943415,
year = {2026},
author = {Zhou, B and Liu, J and Li, L and Yu, J and Sun, X and Wang, J and Shang, S},
title = {Comparative Analysis of Rhizosphere Bacteria of Phragmites australis and Suaeda salsa (L.) Pall. on Chenier Islands.},
journal = {Polish journal of microbiology},
volume = {75},
number = {1},
pages = {55-74},
pmid = {41943415},
issn = {2544-4646},
mesh = {*Rhizosphere ; *Chenopodiaceae/microbiology ; *Poaceae/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; Microbiota ; Phylogeny ; Islands ; },
abstract = {The Chenier Islands are depositional areas within intertidal zones, characterized by unique soil textures and distinctive environmental conditions that shape specific vegetation distribution patterns. However, the adaptive mechanisms of Phragmites australis (common reed) and Suaeda salsa (L.) Pall. (common seepweed) two prevalent plant species in this region-in saline stress environments, as well as the composition and functional characteristics of their rhizosphere bacterial communities, remain largely unclear. In this study, rhizosphere soil samples were collected from common reed and common seepweed. DNA was extracted and subjected to high-throughput sequencing to analyze the composition and predictive functional profiles of the rhizosphere microbial communities. The results indicated that no significant differences were observed in the alpha diversity indices (Chao1, ACE, Simpson, and Shannon), indicating similar microbial species richness and evenness in the rhizospheres of common reed and common seepweed. Taxonomic analysis at the phylum level showed that the dominant bacterial phyla shared by both plants were Proteobacteria, Bacteroidota, Chloroflexota, and Actinomycetota. Notably, Acidobacteriota and Cyanobacteria were uniquely enriched in the common reed and common seepweed rhizospheres, respectively. At the genus level, the microbial communities of both plants were largely composed of unclassified taxa and minor groups, with Zeaxanthinibacter being the only cultivable dominant genus identified. Principal Coordinates Analysis (PCoA) explained 75.02% of the total β-diversity variance, and the clear separation of samples along the first coordinate axis revealed visually distinct community structures between the two plants. PERMANOVA further confirmed that plant species significantly influenced microbial community assembly, with a moderate explanatory strength (R[2] = 0.205, p = 0.008). Integrated results from LEfSe, PICRUSt2, and FAPROTAX analyses demonstrated that common seepweed rhizospheres were enriched with 19 photosynthesis-related biomarkers, suggesting a stronger photoautotrophic potential compared to common reed. In contrast, the common reed rhizosphere retained only two oligotrophic degraders Acidobacteriota and Chloroflexota. Although PICRUSt2 predictions indicated high overlap in core metabolic pathways between the two plants, FAPROTAX profiling revealed markedly divergent energy-acquisition strategies. Specifically, the common seepweed microbiome exhibited a "photoautotrophy nitrogen fixation" coupling strategy, whereas common reed relied predominantly on a "chemoheterotrophy nitrate reduction" pathway, reflecting niche partitioning in the saline environment. It should be noted that functional predictions derived from PICRUSt2 and FAPROTAX are computational inferences rather than empirical measurements, and thus mechanistic interpretations should be treated with caution. This study identifies a rhizosphere bacterial community assembly pattern characterized by "structural differentiation but functional convergence" offering valuable insights into microbial-mediated plant adaptation to saline stress.},
}
@article {pmid41943876,
year = {2026},
author = {Šunić, I and Šarac, J and Havaš Auguštin, D and Pozdniakova, S and Ferguson, RMW and Jergović, M and Visentin, D and Borràs, S and Archer, E and Henderson, DK and Vitko, S and Ašić, A and Bošnjaković, A and Maglica, &#x17d; and Viegas, C and Novokmet, N and Karlović, N and Marjanović, D and Muszyński, A and Liu, Y and Karisola, P and Alenius, H and Krych, L and Lovrić, M},
title = {The Indoor Microbiome: Sampling, Analysis and Emerging Trends.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70272},
pmid = {41943876},
issn = {1758-2229},
support = {101057497//European Union's Horizon Europe research and innovation programme/ ; 101057779//European Union's Horizon Europe research and innovation programme/ ; 101056883//the European Union/ ; 22.00324//Swiss State Secretariat for Education, Research and Innovation/ ; 10040524//United Kingdom Research and Innovation/ ; APP2017786//Australian National Health and Medical Research Council/ ; APP2008813//Australian National Health and Medical Research Council/ ; 101057693//European Union's Call on Environment and Health (HORIZON-HLTH-2021-ENVHLTH-02)/ ; /AMS_/Academy of Medical Sciences/United Kingdom ; },
mesh = {*Microbiota ; *Fungi/isolation &amp; purification/genetics/classification ; *Air Pollution, Indoor/analysis ; *Bacteria/genetics/classification/isolation &amp; purification ; *Air Microbiology ; Humans ; Dust/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Indoor spaces contain diverse microbial communities that shape human health. These microorganisms are particularly relevant to respiratory diseases, including asthma and allergies. Despite growing recognition of the importance of indoor microbial exposures, research in this field is slowed by differences in methods. These inconsistencies make it difficult to compare results and draw conclusions. This systematic review analyses 106 studies published between 2000 and 2025 that investigated indoor microbiomes in dust, air, and other matrices across homes, schools, and other built environments. We assessed sampling strategies, DNA extraction protocols, sequencing technologies, and bioinformatic pipelines, identifying trends, inconsistencies, and areas requiring harmonisation. Passive sampling, particularly dust collection, was the most common approach, while Illumina-based 16S rRNA and ITS amplicon sequencing dominated molecular analyses. However, variations in targeted gene regions, extraction kits, and analytical tools limited cross-study comparability. Ecological findings revealed consistent detection of bacterial taxa such as Staphylococcus, Streptococcus, and Corynebacterium, and fungal taxa including Cladosporium, Aspergillus, and Penicillium, with diversity shaped by building characteristics, ventilation, humidity, occupancy, and presence of pets. This review highlights the need for standardised protocols in indoor microbiome research to facilitate reproducibility, enable meta-analyses, and inform health-related guidelines for indoor environments.},
}
@article {pmid41943884,
year = {2026},
author = {Fonseca, LRS and Feijó, M and Vaz, CV and Pereira, BJ and Laurentino, S and Palmeira-de-Oliveira, A and Socorro, S},
title = {Urologic Bacteriome: The Hero or the Villain in Prostate Cancer Onset, Progression, and Treatment?.},
journal = {Medicinal research reviews},
volume = {},
number = {},
pages = {},
doi = {10.1002/med.70042},
pmid = {41943884},
issn = {1098-1128},
support = {MOD.PD.NAC.015.01//Liga Portuguesa Contra a Cancro (LPCC) Bolsa LPCC/Gillette-Cancro da Pr&#xf3;stata/ ; 2021.07634//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2021.07367//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
abstract = {Prostate cancer (PCa) is the second most frequently diagnosed cancer in men worldwide and the fifth leading cause of cancer-related mortality, presenting urgent unmet clinical needs in diagnosis and treatment. The recognition of the microbiome as a key factor in human health has prompted numerous studies, revealing an exciting new approach to cancer diagnosis and therapy. The bacteriome is the component of the microbiome that is most metabolically active and influenceable by internal and external factors, which is pivotal in the development of cancer. Initial studies exploring the link between the microbiome and PCa focused primarily on the gut bacteriome, which has been implicated in the onset and progression of the disease, as well as in resistance to therapy. Further research has demonstrated that the urologic bacteriome also plays a crucial role in the development of PCa, serving as an important factor for diagnosis and treatment. This review synthesizes current knowledge concerning the significance of the urologic bacteriome in PCa onset, progression, diagnosis/prognosis, and therapy. It also explores the impact of the bacterial metabolome in PCa, emphasizing the importance of this undervalued dimension of the bacteriome. Overall, the review provides a comprehensive analysis of how bacteria and their bioactive metabolites contribute to PCa, highlighting their clinical and therapeutic relevance. It also identifies the existing knowledge gaps, paving the way for the development of new approaches that could enhance PCa diagnosis and treatment.},
}
@article {pmid41944002,
year = {2026},
author = {Liu, Y and Yang, Y and Zhu, L and Peng, W},
title = {Beyond Weight: Systems Biology and Precision Medicine Redefine Obesity as a Multidimensional Disease.},
journal = {Diabetes, obesity &amp; metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70724},
pmid = {41944002},
issn = {1463-1326},
support = {2025ZZTS0829//Central South University Graduate Student Independent Exploration and Innovation Project/ ; 82374552//the National Natural Science Foundation of China/ ; 20240304076//Support Plan for High-level Health and Medical Talents in Hunan Province/ ; 825B20009//National Natural Science Foundation of China for PhD Students/ ; 2024JJ2086//Hunan Provincial Natural Science Foundation for Distinguished Young Scholars/ ; },
abstract = {BACKGROUND: Traditional weight-centered models do not fully capture the biological complexity of obesity. Systems biology offers a new framework by integrating molecular, cellular, clinical, and environmental information to reframe obesity as a heterogeneous, multidimensional disease.<br><br>AIMS: This review aims to reframe obesity as a heterogeneous, multidimensional disease by integrating molecular, cellular, clinical, and environmental information through the lens of systems biology.<br><br>MATERIALS AND METHODS: This article summarizes findings from recent studies employing systems biology approaches, including single-cell transcriptomics, metabolomics, epigenomics, microbiome profiling, and computational modeling.<br><br>RESULTS: These approaches have revealed marked heterogeneity in adipose remodeling, inflammatory tone, mitochondrial stress, and inter-organ communication. Such insights help explain why individuals with similar body mass index (BMI) can differ substantially in insulin resistance, organ-specific vulnerability, and treatment response.<br><br>DISCUSSION: This review focuses on obesity-relevant mechanisms, including adipose tissue heterogeneity, immunometabolic dysfunction, immune aging, and obesity-related multi-system injury. We also discuss emerging precision obesity care strategies such as biomarker-guided subtyping, cell-specific targeting, microbiome-directed intervention, and artificial intelligence-assisted prediction.<br><br>CONCLUSION: Together, these advances support a shift from BMI-based classification alone toward mechanism-informed obesity prevention and treatment.},
}
@article {pmid41944101,
year = {2026},
author = {Sohel, M and Aktar, S and Khatun, S and Hamidu, S and Nity, NU and Kumar, S and Hossain, MS and Sarker, MR and Das, SR and Dey, BR and Hasan, AMW and Islam, K and Islam, F and Al Mamun, A},
title = {A Narrative Review on Unravelling Bacterial-Mediated Carcinogenesis and Possible Alternative Treatment Strategies.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e6359088},
pmid = {41944101},
issn = {2314-6141},
mesh = {Humans ; *Carcinogenesis/pathology ; *Neoplasms/microbiology/pathology/therapy ; Animals ; *Bacteria/pathogenicity ; *Bacterial Infections/complications/microbiology ; Signal Transduction ; Cytokines/metabolism ; Apoptosis ; },
abstract = {The potential roles of chemical, physical, and viral factors in cancer development are well documented. Similarly, bacterial carcinogenesis has been reported previously, though not extensively. Therefore, we aimed to provide comprehensive, mechanistic evidence on the pathogenesis of bacteria-induced carcinogenesis and possible treatments to halt cancer progression. Infections by bacteria, including Salmonella typhi, Fusobacterium spp., Chlamydia pneumoniae, Staphylococcus aureus, Helicobacter pylori, and Mycobacterium tuberculosis, have been reported as the most common carcinogenic bacteria in humans. These bacteria can produce toxins and carcinogenic metabolites those promote the development of cancer in a variety of ways, including by changing the dynamics of the cell cycle, triggering signaling pathways in the cell, such as NF-κB, MAPK, PI3K-PKB/Akt, and JAK/STAT, and activating anti-apoptosis activities by increasing Bcl-2 and decreasing BAX, and caspases expression along with suppressing p53 and pRb tumor suppressor proteins. Moreover, inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interferon-gamma (INF-γ), interleukin-1β (IL-1β), IL-4, IL-6, IL-10, IL-1, IL-17, IL-23, and other inflammatory cytokines are a few of the factors that promote chronic inflammation and initiate carcinogenesis. In addition, bacterial infection can generate free radicals that induce DNA damage, thereby promoting carcinogenesis. Following these mechanisms, bacteria can cause a wide range of cancers, such as breast, colon, pancreas, stomach, lung, gallbladder, and oral carcinoma. Fortunately, supplementation with active natural phytochemicals and nano-based strategies may counteract bacterial infection-induced carcinogenesis by regulating several cellular proteins, including those that control the cell cycle, induce apoptosis, promote metastasis, interact with growth factor receptors and tyrosine kinases, and function as antioxidants. Therefore, this narrative review aims to provide a consolidated mechanistic overview of bacterial infection-induced carcinogenesis and to highlight emerging phytochemical and nanotechnology strategies as potential therapeutic approaches. Additionally, phytochemical-based interventions and nanotechnology strategies are discussed as potential alternative therapeutic approaches to counteract bacteria-induced carcinogenesis.},
}
@article {pmid41944109,
year = {2026},
author = {Saini, O and Kaur, A and Haneef, M and Kosey, S},
title = {Pathophysiological Role of the Gut Brain Axis in Parkinson's Disease: From Microbial Metabolites and Intestinal Permeability to Central Neuroinflammation.},
journal = {Current neurovascular research},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115672026468149260326045511},
pmid = {41944109},
issn = {1875-5739},
abstract = {INTRODUCTION: Parkinson's Disease (PD) is the second most prevalent neurodegenerative disorder, affecting over 8.5 million individuals worldwide, with its incidence expected to rise. It is characterized by dopaminergic neuronal loss in the substantia nigra pars compacta and pathological aggregation of α-synuclein into Lewy bodies, leading to motor and non-motor symptoms. Increasing evidence implicates the Gut-Brain Axis (GBA) in PD pathophysiology.<br><br>METHODS: This review synthesizes findings from human and animal studies investigating the role of gut microbiota, gut permeability, microbial metabolites, and gastrointestinal dysfunction in the development and progression of PD.<br><br>RESULTS: Gut microbiota dysbiosis is associated with altered production of short-chain fatty acids, tryptophan metabolites, and neurotransmitter precursors, contributing to neuroinflammation, increased intestinal permeability, and &#x3b1;-synuclein misfolding. Gastrointestinal symptoms such as constipation, dysphagia, and gastroparesis often precede motor symptoms by decades, highlighting the gut as a potential origin of pathology. Therapeutic strategies targeting the microbiome, including Mediterranean and ketogenic diets, probiotics, prebiotics, postbiotics, and experimental phage therapy, have demonstrated promising preliminary outcomes.<br><br>DISCUSSION: Despite encouraging results, inconsistencies in methodology, mechanistic uncertainties, and the lack of longitudinal and individualized studies limit current understanding. Standardization and precision-based approaches are required to clarify causality and therapeutic efficacy.<br><br>CONCLUSION: Advancing knowledge of the gut-brain axis in PD presents valuable opportunities for early biomarkers and microbiota-targeted interventions, offering novel strategies to delay disease progression and improve patient quality of life.},
}
@article {pmid41944570,
year = {2026},
author = {Ostner, J and Li, H and Müller, CL},
title = {Score Matching for Differential Abundance Testing of Compositional High-Throughput Sequencing Data.},
journal = {Statistics in medicine},
volume = {45},
number = {8-9},
pages = {e70534},
pmid = {41944570},
issn = {1097-0258},
support = {ZT-I-PF-5-138//Helmholtz-Gemeinschaft/ ; R01GM123056/NH/NIH HHS/United States ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods/statistics &amp; numerical data ; Computer Simulation ; *Models, Statistical ; Humans ; Single-Cell Analysis ; },
abstract = {The class of a-b power interaction models, proposed by [1], provides a general framework for modeling sparse compositional data with pairwise feature interactions. This class includes many distributions as special cases and enables modeling of zero entries through power transformations, making it particularly suitable for modern high-throughput sequencing data with excess zeros, including single-cell RNA-Seq and microbial amplicon data. Here, we present an extension of this class of models that allows inclusion of covariate information, thus enabling accurate characterization of covariate dependencies in heterogeneous populations. Combining this model with a tailored differential abundance (DA) test leads to a novel DA testing scheme, cosmoDA, that can reduce the false positive detection rate caused by correlated features. cosmoDA uses penalized generalized score matching for parsimonious model fitting. We show on simulated benchmarks that cosmoDA can accurately estimate feature interactions in the presence of population heterogeneity and significantly reduces the false discovery rate when testing for differential abundance of correlated features. Using single-cell and amplicon data, we illustrate cosmoDA's ability to estimate data-adaptive Box-Cox-type data transformations and assess the impact of zero replacement and power transformations on downstream differential abundance results. cosmoDA is available at https://github.com/bio-datascience/cosmoDA.},
}
@article {pmid41944618,
year = {2026},
author = {Fróis-Martins, R and Mertens, S and Tran, VDT and Maufrais, C and d'Enfert, C and Sanglard, D and LeibundGut-Landmann, S},
title = {Manipulation of regulators of morphogenesis is not sufficient to render a Candida albicans colonizer strain pathogenic.},
journal = {mBio},
volume = {},
number = {},
pages = {e0041526},
doi = {10.1128/mbio.00415-26},
pmid = {41944618},
issn = {2150-7511},
abstract = {As a member of the microbiome, Candida albicans colonizes the oral cavity and other mucosal surfaces of the human body. While commensalism is tightly controlled by the host immune system, the fungal determinants enabling the fungus to colonize the host mucosa without causing tissue damage and inflammation remain less clear. In search of genetic determinants that may underlie the commensal lifestyle of the low-damage-inducing C. albicans isolate 101, we identified a small sequence duplication in one allele of the Brg1 hyphal morphogenesis regulator gene, resulting in a truncated loss-of-function allele (BRG1[TRUNC]). Replacing BRG1[TRUNC] by the full-length allele (BRG1[FL]) resulted in a modest increase in filamentation but did not alter the phenotype of the fungus in the oral mucosa of experimentally colonized mice. Analysis of a spontaneous hyperfilamentous variant of the BRG1[FL]/BRG1[FL] derivative of C. albicans strain 101 identified a Glu-to-Lys change at position 1541 in the Cyr1 adenylate cyclase (CYR1[E1541K]). While the CYR1[E1541K] mutation led to greatly increased filamentation, expression of hyphae-associated genes, and host cell damage when tested in vitro, it was insufficient to render C. albicans strain 101 more pathogenic in the oral mucosa in vivo, irrespective of the BRG1 status. Together, this highlights that the low-damage-inducing nature of strain 101 cannot be overcome by manipulating BRG1 and CYR1, two genes with known roles in C. albicans virulence.IMPORTANCEDuring homeostasis, the fungus Candida albicans establishes mutualistic interactions with its human host. It can, however, also adopt a pathogenic state and cause infections with diverse clinical manifestations that pose a significant challenge for diagnosis and therapy. Understanding the fungal determinants that underlie C. albicans colonization under steady-state conditions may thus provide new avenues for modulating the fungus-host interaction in candidiasis patients to restore homeostasis. Here, we report gene variants in key regulators of C. albicans morphogenesis and virulence that distinguish strains with distinct capacity to drive inflammation and cause disease. Gene-exchange mutants provided evidence for the impact of a BRG1 loss-of-function allele and a CYR1 gain-of-function mutation toward in vitro biomarkers of fungal pathogenicity. However, in vivo in an experimental model of C. albicans oral colonization, none of these gene variants individually or in combination was sufficient to change the pathogenic state of the fungus. These findings indicate that C. albicans mucosal colonization is regulated by a complex gene network rather than by single genetic determinants.},
}
@article {pmid41944629,
year = {2026},
author = {Poopalarajah, R and Jha, AR},
title = {Human lifestyle-associated factors modulate the gut resistome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0145825},
doi = {10.1128/msystems.01458-25},
pmid = {41944629},
issn = {2379-5077},
abstract = {Antimicrobial resistance poses a serious threat to global public health in the 21st century. The human gut is a major reservoir of antimicrobial resistance genes and is strongly shaped by lifestyle factors linked to urbanization. Antibiotic use is widely known as a main driver of gut antimicrobial resistance; however, lifestyle encompasses other host and environmental determinants that also profoundly impact the gut resistome. These factors restructure gut microbiome composition and diversity, which, in turn, shape the abundance, persistence, and mobility of ARGs within the gut ecosystem. Lifestyle transitions along the urbanization gradient illustrate how antibiotic use, subsistence strategies, diet, agriculturally linked environmental exposures, host health, and global patterns of ARG distribution influence gut microbial diversity and ARG prevalence. Frequent antibiotic use in urban settings disrupts gut homeostasis and promotes resistome expansion. Transitions from traditional subsistence strategies to industrialized food systems are associated with dietary changes, such as reduced fiber intake, contributing to lower gut microbial diversity and increased ARG burden. Agrarian practices involving close human and livestock contact and antimicrobial use in animal husbandry facilitate ARG dissemination through the food chain. Host physiological factors and environmental exposures across diverse geographic regions additionally influence gut microbiome resilience and resistome composition. Integrating microbial community structure with ARG profiles provides insight into how lifestyle factors shape the gut resistome and influence ARG emergence and spread.},
}
@article {pmid41944651,
year = {2026},
author = {Morrison, JM and Steuart, R and Russell, CJ},
title = {Pediatric tracheostomy-associated respiratory infections: an evolving paradigm.},
journal = {Current opinion in pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOP.0000000000001559},
pmid = {41944651},
issn = {1531-698X},
abstract = {PURPOSE OF REVIEW: Children with tracheostomy frequently experience tracheostomy-associated infections (TRAINs) such as pneumonia and tracheitis. This review will summarize current evidence regarding the diagnosis, treatment, and prevention of TRAINs.<br><br>RECENT FINDINGS: Recent evidence highlights limitations of respiratory culture testing in the face of a diverse, dynamic bacterial community within the airways of children with tracheostomy, challenging the notion that a positive bacterial culture is sufficient for diagnosing bacterial TRAIN. For this reason, recent consensus guidelines recommend against the routine obtainment of respiratory cultures for TRAIN diagnosis in the absence of specific clinical symptoms. Additional evidence for microbiome shifts and host inflammation as diagnostic tools may help identify those who will benefit from antibiotic treatment. Recent findings support selective anaerobic coverage when aspiration is suspected and suggest shorter antibiotic courses may be effective. Cycled inhaled tobramycin shows potential for reducing TRAIN frequency and related hospitalizations.<br><br>SUMMARY: With recent advances in TRAIN pathobiology, diagnosis, treatment, and prevention of TRAINs is undergoing a paradigm shift. Future translational research will define the airway microbiome during TRAINs and during wellness and its impact on host inflammation. Antibiotic clinical trials are needed to optimize treatment and prevention of TRAINs.},
}
@article {pmid41944793,
year = {2026},
author = {Kumar, J and Hartzell, C and Abelson, E and Mano, KJ and Chidambaran, V},
title = {Prevalence, Expression, Assessment, Mechanisms, and Management of Pain in Autistic Children: A Scoping Review.},
journal = {A&amp;A practice},
volume = {20},
number = {4},
pages = {e02178},
doi = {10.1213/XAA.0000000000002178},
pmid = {41944793},
issn = {2575-3126},
mesh = {Humans ; Child ; *Pain Management/methods ; *Autism Spectrum Disorder/complications/epidemiology ; Prevalence ; Adolescent ; Child, Preschool ; Pain Measurement ; *Pain/epidemiology ; *Chronic Pain/epidemiology/therapy ; },
abstract = {Autism spectrum disorder is a neurodivergent condition affecting communication, social interaction, and behavior, and is characterized by sensory-processing abnormalities. There is a high incidence of chronic pain in autistic children, and pain can also be a presenting symptom of autism. With improved identification of autism in children, it is increasingly important to understand the implications for pain management. This scoping review describes and summarizes existing literature on pain prevalence, mechanisms, expression, and assessment challenges, as well as acute and chronic pain management in autistic children. A systematic search strategy of MEDLINE, PsycINFO, SCOPUS, and Web of Science was utilized to identify major findings of qualitative, quantitative, observational studies, and reviews reporting on pain in pediatric patients (3-18 years) with concomitant autistic symptomatology. We identified 260 eligible articles, of which 85 were included for review. Our findings challenge earlier assumptions that autistic children are not sensitive to pain. Rather, they react differently to pain than nonautistic peers, have comorbidities that increase pain risk, and are hypersensitive to painful stimuli. Altered sensory-processing, genetic mechanisms, and brain-gut microbiome interactions have been suggested as mechanisms for higher pain sensitivity. The combination of altered pain expression and lack of proper pain assessment tools in this population can lead to unnecessary testing or delays in diagnosis and management. Management of pain requires parental engagement, multidisciplinary coordination, and tailored interventions unique to the individual's responses.},
}
@article {pmid41944837,
year = {2026},
author = {Weirauch, T and Vehreschild, MJGT},
title = {[Modulation of the gut microbiome for the eradication of multidrug-resistant pathogens: current approaches and perspectives].},
journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz},
volume = {},
number = {},
pages = {},
pmid = {41944837},
issn = {1437-1588},
abstract = {The global rise in antibiotic resistance represents one of the greatest threats facing modern medicine. Colonization of the gastrointestinal tract with multidrug-resistant organisms is considered a critical risk factor for nosocomial infections across various patient populations. In this context, targeted decolonization strategies are moving into the focus of clinical research. For a long time, non-absorbable antibiotics were considered a promising approach for local eradication; however, the evidence generated on this question does not suggest sufficient clinical efficacy of this approach. Alternative strategies, such as fecal microbiota transplantation, have shown encouraging results in case reports and small-scale studies for the decolonization of multidrug-resistant organisms. Live biotherapeutic products and certain probiotics are also being explored as potential options for microbiome modulation and reduction of antimicrobial resistance. However, the current evidence base remains heterogeneous, and robust randomized controlled trials are largely lacking. This article aims to provide an overview on the current understanding of gastrointestinal colonization with multidrug-resistant organisms and to discuss the clinical relevance of non-absorbable antibiotics as well as the potential role of microbiome-based therapies in the context of the global antibiotic resistance crisis.},
}
@article {pmid41944841,
year = {2026},
author = {Tom, A and Kurian, PS and Philip, S and Mathew, D and Vijayaraghavan, R and Sumbula, V and Varkey, ME},
title = {Exploratory profiling of microbial communities associated with tapping panel dryness in Hevea brasiliensis.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41944841},
issn = {1432-072X},
}
@article {pmid41945577,
year = {2026},
author = {Faridoun, A and Carvalho, R and Smith, J and Gibb, A and Jain, L and Zhang, A and Sran, A and Redmond, J and Malik, MZ and Gibson, M and Haider, A and Rekhi, U and Bhagirath, A and Rock, LD and Altabtbaei, K},
title = {FAVABEAN and FALAPhyl: Open-source pipelines for scalable 16s rRNA microbiome data processing and visualization.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0331145},
pmid = {41945577},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Humans ; *Software ; Phylogeny ; *Computational Biology/methods ; Bacteria/genetics/classification ; },
abstract = {Reproducible and scalable analysis of 16S rRNA amplicon sequencing data remains a persistent challenge in microbiome research due to the complexity of available tools, incompatibilities between platforms, and the need for extensive bioinformatics expertise. We developed two containerized workflows-FAVABEAN (Fast Amplicon Variant Annotation, Binning, Error-correction And ANalysis) and FALAPhyl (Forays into Automating Laborious Analyses of Phylogeny)-to address these challenges. FAVABEAN and FALAPhyl are Snakemake-based pipelines designed for flexible execution across local, cluster, and cloud environments. FAVABEAN automates preprocessing, ASV inference, and taxonomic assignment using DADA2 and FIGARO, integration of taxonomic knowledge when samples are sequenced with multiple primers using SMURF. FALAPhyl supports downstream analysis including alpha/beta diversity, network analysis, and differential abundance testing, with integrated provenance tracking. We validated both pipelines using three case studies involving oral microbiome datasets. In Case Study 1, we compared oral microbiota across family members and niches, showing primer-dependent variability in ASV-based similarity and minimal reseeding from familial sources after prophylaxis. Case Study 2 analyzed dental aerosol samples, revealing no significant microbial differences between pre-, intra-, and post-procedure air. Case Study 3, a randomized trial of a nitrate mouthrinse, demonstrated no significant microbiome shifts, highlighting oral microbial stability. FALAPhyl's integration of DAtest enabled empirical evaluation of multiple statistical tests, aiding robust differential abundance inference. FAVABEAN and FALAPhyl offer a reproducible, automated solution for 16S rRNA amplicon data analysis. Their modular design, containerization, and provenance tracking enhance accessibility and scientific rigor in microbiome research.},
}
@article {pmid41946252,
year = {2026},
author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP},
title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141985},
doi = {10.1016/j.jhazmat.2026.141985},
pmid = {41946252},
issn = {1873-3336},
abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.},
}
@article {pmid41946778,
year = {2026},
author = {Nazir, I and Perez, D and Vargas, SJR and Ur Rehman, S and Arora, D and Chandra, M and Thimmapuram, J and Ebner, P},
title = {Assessing the impact of phage therapy on growth performance, microbiome and phage specific immune response in chickens.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45338-y},
pmid = {41946778},
issn = {2045-2322},
}
@article {pmid41946922,
year = {2026},
author = {Ding, Y and Zhang, Z and Wang, K and Jiang, C},
title = {The microbiome regulates host metabolic health and diseases through microbial enzymes.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
pmid = {41946922},
issn = {1759-5053},
abstract = {The microbiome is widely involved in host metabolism, with many omics studies suggesting that it is important for metabolic health. Although studies in this area have made great strides in furthering our understanding of the role of the microbiome in health and disease, key challenges still hinder the safe clinical application of gut microbiota-targeted therapies. These limitations include a lack of confirmation of causality between the gut microbiota and host health, insights into the molecular mechanisms by which the gut microbiota functions to affect host health, and the development of therapeutic strategies that accurately regulate the function of the gut microbiota towards specific microbial enzyme targets without affecting its overall composition and viability. Microbial enzymes with various functions and activities have attracted the attention of many researchers in the past few years, especially microbiota-host isozymes, which are enzymes in the microbiome and the host that share a similar function. Such isozymes, as well as microbial-specific enzymes involved in basic biological processes of the gut microbiota, metabolism of nutrients, and synthesis of active metabolites and interactions in microbial-host communities, are the key mediators of gut microbiota-host crosstalk and have received much attention. In this Review, we provide a holistic understanding of the multifaceted role of gut microbial enzymes, including providing guidance for their discovery, while highlighting the great potential of gut microbial enzyme-oriented therapies for precision medicine.},
}
@article {pmid41947036,
year = {2026},
author = {Ali, S and Patel, AJ and Lehman, PC and Fitzjerrells, RL and Kasi, PM and Mangalam, AK},
title = {The distinct roles of Negativicoccus and Fusobacterium in proximal- and late-onset colorectal cancer.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655193},
doi = {10.1080/19490976.2026.2655193},
pmid = {41947036},
issn = {1949-0984},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; Female ; Male ; Feces/microbiology ; Middle Aged ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Aged ; DNA, Ribosomal/chemistry/genetics ; *Fusobacterium/isolation &amp; purification/genetics ; Anal Canal/microbiology ; DNA, Bacterial/genetics/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Adult ; },
abstract = {Despite the emerging role of the gut microbiome in colorectal cancer (CRC), its significance in early-onset CRC (EOCRC, < 50 y) versus late-onset CRC (LOCRC) and the molecular differences between proximal and distal CRC remain poorly understood. To circumvent the logistical and patient compliance challenges of stool collection, we explored the utility of anal swabs as a convenient alternative for characterizing gut microbiome signatures in CRC. We profiled the CRC microbiome using anal swabs (n = 76) and stool samples (n = 33) by 16S rRNA sequencing. Diversity indices were compared using Wilcoxon tests, compositional differences assessed by PERMANOVA, and correlations were performed in paired samples. Correlation analysis revealed strong associations between microbial phyla (Bacteroidetes, R = 0.86, p = 4.7 × 10[-6]; Firmicutes, R = 0.65, p = 3.4 × 10[-3]; Verrucomicrobiota, R = 0.81, p = 4.8 × 10[-5]; and Fusobacterium, R = 0.80, p = 7.3 × 10[-5]) and major genera (Bacteroides, R = 0.88, p = 1.7 × 10[-5]; Fusobacetrium, R = 0.75, p = 1.5 × 10[-3]; Blautia, R = 0.77, p = 8.5 × 10[-4]; and Bifidobacterium, R = 0.81, p = 3.3 × 10[-4]) across sample types, validating the use of anal swabs. However, Actinobacteriota and Prevotella were not correlated, likely reflecting the perianal skin-associated microbiota and underscoring the need for validation against stool or mucosal biopsies. Importantly, anal swabs revealed associations between Negativicoccus and proximal CRC (p = 0.047) and between the Fusobacteriota phylum and LOCRC (p = 0.042), suggesting subtype-specific CRC subtypes. In mechanistic studies, using the mucous-secreting HT-29 MTX cell line, we observed that Negativicoccus was associated with activation the RAS/MAPK pathway, upregulated c-MYC, KRAS, MAPK1, and Cyclin D1 (p < 0.05) and increased proinflammatory cytokines (IL-8) (p < 0.05), thereby increasing cell proliferation. In contrast, Fusobacterium modulates the WNT/β-catenin pathway, increasing β-catenin and AXIN1 (p < 0.05), promoting cell migration (p < 0.05), and extracellular matrix (ECM) remodeling. These findings highlight distinct microbial contributions to CRC pathogenesis, with Negativicoccus influencing proliferation and inflammation, whereas Fusobacterium promotes migration and invasion. Understanding these pathways offers potential for harnessing the gut microbiome's diagnostic and therapeutic power in CRC.},
}
@article {pmid41947046,
year = {2026},
author = {Wieser, NV and Admiraal, I and Weiss, R and Ghiboub, M and Davids, M and Lefèvre, A and Emond, P and Powell, EA and Sim, K and Kroll, JS and de Jonge, WJ and Sovran, B and Kinross, JM},
title = {Fecal tryptophan metabolism predicts the development of infant eczema: a prospective longitudinal study.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655171},
doi = {10.1080/19490976.2026.2655171},
pmid = {41947046},
issn = {1949-0984},
mesh = {Humans ; *Tryptophan/metabolism ; Infant ; *Feces/microbiology/chemistry ; Prospective Studies ; Longitudinal Studies ; Male ; Female ; *Eczema/microbiology/diagnosis/metabolism ; Gastrointestinal Microbiome ; Infant, Newborn ; Metabolomics ; Biomarkers/analysis ; Bifidobacterium/metabolism/genetics ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Indoles/metabolism ; RNA, Ribosomal, 16S/genetics ; Metabolome ; United Kingdom ; },
abstract = {Early-life microbial metabolism of tryptophan plays a critical role in immune modulation and may influence susceptibility to inflammatory disorders such as eczema. However, longitudinal human data linking microbial tryptophan metabolism to eczema onset are limited. We conducted a prospective cohort study of 40 term-born UK infants, followed from birth to 24 months, stratified by early-onset (infants developing eczema <12 months, n = 12) or late-onset (infants developing eczema ≥12 months, n = 7) doctor-diagnosed eczema. Fecal samples underwent targeted tryptophan LC-MS metabolomics and 16S rRNA sequencing. Tryptophan metabolomics revealed dynamic changes in tryptophan metabolites that were associated with disease status compared to healthy infants. Infants with early-onset eczema (<12 months) exhibited elevated tryptophan and tryptamine levels at 6 months, while those with late-onset eczema (≥12 months) showed reduced indole-3-lactic acid (ILA) levels prior to diagnosis at 9 months. 16S and metabolomics correlations highlighted a metabolic shift in Bifidobacterium from ILA, a metabolite that predominated fecal metabolome during early infancy but decreases by 12 months, coinciding with increased indole-3-aldehyde (I3AD) metabolism by Bifidobacterium. Receiver operating characteristic (ROC) curve analysis identified a small panel of early predictive indole-pathway markers, including tryptophan and the indole/indole-3-sulfate (I3S), I3S/ILA, and tryptophan/ILA ratios, discriminating both early- and late-onset eczema development. Our findings reveal distinct, time-dependent disruptions in microbial tryptophan cometabolism associated with eczema onset. ILA may serve as a biomarker for the diagnosis of infantile eczema. Further validation studies to establish its clinical utility are now required.},
}
@article {pmid41947175,
year = {2026},
author = {Xiao, Q and Wen, Z and Zhan, H and Zhao, H and Jiao, Y and Huang, D and Li, H and Chen, C},
title = {Si-Ni-San alleviates depression-like behavior via regulating the gut microbiota-tryptophan metabolism-AhR/NF-κB pathway axis.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {41947175},
issn = {1749-8546},
support = {82405203//the National Nature Science Foundation of China/ ; 20242BAB20451//Jiangxi Provincial Natural Science Foundation/ ; 202610094//The Science and Technology Program of Jiangxi Provincial Health Commission/ ; ZZ17-ND-12//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ17-YQ-054//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; PY-2025004B//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; JSYL2025001//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; },
abstract = {BACKGROUND: Si-Ni-San (SNS), a classic herbal formula from the Treatise on Cold Damage Diseases, is used to treat depression by relieving "liver qi stagnation". However, the underlying mechanism remains unclear.<br><br>PURPOSE OF THE RESEARCH: This study aimed to investigate the mechanism by which SNS alleviates depression-like behavior, specifically focusing on its role in modulating gut microbiota and host tryptophan metabolism.<br><br>METHODS: A depression model was induced in mice by chronic unpredictable mild stress (CUMS). The antidepressant effects of SNS were evaluated through behavioral tests. Integrated untargeted and targeted metabolomics, alongside 16S rRNA sequencing, were utilized to identify potential gut-brain signaling molecules. Molecular interactions between the gut-brain signaling molecule and its target were validated by surface plasmon resonance (SPR) and molecular docking. Key protein expression was measured via Western blot and ELISA. Finally, the function of gut microbiome-derived indole-3-acetic acid (IAA) as a key gut-brain signaling molecule was confirmed by oral supplementation experiments.<br><br>RESULTS: SNS significantly alleviated CUMS-induced depression-like behaviors. Multi-omics analysis revealed that SNS reversed tryptophan metabolic disorders and elevated gut microbiome-derived IAA levels in both the colon and prefrontal cortex, which was attributed to the enrichment of Lactobacillus. Further investigations confirmed that IAA directly binds to and activates the aryl hydrocarbon receptor (AhR), thereby inhibiting NF-&#x3ba;B pathway-mediated neuroinflammation. Moreover, oral supplementation with IAA replicated the antidepressant effects of SNS and suppressed CUMS-induced neuroinflammation via the AhR/NF-&#x3ba;B signaling pathway.<br><br>CONCLUSION: SNS alleviates depression-like behavior by modulating gut microbiota-mediated tryptophan metabolism to enhance IAA production, thereby activating central AhR signaling and suppressing NF-&#x3ba;B-mediated neuroinflammation.},
}
@article {pmid41947210,
year = {2026},
author = {Tang, G and Zhang, C and Zhang, X and Liu, H and Suen, G and Yao, J and Zhang, J},
title = {Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02403-y},
pmid = {41947210},
issn = {2049-2618},
support = {2023YFE0111800//National Key Research and Development Program of China/ ; 2024-JSGG-021//the National Center of Technology Innovation for Dairy/ ; 2024BBF01006//Key Research and Development Project of Ningxia Hui Autonomous Region/ ; },
abstract = {BACKGROUND: The transition period is vitally important to the life cycle of dairy cows. However, the function of the microbiota during both pre- and post-partum and their relationship with ruminal, plasma, and milk metabolites still require systematic investigation. To address this, the 7 highest- and 7 lowest-performing animals among a cohort of 100 dairy cows were selected based on their postpartum energy-corrected milk yield. Rumen fluid and plasma samples were collected during both pre- and post-partum periods, whereas milk samples were obtained postpartum. Shotgun metagenomics of rumen contents in addition to metabolomics of rumen, plasma, and milk samples were performed to evaluate the associations between ruminal microbes and early lactation performance in transition dairy cows.<br><br>RESULTS: Compared with prepartum cows, postpartum high-yield cows had greater concentrations of ruminal volatile fatty acids and plasma total bile acid. Moreover, plasma urea nitrogen and most amino acids, peptides, and their derivatives in plasma and milk were increased in postpartum high-yield cows, relative to postpartum low-yield cows. Metagenomic analysis revealed that the relative abundances of several species within the Prevotella, Succinimonas, Succinatimonas, and Methanosphaera increased, while other bacteria belong to Alistipes and Bacteroides, and archaeal Methanobrevibacter species decreased in postpartum cows, particularly in postpartum high-yield cows. Co-occurrence network and correlation analysis suggested that Prevotella and Succinatimonas were negatively correlated to Alistipes, Bacteroides, and Methanobrevibacter, potentially contributing to the nutritionally efficient phenotype of postpartum high-yield cows. A metabolic pathway analysis of our metagenomic data revealed that postpartum high-yield cows possessed more microbial genes involved in starch utilization and amino acid synthesis, while a wide range of microbial genes involved in cellulose utilization, acetogenesis, and amino acid degradation were found in prepartum cows with low-yield in postpartum. A structural equation model analysis showed that the increased relative abundances of Prevotella tf.2-5 and Succinatimonas CAG_777 were related to greater concentrations of plasma chenodeoxycholic acid glycine conjugate, milk 5-Methoxytryptophan, and energy-corrected milk yield. Finally, pan-genomic analysis confirmed that Alistipes, Bacteroides, and Methanobrevibacter possess genetic conservation of both hydrogenases and dehydrogenases, which may contribute to energy loss in the rumen via hydrogen dissipation.<br><br>CONCLUSION: In summary, our findings provide a fundamental understanding of how microbiome-dependent mechanisms contribute to early lactation performance in dairy cows during the transition period. The increased abundance of Prevotella, Succinimonas, and Succinatimonas in postpartum cows suggest that they are important microbes during the transition period and may help in coping with metabolic challenges, while improving nutrient utilization efficiency during this period. Our study underscores the importance of the ruminal microbiome during the transition period and highlights the need for rumen-based nutritional intervention strategies to improve production efficiency in ruminants. Video Abstract.},
}
@article {pmid41947241,
year = {2026},
author = {Wang, Z and Li, LK and Zhou, NN and Wang, T and Wang, YX and Qiao, F and Du, ZY and Zhang, ML},
title = {Microbiota-gut-muscle axis shapes fish muscle texture by regulating collagen synthesis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02400-1},
pmid = {41947241},
issn = {2049-2618},
support = {2022YFD2400800//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Increasing studies have emphasized the communication network between the gut microbiome and host organs, revealing that such interactions significantly influence host physiological performances. However, whether a gut-muscle axis exists to regulate muscle quality in animal production is unknown.<br><br>RESULTS: In two independent cohorts, the muscle hardness of tilapia subjected to a long-term faba bean diet exhibited significant inter-individual variation. RNA-Seq analyses of the high-hardness (H) and low-hardness (L) groups pointed to collagen-based extracellular matrix as a possible factor driving muscle hardness development. Transplantation of gut microbiota from the H donor resulted in enhanced collagen synthesis in gnotobiotic zebrafish. Muscular collagen deposition was featured with an increased abundance of gut Cetobacterium. Gnotobiotic models colonized with live C. somerae exhibited enhanced collagen synthesis. Integrated analyses of microbiome function, bacterial&#xa0;genome, and metabolic profiles identified acetate as a key effector of C. somerae. Acetate incubation upregulated collagen I expression in TGF-&#x3b2;-activated fibroblasts in an acetylation-dependent manner. Mechanistically, acetate promoted the acetylation of SMAD2/3, enhancing its nuclear transport and stability, which ultimately increased collagen expression. An acetate-supplemented feeding experiment corroborated these findings.<br><br>CONCLUSION: The comprehensive results provided evidences that gut microbes regulated&#xa0;tilapia muscle texture through SMAD2/3 acetylation-driven collagen synthesis. This study expands our understanding of the multifaceted role of the gut-muscle axis in muscle physiology. Furthermore, our findings highlight that targeting gut microbiota and the downstream collagen synthesis pathway could be promising for manipulating muscle quality in animal production. Video Abstract.},
}
@article {pmid41947254,
year = {2026},
author = {Passmore, JS and Nieves Delgado, A and Happel, AU},
title = {Ethical design as a prerequisite for translational microbiome science.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41947254},
issn = {2049-2618},
support = {INV-037612/GATES/Gates Foundation/United States ; VI.Vidi.221F.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; K43TW012864/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Translational Research, Biomedical/ethics ; *Translational Science, Biomedical/ethics ; Research Design ; },
abstract = {Human microbiome research is expanding globally, yet remains dominated by samples, institutions, and leadership from the Global North. This imbalance undermines scientific validity, as microbiomes are shaped by socio-ecological context and temporal dynamics, and risks producing diagnostics and therapeutics that are not applicable across diverse populations. In this comment, we engage with van Daele et al.'s framework of co-laboration and argue for ethical, interdisciplinary, and locally led research models that center community participation, context-rich metadata, and equitable authorship. We outline structural requirements-governance tools, funding mechanisms, and accountability systems-needed to ensure these frameworks are implemented and advance both scientific integrity and global health equity. Video Abstract.},
}
@article {pmid41947255,
year = {2026},
author = {Van Daele, W and Tito Tadeo, RY and Perera, J and Tshokey, T and Iversen, PO and Jayasinghe, S and Raffaetà, R and Wangmo, N and Fjeld, HE and R, SC and Thoradeniya, T and Raes, J},
title = {Toward ethical human microbiome research: improving health through radical interdisciplinary and intercultural co-laboration.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41947255},
issn = {2049-2618},
support = {Project no. 324158//Norwegian Research Council/ ; grant G0B7320N//Fonds Wetenschappelijk Onderzoek/ ; GA n. 949742 ERC-HealthXCross//European Union's Horizon 2020 Research and Innovation Programme/ ; },
mesh = {Humans ; *Microbiota ; *Biomedical Research/ethics ; Global Health ; Europe ; North America ; },
abstract = {As human microbiome research is globalizing, it raises ethical concerns regarding the European and North American dominance in the field, which may reproduce a colonial bias and perpetuate inequities in global health research and outcomes. We suggest disentangling this ethical quandary into three main concerns: 1) scientific bias toward European and North American populations; 2) limited meaningful community inclusion, participation, and ownership, and 3) scant significant inclusion of diverse global researchers. We then formulate three recommendations for their resolution, deploying co-laboration-joint labor of diverse partners in generating synergies between diverse disciplines, cultures, and knowledges around shared concerns-and co-laborative science-a form of citizen science based on such synergies between diverse partners-to guide meaningful inclusive, participatory, and ethical human microbiome research. To conclude, we promote a programmatic list for putting co-laborative ethical science into practice, benefiting global communities, individuals, and researchers alike and decolonizing and improving health worldwide.},
}
@article {pmid41947543,
year = {2026},
author = {Samyn, M and Gasparetto, M},
title = {Is it time to consider oral vancomycin treatment for the management of pediatric inflammatory bowel disease irrespective of the presence of primary sclerosing cholangitis?.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70431},
pmid = {41947543},
issn = {1536-4801},
support = {//None/ ; },
}
@article {pmid41947788,
year = {2026},
author = {Gorczyca, K and Kimber-Trojnar, &#x17b; and Kozioł, MM and Leszczyńska-Gorzelak, B},
title = {Association of culture-detected vaginal microbiota and body composition parameters with gestational diabetes outcomes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1776505},
pmid = {41947788},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; Cross-Sectional Studies ; Adult ; *Diabetes, Gestational/microbiology/epidemiology ; *Vagina/microbiology ; *Body Composition ; *Microbiota ; Candida albicans/isolation &amp; purification ; Life Style ; Streptococcus agalactiae/isolation &amp; purification ; Poland/epidemiology ; Young Adult ; },
abstract = {OBJECTIVE: To evaluate associations between culture-detected vaginal microbial colonization, body composition parameters, and lifestyle factors in women with gestational diabetes (GD).<br><br>DESIGN: Cross-sectional observational study.<br><br>SETTING: Tertiary university hospital, Department of Obstetrics and Perinatology, Lublin, Poland.<br><br>POPULATION: One hundred pregnant women, including 47 with GD and 53 healthy controls.<br><br>METHODS: Anthropometric measurements, bioelectrical impedance analysis (BIA), and vaginal culture-based microbiological assessment were performed. Dietary habits, lifestyle behaviours, and supplement use were evaluated using a validated questionnaire. BIA assessed hydration status and body composition, including total body water, extracellular and intracellular water, lean tissue mass, and body cell mass.<br><br>MAIN OUTCOME MEASURES: Prevalence of selected vaginal microorganisms (Candida albicans, Streptococcus agalactiae), body composition indices, and lifestyle factors.<br><br>RESULTS: Women with GD had significantly higher BMI during pregnancy, greater lean tissue mass and body cell mass, and increased total and extracellular water compared with controls (all p < 0.05). Vaginal swabs showed a higher prevalence of Candida albicans (27.7% vs. 5.7%) and Streptococcus agalactiae (23.4% vs. 0%) in the GD group. Women with GD more frequently reported alcohol and coffee consumption before pregnancy and were less likely to use folic acid or probiotic supplements. Due to multiple comparisons, some findings may reflect type I error and should be interpreted cautiously.<br><br>CONCLUSIONS: GD was associated with a higher prevalence of selected culture-detected vaginal microorganisms, as well as differences in body composition and health-related behaviours. These findings highlight potential interactions between metabolic status, microbial colonization, and lifestyle factors in pregnancy. Given the cross-sectional design, causality cannot be inferred, and comprehensive microbiome studies are needed to confirm broader ecological changes.},
}
@article {pmid41947790,
year = {2026},
author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X},
title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1744020},
pmid = {41947790},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Mycobiome ; *Constipation/microbiology/virology ; Metagenomics ; Feces/microbiology/virology ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Middle Aged ; *Fungi/classification/genetics/isolation &amp; purification ; Adult ; Dysbiosis/microbiology ; Viruses/classification/genetics/isolation &amp; purification ; Metagenome ; Chronic Disease ; Aged ; },
abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.<br><br>METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.<br><br>RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable &#x3b1;-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.<br><br>CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.},
}
@article {pmid41948035,
year = {2026},
author = {Li, Y and Wang, B and Lan, C and Dai, P and Zhao, L and Zhang, M and Fang, Q},
title = {Differential responses of crop pollen microbial communities to insect visitation and host identity: fungi are more sensitive than bacteria.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1789970},
pmid = {41948035},
issn = {1664-302X},
abstract = {INTRODUCTION: In the pollination process, pollen serves not only as a key vehicle for plant reproductive success but also as an important ecological interface for microbial transmission and selection. However, how insect visitation and host plant identity jointly affect the assembly of pollen microbial communities in agroecosystems remains poorly understood.<br><br>METHODS: Here, we employed bagging and open-pollination treatments combined with high-throughput sequencing to investigate the effects of insect visitation and host plant identity on the structure, composition, diversity, interspecific interactions, and core taxa of pollen microbial communities in crops.<br><br>RESULTS: Results showed that insect visitation and host plant identity jointly and significantly influenced the structure of pollen bacterial asnd fungal communities and altered their taxonomic composition, diversity, and interaction patterns, with these effects being mainly evident in cross-pollinated plants and more pronounced in fungal than in bacterial communities. Further analyses revealed that insect visitation increased network connectivity while reducing modularity (0.046) in bacterial communities of cross-pollinated plants, whereas their fungal network exhibited reduced connectivity and increased modularity (0.787). In cross-pollinated plants, fungal core taxa dominated the fungal communities (>87%), while bacterial core taxa contributed relatively little to overall community.<br><br>DICUSSION/CONCLUSION: Overall, insect visitation and host plant identity jointly shape pollen microbial communities, but bacterial and fungal communities exhibit distinct response patterns, with bacterial communities being relatively stable and fungal communities being more sensitive. This study highlights the key roles of insect visitation and host plant identity in pollen microbiome assembly and provides a theoretical basis for understanding crop pollination ecology and plant-pollinator-microbe interactions.},
}
@article {pmid41948039,
year = {2026},
author = {Wang, W and Liao, X and Liu, J and Liu, B and Zhou, C and Liang, P},
title = {Elevated postoperative IL-1β induces disorder of intestinal microenvironment and alteration of gut microbiota.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1744636},
pmid = {41948039},
issn = {1664-302X},
abstract = {INTRODUCTION: Previous research hinted at the importance of postoperative gut dysbiosis prevention, but the mechanisms remained unclear, posing a challenge for prevention and therapy. This study aims to investigate the characteristics of postoperative dysbiosis and the underlying mechanisms.<br><br>METHODS: The clinical cohort investigated the perioperative change of gut microbiota in patients undergoing thoracoscopy and its relationship with peripheral inflammatory indicators. Gut microbiome was characterized by 16S rRNA gene sequencing and Bugbase phenotype analysis. In the laboratory study, a mouse model of surgery/anesthesia stress was established to further investigate the potentially underlying mechanisms.<br><br>RESULTS: Microbiome analysis revealed a decrease in alpha diversity and a shift from obligate anaerobes to aerobes/facultative anaerobes after thoracoscopy. Postoperative IL-1&#x3b2; was negatively correlated with obligate anaerobe abundance and positively correlated with facultative anaerobe abundance. Higher facultative anaerobe abundance was associated with increased risk of postoperative complications and longer hospital stays. In the mouse model, surgery and rIL-1&#x3b2; intervention mirrored the oxygen phenotype changes in clinical cohort, and the colonic epithelium exhibited decreased ATP levels and hypoxic staining scores, with increased lactic acid. Downregulating postoperative IL-1&#x3b2; with IL-1&#x3b2; siRNA mitigated colonic hypoxic environment impairment and gut microbiota oxygen phenotype changes induced by surgery/anesthesia stress.<br><br>CONCLUSION: Postoperative gut dysbiosis involves a phenotypic shift of the gut microbiota from anaerobes toward aerobes and facultative anaerobes. This shift may be driven by an IL-1&#x3b2;-colonic epithelial oxygen metabolism-colonic oxygen environment-gut microbiota regulatory axis, offering potential insights for early risk stratification of severe postoperative complications and strategies to improve postoperative recovery.},
}
@article {pmid41948040,
year = {2026},
author = {Mo, X and Liu, Y and Huang, Z and Yu, H and Huang, J and Wu, Z and Tan, M and Fan, H and Ma, F and Zeng, B},
title = {Soil N and P nutrient metabolism affected by fungal community in larch plantation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1658803},
pmid = {41948040},
issn = {1664-302X},
abstract = {INTRODUCTION: The time-response mechanism of soil nitrogen (N) and phosphorus (P) nutrients across different stand ages remains intricate and inadequately quantified, particularly unclear is the effects of rhizosphere soil microbial communities, which serve as crucial drivers on soil N and P nutrients. This study delved into the effects of soil fungal community on the shifts of soil physicochemical properties and their correlations between N-P distribution within rhizosphere of Larix kaempferi (Japanese larch) with different tree stands.<br><br>METHODS: This study investigated the responses of soil nitrogen (N) and phosphorus (P) along a stand age gradient (young: <20 years; mid-aged: 20-30 years; near-mature: 30-40 years; mature: >40 years) in Larix kaempferi forests, with a focus on the associations between rhizosphere microbial communities and soil nutrient dynamics. By covering key developmental stages of forest succession, we examined age-related changes in rhizosphere soil N and P concentrations, soil physicochemical properties, and fungal community structure.<br><br>RESULTS: The results showed that fungal community structure gradually diversified from young to near-mature forests and became more stable in the mature forest stage. Differences in forest age were associated with changes in the availability and distribution of soil N and P nutrients, accompanied by shifts in the relative abundance of microbial functional genes related to N and P cycling. In particular, the abundance of P cycling-related functional genes showed patterns consistent with soil N and P variations, while N fixation-related functional genes exhibited the highest abundance in the middle-aged forest stage.<br><br>DISCUSSION: Overall, variations in stand development along the forest age gradient were closely linked to changes in soil nutrient distribution and rhizosphere microbial biomass, highlighting the potential role of rhizosphere microbial communities in soil N and P cycling in larch plantation ecosystems.},
}
@article {pmid41948042,
year = {2026},
author = {Dresel, FC and Gourlay, CW},
title = {Investigating the pH dependent antifungal effects of butyrate on Candida albicans.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1793162},
pmid = {41948042},
issn = {1664-302X},
abstract = {INTRODUCTION: Candida species are common members of the human gastrointestinal microbiome but are also associated with a range of diseases when microbial community balance is disrupted. Short-chain fatty acids produced by gut bacteria, particularly butyrate, play important roles in host-microbiome interactions and are increasingly explored as therapeutic modulators of microbial composition. Butyrate is present both as a microbial metabolite and dietary component and has been reported to influence Candida abundance within the gut. However, the antifungal activity of sodium butyrate (NaB) against Candida albicans under physiologically relevant gut pH conditions remains poorly understood.<br><br>METHODS: We examined the effects of NaB on C. albicans growth and physiology under pH conditions representative of the gastrointestinal environment. Growth, hyphal transition, respiration and biofilm formation were assessed in the presence of NaB at neutral pH. Parallel experiments at acidic pH (pH 4.0) evaluated fungicidal activity and associated cellular responses, including mitochondrial membrane potential, reactive oxygen species (ROS) accumulation, and intracellular calcium homeostasis. Histone deacetylase inhibitory activity of NaB was also assessed to determine its early cellular effects.<br><br>RESULTS: NaB displayed rapid histone deacetylase inhibitor activity in C. albicans and significantly inhibited growth, hyphal morphogenesis, respiration, and biofilm formation at neutral pH. In contrast, under acidic conditions (pH 4.0) NaB exhibited fungicidal activity. This lethal effect was associated with mitochondrial depolarisation, elevated ROS levels, and disruption of intracellular calcium regulation. Further analyses indicated that oxidative stress and loss of calcium homeostasis are key contributors to NaB-induced cell death under acidic conditions.<br><br>DISCUSSION: These findings reveal a strong pH dependence in the antifungal activity of butyrate against C. albicans. While NaB acts primarily as a physiological inhibitor of growth and virulence traits at neutral pH, acidic conditions convert its activity to a fungicidal mechanism driven by mitochondrial dysfunction, oxidative stress, and calcium dysregulation. This pH-dependent behaviour has implications for understanding microbiome-derived metabolites in fungal ecology within the gut and highlights the potential of butyrate-based strategies to modulate C. albicans overgrowth.},
}
@article {pmid41948045,
year = {2026},
author = {Dong, Y and Du, B and Xie, C and Zhang, S and Pang, Q and Zhang, D},
title = {Potassium sorbate induces developmental and microbiome changes in Drosophila melanogaster with attenuated trans-generational toxicity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783630},
pmid = {41948045},
issn = {1664-302X},
abstract = {Potassium sorbate (PS) is a widely used antimicrobial additive employed as a preservative in food, cosmetics, and animal feed. Early childhood represents a critical developmental window characterized by rapid growth, immune system maturation, gut microbiota establishment, and physiological homeostasis development, which may be particularly vulnerable to chemical exposures (during which chemical exposures may exert heightened impacts). Nevertheless, the effects of PS on childhood development and gut microbiota remain poorly understood, and its potential trans-generational effects have yet to be elucidated. In this study, we employed Drosophila melanogaster, an established model for studying evolutionarily conserved aspects of development, metabolism, and host-microbiota interactions, to systematically evaluate PS toxicity across multiple parameters: developmental dynamics, gut microbiota composition, gene regulation in adulthood, and trans-generational effects. Our findings demonstrate a dose-dependent biphasic response: while low-dose PS exposure (25 mg/L) accelerated larval pupation and adult emergence, suggesting a potential growth-promoting effect, high-dose exposure (≥ 500 mg/L) significantly delayed development and reduced adult lifespan (observed in females at 1,000 and males at 500-1,000 mg/L). Notably, trans-generational analysis revealed persistent developmental delays in the F1 generation, with offspring of 1,000 mg/L-exposed parents showing prolonged larval pupation time despite normal adult emergence timelines, indicative of partial developmental recovery. Mechanistically, high-dose PS disrupted endocrine signaling and altered expression of key developmental pathway regulators (EcR, InR, TOR, and E74B). These transcriptional changes were largely reversible in offspring, further supporting a similar gradually wash out recovery. While gut microbiota remained stable in exposed parents, offspring of 1,000 mg/L-exposed flies had significant microbiome alterations, highlighting clear trans-generational dysbiosis. This study provides new evidence that PS exposure during a sensitive developmental period in D. melanogaster can perturb development and gut microbial homeostasis across generations, offering insights relevant to understanding how early-life chemical exposures might influence conserved biological processes in higher organisms.},
}
@article {pmid41948046,
year = {2026},
author = {Liu, R and Liu, J and Li, Z and Wang, Z and Ding, J and Yuan, J and Yao, B and Dong, X and Dai, W and Huang, Z and Zhang, CS and Zhang, W and Zheng, Y},
title = {The composting microbiome and a multifunctional Bacillus tequilensis JZF3 with straw degradation and pathogen inhibition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768200},
pmid = {41948046},
issn = {1664-302X},
abstract = {Aerobic composting is a sustainable approach for converting organic waste into bio-fertilizer, where microorganisms play a central role in the degradation of recalcitrant lignocellulose. This study employed high-throughput sequencing to analyze the dynamic changes in bacterial and fungal communities during composting using distillers' grains, oil cake and cattle manure as raw materials. The results revealed pronounced successional changes in both microbial community structure and predicted function over time. Specifically, Firmicutes and Ascomycota were the dominant bacterial and fungal phyla, respectively, with the genus Bacillus maintaining high abundance throughout the process. The predicted functional profile indicated a shift in bacterial functions from initial xenobiotic biodegradation to core metabolic processes (such as energy and carbohydrate metabolism) in later stages. A total of 97 bacterial strains belonging to 38 species were isolated from different composting samples, with four strains (Bacillus licheniformis JZF8, B. altitudinis JZF2, B. tequilensis JZF3, and B. siamensis FJ3-3) showing strong cellulase, ligninase and protease activities. Among them, strain JZF3 not only exhibited these enzymatic activities and significant antagonistic activity against plant pathogens, but also was a dominant culturable species within the compost community. Furthermore, strain JZF3 was able to directly degrade rice straw without chemical pretreatment, achieving a degradation rate of 22.5%. The resulting degradation products also significantly promoted the growth of tobacco seedlings. This study identifies B. tequilensis JZF3 as a multifunctional agent that combines straw degradation with pathogen suppression and plant growth promotion, offering a novel strategy for synergizing agricultural waste recycling with disease control.},
}
@article {pmid41948248,
year = {2026},
author = {Padmavathy, K and Maakhni, E and Biswas, PS and Sheikh, F and Chhabra, T and Das, B},
title = {Oral-Systemic Interactions in Modern Healthcare: A Systematic Review of the Interrelationship Between Dental Pathologies and Systemic Diseases.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e104813},
pmid = {41948248},
issn = {2168-8184},
abstract = {Periodontitis is a prevalent chronic inflammatory disease characterised by destruction of the supporting structures of the teeth, and increasing evidence indicates that periodontal inflammation and oral microbial dysbiosis contribute to systemic diseases through inflammatory, immune, and vascular mechanisms. This systematic review examined associations between periodontitis and cardiovascular, metabolic, autoimmune, neurological, and inflammatory outcomes in adult populations. Studies published from 2015 onward were identified using a structured literature search, including cohort studies, randomised controlled trials, case-control studies, cross-sectional analyses, Mendelian randomisation studies, and microbiome-based investigations. Due to heterogeneity in study designs and outcomes, qualitative synthesis was performed. Eleven studies met the inclusion criteria, demonstrating consistent associations between periodontitis and increased risk of hypertension, atrial fibrillation, rheumatoid arthritis, dementia, and elevated systemic inflammatory markers. Quantitative findings showed higher blood pressure, increased C-reactive protein levels, greater autoantibody positivity, enhanced inflammasome activity, and reduced oral microbiome diversity in individuals with periodontal disease. Periodontal therapy improved periodontal health and systemic inflammation, although cardiometabolic improvements were modest or inconsistent. The evidence supports periodontitis as a chronic inflammatory condition with significant systemic consequences, mediated by inflammatory, immune, and endothelial pathways, underscoring the importance of integrating periodontal health into disease prevention and management strategies in modern healthcare.},
}
@article {pmid41948280,
year = {2026},
author = {Algindan, Y and AboAlsamh, H and Ahmad, S},
title = {Professional perspectives on PN among registered dietitians in Saudi Arabia: a mixed-methods assessment.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1695919},
pmid = {41948280},
issn = {2296-861X},
abstract = {BACKGROUND: The clinical implementation of personalized nutrition (PN) remains limited, despite growing interest. Healthcare professionals' readiness for adoption must be better understood.<br><br>OBJECTIVE: The aim of this study is to explore registered dietitians' perceptions, attitudes, and readiness regarding PN and multi-omics approaches in Saudi Arabia.<br><br>METHOD: A mixed-methods survey of 88 registered dietitians in Saudi Arabia provided quantitative and qualitative data on personalized nutrition technology (PNT) adoption patterns and barriers, analysed using the Consolidated Framework for Implementation Research (CFIR) to identify implementation barriers and facilitators.<br><br>RESULTS: PNT adoption was low (16%). Work experience, but not education level, had a relatively greater correlation with perceived usefulness of PNT (r&#x202f;=&#x202f;0.280, p&#x202f;=&#x202f;0.007). Genomics, metabolomics, and microbiome testing demonstrated strong correlations with PNT usefulness (r&#x202f;=&#x202f;0.321-0.571, p&#x202f;&#x2264;&#x202f;0.004). Qualitative findings identified knowledge gaps as the primary challenge and emphasized education as the key facilitator.<br><br>CONCLUSION: While Saudi dietitians have positive attitudes toward PN, they face significant implementation barriers at both an organizational and educational levels. For PN integration to be achieved within the Kingdom's healthcare system, policy, academic, and institutional interventions are required to enhance organizational support, professional training gaps, and interprofessional collaboration frameworks.},
}
@article {pmid41948282,
year = {2026},
author = {Verstegen, REM and de Bruijn, MJW and Garssen, J and Folkerts, G and Kostadinova, AI and Hendriks, RW and Willemsen, LEM},
title = {Dietary fructo-oligosaccharides dose-dependently modulate the microbiome and suppress type 2 lung inflammation in a murine model of house dust mite-induced allergic asthma.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1705988},
pmid = {41948282},
issn = {2296-861X},
abstract = {INTRODUCTION: A balanced microbiome is crucial for local and systemic immune regulation. Dietary fibers can support the intestinal microbiome, protecting the host from allergic diseases, including asthma. The effects of fibers depend on their type, dose, and disease context. Here, we investigated the preventative effects of four doses of fructooligosaccharides (FOS) in a murine model for house dust mite (HDM)-induced allergic asthma.<br><br>METHODS: BALB/c mice received a diet containing 1%, 2.5%, 5%, or 10% FOS (w/w) both prior to and during sensitization and challenges with HDM. Bronchoalveolar lavage fluid (BALF), lung tissue, serum, and cecum content were collected at the endpoint. Fecal microbiome composition was analyzed, and levels of short-chain fatty acids (SCFAs) were measured in cecum content, serum, and lung samples.<br><br>RESULTS: HDM-allergic mice showed eosinophilic airway inflammation and increased pulmonary type 2 inflammation, while cecal SCFA levels were lower compared to sham mice. Serum acetate concentrations showed a similar decline (p = 0.092). The 10% FOS diet did not prevent allergic sensitization or eosinophilic airway inflammation; however, it significantly reduced the proportions of T helper 2 (Th2) cells and the Th2/Th1 ratio in the lungs, decreased concentrations of chemokine (C-C motif) ligand 2 (CCL22) and interleukin (IL-13) in the BALF, and inhibited IL-13 production upon ex vivo HDM restimulation of lung cells. The 2.5% and 5% FOS diets also decreased Th2 cell frequency in the lungs. High doses of FOS increased the abundance of fecal Prevotellaceae, while reducing fecal Oscillospiraceae and Lactobacillaceae. These microbial shifts were correlated with protective effects against type 2 inflammation. In HDM-allergic mice, fecal Prevotellaceae abundance correlated positively with serum acetate concentrations, which were correlated with type protective effects. In allergic mice, the 2.5% and 5% FOS doses were associated with increased abundance of fecal Muribaculaceae and Bacteroidaceae, respectively, along with elevated cecal SCFA concentrations. In addition, the 5% FOS dose increased the relative abundance of fecal Lachnospiraceae, which correlated negatively with serum acetate levels and type prevention.<br><br>DISCUSSION: Dietary FOS modulated the gut microbiome and attenuated pulmonary type 2 immune responses in a dose-dependent manner. These findings underscore the importance of fiber dosing for precision nutrition strategies in allergy management.},
}
@article {pmid41948296,
year = {2026},
author = {Asad, S and Gu, P and Jiang, F and Liu, J and Chen, M and Karunarathna, SC and Atiq, M and Younas, M and Yapa, PN and Kan, X and Zhang, J},
title = {Pseudomonas parafulva SAPEU-1 as a keystone modulator: reshaping citrus phyllosphere microbiome to suppress citrus canker.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1771742},
pmid = {41948296},
issn = {1664-462X},
abstract = {INTRODUCTION: Citrus canker disease, caused by the pathogen Xanthomonas citri subsp. citri (Xcc) poses a substantial challenge for citrus production due to the limited efficacy of chemical control and increasing pathogen resistance.<br><br>METHODS: In this study, we isolated an endophytic bacterial strain, Endophyte S2, from the phyllosphere of citrus plants in Yunnan Province, China. We evaluated its efficacy both as a biocontrol agent and as a modulator of the citrus leaf microbiome.<br><br>RESULTS AND DISCUSSION: In vitro antagonism assays revealed that Endophyte S2 achieved the highest inhibition rate (68.2%) against Xcc among all tested isolates. Molecular identification based on 16S rRNA gene sequencing classified S2 as Pseudomonas parafulva SAPEU-01. In greenhouse trials, citrus plants with Xcc infestation were treated with SAPEU-01, and phyllosphere samples were collected before treatment and one month after, and analyzed by Illumina MiSeq sequencing. Post-treatment, &#x3b1;-diversity (richness and evenness) increased significantly, and &#x3b2;-diversity (PCoA, Bray-Curtis) showed a clear separation of microbial community structure, with reduced intra-group variability. Taxonomic shifts included the enrichment of Proteobacteria (particularly Pseudomonadaceae and Sphingomonadaceae), as well as genera such as Pseudomonas, Sphingomonas, and Methylobacterium, concomitant with a marked decline in Xanthomonadaceae (including X. citri) and opportunistic taxa such as Escherichia coli O157:H7 and Klebsiella aerogenes. Beneficial taxa, including Leuconostoc tardus, Sphingomonas, and Curtobacterium luteum, also increased. These results suggest Pseudomonas parafulva SAPEU-01 not only suppresses the pathogen but also restructures the phyllosphere microbiome toward greater stability and potential resilience.},
}
@article {pmid41948323,
year = {2026},
author = {Chao, K and Ding, Y and Ji, W and Wang, D and Liang, Q and Sun, S and Li, L and Yang, H and Zhao, J},
title = {Indole-3-acetic acid derived from Blautia protects against sepsis-induced acute lung injury.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1707493},
pmid = {41948323},
issn = {1664-3224},
mesh = {Animals ; *Sepsis/complications/microbiology/immunology ; Rats ; *Acute Lung Injury/etiology/prevention &amp; control/microbiology/immunology/metabolism ; Male ; Humans ; Gastrointestinal Microbiome/drug effects ; *Indoleacetic Acids/pharmacology/metabolism ; Disease Models, Animal ; Female ; CD8-Positive T-Lymphocytes/immunology ; Middle Aged ; Rats, Sprague-Dawley ; Aged ; },
abstract = {OBJECTIVES: Sepsis-induced acute lung injury (SI-ALI) significantly contributes to sepsis mortality, with CD8[+] T cell depletion being a critical pathogenic factor. While Blautia, a gut commensal bacterium with established probiotic benefits in diverse diseases, its role in SI-ALI pathogenesis remains undefined. Here, we investigated the therapeutic potential of Blautia in lethal SI-ALI.<br><br>METHODS: Gut microbiome profiling was performed in SI-ALI patients and healthy controls to identify disease-associated microbial alterations. A cecal ligation and puncture (CLP) rat model of sepsis was used to validate microbiota changes and evaluate the therapeutic effects of Blautia supplementation. Untargeted metabolomic analysis was conducted to identify key metabolites associated with Blautia. Functional studies were performed to assess lung injury, immune responses, CD8[+] T cell abundance, and survival following Blautia or metabolite administration.<br><br>RESULTS: Gut microbiome analysis identified significant Blautia depletion in SI-ALI patients compared to healthy controls. This pathogenic alteration was faithfully reproduced in cecal ligation and puncture (CLP) -modeled septic rats, in which Blautia supplementation attenuated lung injury, enhanced systemic immune responses,and improved survival. Untargeted metabolomic profiling identified indole-3-acetic acid (IAA) as a key Blautia-derived metabolite. Administration of IAA alone recapitulated the protective effects of Blautia, significantly ameliorating SI-ALI. Crucially, both interventions restored CD8[+] T cell populations and augmented their functional responses. Clinical analysis revealed that elevated Blautia abundance in sepsis patients inversely correlated with pulmonary injury severity and positively associated with augmented CD8[+] T cell effector functions.<br><br>DISCUSSION: Our findings establish that Blautia and Blautia-derived IAA mitigates SI-ALI by counteracting CD8[+] T cell depletion and dysfunction, highlighting a novel and promising mechanism-based therapeutic strategy for life-threatening sepsis.},
}
@article {pmid41948342,
year = {2026},
author = {Gao, KP and Dou, JR and Ma, BB and Ma, TB and Li, N and Qian, AD and Shan, XF and Sun, WW and Zhang, L and Zhang, D and Wang, CF and Zhang, DX},
title = {Engineered Lactobacillus casei targets the IgT-pIgR axis to confer mucosal protection against Aeromonas veronii in snakehead (Channa argus).},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1759765},
pmid = {41948342},
issn = {1664-3224},
mesh = {Animals ; *Lacticaseibacillus casei/genetics/immunology ; *Aeromonas veronii/immunology ; *Fish Diseases/immunology/microbiology/prevention &amp; control ; *Gram-Negative Bacterial Infections/immunology/prevention &amp; control/veterinary/microbiology ; *Immunity, Mucosal ; Probiotics/administration &amp; dosage ; *Bacterial Outer Membrane Proteins/immunology/genetics ; Bacterial Vaccines/immunology ; *Fish Proteins/immunology/genetics ; *Fishes/immunology/microbiology ; },
abstract = {INTRODUCTION: Aeromonas veronii remains a pervasive aquatic pathogen precipitating catastrophic economic depletion and threats to global food security. Conventional therapeutic modalities are constrained by inadequate stability, prohibitive costs, and biosafety risks.<br><br>METHODS: To address such challenges, an engineered Lactobacillus casei strain was developed to constitutively express the A. veronii outer membrane protein OmpAI through a tandem promoter system to ensure optimized antigen delivery.<br><br>RESULTS: Anal intubation with engineered L. casei in Channa argus stimulated compartmentalized mucosal immunity, evidenced by a six-fold elevation in hindgut IgT transcripts, significant infiltration of IgT[+] B cells, and pIgR mediated transcytosis, synchronized with systemic IgM activation. The probiotic treament accelerated pathogen clearance, improved survival rates to 42.9% compared to 12.5% in control group, and reorganized the commensal microbiome through a specific enrichment of beneficial Firmicutes.<br><br>DISCUSSION: This study elucidated a novel engineered-probiotic mucosal vaccination strategy for teleosts, providing a noninvasive, mucosal targeted immunoprophylactic strategy to decrease antibiotic dependency in aquaculture.},
}
@article {pmid41948584,
year = {2026},
author = {Yu, J and Liu, X},
title = {Gut microbiota and sepsis: mechanisms, clinical correlations, and therapeutic prospects.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1793041},
pmid = {41948584},
issn = {2296-858X},
abstract = {Sepsis is a life-threatening organ dysfunction triggered by a dysregulated host response to infection. According to the Global Burden of Disease Study, this condition affects over 50 million people annually and causes approximately 5.3 million deaths, with fatality rates varying significantly across populations and healthcare settings, ranging from about 20% to 50%, representing a major challenge in critical care medicine. In recent years, the gut microbiota, as the largest microbial ecosystem in the human body, has increasingly demonstrated a central role. It is not only essential for maintaining intestinal barrier integrity, immune homeostasis, and metabolic balance but also actively participates in the pathogenesis, progression, and outcomes of sepsis through modulating immune responses, influencing the production of key metabolites, and mediating gut-organ axes. This article systematically reviews the characteristics of sepsis-induced gut microbiota dysbiosis, delves into the molecular mechanisms by which dysbiosis drives immune disorders, metabolic disturbances, and multi-organ injury, evaluates the clinical potential and current limitations of microbiome-associated biomarkers, and summarizes recent advances and controversies in microbiota-targeted therapeutic strategies, including probiotics, fecal microbiota transplantation, precision nutrition, and antibiotic stewardship. This review aims to analyze the shortcomings and translational challenges in current research, providing a theoretical basis and forward-looking perspective for developing precise microbiome-based individualized management strategies for sepsis.},
}
@article {pmid41948629,
year = {2026},
author = {Osei-Poku, P and Wilson, MB and Shardow, ALK and Abakah, A and Amewu, EKA and Kyerewaa, CA and Larbi, A and Kwarteng, A},
title = {Tetracycline Resistance Pattern Among Lymphatic Filariasis-Hyperendemic Communities in Southern Ghana: A Mixed-Method Approach.},
journal = {Health science reports},
volume = {9},
number = {4},
pages = {e72242},
pmid = {41948629},
issn = {2398-8835},
abstract = {BACKGROUND AND AIM: Tetracyclines continue to serve as a cost-effective and essential treatment for common infections, particularly in resource-limited regions such as lymphatic filariasis (LF)-hyperendemic communities. The growing use of tetracycline-based antibiotics by symptomatic filarial lymphedema patients, likely influenced by the demonstrated benefits of anti-Wolbachia therapy, especially following doxycycline trials, underlines the necessity for vigilant monitoring of tetracycline resistance patterns. This study evaluated patients' antibiotic knowledge, attitude and practice in LF-endemic communities, and the resistance profiles of tetracycline-class antibiotics to assess the clinical impact of resistance on current anti-Wolbachia treatments.<br><br>METHODS: This cross-sectional study in Ghana's Ahanta West District enrolled 71 filarial lymphedema patients from four LF-hyperendemic communities. Structured questionnaires evaluated KAP on antibiotic use and resistance, complemented by microbiological analysis of wound swabs from 28 patients to profile the wound microbiome and assess tetracycline resistance.<br><br>RESULTS: Mean antibiotic knowledge (1.8&#x2009;&#xb1;&#x2009;1.0), attitude (1.4&#x2009;&#xb1;&#x2009;1.1), and practice (1.9&#x2009;&#xb1;&#x2009;1.1) scores were low, yielding a combined KAP score of 5.0&#x2009;&#xb1;&#x2009;1.9 (31.2%&#x2009;&#xb1;&#x2009;11.9%) with no significant correlation to the educational level of patients. the facilities survey, the primary healthcare facilities in the area stocked at least one tetracycline-class antibiotic (specifically tetracycline and/or doxycycline). Microbiological testing identified 68 distinct bacterial isolates (20 genera, 36 species; dominated by S. sciuri, S. aureus). Varied tetracycline resistance observed: doxycycline (35.3%), tetracycline (26.5%), and minocycline (17.6%), with nine (13.2%) isolates resistant to all three. High-resolution melting analysis detected tet(M) gene in 34.1% (14) of isolates with Tm variation (69.27&#xb0;C-73.06&#xb0;C), suggesting variants.<br><br>CONCLUSION: Multifaceted strategies are essential to curb tetracycline resistance and overuse. These include culturally adapted education to enhance antibiotic stewardship among patients and providers, optimized wound care protocols addressing polymicrobial infections through improved hygiene and tailored regimens, and ongoing resistance surveillance to track trends while promoting therapeutic alternatives.},
}
@article {pmid41948819,
year = {2026},
author = {Cheng, L and Cai, J and Auster, A and Cho, S and Keir, M and Rhee, H and Kapili, B and Shalon, D and Ning, M},
title = {Translational Modeling of Gut Microbiome-Mediated Drug Metabolism: A Case Example of Sulfasalazine.},
journal = {CPT: pharmacometrics &amp; systems pharmacology},
volume = {15},
number = {4},
pages = {e70246},
doi = {10.1002/psp4.70246},
pmid = {41948819},
issn = {2163-8306},
mesh = {Humans ; *Sulfasalazine/pharmacokinetics/administration &amp; dosage ; *Gastrointestinal Microbiome/physiology ; *Models, Biological ; Feces/microbiology ; Sulfapyridine/pharmacokinetics/metabolism ; Male ; Mesalamine/pharmacokinetics/metabolism ; Adult ; *Anti-Inflammatory Agents, Non-Steroidal/pharmacokinetics ; Female ; },
abstract = {The gut microbiome can contribute to drug metabolism and significantly influence pharmacokinetic (PK) behavior. Sulfasalazine is well-known to be metabolized by gut bacterial azoreductases into sulfapyridine and mesalamine. Despite in vitro and in vivo evidence of the gut microbiome's role in drug metabolism, quantitative predictions of its impact on drug PK are lacking. To address this gap, we used sulfasalazine and its metabolites as a case example to build a translational modeling framework to predict the extent of gut microbiome-mediated drug metabolism and subsequent PK of the metabolites. First, sulfasalazine conversion kinetics was measured in vitro using pooled human fecal homogenate incubation. In vitro Vmax was 650.5 and 200.9 pmol/min/mg feces, and Km was 3648 and 1605 μM for sulfapyridine and mesalamine formation, respectively. Based on colon and feces bacterial counts from nine healthy humans, a ratio of 0.47 was used to scale in vitro fecal Vmax to the colon level. Second, physiologically-based pharmacokinetic (PBPK) models for sulfasalazine, sulfapyridine, and mesalamine were built in Simcyp and verified to predict their oral PK when dosed directly. Lastly, sulfapyridine or mesalamine PK after dosing sulfasalazine was predicted by linking the parent and metabolite PBPK models with colon luminal metabolism kinetics. The observed sulfapyridine and mesalamine PK after dosing sulfasalazine were predicted with weighted average fold-errors of 1.21, 1.22, and 1.05 for Cmax, Tmax, and AUC, respectively. Overall, this in vitro to in vivo translation and modeling framework provides valuable insights for quantitatively predicting the in vivo impact of gut microbiome-mediated drug metabolism.},
}
@article {pmid41948926,
year = {2026},
author = {Garg, I and Singh, N and Rawat, S and Negi, T and Chaurasia, U and Gupta, P},
title = {Decoding the Skin Micro-Immune Milieu, Homeostasis, and Keratinocyte Trafficking in Psoriatic Disease.},
journal = {Immunological investigations},
volume = {},
number = {},
pages = {1-31},
doi = {10.1080/08820139.2026.2651752},
pmid = {41948926},
issn = {1532-4311},
abstract = {INTRODUCTION: The skin, acting as a complex interface between the immune system and microbiome, maintains balance through coordinated interactions among the epidermal barrier, microbiome, and immune responses. Psoriasis, a chronic autoimmune and inflammatory disorder, disrupts this balance by altering keratinocyte growth, immune signaling, and microbial diversity.<br><br>RESULTS AND DISCUSSION: The psoriatic environment exhibits dysbiosis, with reduced &#x3b1;-diversity and increased &#x3b2;-diversity, thereby worsening lesions. Beneficial microbes like Staphylococcus epidermidis provide protection, while opportunistic pathogens such as Staphylococcus aureus, Streptococcus pyogenes, Malassezia, Candida albicans, and HPV can trigger psoriatic outbreaks. Keratinocytes, essential to disease development and progression, interact actively with immune cells, fibroblasts, and Langerhans cells through cytokines, chemokines, and extracellular vesicles, influencing cell movement and inflammation. Changes in pathways like GLUT-1-mediated glucose metabolism and PI3K/Akt/mTOR signaling promote epidermal overgrowth, new blood vessel formation, and immune imbalance. Oxidative stress and mitochondrial dysfunction also weaken skin homeostasis. The skin's lymphoid tissue (SALT) and inducible SALT are crucial for immune surveillance and autoimmunity but become hyperactive in psoriasis.<br><br>CONCLUSION: Understanding the complex network linking the skin microbiome, immune system, and keratinocyte behavior is essential for developing advanced treatments. Combining immunology, molecular biology, and drug delivery science, using molecular docking, in-silico modeling, and nanotherapy, offers promising options for targeted psoriasis therapy.},
}
@article {pmid41949018,
year = {2026},
author = {Grabska, M and Gorecki, A and Pye, HV and Adriaenssens, EM and Grzesiuk, M},
title = {Phage Cocktail Designed for Wastewater Bioremediation Has Limited Effect on Crustacean Filtrator Microbiome Diversity and Health.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70329},
pmid = {41949018},
issn = {1758-2229},
support = {UMO-2021/03/Y/NZ9/00141 under the frame work of JPIAMR-ACTIONGA no. 963864//National Science Centre/ ; MR/W031205/1/MRC_/Medical Research Council/United Kingdom ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13631/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13633/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011011/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13634/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13635/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13636/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Bacteriophages/physiology ; *Microbiota ; *Wastewater/microbiology/virology ; *Daphnia/microbiology/virology/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; Bacteria/genetics/classification/virology ; Klebsiella pneumoniae/virology ; Pseudomonas aeruginosa/virology ; Enterobacter/virology ; Female ; Biodiversity ; },
abstract = {In this study we investigated the impact of a phage cocktail on Daphnia magna microbiome and the life-history parameters. A mixture of four phages able to infect strains of Klebsiella pneumoniae, Enterobacter sp. and Pseudomonas aeruginosa was tested on three D. magna clones. The host-associated microbiome composition in both the examined variants and the control was analysed using 16S rRNA amplicon sequencing. Additionally, the survival, growth rate, age, size at the first reproduction, and neonate per female were assessed. The analysis revealed minor shifts in microbial composition following phage exposure. Nevertheless, results showed that the phage cocktail increased microbiome diversity. None of the life-history parameters studied were affected by the presence of the phage cocktail, and no adverse effects were observed. The results indicated that under laboratory conditions the phage cocktail is safe for D. magna and its microbiome.},
}
@article {pmid41949064,
year = {2026},
author = {Chongtham, C and Biswas, T and Kumari, N and Kar, R and Jyotsna, and S, J and Pant, A and S Patil, V and Arimbasseri, GA},
title = {The JNK2-microbiome axis modulates gut barrier integrity through microbial acetate.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2651962},
doi = {10.1080/19490976.2026.2651962},
pmid = {41949064},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Acetates/metabolism ; *Intestinal Mucosa/microbiology/metabolism ; Mice, Inbred C57BL ; Milk ; *Mitogen-Activated Protein Kinase 9/metabolism/genetics ; Female ; Weaning ; Dextran Sulfate ; Male ; Diet, High-Fat ; },
abstract = {BACKGROUND: Weaning involves a nutritional shift from fat-rich milk to carbohydrate-based solid food, reshaping metabolism, microbiota, and gut immune tolerance. While dairy remains a component of the human diet beyond weaning, the impact of continued milk supplementation on gut epithelial homeostasis remains poorly understood.<br><br>RESULT: Here, using a mouse model, we show that continued milk-based feeding post-weaning promotes intestinal barrier function by enriching the commensal bacterium Dubosiella newyorkensis, which produces acetate to activate epithelial JNK2 signaling. This pathway enhances barrier integrity and suppresses inflammation induced by mild dextran sodium sulfate (DSS) treatment. In contrast, feeding a lard-based high-fat diet or transient pharmacologic inhibition of JNK2 induces epithelial P38 activation, resulting in barrier disruption and inflammation. Importantly, the beneficial effects of milk were observed only if they were initiated during the weaning period, when the microbiome is in a metastable transitional state. Initiation of the same intervention two weeks after weaning led to P38 activation and inflammatory responses.<br><br>CONCLUSION: Our findings show that immediate post-weaning milk supplementation preserves a beneficial gut microbiome, marked by the persistence of D. newyorkensis and enhanced gut barrier integrity. Even a one-week delay eliminates this protective effect, emphasizing the critical timing of post-weaning nutritional intervention for maintaining intestinal health.},
}
@article {pmid41949254,
year = {2026},
author = {Du, J and Sun, Y and Yu, D and Lu, S and Yu, S and Wang, M and Zhou, G and Xu, S and Zhang, L and Zhu, Y and Zhou, L},
title = {Oral liposomal co-delivery of ultrasmall ceria and 5-aminosalicylic acid alleviates DSS colitis via ROS scavenging and microbiome remodeling.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6tb00173d},
pmid = {41949254},
issn = {2050-7518},
abstract = {Inflammatory bowel disease (IBD) is a refractory gastrointestinal disorder characterized by sustained intestinal inflammation, mucosal barrier dysfunction, and gut dysbiosis. Excess reactive oxygen species (ROS) is a key driver of these pathological processes. Although CeO2-based nanozymes can scavenge ROS, their clinical application is limited by poor aqueous stability. Here, we developed an oral nanozyme by co-encapsulating ultrasmall CeO2 nanoparticles and the clinical drug 5-aminosalicylic acid (5-ASA) within liposomes. The resulting formulation (CeLA) exhibited excellent colloidal stability and robust ROS-scavenging activity and provided marked cytoprotection against oxidative stress in vitro. In a dextran sulfate sodium (DSS)-induced colitis model, CeLA alleviated clinical symptoms, restored intestinal barrier integrity, and suppressed pro-inflammatory cytokine expression. Notably, CeLA also reshaped the dysbiotic gut microbiome by reducing pro-inflammatory bacterial taxa. This multifunctional nanozyme integrates antioxidant, anti-inflammatory, and microbiome-modulating effects, offering a promising therapeutic strategy for IBD.},
}
@article {pmid41949255,
year = {2026},
author = {Wang, W and Guan, R and Wang, Q and Xiong, L and He, A and Bai, L and Li, Z and Lu, C and Zhang, S and Zhao, C and Yin, Y and Li, J and Wang, Y and Jiang, G},
title = {Traditional Fermentation Amplifies PFAS Bioaccessibility: Defining Fermented Fish Products as an Unrecognized Source of Dietary Exposure.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15723},
pmid = {41949255},
issn = {1520-5851},
abstract = {Per- and polyfluoroalkyl substances (PFAS), as a class of persistent organic pollutants, are well-characterized environmental and human health threats; however, their behavior in food systems, particularly during fermentation, remains poorly understood. Here, we show that traditional fermentation significantly enhances the PFAS bioaccessibility. Through a 300 day model fermentation system, we observed near-complete release of several major PFAS congeners. While microbial transformation of the PFAS precursor of N-ethyl perfluorooctane sulfonamide (N-EtFOSA) was observed, persistent congeners of perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) remained unaffected during microbiome restructuring. We demonstrate that matrix degradation and microbial activity synergistically modify the PFAS binding states. In silico modeling reveals a shift in bioaccessibility determinants from specific binding to partitioning behavior, establishing that fermentation liberates PFAS via two key pathways: microbial degradation of structural components, releasing bound contaminants and altered PFAS partitioning during digestion. Our findings establish fermentation as a previously unrecognized amplifier of dietary PFAS exposure, with substantial implications for food safety and public health, especially in populations with high consumption of traditionally fermented products.},
}
@article {pmid41949309,
year = {2026},
author = {Yang, P and Wu, Z and Zhang, S and Yan, L and Yan, Y and Zhou, F and Ren, X and Li, Y and Gu, S and Gao, S and Zhang, Z and Zhang, Y and Zhu, H and Li, H and Zhang, Z},
title = {Predicting dairy cattle PL via longitudinal rumen microbiome dynamics using machine learning approaches.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0296925},
doi = {10.1128/spectrum.02969-25},
pmid = {41949309},
issn = {2165-0497},
abstract = {Aging is a spontaneous biological process involving intricate regulatory mechanisms over time. Studies in mice and humans indicate that the gut microbiota is closely linked to the aging process and plays an important role in it. However, the relationship between the rumen microbiota and aging in dairy cows remains unclear. In this study, we characterized rumen microbial differences across different parities in 341 dairy cows using 16S rRNA amplicon sequencing and identified microbial markers associated with productive lifespan (PL) and farm profitability through machine learning analysis. Our findings reveal that as parity increases, the rumen microbiota undergoes systematic succession: alpha diversity indices significantly decrease, microbial interactions weaken, the abundance of Proteobacteria increases, while the abundance of Bacteroidetes decreases in higher-parity cows. By integrating machine learning with 16S sequencing, we identified characteristic microbial markers predictive of PL and farm profitability. Specifically, the support vector regression model achieved a predictive performance with an area under the curve (AUC) of 0.788 and identified eight key genera associated with the PL of dairy cows. Meanwhile, the random forest (RFTEST) model attained an AUC of 0.763 and selected eight key microorganisms linked to the economic benefits of the farm, with fivefold cross-validation confirming the reliability of RFTEST. Combined with SHapley Additive exPlanations (SHAP) analysis, the genus-level taxa Eubacterium_hallii_group and Prevotella_7 can serve as indicator strains for PL and farm profitability in dairy cows. Therefore, alterations in the rumen microbiota may serve as a key driver of aging in dairy cows. This study aims to provide insights for improving PL and farm profitability through the modulation of rumen microbiota.IMPORTANCEIn the dairy industry, longevity is a critical economic trait that directly impacts overall farm profitability. Although dairy cows have a natural lifespan of approximately 20 years-with optimal productivity often extending beyond the fifth parity-their average PL is only about 2.7 parities. Identifying factors influencing PL is therefore crucial. Given the vital role of the rumen microbiota in regulating dairy performance, milk fat/protein synthesis, and other key physiological processes, elucidating its correlation with PL is essential for developing probiotic interventions to enhance longevity. Furthermore, early detection of aging-associated microbial signatures could facilitate proactive adjustments to feeding strategies. Notably, this is the first study to link parity-driven microbiome succession with PL prediction in dairy cattle. Consequently, by identifying microbial molecular markers linked to PL and potential probiotic targets, this study highlights promising opportunities to improve dairy cow health and advance sustainable dairy farming practices.},
}
@article {pmid41949699,
year = {2026},
author = {Shen, H and Zhang, L and Ma, X and Yin, Y and Wang, J and Tan, B},
title = {Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41949699},
issn = {1869-1889},
abstract = {The human microbiome is a dynamic ecosystem that profoundly influences host physiology through complex molecular interactions. Advances in high-throughput profiling now enable multi-omics measurements at scale, yet integration remains difficult due to biological complexity, technical variability, sparsity, and small cohorts. This review targets bioinformatics practitioners and clinical microbiology researchers applying machine learning to host-microbiome studies. Here, we survey state-of-the-art methods for integrating heterogeneous data types and highlight algorithmic innovations for high dimensionality and small cohorts. We also examine approaches for interpretability that translate mechanistic insight into clinically actionable models. Finally, we outline a standardized benchmarking framework emphasizing open data, rigorous evaluation, and biologically informed architectures. By synthesizing multi-omics measurements with advanced analytics, we chart a pathway toward personalized, microbiome-based therapies while deepening our understanding of host-microbiome crosstalk.},
}
@article {pmid41950008,
year = {2026},
author = {Mifflin, KA and Kigerl, KA and Hudson, LC and Guan, Z and Popovich, PG},
title = {Protocol for performing traumatic spinal cord injury surgery on mice in germ-free isolators and assessing injury recovery and pathophysiology.},
journal = {STAR protocols},
volume = {7},
number = {2},
pages = {104488},
doi = {10.1016/j.xpro.2026.104488},
pmid = {41950008},
issn = {2666-1667},
abstract = {An altered gut microbiome affects recovery from traumatic spinal cord injury (SCI). Here, we present a protocol for performing SCI survival surgery on mice in germ-free isolators. Specifically, we describe steps for colonization, preparing surgical tools, performing surgery, and post-surgical care. We then outline procedures for behavioral assessment, followed by collecting and processing tissue to assess injury recovery and pathophysiology. This protocol can be easily adapted to study the gut microbiome's influence on other forms of central nervous system injury.},
}
@article {pmid41950061,
year = {2026},
author = {Dayman, NA and Patel, D and Wisniewska, A and Fletcher, E and Ahmed, MI and Modha, D and Barer, MR and Gaillard, EA},
title = {Face mask sampling for the detection of microbes in expelled aerosols and the impact of airway clearance on microbial yield in children with cystic fibrosis: a feasibility trial.},
journal = {Journal of medical microbiology},
volume = {75},
number = {4},
pages = {},
doi = {10.1099/jmm.0.002150},
pmid = {41950061},
issn = {1473-5644},
mesh = {Humans ; *Cystic Fibrosis/microbiology ; Child ; Male ; Female ; Adolescent ; Child, Preschool ; *Masks/microbiology ; Prospective Studies ; Cross-Sectional Studies ; Feasibility Studies ; Infant ; Sputum/microbiology ; *Bacteria/isolation &amp; purification/classification ; Specimen Handling/methods ; Pseudomonas aeruginosa/isolation &amp; purification ; Aerosols ; *Respiratory Tract Infections/microbiology/diagnosis ; },
abstract = {Background. Early identification of pulmonary exacerbations is vital for the management of cystic fibrosis (CF). Non-invasive airway sampling in preschool children can be inaccurate. Face mask sampling (FMS) is a novel non-invasive approach that can be used to assess microbial airway pathogens in patients with CF.Methods. Prospective cross-sectional study in children with CF. Children wore a suitably sized face mask fitted with two strips of a polyvinyl alcohol sampling matrix for a period of 15 min. Routine microbiology sampling using cough swab, sputum and/or bronchoalveolar lavage was completed following FMS. Children then completed their routine airway clearance with their physiotherapist. Following this, a separate face mask was worn for a further 15 min, after which further routine microbiology sampling (cough swab or sputum) was completed. The face masks were stored at room temperature before transfer and processing in the laboratory to quantify bacterial burden and identify key pathogens such as Mycobacterium abscessus and Pseudomonas aeruginosa.Results. Eleven children (six male, median age 12 years, range 1-16 years), from the Leicester CF cohort were included. All patients tolerated the FMS. Nine face mask samples from 11 participants isolated respiratory pathogens, including M. abscessus (n=3). P. aeruginosa was not detected on face mask samples. There was a trend towards an increase in microbial yield (prGen16s) following airway clearance (n=5), but this did not reach statistical significance.Conclusions. FMS systems are feasible for children and young people with CF. They may provide an effective method to detect exhaled lower airway pathogens including non-tuberculous mycobacteria. The effect of physiotherapy on the exhaled microbiome needs to be explored further.},
}
@article {pmid41950213,
year = {2026},
author = {Babbo, CC and van Rensburg, J and Mellet, J and Velaphi, SC and Nakwa, FL and Masemola, MYK and Kali, GTJ and Foden, CJ and Oosthuizen-Vosloo, S and Chellan, V and Mosuwe, O and Mistry, P and Buyens, ARM and Barmania, F and Pillay, S and Ballot, DE and Coetzee, M and Horn, AR and Wright, C and Schubertand, PT and Pepper, MS},
title = {Protocol: A multi-factorial, multi-centre study, for biomarker identification in healthy controls for comparison to babies with moderate-severe NESHIE.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346798},
pmid = {41950213},
issn = {1932-6203},
mesh = {Humans ; Infant, Newborn ; *Biomarkers/blood/analysis/metabolism ; *Hypoxia-Ischemia, Brain/genetics/metabolism/diagnosis ; Female ; Male ; DNA Methylation ; Case-Control Studies ; },
abstract = {Neonatal encephalopathy suspected to be hypoxic-ischaemic encephalopathy (NESHIE) remains a leading cause of neonatal mortality and long-term neurodevelopmental impairment, particularly in low- and middle-income countries. While therapeutic hypothermia reduces mortality in moderate to severe cases, a significant proportion of affected infants continue to experience adverse neurological outcomes. This multi-centre observational study aims to elucidate the clinical and biological mechanisms underlying NESHIE by conducting a comprehensive comparative analysis of neonates with moderate to severe NESHIE and healthy term controls. Participants with NESHIE were previously recruited under an existing approved protocol (University of Pretoria ethics reference: 481/2017), and healthy neonates will be newly enrolled. The study will integrate clinical and molecular data to: (1) identify clinical risk factors associated with NESHIE; (2) perform whole genome sequencing to detect relevant genetic variants; (3) analyse DNA methylation patterns via bisulfite sequencing; (4) assess gene expression using bulk and single-cell RNA sequencing (RNA-seq); (5) characterise proteomic and metabolomic profiles through liquid chromatography-mass spectrometry of dried blood spot samples; (6) examine the placental microbiome; and (7) evaluate placental histopathological differences between groups. By offering a multi-dimensional view of the molecular and microbial landscape of NESHIE in a South African cohort, this study aims to enhance understanding of the disease pathogenesis. Ultimately, the findings may support the development of biomarkers for early diagnosis, improve risk stratification, and guide novel therapeutic strategies for affected neonates. The study has received National Health Research Database (NHRD) registration under GP_202411_053 (Gauteng) and WC_202411_026 (Western Cape), with ethics approvals granted by the University of Pretoria (184/2024), University of the Witwatersrand (250406B), and Stellenbosch University (N24/12/154_RECIP_UP184/2024) as well as their respective tertiary academic hospitals.},
}
@article {pmid41950528,
year = {2026},
author = {Federico, VA and Cliffel, DE and Gaddy, JA and Townsend, SD},
title = {Shaping of the Infant Gut Microbiome by Milk Oligosaccharides.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051024-062915},
pmid = {41950528},
issn = {1545-4509},
abstract = {The gut microbiome governs aspects of human growth and development. While human milk's primary purpose is metabolism, it also provides nonnutritious biologics and macromolecules. This mixture includes the human milk oligosaccharides (HMOs), which are indigestible and survive the low pH of the stomach and small intestine, reaching the large intestine intact. Here, HMOs serve as prebiotics for beneficial bacteria, providing a competitive growth advantage over potential pathogens. Upon metabolizing HMOs, commensals generate short-chain fatty acids and metabolites that enhance the gut community. Therefore, HMOs work to develop and sustain the gut microbial community as a living therapeutic that prevents illness from potential microbial pathogens and modulates development of the infant gut. The goal of this targeted review is to characterize the roles HMOs play in governing bacterial and viral members of the infant gut microbiome, describing how HMOs both define a healthy microbiota and prevent microbial dysbiosis.},
}
@article {pmid41950533,
year = {2026},
author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X},
title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128511},
doi = {10.1016/j.micres.2026.128511},
pmid = {41950533},
issn = {1618-0623},
abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.},
}
@article {pmid41950535,
year = {2026},
author = {Adeniji, A and Liu, Q and Huang, X and Lu, X and Li, S and Guo, R},
title = {Correlation between root exudate composition and beneficial bacteria underlies Fusarium wilt resistance in cucumber.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128512},
doi = {10.1016/j.micres.2026.128512},
pmid = {41950535},
issn = {1618-0623},
abstract = {Rhizosphere microbes regulated by root exudates play important roles in promoting plant growth and suppressing soil-borne diseases. However, their functions in monoculture systems are not well studied. Here, we integrated metabolomic and microbiome analyses to compare root exudate profiles and rhizosphere communities of Fusarium oxysporum f. sp. cucumerinum (Foc) resistant (CL11) and susceptible (ZN6) cultivars grown in naturally infested, continuous-cropping soil. The asymptomatic, resistant cultivar CL11 (CL11H) exhibited a metabolic signature enriched in defensive compounds (ganoderic acid I and L-isoleucine) and harbored a beneficial bacterial community dominated by Streptomyces, Cellvibrio, and Ensifer. While the asymptomatic susceptible cultivar ZN6 (ZN6H) showed elevated levels of primary metabolites (methylmalonic and succinic acids) and an enrichment in the relative abundance of Amycolatopsis and Flavobacterium. Upon symptom development, susceptible symptomatic ZN6 (ZN6D) mounted a "cry-for-help" response, accumulating L-tryptophan and citric acid, which correlated with recruitment of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. Conversely, resistant symptomatic CL11 (CL11D) deployed a metabolic profile (L-3-cyanoalanine, 4-hydroxybenzoyl glucose, D-fructose), which enriched Bacillus and Cellvibrio. Exogenous application of citric acid, L-isoleucine, L-tryptophan, hexadecanedioic acid, and succinic acid to susceptible ZN6 plants significantly suppressed wilt disease. These metabolites restructured the rhizosphere bacterial communities, demonstrated by enrichments of Pseudomonas, Burkholderia-Caballeronia-Paraburkholderia, and Comamonadaceae by L-tryptophan, as well as Pseudomonas and Bacillus promoted by L-isoleucine and citric acid, respectively. Moreover, succinic acid suppressed disease through microbiome-mediated mechanisms despite its in vitro positive effect on Foc growth. These findings demonstrate that root exudates are linked to cultivar-specific disease outcomes, and that target metabolite application can suppress Fusarium wilt through microbiome-mediated mechanisms or a combined antifungal mode.},
}
@article {pmid41950737,
year = {2026},
author = {Jung, Y and Yeo, S and Kim, RH and Seo, CH and Joo, SY and Shin, JH and Cho, YS},
title = {Response to antihistamines in post-burn pruritus is associated with gut microbiota composition and function: A prospective cohort study with a nested case-control analysis.},
journal = {Burns : journal of the International Society for Burn Injuries},
volume = {52},
number = {5},
pages = {108005},
doi = {10.1016/j.burns.2026.108005},
pmid = {41950737},
issn = {1879-1409},
abstract = {Post-burn pruritus (PBP) is a common complication following burn injuries, with substantial interindividual variability in response to antihistamine treatment. While altered gut microbial communities have been observed in patients with histamine intolerance, no studies have examined the relationship between gut microbiota and antihistamine responsiveness in burn patients. Therefore, we hypothesized that the gut microbiome composition differs according to antihistamine responsiveness in patients with PBP. A total of 56 male burn patients categorized into no-pruritus, antihistamine-responsive (HR), and antihistamine-nonresponsive (HNR) groups. Fecal samples were collected at baseline and after 8 weeks of antihistamine treatment. Microbial composition was analyzed using 16S rRNA gene sequencing, and functional prediction was conducted with PICRUSt2. Overall microbial diversity did not differ significantly between groups; however, distinct taxonomic and functional features were identified. The HR group was characterized by enrichment of Sutterella and showed a temporal increase in microbial diversity and Bifidobacterium abundance after 8 weeks of treatment, accompanied by enrichment of redox-related microbial functions. In contrast, the HNR group showed increased Akkermansia and Acidaminococcus with reduced antioxidant defenses and activation of non-histaminergic pruritic pathways. This study is the first to suggest that gut microbiota composition and function are associated with antihistamine responsiveness in patients with PBP. Distinct microbial signatures and functional pathways were identified among non-pruritic individuals, antihistamine responders, and non-responders. Our findings indicate a potential involvement of gut microbes in the pathophysiology of PBP and highlight the possibility of microbiota-targeted therapeutic strategies.},
}
@article {pmid41938779,
year = {2026},
author = {Luttenschlager, H and Noel, G and Alabi, T and Carpentier, J and Francis, F and Megido, RC},
title = {Microbial drivers of Black Soldier Fly biowaste valorization: from microbiome functions to scalable insect-microbe systems.},
journal = {AIMS microbiology},
volume = {12},
number = {1},
pages = {126-149},
pmid = {41938779},
issn = {2471-1888},
abstract = {Biowaste and agro-industrial co-products continue to increase with population growth and rising living standards, calling for scalable valorization strategies that go beyond simple mineralization. The black soldier fly (BSF) has emerged as a practical bioconversion platform capable of channeling biodegradable organic waste into high-value proteins, lipids, and chitin. In parallel, microbial interventions are increasingly recognized as key levers for substrate conditioning, process stabilization, and performance optimization in BSF-based systems. In this review, we adopted a function-first perspective to examine how microbial processes shape and connect three major biological valorization routes: aerobic composting, anaerobic digestion (AD), and BSF bioconversion. Rather than focus on taxonomic inventories, we synthesized evidence on microbial functions that matter in practice, including extracellular hydrolysis of complex polymers, regulation of short-chain fatty acids, detoxification and pathogen suppression, and process stabilization. We further reviewed microbe-assisted strategies, such as lactic pre-fermentation, directed acidogenesis, and probiotic or defined consortia and their effects on waste reduction, conversion efficiency, product quality, and sanitary safety. Finally, we translated these microbial mechanisms into scalable design principles for configuring and operating integrated insect-microbe systems, highlighting how microbial functions underpin reproducible, enterprise-ready performance across composting, AD, and BSF-integrated workflows.},
}
@article {pmid41938782,
year = {2026},
author = {Mataragka, A and Ringø, E and Papastathis, AK},
title = {Climate-driven restructuring of sediment microbiomes and ecosystem functions in aquaculture systems.},
journal = {AIMS microbiology},
volume = {12},
number = {1},
pages = {150-172},
pmid = {41938782},
issn = {2471-1888},
abstract = {Aquaculture expansion is occurring under accelerating climatic pressure. Warming, marine heatwaves, deoxygenation, salinity fluctuation, and intensified nutrient loading act simultaneously in aquaculture sediments, altering redox gradients and substrate fluxes that structure microbial communities. These stressors strengthen deterministic environmental filtering, reorganize interaction networks toward reduced-state dominance, and redistribute functional investment within sediment microbiomes; the biogeochemical engines regulating nutrient cycling, water quality, and disease dynamics. Such restructuring is associated with altered nitrogen processing, modified greenhouse gas fluxes, sulfide accumulation, enhanced pathogen performance, and enrichment of antimicrobial resistance determinants, with direct implications for production stability and disease risk. Evidence is synthesized to integrate quantified environmental forcing, ecological assembly mechanisms, and molecular functional responses into a unified framework linking microbial restructuring to ecosystem performance and operational resilience. Structural and functional microbial indicators suitable for early detection of redox compression and functional destabilization are evaluated, alongside resilience-oriented strategies spanning ecological design, microbiome management, engineering control, and adaptive monitoring. Despite substantial empirical progress, major gaps remain in resolving compound-stressor interactions, temporal reversibility, cross-system threshold comparability, and predictive modeling of microbial assembly under multi-driver forcing. Addressing these gaps is essential for developing mechanistically grounded, climate-resilient aquaculture systems.},
}
@article {pmid41938867,
year = {2026},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R},
title = {Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779554},
pmid = {41938867},
issn = {2235-2988},
mesh = {Female ; Humans ; Phylogeny ; *Candidiasis, Vulvovaginal/virology/microbiology ; Genome, Viral ; Vagina/virology/microbiology ; Metagenomics ; Capsid Proteins/genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Adult ; *Double Stranded RNA Viruses/genetics/isolation &amp; purification/classification ; },
abstract = {INTRODUCTION: Vulvovaginal candidiasis (VVC) is a common fungal infection affecting women worldwide. Although the vaginal microbiome has been extensively studied, the diversity of viruses present in the vaginal microenvironment remains poorly characterized.<br><br>METHODS: Vaginal swab samples from patients diagnosed with VVC were subjected to viral metagenomic sequencing using an Illumina NovaSeq platform. Viral contigs were assembled, annotated, and screened against public databases. Genome organization, pairwise sequence identity, and phylogenetic relationships were analyzed to determine the evolutionary position of the detected virus.<br><br>RESULTS: Here, we identified a novel double-stranded RNA virus, tentatively named Vaginal-associated orthototivirus-like 1 (VAOTV-1), in vaginal swab samples from patients with vulvovaginal candidiasis. VAOTV-1 was represented by a partial genome sequence of 4,332 bp, encoding a complete RNA-dependent RNA polymerase (RdRp; 729 amino acids) and a partial capsid protein (CP; 532 amino acids). The encoded RdRp protein shared a maximum amino acid sequence identity of 47.43% with Totiviridae sp. isolate 22AP502 (GenBank accession no. XTJ93729.1), reported from Bandicota indica. In contrast, the CP showed no significant similarity to any sequences currently available in public databases, and BLASTn searches against the NCBI nucleotide database did not yield any significant matches. Phylogenetic analysis, together with the relatively low amino acid sequence identity to known members of the genus Totivirus within the family Orthototiviridae, suggests that VAOTV-1 represents a distinct and highly divergent orthototivirus-like lineage.<br><br>DISCUSSION: These findings indicate that VAOTV-1 represents a highly divergent orthototivirus-like virus and expands the known diversity of totiviruses detected in human-associated mucosal environments. This discovery highlights previously unrecognized viral diversity in the vaginal virome and provides new insights into viruses associated with vulvovaginal candidiasis.},
}
@article {pmid41939093,
year = {2026},
author = {},
title = {Gut microbiome metaproteomics for colorectal cancer risk stratification: moving from taxonomic signatures to functional protein biomarkers: Retraction.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {4},
pages = {2724},
pmid = {41939093},
issn = {2049-0801},
abstract = {[This retracts the article DOI: 10.1097/MS9.0000000000004567.].},
}
@article {pmid41939102,
year = {2026},
author = {Mohan, A and Sultany, A and Fatima, SB and Hasan, ZW and Butt, MD and Alkhazender, AHJ and Lal, PM and Aminpoor, H and Karimi, H and Kumar, V and Tejwaney, U and Kumar, S},
title = {Association between atrial fibrillation and gastrointestinal bleeding: pathophysiology, risk stratification, and management - a narrative review.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {4},
pages = {2566-2573},
pmid = {41939102},
issn = {2049-0801},
abstract = {Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, significantly increasing the risk of thromboembolic events, necessitating anticoagulation therapy. However, anticoagulation, particularly with novel oral anticoagulants, elevates the risk of gastrointestinal bleeding (GIB), creating a clinical dilemma in managing AF patients. This narrative review explores the pathophysiology linking AF and GIB, emphasizing the hypercoagulable state in AF and the mucosal damage caused by anticoagulants. Epidemiological data reveal that GIB incidence in AF patients ranges from 1.32% to 5.4% annually, with risk factors including older age, prior GIB, and concomitant antiplatelet use. Risk stratification tools such as CHA2DS2-VASc and HAS-BLED aid in balancing thromboembolic and bleeding risks, though their predictive performance remains modest. Comparative studies highlight that rivaroxaban carries a higher GIB risk, while apixaban offers a safer profile. Management strategies include proton pump inhibitors for prophylaxis, endoscopic interventions for acute bleeding, and individualized decisions on resuming anticoagulation post-GIB, typically within 7-30 days. Emerging research on the gut microbiome's role in AF pathogenesis suggests potential novel therapeutic avenues. A multidisciplinary approach involving cardiologists, gastroenterologists, and hematologists is essential to optimize outcomes. Future directions include developing safer anticoagulants, refining risk prediction models, and exploring microbiome-targeted therapies.},
}
@article {pmid41939187,
year = {2026},
author = {Zhang, H and Wu, ZH and Sun, XM and Sun, C and Chang, J and Yuan, L},
title = {Gender-specific and dose-dependent responses to L-se-methylselenocysteine are mediated by the gut microbiota-metabolite axis: implications for intestinal homeostasis and safe clinical application.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1803630},
pmid = {41939187},
issn = {2296-861X},
abstract = {INTRODUCTION: L-Se-methylselenocysteine is a prominent naturally occurring organic selenium compound with notable health benefits and validated efficacy in managing various diseases. However, its impacts on intestinal microecology and the role of the gut microbiota-metabolite axis in mediating host health outcomes remain unclear.<br><br>METHODS: Sprague-Dawley rats were subjected to a 90-day chronic toxicity study, combined with integrated intestinal microbiome and metabolome analysis, to explore L-Se-methylselenocysteine's effects and underlying mechanisms.<br><br>RESULTS: L-Se-methylselenocysteine at doses of 0.25-0.75 mg/kg bw/ day enhanced gut microbiota biodiversity, enriched probiotic abundance, ameliorated hematological and serum biochemical indices, and promoted synthesis of beneficial metabolites via modulating the gut microbiota-metabolite axis. Notably, high-dose L-Se-methylselenocysteine (2.25 mg/kg bw/day) induced irreversible hepatosplenic injury in female rats but not males, with gender-specific responses mediated by the axis.<br><br>DISCUSSION: L-Se-methylselenocysteine confers intestinal health benefits through the gut microbiota-metabolite axis, while defining a safe dosage range. This study provides a solid scientific basis for the rational application of L-Se-methylselenocysteine as a selenium supplement.},
}
@article {pmid41939240,
year = {2026},
author = {Barrera-Suarez, MA and Zhao, CY and Karnatovskaia, LV and Sung, J},
title = {Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2650247},
pmid = {41939240},
issn = {2993-3935},
abstract = {Diet-gut microbiome interactions drive substantial inter-individual variability in metabolic responses to food, a fact that challenges the efficacy of uniform dietary recommendations. To address this complexity, advances in multi-omics profiling, dietary assessment technologies, and host clinical phenotyping now generate high-resolution multimodal datasets. However, managing these vast amounts of data necessitates the integration of artificial intelligence (AI) and machine learning (ML) approaches. In this review, we first delineate the multimodal data landscape and its associated computational workflows. These range from the initial preprocessing of heterogeneous inputs (filtering, normalization, dimensionality reduction) to ML modeling strategies designed to address high dimensionality, sparsity, and compositionality through feature engineering and regularization. We then summarize core ML applications, including the classification of habitual dietary patterns from microbiome signatures, prediction of postprandial metabolic responses, responder stratification, and in silico simulation of dietary perturbations. Furthermore, recent randomized controlled trials demonstrate the tangible clinical potential of AI-guided personalization. Next, we highlight composite microbiome health metrics and diet-specific indices, such as GMWI2 and DI-GM. These tools are essential because they condense high-dimensional taxonomic profiles into interpretable wellness scores for monitoring diet-induced shifts. We subsequently examine genome-scale metabolic models and microbiome "digital twins" that mechanistically link dietary substrates to community metabolism and host-relevant metabolites. We also discuss emerging hybrid AI-mechanistic frameworks that enhance interpretability, biological plausibility, and scalability. Finally, we outline translational priorities-including the development of diverse longitudinal cohorts, standardized benchmarking, and clinically trustworthy AI-that are required to realize equitable, microbiome-informed precision nutrition.},
}
@article {pmid41939241,
year = {2026},
author = {Pereira, FC and El Aidy, S},
title = {Drug-microbiome interactions: What we know and why predictive translation remains elusive.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2649166},
pmid = {41939241},
issn = {2993-3935},
abstract = {Medication-induced alterations of the gut microbiome influence drug efficacy, toxicity, and long-term outcomes. Despite extensive evidence for drug-microbe interactions, predictive translation into clinical practice remains limited. Generalization from shifts in taxonomic profiles, mechanistic studies or isolated enzymatic assays is challenging because microbial activity is highly context-dependent. Drug-microbiome interactions are shaped by host factors including pH, transit time, nutrient and cofactor availability, and spatial organization along the gastrointestinal tract. Here, we argue that predictive translation requires measuring functional outputs, site-specific activity, ecological interactions, and host-contextual modulation, rather than static microbial properties.},
}
@article {pmid41939697,
year = {2026},
author = {Bagul, SY and S, S and Saran, PL and Khadke, GN and Das, M},
title = {Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786817},
pmid = {41939697},
issn = {1664-302X},
abstract = {Ashwagandha, Withania somnifera (L.) Dunal is a perennial evergreen shrub widely used to treat mental health disorders and physical debility, and to enhance overall physiological function. Variations in genotype and geographic origin significantly influence rhizospheric microbial communities by altering soil physicochemical properties. This study applied shotgun metagenomic sequencing to investigate microbial community shifts in the rhizosphere of Nagori Ashwagandha (RN) from Rajasthan, Vallabh Ashwagandha-1 (GV) from Gujarat, and Nagori Ashwagandha from Rajasthan cultivated in Gujarat (GN). Fusarium wilt incidence was 67%, affecting the roots, which represent the most economically important part of ashwagandha. Taxonomic analysis identified Actinomycetota (46-60%) and Pseudomonadota (35-42%) as the predominant phyla, with Nocardioides (3.1-8.8%), Streptomyces (4.5-6.5%), and Bradyrhizobium (1-1.6%) as dominant genera across all groups in metagenomic analysis. Alpha-diversity analysis revealed higher species richness and Simpson's index in the GV group compared to the GN and RN groups. Beta-diversity assessment using Bray-Curtis distances showed partial clustering of GN and RN relative to GV in principal coordinate analysis and hierarchical dendrograms. Functional profiling based on KEGG annotation indicated that core metabolic and cellular pathways predominated across all genotypes, with no significant differences in Tier 1 and Tier 2 functional categories. To our knowledge, this represents the first shotgun metagenomic analysis of ashwagandha. Culturomics analysis yielded seventeen isolates from two rhizospheric locations; among these, Bacillus subtilis DMA1 exhibited the highest mycelial inhibition against Fusarium solani (64%), with a germination rate of 98%, root length of 2.1 cm, shoot length of 1.3 cm, seed vigor index of 333.2, and maximum fresh biomass of 1.12 g. Co-inoculation with F. solani and Bacillus subtilis DMA1 in pot trials significantly increased root length (20.1 cm), shoot length (39.5 cm), root girth (14.9 mm), and total biomass (51.1 g) compared to control and Fusarium-only treatments. These findings indicate that Bacillus subtilis DMA1 reduced wilt incidence by 70% and enhanced plant growth under pathogen-stress conditions.},
}
@article {pmid41939699,
year = {2026},
author = {Zeng, H and Gao, Z and Wang, Z and Li, K and Xu, B and Yan, Z and Gu, Y and Du, W and Ding, H and Wang, J},
title = {Temporal succession and assembly of marine bacterial communities in Maxwell Bay, Antarctica during summer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1748960},
pmid = {41939699},
issn = {1664-302X},
abstract = {INTRODUCTION: In recent years, ecological feedbacks driven by climate change have become increasingly prominent. The polar amplification effect has made Antarctic ecosystems pivotal indicators for reflecting global climatic impacts. As core drivers of biogeochemical cycling, marine microbes play a central role. Therefore, deciphering their temporal dynamics and assembly mechanisms is crucial for projecting the trajectories of polar ecosystems. However, the intrinsic ecological processes regulating microbial summer succession, particularly the relative contribution of deterministic processes, remain insufficiently quantified.<br><br>METHODS: In the present study, Maxwell Bay, Antarctica-a coastal marine region heavily influenced by glacial melt-was selected as the model system. Surface seawater samples were collected sequentially during the 2022 austral summer, followed by 16S rRNA gene amplicon sequencing and phylogenetic null model analysis.<br><br>RESULTS: Our results revealed a distinct shift in the assembly mechanisms of bacterial communities. In January, community structure was shaped jointly by stochastic and deterministic processes, with stochastic processes contributing a greater proportion to assembly. This state transitioned to the predominance of deterministic homogeneous selection (84.68%) in February. Mantel tests, followed by linear regression analyses, confirmed that this phylogenetic transition was driven by shifting environmental factors. Specifically, water temperature served as the primary influencing factor in January, whereas silicate and nitrate concentrations emerged as the key factors in February. Subsequent partial least squares path modeling (PLS-PM) and redundancy analysis (RDA) further validated these findings, demonstrating that the identified environmental variables collectively explained more than 50% of the observed variation in community structure. Notably, nitrate drawdown was significantly correlated with the increased relative abundances of dominant bacterial genera in February.<br><br>DISCUSSION: By quantifying the relative roles of deterministic and stochastic processes in microbial community assembly, this study demonstrates that environmental selection is the dominant factor mediating microbial responses to polar warming. These findings provide a mechanistic foundation for the development of predictive models for future marine biogeochemical cycles in polar regions.},
}
@article {pmid41939702,
year = {2026},
author = {Shi, Y and Chu, H and He, R and Ma, W and Liang, Q and Li, Z and Gao, Y and Luo, C},
title = {Harnessing rhizosphere microbes: the synergistic roles of PGPR and AMF in sustainable tomato production under stress.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1746930},
pmid = {41939702},
issn = {1664-302X},
abstract = {Tomato (Lycopersicon esculentum L.) is among the most economically important vegetable crops worldwide, yet its production is severely constrained by multiple biotic and abiotic stresses, including pathogens, pests, drought, salinity, and heavy metal toxicity. Amid intensifying climate change and increasing demands for sustainable agriculture, plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) have emerged as key beneficial rhizospheric microorganisms with significant potential for enhancing plant stress tolerance and promoting growth. PGPR directly promote the growth of tomato plants through biological nitrogen fixation, solubilization of phosphate and potassium, siderophore-mediated iron uptake, and the production of phytohormones. Indirectly, PGPR suppress pathogens, activate induced systemic resistance (ISR), reinforce cell walls, enhance the activities of antioxidant enzymes, and regulate the accumulation of osmolytes. AMF form symbiotic associations with the roots of tomato plants, enhancing nutrient and water absorption via extraradical mycelial networks, improving phosphorus and nitrogen uptake, modulating abscisic acid (ABA), jasmonic acid (JA), and strigolactone signaling pathways, activating mycorrhiza-induced resistance (MIR), and enhancing photosynthetic efficiency and water-use efficiency under stress. The co-inoculation of PGPR and AMF yields synergistic effects by facilitating mutual colonization, optimizing nutrient bioavailability, coordinately strengthening antioxidant and osmotic regulation systems, and reinforcing systemic defense responses, thereby conferring more robust and efficient stress tolerance than single inoculations. Despite significant advances, key challenges persist in elucidating tripartite molecular crosstalk, maintaining stability during field applications, and developing tailored microbial consortia. This review synthesizes the individual and synergistic mechanisms through which PGPR and AMF enhance the resilience of tomato plants to biotic and abiotic stresses, offering valuable insights for engineering microbial communities to enhance stress resistance in crops.},
}
@article {pmid41939703,
year = {2026},
author = {Liao, HY and Ren, YS and Li, J and Huang, HT and Li, ZL and Zeng, Y and Zhu, DH},
title = {Geographical variation of Ceracris kiangsu gut microbiota and its association with environmental factors.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1752887},
pmid = {41939703},
issn = {1664-302X},
abstract = {The yellow-spined bamboo locust (Ceracris kiangsu) is one of the most destructive forest pests in China, causing severe damage to bamboo forests across multiple provinces. Understanding the relationship between its gut microbiota and environmental factors is crucial for revealing its ecological adaptability and migration potential. This study used 16S rRNA high-throughput sequencing to analyze gut bacterial communities of C. kiangsu from six geographically distinct populations in China. The results showed that Firmicutes and Proteobacteria were the dominant phyla, while bacterial diversity and composition varied significantly among populations. Precipitation and sunshine duration were identified as the main environmental factors most strongly associated with microbial community structure. These findings suggest that environmental conditions are strongly associated with variation in the gut microbiota of C. kiangsu, potentially affecting its adaptability and outbreak dynamics. This research provides new insights into the ecological mechanisms underlying pest distribution and offers a microbiome-based foundation for developing sustainable control strategies to reduce the agricultural and forestry losses caused by this species.},
}
@article {pmid41939705,
year = {2026},
author = {Rey-Mariño, A and Ruiz-Ruiz, S and Jiménez-Hernández, N and Pons, X and Artacho, A and Codoñer-Franch, P and Francino, MP},
title = {Patterns of gut microbiome composition, function and dynamics in toddlers, adolescents and adults over a three-year period.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768977},
pmid = {41939705},
issn = {1664-302X},
abstract = {Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.},
}
@article {pmid41939710,
year = {2026},
author = {Alibrandi, A and Plewka, J and di Primio, R and Bartholomäus, A and Vuillemin, A and Probst, AJ and Kallmeyer, J},
title = {Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741638},
pmid = {41939710},
issn = {1664-302X},
abstract = {Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production, when processes like water injection introduce external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough using 16S rRNA gene and metagenomic sequencing of produced fluids, production water, and injection water samples from the Edvard Grieg oil reservoir offshore Norway. We found clear regional heterogeneity in community composition, characterized by overall low diversity, dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while the microbial community composition of well A07 showed a distinct signature. The prevailing genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not because of widespread replacement by injected microbes, but due to the increase in sulfate-reducing bacteria. Comparison between sequence data from production fluids and water samples allowed the identification of microbial signatures that can act as cost-effective tools for monitoring oil reservoir processes and integrity.},
}
@article {pmid41939716,
year = {2026},
author = {Zhang, B and Zhao, J and Zhuang, L and Liu, Y and Meng, P and Wang, S and Liu, Y and Zhang, T and Xu, J and Qin, W},
title = {Peat promotes production of the edible mushroom Oudemansiella raphanipes by regulating casing soil microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1774800},
pmid = {41939716},
issn = {1664-302X},
abstract = {INTRODUCTION: As an exotic edible mushroom, Oudemansiella raphanipes has attracted extensive attention for efficient cultivation. Peat-amended casing soil is known to increase its productivity, while the underlying mechanisms remain unclear.<br><br>METHODS: In this study, high-throughput 16S rRNA gene sequencing was performed to characterize bacterial communities in casing soils with five peat proportions.<br><br>RESULTS: Results showed that peat proportion had a significant effect on O. raphanipes yield, with the 70% peat treatment achieving the maximum yield of 279.21&#x202f;g per cultivation bag, 38.12% higher than the control without peat. Casing soil with 70% peat harbored higher bacterial richness, enriched beneficial taxa such as Paenisporosarcina, enhanced chemoheterotrophy and nitrogen fixation functions, and more deterministic community assembly compared with other treatments. The bacterial ecological network in casing soil with 70% peat also showed the highest average connectivity, shortest average path length, and strongest robustness. Further, soil physical properties had a greater influence on bacterial community structure in the casing soil than chemical properties. Soil density, available phosphorus and potassium significantly influenced the bacterial community in the 70% peat group.<br><br>CONCLUSION: Together, this study suggested that peat promoted O. raphanipes production by regulating the casing soil microbiome, providing a theoretical basis for optimizing practical cultivation strategies.},
}
@article {pmid41939722,
year = {2026},
author = {Ryan, SM and Brayden, DJ},
title = {Food-derived molecules as regulators of intestinal tight junctions and barrier function: mechanisms and implications.},
journal = {Frontiers in drug delivery},
volume = {6},
number = {},
pages = {1692219},
pmid = {41939722},
issn = {2674-0850},
abstract = {Controlling TJ permeability in the small intestine facilitates nutrient absorption, maintains luminal osmotic balance, and prevents the paracellular entry of pathogens. The pharmaceutical industry has leveraged the capacity of medium-chain fatty acids and their derivatives to transiently and reversibly open epithelial TJs in formulations to enable oral administration of therapeutic peptides, some of which have received regulatory approval or are progressing in advanced clinical trials. Other food-derived agent including chitosan and its analogues enhance mucoadhesion and also modulate TJ permeability in the intestine. Recently, pelargonidin, a polyphenolic pigment isolated from strawberries, has emerged as a promising food-derived TJ opener, facilitating oral insulin delivery in rat models. Conversely, other food or food-derived molecules reinforce TJ integrity while exerting antioxidant effects, thereby offering potential therapeutic benefits for conditions characterized by increased intestinal permeability including inflammatory bowel disease, sepsis, and coeliac disease. Examples of such agents include the short-chain fatty acid (SCFA), sodium butyrate, various essential and non-essential amino acids, fermented food, the trace element, zinc, and anthocyanins. The exploration of food-derived substances as modulators of intestinal epithelial TJ dynamics is still in its early stages but holds significant promise for future health applications.},
}
@article {pmid41939734,
year = {2026},
author = {Puppo, F and Carbone, RG},
title = {Microbiome in connective tissue diseases associated interstitial lung disease.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1738689},
pmid = {41939734},
issn = {2296-858X},
abstract = {Microbiome consists of a large community of bacteria, yeast, protozoa, and viruses that co-exist in symbiosis with human hosts. Changes in microbiome, named "dysbiosis," alter the interplay between microbiome and immune system triggering inflammation and contributing to the pathogenesis of connective tissue diseases (CTD). Interstitial lung diseases (ILD) are a group of pulmonary disorders characterized by lung tissue fibrosis and impaired lung function. The existence of a gut-lung axis is well demonstrated; however, it is not established whether gastrointestinal dysbiosis contributes to ILD development. ILD represent a major cause of morbidity and mortality in CTD patients. Lung microbiome changes and high microbial load are associated with worse prognosis and acute exacerbations in patients with CTD-ILD and especially in those affected by rheumatoid arthritis, systemic sclerosis and dermatomyositis. Probiotics are active microorganisms that normalize the intestinal flora and their use has been proposed as potential supportive treatment of CTD-ILD. Present knowledge of the relationships between dysbiosis and CTD-ILD development is largely incomplete and further studies are needed to validate this issue. Aim of this concise review is to report current knowledge on microbiome in CTD-ILD focusing on clinical lung aspects and therapeutic options.},
}
@article {pmid41939772,
year = {2026},
author = {Zheng, B and Shen, X and Han, N and Guo, X and Wan, S},
title = {The microbiota-gut-brain-epigenome axis as a novel therapeutic target for decoding postpartum depression.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1778348},
pmid = {41939772},
issn = {2296-858X},
abstract = {BACKGROUND: Postpartum depression (PPD) is a psychological disorder affecting approximately 10-15% of women following childbirth, with significant implications for maternal and infant well-being. While hormonal fluctuations and psychosocial factors have long been considered primary contributors, recent reports demonstrated that gut microbiome is implicated in modulating maternal mood and behavior. The bidirectional communication between the gut and brain, mediated by microbiota-gut-brain axis, along with genetic and epigenetic modifications, has gained increasing attention as a potential mechanistic pathway in PPD. However, the precise genetic and epigenetic underpinnings of this interaction remain to be elucidated.<br><br>OBJECTIVE: This review aims to explore the genetic and epigenetic landscape of postpartum depression, with a significant focus pertinent to gut microbiota role in shaping neurobiological outcomes. By integrating recent findings from genomic, epigenomic, and microbiome research, we seek to elucidate novel mechanistic insights and potential therapeutic avenues.<br><br>METHODS: A comprehensive literature search was conducted using public databases, including PubMed, Google Scholar, and NCBI, to identify relevant studies on PPD, gut microbiota, genetics, and epigenetics.<br><br>RESULTS: Gut microbiota and neuroimmune modulation: peripartum changes in gut microbiota composition have been linked to immune dysregulation, inflammation, and neurotransmitter imbalances, all of which are implicated in PPD pathophysiology. Genetics and epigenetics of PPD: Genome-wide association studies (GWAS) revealed a profound genetic risk loci associated with PPD. Additionally, DNA methylation, histone modifications, and non-coding RNAs have profound functional implications in gene expression regulation, influencing PPD susceptibility. Epigenetic influence of the gut microbiome: The gut microbiome affects epigenetic modifications, such as DNA methylation and histone acetylation, which may lead to fetal programming and maternal mental health disorders. Choline metabolism and maternal mental health: Choline, an essential nutrient involved in epigenetic regulation, influences gut microbiota composition and brain function. Dysregulation in choline metabolism is associated with higher risk of PPD. Clinical and therapeutic implications: Understanding the genetic and epigenetic mechanisms underlying PPD offers new avenues for personalized therapeutic interventions, including probiotic and prebiotic strategies, microbiome-based treatments, and targeted epigenetic therapies.<br><br>CONCLUSION: The interplay between genetics, epigenetics, and gut microbiota represents a novel and promising area of research in understanding postpartum depression. The microbiota-gut-brain axis serves as a crucial mediator in this relationship, influencing neuroimmune regulation, neurotransmitter synthesis, and epigenetic modifications. Future studies should focus on integrating multi-omics approaches to unravel the molecular complexity of PPD and develop targeted interventions aimed at restoring microbiome and epigenetic homeostasis.},
}
@article {pmid41939831,
year = {2026},
author = {Omolo, CA and Yata, VK and Janapati, YK and Dachani, SR},
title = {Editorial: Innovative therapeutic strategies for managing diabetic foot ulcers and mitigating associated complications.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1788742},
pmid = {41939831},
issn = {1663-9812},
}
@article {pmid41939871,
year = {2026},
author = {Tonk-Rügen, M and Schilling, T and Cabezas-Cruz, A and Hoelzle, LE},
title = {Microbiota-immune crosstalk in livestock: implications for tick-borne disease control.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1731518},
pmid = {41939871},
issn = {1664-3224},
mesh = {Animals ; *Livestock/immunology/microbiology ; *Tick-Borne Diseases/immunology/prevention &amp; control/veterinary/microbiology ; *Microbiota/immunology ; Ticks/microbiology/immunology ; },
abstract = {Globally, livestock health, which impacts animal welfare and agricultural productivity, is continuously threatened by tick-borne diseases (TBDs). The growing issues of acaricide overuse in livestock, emerging resistance, and vector adaptation to climate change require novel and sustainable intervention strategies. Recent advances in microbiome research reveal how host and vector microbiota influence immune responses, particularly through natural antibodies (nAbs) that modulate vector competence and pathogen transmission. In livestock, nAbs targeting microbial glycans are heritable, measurable, and linked to health outcomes. In cattle, nAb titers to bacterial antigens are associated with mastitis risk and longevity, while in pigs, early-life nAb levels are proposed as resilience markers. Studies in poultry further demonstrate the importance of high nAb phenotypes for health and production. These findings highlight nAbs as both immunological markers and potential targets for genetic selection to improve disease resistance. Emerging interventions, such as anti-microbiota vaccines and immunobiotics, aim to modulate nAb repertoires, disrupt pathogen colonization, and enhance disease resilience. Additionally, microbial glycans serve as key targets for inducing cross-reactive immunity against TBDs. Manipulation of the livestock microbiota through diet, probiotics, and prebiotics shows promise in diversifying nAb profiles and improving robustness against infection. Despite these advances, research gaps remain, particularly in establishing causality and practical feasibility in livestock systems. This review emphasizes the need for integrative research across immunology, microbiology, and veterinary sciences to leverage microbiota-immune interactions in enhancing livestock resilience against TBDs, exploring how nAbs shaped by the gut microbiota can modulate tick microbiomes and impact pathogen transmission.},
}
@article {pmid41939876,
year = {2026},
author = {Li, L and Zhu, G and Chen, M and Qiu, B and Li, Y and Liu, S and Gu, W and Liu, L},
title = {ARG1-polyamine axis: cell-type-specific functions in disease pathogenesis and therapeutic targeting.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1744890},
pmid = {41939876},
issn = {1664-3224},
mesh = {Humans ; *Polyamines/metabolism ; *Arginase/metabolism/antagonists &amp; inhibitors ; Animals ; Neoplasms/metabolism ; },
abstract = {ARG1 catalyzes the conversion of L-arginine to L-ornithine, urea, polyamines, and L-proline, thereby balancing nitrogen detoxification with tissue-specific roles in proliferation and immunity. This review delineates the context-dependent functions of ARG1 across diverse cell types-including tumor cells, immune cells, endothelial cells, keratinocytes, and stem cells. In tumors, ARG1 drives immunosuppression and metabolic reprogramming but can paradoxically suppress tumorigenesis. Immune modulation via ARG1-polyamine crosstalk regulates T cell differentiation, macrophage polarization, and microbiota interactions, influencing infection and autoimmunity. Endothelial ARG1 exacerbates obesity-related vascular dysfunction, while keratinocyte ARG1 impacts wound healing and psoriasis. Emerging therapies-such as ARG1 inhibitors, engineered extracellular vesicles, and microbiome interventions-show preclinical promise in cancer, cardiovascular, and neurodegenerative diseases. By mapping ARG1's spatiotemporal metabolic networks, this work highlights its dual roles and positions ARG1 as a central player for precision medicine in complex pathologies.},
}
@article {pmid41939907,
year = {2026},
author = {Jayaraman, S and Mahalingam, SS and Zhu, Z and Faddoul, F and Paes da Silva, A and Asaad, R and Bhaskaran, N and Schneider, E and Taylor, T and Horne, S and Yoo, A and Zhang, L and Burgener, A and Pandiyan, P},
title = {Enrichment of Candida associated with dysbiosis contributes to mucosal CD4[+]FOXP3[+] regulatory T cell accrual and their dysfunction in aging.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1714595},
pmid = {41939907},
issn = {1664-3224},
mesh = {Humans ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Dysbiosis/immunology/microbiology ; Middle Aged ; *Aging/immunology ; *Mouth Mucosa/immunology/microbiology ; Male ; Female ; Aged ; *Candida/immunology ; Adult ; Forkhead Transcription Factors/metabolism/immunology ; },
abstract = {Age-associated T cell dysfunction is a defining feature of inflammaging and immunosenescence, the progressive decline in immune competence observed with advancing age. Here we identified the association between aging (defined as age >60) and fungal dysbiosis, notably characterized by increased colonization of Candida species in the oral mucosa. There is also a notable enrichment of other taxa related to the order Saccharomycetales in older individuals. In contrast, younger individuals exhibit a greater abundance of Cryptococcus, Yarrowia, Kluyveromyces, and various Incertae sedis lineages. Further analysis, stratified by HIV status, shows that older individuals in both healthy and HIV+ groups display significantly higher levels of Candida. Gingival tissues reveal that both healthy older group and HIV-positive group exhibit elevated levels of CD4[+]FOXP3[+] regulatory T cells (Tregs) along with increased salivary concentrations of soluble TLR-2 and IL-6 compared to younger healthy group. Importantly, the abundance of Candida is positively correlated with elevated levels of mucosal Tregs, dysfunctional Tregs (TregDys), and hyperactivated CD4[+] T cells. In vitro experiments provided mechanistic insights by further demonstrating that Candida can induce both proliferation and dysfunction of Tregs in an IL-6 dependent manner, supporting the notion that Candida plays a role in oral T cell senescence and inflammaging. Collectively, these findings underscore a direct relationship between the commensal mycobiome and Treg population, which normally promotes mucosal homeostasis but becomes susceptible to dysfunction with aging.},
}
@article {pmid41939911,
year = {2026},
author = {Zhao, WY and Zhao, JW},
title = {Pancreatic cancer immunotherapy biomarkers: from traditional markers to multimodal integration and dynamic monitoring.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1686658},
pmid = {41939911},
issn = {1664-3224},
mesh = {Humans ; *Pancreatic Neoplasms/therapy/diagnosis/immunology ; *Biomarkers, Tumor ; *Immunotherapy/methods ; *Carcinoma, Pancreatic Ductal/therapy/immunology/diagnosis ; Animals ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains an intractable cancer marked by delayed diagnosis, rapid progression, and significant resistance to current treatments. Conventional biomarkers, such as CA19-9, have insufficient sensitivity and specificity. Meanwhile, the practical use of newer markers such as the tumor mutational burden and microsatellite instability is limited by the absence of standardized testing protocols and definitive threshold values. Circulating tumor DNA and exosomal miRNA hold promise for continuously tracking tumor dynamics and effectiveness of immunotherapy, but additional validation is necessary before their routine clinical application. Recent advancements in multiomics, nanotechnology, and artificial intelligence have opened new possibilities for more accurate and comprehensive biomarkers. For instance, Shah et al. developed shortwave-infrared-emitting nanoprobes to specifically target CD8[+] cytotoxic T cells, permitting high-sensitivity in vivo imaging in breast cancer models. Batool et al. utilized nanoplasmonic sensors to detect changes in serum programmed death-ligand 1 and cytokine levels within 1-2 weeks post-treatment, achieving picomolar sensitivity. Chang et al. combined fluorescence and photoacoustic imaging in the NanoTrackThera platform, facilitating the real-time monitoring of immunotherapy efficacy. This review highlights the evolution of PDAC biomarkers from traditional markers to multimodal integration and dynamic monitoring. The limitations of current markers and potential of emerging technologies, including metabolic reprogramming markers, epigenetic regulators, and AI-driven predictive models, are discussed. Future directions include multicenter prospective trials to validate multimodal models, standardize detection methods, and increase interdisciplinary collaboration. By integrating genomic, epigenetic, metabolic, and microbiome data, these models can better capture the complexity of PDAC, thereby improving patient outcomes through precision immunotherapy.},
}
@article {pmid41939913,
year = {2026},
author = {Van Doorn, J and Brooks, SR and LiCausi, F and Zhou, K and Betrapally, NS and Gubitz-Hess, E and Cougnoux, A and Dell'Orso, S and Islam, S and Colbert, RA and Navid, F},
title = {Rapamycin treatment ameliorates HLA-B27-mediated gut inflammation and alters the microbiome in experimental spondyloarthritis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1755132},
pmid = {41939913},
issn = {1664-3224},
mesh = {Animals ; *HLA-B27 Antigen/genetics/immunology ; *Sirolimus/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Rats ; Rats, Transgenic ; Disease Models, Animal ; Cytokines/metabolism/genetics ; *Spondylarthritis/drug therapy/immunology/microbiology ; Humans ; Male ; Inflammation/drug therapy ; Colon/drug effects/immunology/microbiology/pathology ; },
abstract = {OBJECTIVE: To determine whether rapamycin affects HLA-B27-mediated gut inflammation in experimental spondyloarthritis (SpA).<br><br>METHODS: HLA-B27/human &#x3b2;2-microglobulin transgenic (B27-Tg) rats with gut inflammation were treated with rapamycin (1.5 mg/kg intraperitoneally, 3 times a week) or vehicle for 5 weeks. Healthy age-matched wild type (WT) rats were treated in parallel. Gut inflammation was evaluated via stool scoring and histological assessment. Transcriptome and microbiome analyses were performed on colon tissue and cecal luminal contents, respectively. Bulk immune cells were isolated from the colonic lamina propria of B27-Tg and WT animals, treated with rapamycin ex vivo, and pro-inflammatory cytokine expression was measured using qPCR.<br><br>RESULTS: Rapamycin treatment reduced stool and colon histological scores in B27-Tg rats compared to vehicle-treated B27-Tg controls. Transcriptome analysis revealed that rapamycin reduced expression of key pro-inflammatory cytokines like Il17a, Il17f, Tnf, Il1a, IL1b, and Il22 in B27-Tg colon tissue compared to vehicle-treated B27-Tg controls. Ex vivo treatment of bulk immune cells isolated from B27-Tg rat colon with rapamycin reduced expression of Il17a, Il17f, Ifng, and Il22 compared to vehicle-treated cells. Rapamycin treatment decreased the abundance of cecum microbiota associated with inflammation in B27-Tg rats. Rapamycin also altered the gut microbiome in WT rats, without associated changes in the tissue transcriptome.<br><br>CONCLUSION: Our study demonstrates that rapamycin treatment substantially reduces HLA-B27-mediated gut inflammation in experimental SpA. Results from this pre-clinical model suggest further evaluation of rapamycin as a therapeutic strategy in HLA-B27 associated diseases is warranted.},
}
@article {pmid41940020,
year = {2026},
author = {Usman, S and Yan, Q and Gao, L and Deng, S and Lu, L and Pang, T and Lai, D and Jones, CS and Yi, X and Zhang, J},
title = {Inclusion of different levels of fermented elephant grass in broiler chicken diet: effects on growth, physiology, carcass traits and gut microbial community.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1767570},
pmid = {41940020},
issn = {1664-042X},
abstract = {The physiological and microbiome-modulating benefits of dietary forage in monogastrics are impeded by recalcitrant fiber and anti-nutritional factors. However, fermentation and appropriate inclusion levels may overcome these limitations. This study evaluated the effects of two fermented cultivars of elephant grass (Cenchrus purpureus cv. Guiminyin and cv. Purple) incorporated into broiler diets at different inclusion levels, with emphasis on cultivar-specific responses, growth performance, physiological status, and gut microbial composition. A total of 240 male (30-days old) Jinling earth-neck chickens were housed in four replicate pens of 12 birds each, and randomly assigned to five dietary treatments (48 birds per treatment): a control diet with no inclusion (0%), CpGui5 (5% Guiminyin inclusion), CpGui10 (10% Guiminyin inclusion), CpPur5 (5% Purple inclusion), and CpPur10 (10% Purple inclusion). CpGui5 and Control diets had statistically similar and higher final weight, total weight gain, average daily gain and feed efficiency which were higher than the other treatments (P < 0.05). On the other hand, Control, CpGui5 and CpPur5 had higher daily feed intake compared to CpGui10 and CpPur10 which had the lower daily feed intake (P < 0.05). Slaughter performance revealed significant differences (P < 0.05), with the control, CpGui5, CpPur5 and CpPur10 groups maintaining higher live weight, dressed weight, half-bore, and breast muscle rate while CpGui10 recorded the lowest values. Blood biochemical indices, including total protein, albumin, liver enzymes, and renal function markers, were unaffected by dietary treatments (P > 0.05), indicating no adverse physiological effects. Gut microbiome analysis showed stable richness (Chao1, ACE) across treatments, while diversity (Shannon, Simpson) was reduced in CpPur5 relative to other groups (P < 0.05). A shared core microbiome of 202 OTUs was detected across all treatments, alongside treatment-specific enrichment of taxa. LEfSe (Linear Discriminant Analysis Effect Size) analysis identified treatment-specific enrichment of functionally relevant bacterial genera, including Megamonas in CpGui5 and Ruminococcaceae_UCG-014 and unclassified Lachnospiraceae at higher inclusion levels (CpGui10). Overall, moderate inclusion of fermented elephant grass, especially CpGui5 supports broiler performance while maintaining physiological health and gut microbial stability, highlighting its potential as a sustainable functional feed resource for poultry production.},
}
@article {pmid41940149,
year = {2026},
author = {Etesami, H and Yadegari, AH and Otabek, U and Zahro, B and Shavakatullo, N and Tolqinjon, A},
title = {The root's hidden ally: How the rhizosheath microbiome fortifies crops against drought.},
journal = {aBIOTECH},
volume = {7},
number = {1},
pages = {100015},
pmid = {41940149},
issn = {2662-1738},
abstract = {Drought stress poses a significant threat to global agriculture, necessitating innovative strategies to enhance plant resilience. This review highlights the rhizosheath-the soil layer tightly bound to roots by mucilage and microbial biofilms-as a critical but underexplored microbial niche for sustainable drought mitigation. Unlike the vulnerable rhizosphere, the rhizosheath has a cohesive structure that acts as a protective "mini-oasis," preserving moisture and sustaining microbial activity when water is scarce. We synthesize evidence showing that resident rhizosheath bacteria, including genera such as Bacillus, Pseudomonas, and Azospirillum, enhance plant drought tolerance through multiple mechanisms: improving soil structure and water retention, modulating phytohormone levels, facilitating nutrient acquisition, and activating antioxidant and genetic defense pathways in the plant. Despite promising laboratory findings, there has been little field-scale validation of these effects. Here, we critically assess translational challenges and outline future research priorities, such as understanding plant-microbe specificity and optimizing synthetic microbial consortia. Addressing these questions will enable manipulation of the rhizosheath microbiome for development of climate-resilient crops and securing food production in water-limited environments.},
}
@article {pmid41940156,
year = {2026},
author = {Ma, J and Qiao, J and Cao, Y and Cheng, Z},
title = {Harnessing artificial intelligence to decode the rhizosphere microbiome.},
journal = {aBIOTECH},
volume = {7},
number = {1},
pages = {100005},
pmid = {41940156},
issn = {2662-1738},
abstract = {The rhizosphere microbiome plays crucial roles in plant health by regulating nutrient cycling and enhancing stress resilience. However, due to its complexity, the rhizosphere microbiome is quite challenging to analyze using conventional approaches. Recent advances in artificial intelligence (AI) offer unprecedented opportunities to decipher intricate microbial interactions and leverage their potential for crop breeding. In this review, we assess AI methodologies derived from human microbiome studies that address foundational data challenges, including high dimensionality, compositionality, and sparsity. Next, we examine the uses of these methods for the functional prediction of microbial traits. We then shift our focus to the rhizosphere, exploring AI-driven approaches for predictive modeling of rhizosphere dynamics, integrating plant phenotypic and microbiome data, and designing synthetic microbial communities (SynComs). Finally, we discuss the major challenges and future prospects of using AI in rhizosphere microbiome research. Specifically, we propose an emerging AI paradigm that integrates complementary inside-out (hologenome-based genomic selection) and outside-in (SynCom design) strategies, powered by transformative technologies such as federated learning, large language models, digital twins, and autonomous AI agents. This review underscores the potential for AI to revolutionize microbiome science and crop improvement.},
}
@article {pmid41940273,
year = {2026},
author = {Huang, F and Shi, X and Chen, P and Hu, Q and Zhao, Y and Chen, Z and Ma, W and Tan, Q and Feng, X and Zhang, X},
title = {Dietary drivers of gut microbiota diversity and function in wildlife of Wolong Nature Reserve: a metagenomic study.},
journal = {Current zoology},
volume = {72},
number = {1},
pages = {14-29},
pmid = {41940273},
issn = {1674-5507},
abstract = {While diet is known to regulate the composition, function, and diversity of the human gut microbiome, its effects on wildlife remain understudied. Here, noninvasive sampling methods were first used to conduct metagenomic analyses of the gut microbiomes of 10 protected wild animals in the Wolong Nature Reserve. There were significant differences in microbiota composition and function between herbivores and carnivores. Herbivores exhibited higher microbial diversity and evenness (Shannon and Pielou indices), with Bacillota and Acinetobacter predominating, whereas carnivores were enriched in Pseudomonadota and Escherichia. Cellulose-degrading bacterium Ruminococcus champanellensis was abundant in herbivores, while Rhodococcus and Pediococcus, which were associated with toxin degradation and pathogen inhibition, were more prevalent in carnivores. Carnivores showed higher lipid metabolism and protein degradation, as evidenced by the enrichment of leucyl aminopeptidase and oligopeptidase B, while herbivores demonstrated superior cellulose and starch digestion, characterized by the enrichment of cellulose 1,4-beta-cellobiosidase. Stochastic processes shaped gut microbiome assembly, especially in herbivores. Potential health risks from pathogens such as Escherichia and Listeria were identified, and Escherichia abundance was positively correlated with niche width. Furthermore, the findings suggest that high-altitude environments may promote the persistence and spread of pathogens. Overall, our findings underscore the intricate linkages between diet, gut microbiota composition, assembly processes, and host ecology in protected wildlife, address a key knowledge gap, and provide important theoretical and practical insights for ecological conservation, species restoration, and environmental management.},
}
@article {pmid41940285,
year = {2025},
author = {Jeong, GH and Lim, KS},
title = {Exploring the potential of salivary small RNAs as non-invasive biomarkers in pigs.},
journal = {Journal of animal science and technology},
volume = {67},
number = {6},
pages = {1207-1214},
pmid = {41940285},
issn = {2055-0391},
abstract = {Saliva, a non-invasive potential source of circulating microRNAs (miRNAs) and microbiomes, is not well described in pigs. Salivary miRNA expression profiles and the functional significance in pigs were investigated in this study. Saliva samples were extracted from adult female pigs, and small RNA sequencing revealed 26 known and 223 novel miRNAs. The large number of novel miRNAs also demonstrates the differences between salivary miRNAs in pigs and other biological samples. Functional analysis of miRNA target genes indicated enrichments in molecular functions related to transcription regulator activity, cytoskeleton organization, and protein binding, suggesting roles for this interaction in gene expression and physiological control. Moreover, metagenomic analysis revealed microbial sequences representing around 39% of the total reads, with Corynebacterium genus, an important member of the oral microbiota, being the most prevalent. Combining miRNA with microbiome data indicates that porcine saliva is rich in molecular information that will be useful for salivary health monitoring and microbiome studies. This study underscores the potential of salivary miRNAs as biomarkers for physiological processes and microbiome interactions in pigs, paving the way for further research into their diagnostic and monitoring applications.},
}
@article {pmid41940567,
year = {2026},
author = {De Zutter, N and Audenaert, K},
title = {Can We Breed Microbiomes to Sustain Plant Productivity?.},
journal = {Microbial biotechnology},
volume = {19},
number = {4},
pages = {e70351},
pmid = {41940567},
issn = {1751-7915},
mesh = {*Microbiota ; *Plant Breeding/methods ; *Crops, Agricultural/microbiology/genetics/growth &amp; development ; Quantitative Trait Loci ; *Plants/microbiology/genetics ; },
abstract = {Global food systems face challenges from population growth, shifting diets and climate change. While decades of plant-centric breeding and high-input agriculture have generated high yielding crops, this strategy has unintentionally reshaped the plant associated microbiomes, often coinciding with a depletion of their functional diversity. We revisit these breeding strategies and propose extending breeding targets beyond the plant genome to include the plant microbiome. In this regard, resistance breeding shows, albeit unintended, that plant genetics shape the microbiome: by narrowing the genetic base, we have selected for highly specialised pathogenic microbiomes. This raises a key question: can we intentionally apply the same principle to select for beneficial microbiomes? To answer this question, a thorough insight into microbial community architecture, hubs and functional redundancy is key. We outline two complementary avenues: (i) rewilding to restore ancestral microbial partners and (ii) microbiome breeding guided by QTL/GWAS mapped host loci that gate microbial recruitment, immune filtering and exudate composition. This approach comprises the integration of trait-based phenotyping, multi-omics, network-informed SynCom design and field testing across environments to capture G × E × M (genotype × environment × microbiome) interactions. Treating the microbiome as a selectable, designable and heritable trait can convert small gains into durable long-lasting crop resilience.},
}
@article {pmid41940646,
year = {2026},
author = {Yin, X and Niu, Y and Chen, B and Zhang, H and Guo, R and Niu, C and Kang, J and Shi, H and Kong, X and Ma, W and Ma, Z and Wei, Y and Hua, Y},
title = {Screening and dynamic change study of microbial and metabolite markers for calf diarrhea based on multi-omics and machine learning.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0000526},
doi = {10.1128/msystems.00005-26},
pmid = {41940646},
issn = {2379-5077},
abstract = {UNLABELLED: Neonatal calf diarrhea is a leading cause of calf mortality and substantial economic loss in the livestock industry, yet the dynamic microbial and metabolic signatures accompanying disease onset remain poorly defined. Here, we integrated 16S rRNA high-throughput sequencing, untargeted metabolomics, and machine learning approaches to longitudinally profile fecal samples from neonatal calves at 0, 5, 10, 15, and 20 days of age. Diarrheic calves exhibited significantly reduced gut microbial α-diversity, as indicated by lower Chao1 richness and Shannon index compared with healthy counterparts. At the genus level, Tyzzerella and Fusobacterium emerged as core differential taxa associated with diarrhea and were further validated as robust biomarkers using an XGBoost predictive model. Metabolomic analysis showed that differential metabolites were mainly enriched in pathways including the phosphotransferase system. Notably, dulcitol, N-acetylmuramate, and D-fructose were highlighted as potential contributors to diarrhea, possibly through modulating intestinal osmolality and inflammatory responses. Pearson correlation analysis revealed significant associations between Tyzzerella/Fusobacterium and key metabolites, suggesting coordinated microbe-metabolite interactions during disease progression. Temporal pattern analysis identified an early-life signal: a high abundance of Escherichia-Shigella at birth may act as an important trigger for subsequent diarrhea. In addition, several metabolites displayed distinct age-dependent trajectories, indicating their potential as time-resolved metabolic biomarkers. Collectively, this study delineates dynamic shifts in the gut microbiome and metabolome during neonatal calf diarrhea, identifies Tyzzerella and Fusobacterium, together with characteristic metabolites such as dulcitol and N-acetylmuramate, as candidate biomarkers, and provides a high-performance predictive framework to support early diagnosis and targeted microbiota-based interventions.<br><br>IMPORTANCE: Neonatal calf diarrhea causes substantial early-life mortality and economic losses, yet the dynamic microbiota-metabolite alterations and early-warning biomarkers during disease onset remain poorly defined. Here, we longitudinally profiled fecal microbiota and metabolites in calves from birth to day 20 and integrated machine learning approaches to systematically characterize diarrhea-associated signatures. Diarrheic calves showed reduced &#x3b1;-diversity, and Tyzzerella and Fusobacterium emerged as core differential genera with predictive value validated using an XGBoost model. Differential metabolites were mainly enriched in pathways such as the phosphotransferase system (PTS), and dulcitol and N-acetylmuramate may contribute to diarrhea by modulating intestinal osmolality or inflammatory responses. Notably, a higher abundance of Escherichia-Shigella at birth was potentially associated with subsequent diarrhea risk, while L-glutamic acid, choline, and LysoPC exhibited distinct temporal trajectories. Collectively, these findings provide translational candidate biomarkers to support early warning and microbiota-targeted precision interventions for neonatal calf diarrhea.},
}
@article {pmid41940665,
year = {2026},
author = {Huang, C and Feng, Q and Yu, B and Zou, H and Cai, Y and Liu, J and Li, D and Zhang, H and Zou, X},
title = {Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191125},
doi = {10.1128/spectrum.01911-25},
pmid = {41940665},
issn = {2165-0497},
abstract = {UNLABELLED: Research shows that patients with viral pneumonia complicated by diabetes have a worse prognosis and higher mortality. Our study aimed to assess the effect of diabetes on respiratory tract microbes and the transcriptome in patients with viral pneumonia. We included 76 subjects from China-Japan Friendship Hospital, including 16 healthy people, 17 patients with viral pneumonia and diabetes (VD), and 43 patients with viral pneumonia without diabetes (VP). We collected their sputum samples for both metagenomic and 16S rRNA sequencing and collected blood samples for RNA sequencing. In transcriptome analysis, the VD group downregulated the expression of PTCH1 and upregulated the expression of ANK1, RBM38, BPGM, CRYM, TAL1, and HBD. The differential pathways are mainly reflected in the formation, development, and maintenance of red blood cells, the activity of immunoglobulins, and the membrane transport and transportation of substances. There is a significant difference in microbial diversity between the two groups. Both analysis methods demonstrate a significant increase in the abundance of g__Treponema, s__Treponema_denticola, and s__Campylobacter_rectus in the VP group. The host genes AGAP1, RNF182, and ANKRD9 are particularly closely associated with microorganisms. Our results suggest that diabetes may inhibit the expression of genes related to immune regulation, energy metabolism, and oxygen utilization in patients with viral pneumonia. Meanwhile, we predict that VD may be associated with a decrease in microbial diversity and a decline in microbial functions in cellular processes, environmental adaptation, metabolism, and genetic activity. These abnormalities can worsen the course of viral pneumonia and affect the prognosis of patients.<br><br>IMPORTANCE: We used 16S rRNA and metagenome sequencing to analyze the respiratory microbial composition of patients with viral pneumonia complicated by diabetes (VD) and patients with viral pneumonia without diabetes (VP) and used transcriptome sequencing to compare the gene expression of patients in VD, VP, and healthy people. Our results indicate significant differences in gene expression and respiratory microbiota profiles between VD and VP. VD may inhibit the immune regulatory response and affect cell energy metabolism and oxygen transport and utilization by regulating related gene pathways. The abundance of Treponema denticola in the VP group was significantly higher than that in the VD group. We predicted that the functions of differential microorganisms may be related to cellular processes, environmental information processing, genetic information processing, human diseases, and metabolism. This study found characteristic biomarkers related to viral pneumonia with diabetes, providing a new strategy for further research and clinical treatment.},
}
@article {pmid41940696,
year = {2026},
author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M},
title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0190325},
doi = {10.1128/aem.01903-25},
pmid = {41940696},
issn = {1098-5336},
abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.},
}
@article {pmid41940869,
year = {2026},
author = {Sharif-Askari, Z and Atoui, K and El Zein, W and Rizk, M and Sharif Askari, E},
title = {From periodontitis to neurodegeneration: Can probiotics modulate the P. gingivalis-amyloid pathway in Alzheimer's disease?.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261432686},
doi = {10.1177/13872877261432686},
pmid = {41940869},
issn = {1875-8908},
abstract = {Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the gradual destruction of cognitive and behavioral functions. Despite the continuous research efforts, there is still no cure for this disease. In recent years, researchers have investigated Porphyromonas gingivalis (P. gingivalis) as a potential cause of AD. P. gingivalis-lipopolysaccharides (LPS) and gingipains have been implicated in neuroinflammatory cascades relevant to AD. The gut-brain axis provides a pathway for microbial migration, immune activation, and regulation of the central nervous system function. Emerging evidence suggests that selected probiotics may modulate these pathways by restoring microbial balance, reinforcing epithelial barrier function, and regulating innate and adaptive immunity. Importantly, much of the evidence and mechanistic support for these effects derives from preclinical and animal studies, whereas human data remain limited to associative findings and early-stage clinical trials. Early clinical trials report modest improvements in cognitive scores and systemic inflammatory markers. Strain selection, dose, and treatment duration make direct comparisons challenging. This review integrates the literature on the links between P. gingivalis and AD, suggesting that probiotics may be used as neuroprotective agents. Taken together, current preclinical signals are consistent with the potential of probiotics as feasible adjuncts, pending confirmatory trials with standardized formulations.},
}
@article {pmid41941327,
year = {2026},
author = {Strope, TA and Easson, CG and Fiore, CL},
title = {Low Abundance Taxa Show Diverse Microbial Symbiotic Interactions With the Freshwater Sponge, Radiospongilla crateriformis, Pre and Post Gemmulation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70331},
pmid = {41941327},
issn = {1758-2229},
support = {//Appalachian State University/ ; 1924540//National Science Foundation/ ; },
mesh = {*Symbiosis ; *Porifera/microbiology/growth &amp; development/physiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Fresh Water/microbiology ; *Microbiota ; Flavobacterium/genetics ; Phylogeny ; },
abstract = {Freshwater sponges, most of which have a dormant stage with gemmules, are well poised for microbiome focused experiments. Here, we leveraged field collections of freshwater sponges pre-gemmule (Pre) and post-gemmule (Post) formation to compare the microbial symbiont metatranscriptome at the two developmental stages. There were no broad changes to the microbiome in composition between the two stages; however, there were significant differences in the abundance of several bacterial taxa and functional genes between Pre and Post sponge samples. For example, many Polynucleobacter spp. increased from Pre to Post samples, but no putative symbiosis factors were associated with Polynucleobacter and these may be loosely associated with the sponges. In contrast, we hypothesise that Flavobacterium spp. are facultative symbionts of freshwater sponges that begin to leave when the sponge tissue degrades, or they may decrease their metabolic activity. Functions attributed to Flavobacterium spp. such as type IX secretion system (T9SS) component and ankyrin repeat domains, all decreased in the Post samples and suggests that this group can interact with the sponge host or be free-living. These results provide a foundation for future hypothesis testing and experimental work with the microbiomes of freshwater sponges.},
}
@article {pmid41941330,
year = {2026},
author = {Dunn, ES and Spalding, HL and Hill-Spanik, KM and Fullerton, H},
title = {Examining Short Temporal Changes in Intertidal Macroalgal Microbiomes at 'Ewa Beach, O'Ahu, Hawai'i: Some Hosts Varied While Others Remained Stable.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70333},
pmid = {41941330},
issn = {1758-2229},
mesh = {Hawaii ; *Microbiota ; *Seaweed/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Climate Change ; Rhodophyta/microbiology ; Seawater/microbiology ; Phaeophyceae/microbiology ; },
abstract = {Understanding the temporal variability of microbiomes is crucial for predicting dynamics within macroalgal communities under future climate change scenarios, rising temperatures, and increased marine heatwave events. Short-term variation has been observed in human- and coral-associated microbes, but these dynamics are less understood in macroalgae. Intertidal macroalgal communities are ideal systems for investigating microbiome temporal variation due to their exposure to daily fluctuations in abiotic conditions. We characterised and examined the variability in the microbiota of seven macroalgal species, with representatives from three different phyla, across five sequential low tides in May 2021 at a single intertidal bench at 'Ewa Beach, O'ahu, Hawai'i, USA. Bacterial community compositions found in two red algae, Acanthophora spicifera and Laurencia dendroidea, and one brown alga, Dictyota sandvicensis, had variable abundances of several amplicon sequence variants contributing to significant dissimilarity through time. Two green macroalgae (Avrainvillea lacerata and Halimeda discoidea) were stable over time. Temporal stability of the macroalgal microbiotas, therefore, was variable amongst macroalgal species, but may be dependent on its horizontal or vertical positioning within the intertidal zone, which can vary the level of environmental stress (e.g., temperature, light, desiccation). Additional work exploring the drivers of the temporal variability observed herein is needed.},
}
@article {pmid41941490,
year = {2026},
author = {Ventero, MP and Herrero, R and Tyshkovska, I and Valverde-Fredet, MD and Rodríguez, JC and Rodríguez-Fernández, M and González-De-La-Aleja, P and Trigo, M and Parra, M and Aller, AI and Otero, S and Espindola-Gomez, R and Ramos, JM and León, EM and García, M and Navarrete-Lorite, MN and Llenas-García, J and Portillo, I and Jover, F and Tasias, M and Caston, JJ and Gil, C and Vinuesa-Garcia, D and Gomez-Ayerbe, C and Martínez Marcos, FJ and Merchante, N and De Lucas, EM},
title = {Dynamics of the microbiota in patients with Clostridioides difficile: Recurrence, treatment, sex, and immunosuppression.},
journal = {PLoS pathogens},
volume = {22},
number = {4},
pages = {e1014063},
doi = {10.1371/journal.ppat.1014063},
pmid = {41941490},
issn = {1553-7374},
abstract = {BACKGROUND: Alterations in the gut microbiome are central to the pathogenesis and recurrence of Clostridioides difficile infection (CDI).<br><br>OBJECTIVE: To evaluate intestinal microbiome changes during CDI and their association with recurrence, sex, age, and immunosuppression.<br><br>METHODS: Patients from the CDI-ANCRAID-SEICV cohort were consecutively enrolled. Stool samples were obtained at diagnosis (Dx), end of treatment (ET), and eight weeks post-treatment (8W) or upon recurrence. Microbiota composition was analyzed by 16S rRNA sequencing using QIIME2 and R. Outcomes were compared by demographics, immunosuppression, and treatment (vancomycin [VNC], vancomycin-bezlotuzumab [VNC-BZL], fidaxomicin [FDX]).<br><br>RESULTS: Among 143 patients, non-recurrent cases showed higher biodiversity at 8W versus diagnosis (H p&#x2009;=&#x2009;0.002, ASVs p&#x2009;<&#x2009;0.001), unlike recurrent cases. Diversity decreased with VNC (H p&#x2009;>&#x2009;0.001, ASVs p&#x2009;<&#x2009;0.001) but was preserved with FDX (H p&#x2009;=&#x2009;0.15). Recovery of Shannon diversity was limited in women (p&#x2009;=&#x2009;0.50) and immunocompromised patients (p&#x2009;=&#x2009;0.31). At ET, Fusobacteria and Verrucomicrobiota were less abundant in recurrent than non-recurrent cases (0.77%, 0.53% vs 3.43%, 3.50%). FDX-treated samples showed higher Bacteroidetes (31.33%) compared to VNC (5.23%) or VNC-BZL (3.12%). Women exhibited increased Firmicutes abundance (p&#x2009;=&#x2009;0.034).<br><br>CONCLUSIONS: Restoration of microbial diversity correlates with CDI resolution. FDX preserves gut microbiota better than VNC or VNC-BZL. Women and immunocompromised patients demonstrate impaired microbiota recovery.},
}
@article {pmid41941984,
year = {2026},
author = {Margaux, E and Elise, T and Muriel, D and Matthijs, M and Jellina, P and Arnau, VV and Jean, S and Nicky, D and Bart, B and Jeroen, R and Kaat, A},
title = {A pilot study on the role of the oxytocinergic system in gut microbiome composition in children with autism: baseline associations and effects of intranasal oxytocin.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106579},
doi = {10.1016/j.bbi.2026.106579},
pmid = {41941984},
issn = {1090-2139},
abstract = {Autistic children often experience behavioral difficulties alongside nutritional and gastro-intestinal (GI) problems, including gut dysbiosis. Recent research has highlighted important interactions between the oxytocinergic system and gut microbiome compositions, however, insights into how exogenous administration of oxytocin may influence GI health remain largely unexplored. Here, we first examined whether nutrition, GI symptoms and microbiome compositions vary in autistic versus non-autistic children, and how alterations link to clinical-behavioral difficulties and oxytocinergic signaling. Next, we examined the effect of a four-week intranasal oxytocin administration regimen on GI health/dysbiosis in autistic children enrolled in a randomized placebo-controlled trial. Compared to non-autistic children, autistic children consumed more soft drinks, and fewer vegetables and experienced abdominal pain more frequently over the past three months. Notably, epigenetic variations in the oxytocin receptor gene (OXTR) were associated with stool consistency, indicating that children with looser stools exhibited lower OXTR methylation levels, indicative of increased receptor expression. Additionally, a higher abundance of Romboutsia was associated with OXTR hypo-methylation and more anxiety-like behavior. In autistic children, the four-week oxytocin regimen had no effect on bacterial diversity but did modify stool consistency, leading to less dense stools with an overall more normal stool consistency, and an increased abundance of the potentially anti-inflammatory genus Fusicatenibacter. To conclude, this study provides novel insights into the role of the oxytocinergic system in GI symptoms and gut microbiome compositions in autistic children, and preliminary evidence suggesting a modulatory effect of exogenously administered oxytocin on these parameters.},
}
@article {pmid41941985,
year = {2026},
author = {Bettio, MK and Vidal, T and Rose, JJ and Jois, M and Flavel, M and Petrovski, S},
title = {Polyphenol-Rich Feed Material increases Anaerostipes and reduces methanogenic archaea in the horse hindgut microbiome.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {105885},
doi = {10.1016/j.jevs.2026.105885},
pmid = {41941985},
issn = {0737-0806},
abstract = {BACKGROUND: The gastrointestinal microbiota plays a critical role in horse health and performance. While sugarcane-derived polyphenols have shown microbiota-modulating properties in other species, their effects in horses remain unexplored.<br><br>AIMS/OBJECTIVES: This study investigated whether supplementation with a sugarcane-derived polyphenol feed material modulates the hindgut microbiota of healthy adult horses.<br><br>METHODS: An observational longitudinal study was conducted on six horses over 12 weeks. Faecal samples were collected at three time points: baseline (P1), during supplementation (P2), and post-supplementation (P3). Microbial composition was assessed by 16S rRNA gene sequencing targeting the V3-V4 region. Alpha and beta diversity, as well as differential abundance analyses, were performed.<br><br>RESULTS: Alpha diversity metrics (Chao1, Shannon, Simpson) showed no significant differences across time points. However, Anaerostipes increased by 105.3% during supplementation and 23.6% post-supplementation. Prevotella abundance also rose post-supplementation. Methanogenic Archaea, including Methanomassiliicoccus, decreased by 79.1% during supplementation, while members of Methanobacteriales were reduced by 61.8%. These changes partially reversed in the post-supplementation phase. Core microbiota genera remained stable throughout.<br><br>CONCLUSION: Supplementation with a sugarcane-derived polyphenol feed material modulated specific microbial taxa without disrupting overall microbial diversity. The intervention enhanced fermentative SCFA-producing bacteria and suppressed methanogenic Archaea, supporting the potential use of this feed material as a microbiome enhancer for improving hindgut health and reducing methanogenesis in horses.},
}
@article {pmid41942049,
year = {2026},
author = {Chen, W and Zhang, Y and Tian, Y and Dai, W and Huang, D and Zhao, Z and Henawy, AR and Shao, Z and Cai, M and Huang, F and Zheng, L and Cheng, W and Zhang, J},
title = {Multi-cycle application of Virgibacillus dokdonensis induces a root-knot nematode-suppressive soil via specifically recruiting functional Pseudomonas.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.004},
pmid = {41942049},
issn = {2090-1224},
abstract = {INTRODUCTION: Inducing the development of disease-suppressive soils against root-knot nematodes (RKNs) represents a sustainable strategy for reducing pesticide dependence, with microbial management serving as a core approach. However, the formation mechanisms, key microbial drivers, and functional stability of RKN disease suppressive soil remain poorly understood.<br><br>OBJECTIVES: This study aimed to elucidate the ecological mechanisms underlying soil microbiome-mediated suppressiveness against RKNs induced by multi-cycle application of the deep-sea biocontrol bacterium Virgibacillus dokdonensis MCCC 1A00493.<br><br>METHODS: Using a three-cycle consecutive microcosm experiment, we tracked RKN disease incidence and soil microbial community dynamics. We combined microbiome sequencing with functional assays to identify key functional taxa, and constructed synthetic microbial communities (SynComs) to validate their synergistic suppression with V. dokdonensis.<br><br>RESULTS: Continuous application of V. dokdonensis significantly reduced RKN disease, with the control efficacy reaching 37.86%, 51.11%, and 65.85% over three cropping cycles. This suppressiveness was achieved through direct antagonism and the reshaping of the soil bacterial community, which involved the successful colonization of V. dokdonensis and specific enrichment of indigenous functional Pseudomonas. Metagenomic analysis indicated a significant upregulation of bacterial chemotaxis genes. Further chemotaxis assays confirmed that the fermentation supernatant of V. dokdonensis specifically attracts high-nematicidal Pseudomonas, achieving a relative chemotaxis index reaching 3.0 to 9.1. Based on this, we constructed synthetic communities of functional Pseudomonas with varying complexity levels. Among them, a simplified SynComV1, consisting of Pseudomonas monteilii, P. parafulva, P. fulva, P. plecoglossicida, and P. putida, exhibited the greatest disease suppression, reaching 48.38%. Notably, co-application of V. dokdonensis and SynComV1 demonstrated significant synergistic effects, enhancing the control efficacy to 58.33%.<br><br>CONCLUSIONS: Overall, this study revealed that multi-cycle application of V. dokdonensis induces a RKN-suppressive soil by specifically recruiting indigenous high-nematicidal Pseudomonas to synergistically suppress RKN disease. These findings provide a practical strategy for developing efficient and sustainable technologies for RKN management.},
}
@article {pmid41942109,
year = {2026},
author = {Alsarahead, RA and El-Shehabi, FS and Hijjawi, NS},
title = {Prevalence and subtype diversity of Blastocystis hominis among gastroenteritis patients in northern and central Jordan.},
journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
volume = {},
number = {},
pages = {},
doi = {10.1093/trstmh/trag033},
pmid = {41942109},
issn = {1878-3503},
support = {49//Deanship of Scientific Research at Hashemite University/ ; //Department of Graduate Studies/ ; },
abstract = {BACKGROUND: Blastocystis hominis is a common intestinal eukaryotic organism that infects both humans and animals. Although its pathogenicity remains debated, it has been associated with diarrhoea and gastroenteritis. This study aimed to determine its prevalence and characterize its genetic subtypes (STs) in symptomatic patients presenting with gastrointestinal complaints.<br><br>METHODS: DNA was extracted from 279 stool samples collected from patients in northern and central regions of Jordan. Nested polymerase chain reaction targeting the 18S rRNA gene locus and Sanger sequencing of positive samples were used for B. hominis detection and subtype identification. Phylogenetic relationships were analysed using Unipro UGENE and MEGA software. Statistical analyses, prevalence, Pearson's &#x3c7;2 test (p<0.05) were conducted using SPSS.<br><br>RESULTS: The present study found a B. hominis prevalence of 7.2% (20/279). Three subtypes were identified: ST1 35% (7/20), ST2 10% (2/20) and ST3 55% (11/20). No mixed-subtype infections were detected. A statistically significant association was observed between B. hominis infection and patient age (p<0.05), with infection rates influenced by age and not by gender. The highest prevalence, based on sequencing, was observed in the 6- to <12-y age group. The association between B. hominis infection and gender was not statistically significant.<br><br>CONCLUSIONS: The relatively low prevalence of B. hominis among patients suggests it may function more as an indicator of gut health rather than as a primary pathogen. However, confirmation of this hypothesis requires additional microbiome and longitudinal studies. The frequent detection of ST1 and ST3 aligns with previous findings that link these subtypes to clinical symptoms. Broader epidemiological studies are needed to clarify the distribution patterns and clinical significance of B. hominis in human populations.},
}
@article {pmid41942178,
year = {2026},
author = {Opperman, C and Lloyd, C and Ratanpaul, V and Van, TTH and Brennan, C and Eri, R},
title = {Engineering SCFAs with dietary fibre combinations: insights from a kinetic-microbiome single-subject longitudinal study.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 1},
pages = {118846},
doi = {10.1016/j.foodres.2026.118846},
pmid = {41942178},
issn = {1873-7145},
mesh = {*Dietary Fiber/metabolism/analysis ; Humans ; Fermentation ; Longitudinal Studies ; *Gastrointestinal Microbiome/physiology ; Male ; Manihot/chemistry ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Adult ; Saccharum ; Inulin/metabolism ; Female ; Starch/metabolism ; Kinetics ; Young Adult ; Musa ; Bifidobacterium/metabolism ; Psyllium ; },
abstract = {The human diet plays a pivotal role in health, yet many studies seeking to identify health-promoting foods rely on experimental designs that poorly reflect natural circumstances. The effects of dietary fibres on the microbiota are typically examined using pooled faecal material and isolated fibres, creating unrealistic environments. Additionally, little progress has been made in distinctly characterising the fermentation rates of dietary fibres. To evaluate the temporal dynamics of gut microbial composition and metabolite production, as well as to characterise the fermentation rates of dietary fibres at an individual level, we conducted an n-of-1 longitudinal study examining responses to eight distinct dietary fibres, fermented both individually and in combination. A blend of sugarcane fibre and cassava resistant starch produced significantly higher butyrate levels (p < 0.0001) than either fibre alone. Microbial profiling showed that inulin and pectin selectively enriched Bifidobacterium spp. Anaerobutyricum hallii was increased with psyllium husk, wheat dextrin, and banana resistant starch, but decreased with a mixture of sugarcane fibre and cassava resistant starch (p < 0.0001). Fermentation kinetics were distinctly categorised into "fast", "medium", "slow" and "poorly-fermentable". These findings indicate that combinations of dietary fibres can be used as a strategy to engineer synergistic health-promoting metabolite responses in an individual, while establishing a standardised framework for describing fermentation rates across studies.},
}
@article {pmid41942241,
year = {2026},
author = {Cheng, W and Jiang, C and Pan, T and Zhu, Q and Liu, G and Li, N and Wu, Z and Li, X},
title = {Corrigendum to "Effects of quinoa addition on physicochemical properties, microbiome profiles, and volatile organic compounds in medium-temperature Daqu" [Food Res. Int. 223 (2026) 117868].},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 1},
pages = {119013},
doi = {10.1016/j.foodres.2026.119013},
pmid = {41942241},
issn = {1873-7145},
}
@article {pmid41942569,
year = {2026},
author = {Connolly, JA and Del Carratore, F and Schmidt, K and Bisesi, AT and Martinson, JNV and Chua, J and Kuhs, M and Boneza, MM and Heinsch, SC and Kinkel, LL and Smanski, MJ and Harcombe, WR and Breitling, R and Takano, E},
title = {Multi-omics analysis of interspecies interactions in a soil Streptomyces community provides functional insights into siderophore ecology.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41942569},
issn = {2045-2322},
support = {NE/T010959/1//UK Research and Innovation/ ; 1935458//National Science Foundation/ ; },
mesh = {*Streptomyces/metabolism/genetics ; *Siderophores/metabolism ; *Soil Microbiology ; Metabolomics/methods ; Iron/metabolism ; *Microbiota ; Deferoxamine/metabolism ; Transcriptome ; Multigene Family ; Multiomics ; },
abstract = {Streptomyces are key contributors to soil microbiome function, known for their biosynthetic diversity. While advances in -omics technologies have improved our understanding of microbiome composition and metabolic potential, the mechanisms underpinning interspecies interactions remain poorly resolved. Here, we investigate the molecular basis of interactions among four sympatric Streptomyces soil microbiome isolates, focusing on phenotypic, metabolomic and transcriptomic responses. Co-culture experiments revealed that one isolate, strain A, exhibited pronounced phenotypic changes when grown alongside each of the other three strains. Untargeted metabolomics and RNA-seq analyses showed that strain A undergoes distinct metabolic and transcriptional shifts depending on its partner, with the strongest response elicited by strain C. Despite all four strains possessing a conserved desferrioxamine biosynthetic gene cluster, only strain C constitutively produced desferrioxamine B (DFO-B), a hydroxamate siderophore, indicating a role for iron bioavailability in the interaction. Supplementation with DFO-B or iron mimicked the growth stimulation of strain A observed in co-culture with strain C, and CRISPR base editing of desD in strain C abolished both DFO production and the phenotypic induction of strain A. However, transcriptomic profiles of strain A varied significantly depending on the partner strain, with distinct sets of biosynthetic gene clusters and metabolic pathways activated in response to strains B and C, suggesting additional cues beyond DFO-B. In contrast, strain D did not elicit growth stimulation in its partners, and itself showed downregulation of amino acid and carbon metabolism when co-cultured with strain C. These findings indicate that Streptomyces interactions are not only mediated by siderophore piracy but also involve complex, strain-specific molecular responses. Our findings demonstrate that Streptomyces interactions are highly strain-specific and only partly mediated by siderophore piracy, with DFO-B acting as a potent interspecies cue. The divergent molecular responses to different partners suggest nuanced mechanisms of microbial sensing and competition. These insights advance our understanding of microbial crosstalk and highlight the ecological and evolutionary complexity of siderophore-mediated interactions. By integrating transcriptomics, metabolomics, and biochemical assays, we present a robust framework for dissecting microbial interactions, with implications for microbiome engineering and synthetic community design.},
}
@article {pmid41942702,
year = {2026},
author = {Zhang, YK and Iskandar, MM and Kubow, S and Komarova, SV and Tauer, JT},
title = {Exploring the impact of collagen-I genetic variants on intestinal structure and gut microbiota in mouse models of osteogenesis imperfecta.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47221-2},
pmid = {41942702},
issn = {2045-2322},
support = {87500//Shriners of North America/ ; },
}
@article {pmid41942777,
year = {2026},
author = {Verdegaal, AA and Oh, J and Javdan, B and Wang, R and Wu, Q and Wang, TRW and González-Hernández, JA and Donia, MS and Crawford, JM and Goodman, AL},
title = {A drug-microbiome-drug interaction impacts co-prescribed medications for Parkinson's disease.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41942777},
issn = {2058-5276},
support = {R35GM118159//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AT010014//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; F31DK132941//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AI172144//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RM1GM141649//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Simultaneous prescription of multiple drugs is widespread in medicine. Although the gut microbiome is implicated in drug responses, its role in mediating drug-drug interactions is unexplored. Catechol-O-methyltransferase inhibitors (COMT-I), a class of drugs used alongside levodopa (L-DOPA) to treat Parkinson's disease symptoms, can alter microbiome composition in patients. Here we characterize the antibiotic properties of COMT-I drugs in vitro, ex vivo and in vivo and dissect how these interactions alter microbiome-mediated L-DOPA metabolism in vitro and ex vivo. Notably, in vitro iron availability determines COMT-I antibiotic activity at multiple levels: extracellular iron can drive non-enzymatic inactivation of COMT-I, rescuing COMT-I-mediated bacterial iron starvation responses. However, limitation of intracellular iron can protect sensitive bacteria from COMT-I antibiotic activity. Co-administration of COMT-I and L-DOPA to human faecal microbial communities ex vivo results in COMT-I-dependent alterations to L-DOPA metabolism in an individual-specific manner. These studies highlight a role for the gut microbiome in mediating drug-drug interactions and identify microbial features that could predict individual responses to co-prescribed drugs.},
}
@article {pmid41943076,
year = {2026},
author = {Ghathian, KSA and Halkjær, SI and Krogfelt, KA and Frimodt-Møller, N and Hansen, KH and Frederiksen, AKS and Holm, A and Petersen, AM},
title = {The effect of the probiotic supplement-ASTARTE™-on the reduction of recurrent urinary tract infection in women aged 18-40 years: protocol for a randomized, double-blind, placebo-controlled study.},
journal = {Trials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13063-026-09679-3},
pmid = {41943076},
issn = {1745-6215},
abstract = {BACKGROUND: Urinary tract infection (UTI) is one of the most common bacterial infections, contributing to increased antibiotic consumption and high healthcare costs. Clinical studies suggest that probiotics can be effective dietary supplements reducing the risk factors for the development of infections in the intestine and vagina. In this study, we investigate the effect of the orally ingested probiotic combination ASTARTE™ on the composition of bacteria in vaginal and fecal samples, as well as on the occurrence of bacteriologically confirmed UTIs in women of reproductive age.<br><br>METHODS: A randomized, placebo-controlled, double-blind study evaluating the effect of the probiotic combination ASTARTE&#x2122; (Chr. Hansen A/S, Part of Novonesis Group, Denmark) on reducing the number of recurrent urinary tract infections (rUTIs) in women aged 18-40&#xa0;years. Participants are randomized (1:1) to receive one daily probiotic capsule (5 &#xd7; 10[9] CFU) containing Lactobacillus crispatus LBV 88&#x2122; (DSM22566), Lacticaseibacillus rhamnosus LBV 96&#x2122; (DSM22560), Lactobacillus jensenii LBV 116&#x2122; (DSM22567), and Lactobacillus gasseri LBV 150N&#x2122; (DSM22583), or placebo, for 6 months. Assessments, including symptom questionnaires, urine culturing and microbiome analysis of vaginal and rectal samples by shotgun sequencing, are conducted at baseline, 2, 4, and 6&#xa0;months. Compliance is tracked by unused capsule counts. Follow-up visits occur at 8, 10, and 12&#xa0;months. The primary outcome is the incidence of symptomatic bacteriologically confirmed UTIs during the 6&#xa0;months intervention period. The secondary objective is the effect of ASTARTE&#x2122; on changes in vaginal and gut microbiome.<br><br>DISCUSSION: This randomized, placebo-controlled, double-blind study investigates the effectiveness of ASTARTE&#x2122; in restoring beneficial microbiomes and reducing UTI recurrence. The findings will provide valuable evidence on the effectiveness of a non-antibiotic strategy for the prevention of rUTI as well as insights into the complex interactions between the vaginal and gut microbiome and the risk of rUTI.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT05553652. Registered 21 September 2022.},
}
@article {pmid41943109,
year = {2026},
author = {Crouzet, L and Kelly, W and Andrews, C and Soni, P and Tong, B and Tavendale, R and Rajasekaran, K and Wieliczko, K and Pilkington, K and Kaminsky, R and Matiya, F and Molano, G and Sandoval, E and Dobson-Hill, B and Reid, P and Muetzel, S and Khan, A and Maclean, P and Doohan, H and Burgess-Smith, T and Atkins, N and Bassett, S and Dekker, J and Hill, J and Bermingham, E and Attwood, G},
title = {Early life treatment with Lacticaseibacillus rhamnosus strains drives reduced enteric methane emissions in dairy heifers.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41943109},
issn = {1674-9782},
support = {PGGRC-Fonterra project contract 20-FONT- LAB AGR MET 5.4, Contract AgR: A27147.//This study was funded by the Pastoral Greenhouse Gas Research Consortium (PGgRc) and Fonterra Ltd./ ; },
abstract = {BACKGROUND: Methane emissions from enteric fermentation in ruminant livestock make up 27% of anthropogenic methane emissions.<br><br>RESULTS: Screening&#x2009;>&#x2009;1,700 lactic acid bacteria identified Lacticaseibacillus rhamnosus FNZ118 (Kowbucha&#x2122; FNZ118) and L. rhamnosus FNZ142, (Kowbucha&#x2122; FNZ142) as capable of inhibiting rumen methanogens and methane production in vitro. FNZ118 or FNZ142 fed daily to Friesian heifer calves from birth to 14&#xa0;weeks substantially lowered methane production through the first year of life compared to control animals. These strains also decreased feed intake and reduced ruminal metabolite concentrations without affecting animal live weight, suggesting an improvement in feed conversion efficiency. The observed effects did not cause major changes in the structure of the rumen microbiome.<br><br>CONCLUSIONS: These findings demonstrate that early life provision of specific L. rhamnosus strains lower CH4 production and have potential for the mitigation of enteric greenhouse gas emissions from growing dairy cattle.},
}
@article {pmid41943321,
year = {2026},
author = {Pu, D and Liang, T and Li, X and Xing, W and Luo, L and Ding, Y and Wan, C and Wu, M},
title = {Physicochemical properties and molecular weight-dependent gut microbiota modulation of inulin-type fructans from Codonopsis bulleynana.},
journal = {Carbohydrate polymers},
volume = {381},
number = {},
pages = {125217},
doi = {10.1016/j.carbpol.2026.125217},
pmid = {41943321},
issn = {1879-1344},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Fructans/chemistry/pharmacology/isolation &amp; purification ; *Codonopsis/chemistry ; *Inulin/chemistry/pharmacology ; Molecular Weight ; Mice ; Fermentation ; Molecular Dynamics Simulation ; },
abstract = {The therapeutic efficacy of dietary fibers is closely related to structural heterogeneity, yet the impact of chain length on physicochemical behavior and gut microbiota modulation remains unclear. Herein, three homologous linear β-(2 → 1)-linked inulin-type fructans with distinct molecular weights, hereafter referred to as CBP1-3, were isolated from Codonopsis bulleynana. All fractions spontaneously assembled into stable supramolecular nanoparticles/disks in water, a process thermodynamically driven by intermolecular hydrogen bonding according to molecular dynamics simulations. Biological evaluation revealed a striking divergence: while low-molecular-weight fractions showed superior efficacy in in vitro fermentation, the relatively high-molecular-weight CBP1 exhibited superior in vivo potency. Multi-omics analysis supports the hypothesis that this supramolecular structure, in synergy with extended chain length, may function as a structural barrier and confer sustained-release characteristics. This likely limits mucin-degrading Akkermansia proliferation via a nutrient-sparing effect, thereby maintaining metabolic homeostasis. These findings demonstrate that relatively high-molecular-weight polysaccharides possess unique ecological advantages in physiological contexts, challenging traditional in vitro screening paradigms and positioning CBP1 as a promising candidate for precision microbiome restoration.},
}
@article {pmid41936486,
year = {2026},
author = {Pasta, A and Formisano, E and Calabrese, F and Navazzotti, G and Giannini, EG and Savarino, V and Savarino, EV and Marabotto, E},
title = {Dietary and nutraceutical interventions for functional dyspepsia: A narrative review.},
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.2026.03.010},
pmid = {41936486},
issn = {1878-3562},
abstract = {Functional dyspepsia (FD) is a prevalent disorder of gut-brain interaction. Commonly, meals may exacerbate FD symptoms like postprandial fullness, early satiation, epigastric pain, and nausea. We narratively synthesize meta-analyses, randomized trials, and observational evidence to outline mechanism-based dietary and nutraceutical options. Evidence favors small, regular, lower-fat meals and adjusting texture/osmolarity to minimize gastric distension. In selected phenotypes-particularly postprandial distress with bloating-a brief, dietitian-supervised low-FODMAP trial with staged reintroduction can define personal thresholds. Among nutraceuticals, peppermint-caraway, ginger, STW-5, curcumin, and selected probiotics show benefit, with melatonin and barrier-forming agents promising in subsets, while safety remains product-specific.},
}
@article {pmid41936491,
year = {2026},
author = {Burns, KF and Blair, RH and Mares, JA and LaMonte, MJ and Wactawski-Wende, J and McSkimming, D and Liu, Z and Millen, AE},
title = {Gut bacteria associated with an atherogenic TMAO-dietary pattern and choline-rich foods among aging women.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104635},
doi = {10.1016/j.numecd.2026.104635},
pmid = {41936491},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: Choline can be metabolized by gut bacteria with a choline utilization gene, CutC, as identified through genome sequencing studies. This metabolism produces trimethylamine, the precursor to the atherosclerotic metabolite trimethylamine N-oxide (TMAO). Bacterial species involved in trimethylamine production in free-living humans have been under-investigated. We previously developed the TMAO dietary pattern (TMAO-DP), which is predictive of plasma TMAO and choline. We evaluated associations between the TMAO-DP, dietary choline, and choline-rich foods (fish, red meat, eggs) with the abundance of species with CutC. We also explored associations between the TMAO-DP and microbiome diversity.<br><br>METHODS AND RESULTS: This cross-sectional analysis included 287 women (mean age&#xa0;=&#xa0;79.6 years) from the Women's Health Initiative. Diet was assessed using a food frequency questionnaire. Stool samples were collected and the V3-V4 regions of the 16S ribosomal RNA were sequenced. Adjusted linear regression models evaluated associations between the TMAO-DP with the CLR-transformed abundance of species with CutC and with alpha-diversity indices. For beta-diversity, PERMANOVA examined measures of Aitchison distance within and between quartiles of the TMAO-DP. Associations between dietary choline and choline-rich foods with the abundance of species were evaluated using linear regression. The TMAO-DP was associated with Acidaminococcus intestini [Beta (SE): 0.23 (0.09), p-value&#xa0;=&#xa0;0.035] and Desulfovibrio desulfuricans [Beta (SE): 0.16 (0.6), p&#xa0;=&#xa0;0.035]. The TMAO-DP was not associated with alpha- or beta-diversity.<br><br>CONCLUSION: This study provides evidence that Desulfovibrio desulfuricans and Acidaminococcus intestini, two species identified as having CutC by gene sequencing, may produce trimethylamine from diet in free-living women.},
}
@article {pmid41936687,
year = {2026},
author = {Viswan, A and Augustine, N},
title = {Insect Gut Microbiota as a Reservoir of Industrially Relevant Enzymes: A Comprehensive Review.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02726-1},
pmid = {41936687},
issn = {1432-184X},
}
@article {pmid41936794,
year = {2026},
author = {Evans, C and Petry, A and Johnson, T and Kogut, MH and Walk, CL and York, T},
title = {A NEW FOCUS ON FIBER.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106863},
doi = {10.1016/j.psj.2026.106863},
pmid = {41936794},
issn = {1525-3171},
abstract = {Dietary fiber (DF) in poultry nutrition was once viewed mainly as an anti-nutritional factor that reduced energy density and nutrient digestibility. Current research shows DF can play important functional roles in gut health, nutrient utilization, and overall performance when its type and inclusion level are carefully managed. Fiber fractions differ widely in chemical composition and physical properties such as solubility, water-holding capacity, and water-binding capacity. These factors influence digesta viscosity, passage rate, microbial fermentation, and satiety, making precise fiber characterization critical for effective diet formulation. Traditional methods like crude fiber analysis underestimate total fiber and miss key soluble fractions. Modern approaches, including total dietary fiber analysis and near-infrared spectroscopy allow for better quantification of both insoluble and soluble components and support incorporation into real-time feed formulation. By understanding and targeting specific non-starch polysaccharides or oligosaccharides, nutritionists can promote beneficial fermentation, encourage short-chain fatty acid (SCFA) production, and minimize undesirable protein fermentation or pathogen growth. Dietary fiber also supports intestinal barrier function by stimulating gut development, increasing villus height, and fueling epithelial cells through SCFAs. However, poorly balanced fiber can impair nutrient absorption, increase maintenance energy needs, or elevate digesta viscosity, particularly in young birds. Monitoring gut health is now possible by using biomarkers as tools to evaluate intestinal integrity, inflammation, and microbial balance as we investigate the impact of dietary fiber, but further work is needed to standardize these measures and account for flock variability When properly applied, DF can enhance feed efficiency, improve welfare by reducing hunger-driven behaviors, support reproductive performance, and strengthen disease resilience. A data-driven, precision approach combining accurate fiber analysis, enzyme supplementation, microbiome profiling, and non-invasive gut health biomarkers offers the greatest potential to optimize both productivity and sustainability in poultry systems. The purpose of this symposium was to stimulate discussion and enhance understanding of dietary fiber and its potential benefits in improving poultry production. This paper provides an overview of each contributing author's role in the symposium. Dr. Caitlin Evans addressed the challenges associated with current fiber nomenclature and emphasized the need to improve analytical methods and overall understanding of fiber. She brings strong credibility to this topic as a Technical Manager for Near-Infrared Spectroscopy and Feed Milling Engineer at AB Vista, and as a Ph.D. graduate of Kansas State University. Dr. Amy Petry shared her expertise on the impact of fiber in swine nutrition and how these findings can be applied to poultry. She is an Assistant Professor in the Division of Animal Sciences at the University of Missouri, where her research focuses on improving fiber utilization and its effects on energy efficiency and animal health. Dr. Tim Johnson, Professor in the Department of Veterinary and Biomedical Sciences at the University of Minnesota, highlighted the importance of understanding the poultry microbiome and its role in developing strategies to enhance bird performance. Dr. Mike Kogut contributed his expertise as a Research Microbiologist and Lead Scientist with the Food and Feed Safety Research Unit at the Southern Plains Agricultural Research Center. Finally, Dr. Carrie Walk, Head of Research at AB Vista, along with Dr. Tara York, AB Vista's Technical Director for North America, integrated the key themes of the symposium, connecting the presented research and practical applications.},
}
@article {pmid41936807,
year = {2026},
author = {Nualart C, D and Schwob, G and Orlando, J and Pashcke, K and Guerreiro, PM and McCormick, SD and Cheng, CC and Vargas-Chacoff, L},
title = {Microplastic pollution and thermal increase alter cellular stress responses and microbiomes in Antarctic and Sub-Antarctic fish.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128039},
doi = {10.1016/j.envpol.2026.128039},
pmid = {41936807},
issn = {1873-6424},
abstract = {Antarctic and sub-Antarctic fishes of the genus Harpagifer inhabit extreme environments and face emerging anthropogenic stressors, including plastic pollution and warming. While each factor is known to affect fish physiology, their acute combined impacts on molecular responses and host-microbe interactions remain poorly understood. In this study, we investigated the immediate (24 h) transcriptional response of stress-related genes heat shock protein 70 (hsp70), S100 calcium binding protein (s100), High Mobility Group 1 box (hmg1b), E3 Ubiquitin Ligases (E3), and BCL2 Associated X (Bax) and gut microbiome diversity in H. antarcticus (King George Island, Antarctica) and H. bispinis (Punta Arenas, Chile) exposed to elevated temperature (TI), PVC microplastics (MP), or their combination (TI+MP). Both stressors altered gene transcription in a tissue- and species-specific manner, suggesting a synergistic stress response under combined treatment. Temperature rise consistently modulated stress markers, while acute PVC exposure intensified apoptotic signaling. Notably, species-specific patterns emerged: H. bispinis showed a more pronounced induction of pro-apoptotic pathways, whereas H. antarcticus maintained a higher induction of protective chaperones within this short temporal window. At the microbial level, while community-wide diversity metrics remained statistically stable, an exploratory analysis revealed increased inter-individual variability and the enrichment of specific stress-tolerant bacterial taxa. These results reveal that acute warming and microplastic exposure interactively disturb host, cellular homeostasis, with distinct transcriptional plasticity across closely related species. Our study provides mechanistic insights into the early physiological challenges faced by Notothenioids, highlighting the importance of coupling molecular biomarkers with microbiome analyses to assess the initial stages of response in cold-adapted fishes to environmental change.},
}
@article {pmid41936881,
year = {2026},
author = {Liang, L and Fu, Y and Guan, D and Zeng, H and Wang, H and Peng, J and Shao, Y and Zhang, S and Liu, L},
title = {Effects of 16S rRNA hypervariable region selection on respiratory Microbiome profiling in healthy adults.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107493},
doi = {10.1016/j.mimet.2026.107493},
pmid = {41936881},
issn = {1872-8359},
abstract = {Selection of the 16S rRNA gene target region can substantially influence inferred respiratory microbiome profiles, particularly in low-biomass samples. In this study, we compared full-length V1-V9 (Pacific Biosciences) and V3-V4 (Illumina) amplicon sequencing using exhaled breath condensate collected from 50 healthy adults. Samples that yielded successful amplification for both approaches were included in paired, within-subject comparisons of sequencing depth, alpha diversity, and taxonomic composition. Sequencing of the V3-V4 region yielded significantly higher read counts and greater alpha diversity (richness and Shannon index) than full-length V1-V9 sequencing (all p < 0.001). Both approaches consistently identified a shared set of dominant respiratory-associated genera, including Acinetobacter, Streptococcus, Psychrobacter, Gemella, Neisseria, and Granulicatella. However, relative abundance estimates differed by target region, with Acinetobacter enriched in V1-V9 profiles, whereas Streptococcus and Neisseria were more abundant in V3-V4 data. In contrast, several genera showed comparable abundances across regions. These findings indicate that while overall community membership is broadly conserved, quantitative diversity metrics and genus-level abundance estimates are strongly influenced by primer and target-region selection. Overall, these results provide methodological guidance for interpreting respiratory microbiome data derived from exhaled breath condensate and highlight the importance of aligning sequencing strategies with specific study objectives.},
}
@article {pmid41936917,
year = {2026},
author = {Zhang, S and Yue, T and Jin, P and Zhang, X and Huo, Q and Li, W and Tian, C and Dong, H and Dong, Y and Zhao, Y and Li, D},
title = {4-Octyl itaconate attenuates radiation-induced intestinal injury associated with ferroptosis inhibition and microbiota rebalance.},
journal = {Free radical biology &amp; medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2026.04.006},
pmid = {41936917},
issn = {1873-4596},
abstract = {Radiation-induced intestinal injury (RIII) is a serious and common complication of radiotherapy, and there are currently no effective therapeutic strategies. This study investigates the protective role of 4-octyl itaconate (4-OI), a cell-permeable itaconate derivative, against RIII. In vitro, 4-OI pretreatment enhanced the viability of irradiated intestinal epithelial cells, reduced reactive oxygen species (ROS) accumulation, and alleviated DNA damage. In a murine model of total body irradiation, 4-OI administration mitigated intestinal structural disruption, promoted crypt stem cell regeneration, and suppressed epithelial apoptosis. Mechanistically, 4-OI exerted its cytoprotective effects by modulating the SLC7A11/GPX4 axis to inhibit ferroptosis and enhancing glutathione biosynthesis. Furthermore, 16S rRNA sequencing revealed that 4-OI treatment recalibrated radiation-induced gut microbiota dysbiosis, suggesting an additional microbiome-mediated protective pathway. To our knowledge, the results represent the first demonstration of 4-OI's protective effects in RIII pathogenesis, positioning it as a novel therapeutic candidate for clinical radioprotection through dual mechanism targeting.},
}
@article {pmid41936935,
year = {2026},
author = {Wang, J and Bi, Y and Fu, Z and Qiao, H and Liu, F},
title = {Harvesting reed (Phragmites australis) for wetland nitrogen removal: Productivity, microbial communities, and underlying mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134553},
doi = {10.1016/j.biortech.2026.134553},
pmid = {41936935},
issn = {1873-2976},
abstract = {Non-point source nitrogen (N) pollution is a primary driver of aquatic eutrophication. While reed (Phragmites australis) wetlands effectively intercept N, the optimal harvesting strategy for maximizing N removal while maintaining ecosystem function remains unclear. This study investigated the effects of different harvesting frequencies on N removal, plant productivity, and associated microbial mechanisms in wetland microcosms over a three-year period. Four treatments were evaluated: unplanted control (CK), planted with no harvest (T0), annual harvest (T1), and biennial harvest (T2). Results demonstrated that all planted treatments significantly enhanced N removal compared to CK. Although not statistically significant among planted groups, T1 consistently achieved the highest average removal efficiencies for total nitrogen, ammonium-nitrogen, and nitrate-nitrogen. Furthermore, T1 produced the greatest aboveground biomass, facilitating the largest export of N and other nutrients. Metagenomic analysis revealed that reed planting shifted the microbial community, suppressing Cyanobacteria (e.g., Stanieria) and Nitrospirota (e.g., Nitrospira F), while enriching Proteobacteria and Chloroflexota. These compositional changes were coupled with a functional shift that key dissimilatory pathways (denitrification and dissimilatory nitrate reduction) were upregulated, while assimilatory nitrate reduction was suppressed. Additionally, annual harvesting fostered a more complex and stable microbial co-occurrence network. Structural equation modeling indicated that harvesting enhanced N removal primarily through plant-microbe interactions, with increased plant N accumulation promoting microbial N-functional gene abundance, and ultimately driving N removal. Overall, annual harvesting optimally coupled high biomass production with microbial N removal, presenting a sustainable management strategy for wetlands that balances water purification with resource recovery.},
}
@article {pmid41937023,
year = {2026},
author = {Field, CM and Keller, PM and Schultheiss, E and Gewitsch, B and Wiemer, DF and Schawaller, M and Halfter, M and Frickmann, H},
title = {Potential impact of antimalarial chemoprophylaxis with doxycycline on antimicrobial resistance genes in the enteric microbiome of deployed German soldiers - a case-control-study.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102978},
doi = {10.1016/j.tmaid.2026.102978},
pmid = {41937023},
issn = {1873-0442},
abstract = {BACKGROUND: Antimalarial chemoprophylaxis with doxycycline is taken by German soldiers on tropical deployments. In a case-control-assessment, diagnostic metagenomics was applied to comparatively assess antimicrobial resistance genes in enteric microbiomes of soldiers with and without medical history of doxycycline-based antimalarial chemoprophylaxis on deployment.<br><br>METHODS: Two groups of 26 military deployment returnees, each either exposed or non-exposed to antimalarial chemoprophylaxis with doxycycline, were matched by deployment site and period, age and sex in declining order of prioritization. Metagenomic analysis of stool samples was applied to detect resistance gene sequences within the sample materials.<br><br>RESULTS: In total, 3,770 different antibiotic resistance genes were detected across all samples. No significant differences were found in the frequency of antibiotic resistance genes in each sample compared between the doxycycline group and the control group. Approximately one third of metagenomically assembled genomes could be identified taxonomically at the species level (32.2%) and over half at the genus level (53.9%). The overall distribution of ABR genes at the species level showed that Escherichia coli was host for over a quarter of detected genes - 1,021 genes in only 42 identified genomes. Hosts with the next highest number of ABR genes were Escherichia marmotae (156 genes), Staphylococcus aureus (85 genes), Klebsiella michiganensis (63 genes) and Leclercia adecarboxylata (62 genes).<br><br>CONCLUSIONS: The study suggests - if any - only a low impact of doxycycline intake during military deployments on the enteric resistome of soldiers at post-deployment assessments. Reasons for Escherichia's high ABR gene load remain to be investigated.},
}
@article {pmid41937169,
year = {2026},
author = {Mullin, CE and Louca, S},
title = {Effects of heat-assisted sample desiccation on microbiome surveys.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00889-5},
pmid = {41937169},
issn = {2524-6372},
abstract = {Sample preservation remains a challenge in microbiome surveys, particularly in remote areas. Drying samples eliminates the need for cold chains and preservatives, but sophisticated desiccation tools such as lyophilization are impractical in the field. Further, the effects of sample drying on modern analyses, such as gene-centric metagenomics and metagenome-assembled genome (MAG) recovery, remain poorly understood. Here we explore heat-assisted sample desiccation followed by storage at room temperature as a cost-effective and practical solution in the field. We assess its effects relative to freezing on typical metagenomic and 16 S rRNA amplicon sequence analyses of bacterial and archaeal communities, using 60 samples from 6 different source materials (soils from 3 locations, feces from 3 animals). We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG recovery, as well as impacts on inferred microbial community composition. We find that, while desiccation had a significant negative impact on multiple metrics related to DNA extraction success, its impacts on downstream metrics such as OTU richness, Shannon diversity, gene annotation and MAG recovery were more nuanced and often insignificant. Further, while the preservation method had a significant influence on the inferred microbial community composition, samples from different source materials (e.g., soils from different locations, or feces from different individuals) remained clearly distinguishable. We conclude that heat-assisted desiccation can be a viable sample preservation method for microbiome studies, when a high consistency with frozen samples is not a requirement.},
}
@article {pmid41937467,
year = {2026},
author = {Lee, HJ and Lee, JH and Kwak, YS},
title = {A Keystone-Taxa SynCom Reveals Chlorella-Microbiome-Plant Communication and Enhances Suppression of Fusarium oxysporum.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2601023},
doi = {10.4014/jmb.2601.01023},
pmid = {41937467},
issn = {1738-8872},
mesh = {*Chlorella/physiology ; *Fusarium/drug effects/growth &amp; development ; *Plant Diseases/microbiology/prevention &amp; control ; *Microbiota ; Solanum lycopersicum/microbiology/growth &amp; development ; Antifungal Agents/pharmacology ; Mannitol/pharmacology ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Chlorella, a microalga renowned for its high protein and lipid content, is extensively used as a biofertilizer due to its plant growth promotion and disease suppression capabilities. To reveal, Chlorella-microbiome-plant communication, in-depth microbiota structure and network analyses were conducted. As a result, keystone taxa, which are microbial element in interaction with Chlorella, keystone taxa (Psedomonas, Duganella, Brevibacterium) interaction with C. fusca CHK0059 within plant hosts were identified. Here, however, the mechanistic insights into these interactions remain limited. Therefore, we aimed to investigate the characteristics of keystone taxa to elucidate Chlorella effects on plants. By applying various substances, including Chlorella, Chlorella methanol extract (methanol extract), and D-mannitol, we observed changes in microbial distribution and diversity, with a notable increase in Pseudomonas abundance following 2% D-mannitol treatment. Additionally, we assessed the impact of Chlorella on plant growth and disease suppression, finding that a synthetic community (SynCom) of keystone taxa exhibited enhanced antifungal effects against Fusarium oxysporum in both strawberry and tomato, compared to individual strains. The findings in this study suggested the fundamental data that the SynCom can contribute to the mechanism of action of C. fusca CHK0059 and expect to maximize the effect of Chlorella when combined.},
}
@article {pmid41937585,
year = {2026},
author = {Chen, X and Dong, T and Wu, D and Pan, Q and Wei, J and Liang, G and Lin, Z},
title = {Shifts in the Lung Microbiota and Antibiotic Resistance Genes Occur With Aging in Patients With Lower Respiratory Tract Infections.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e9038281},
pmid = {41937585},
issn = {2314-6141},
mesh = {Humans ; Adult ; Aged ; *Microbiota/genetics ; Middle Aged ; Adolescent ; Child ; *Aging/genetics ; Female ; *Respiratory Tract Infections/microbiology/drug therapy/genetics ; Male ; Aged, 80 and over ; *Lung/microbiology ; Child, Preschool ; Young Adult ; *Drug Resistance, Microbial/genetics ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Lower respiratory tract infections (LRTIs) are a leading cause of critical illness and mortality. The lung microbiome represents an important reservoir for the exchange of antibiotic resistance genes (ARGs). The pathogenic microbes remain poorly understood among different age groups, including children (0-17 years), youth (18-39 years), middle-aged adults (40-64 years), and older adults (65-99 years). We conducted a retrospective study of 699 bronchoalveolar lavage fluid (BALF) samples from LRTI patients aged 30 days to 99 years. The differences in the lung microbiome and ARG expression shift with age were evaluated based on targeted next-generation sequencing (tNGS) results. Correlation analysis revealed that age had a strongly positive correlation effect on the relative abundances of Candida albicans, Candida glabrata, Corynebacterium striatum, and Stenotrophomonas maltophilia. Meanwhile, age had a largely negative correlation effect on Enterococcus faecium and Mycoplasma pneumoniae. We found that ARG expression was significantly higher in adults compared with children. The beta-lactam ARG TEM was the most abundant, and the primary carrier of ARGs was Streptococcus in the LRTI microbiota. The proportion of adults expressing beta-lactams, aminoglycosides, and phenicol antibiotic types was higher compared to children. Our results indicated that ARGs in the human LRTI microbiota accumulate and become more complex with age, as older groups tend to harbor the highest abundance of these genes. Collectively, these results presented the respiratory tract core microbiota and ARGs in different age groups, supplying a foundation for microbiome-targeted interventions and emphasizing the potential of tNGS to improve clinical diagnosis.},
}
@article {pmid41937700,
year = {2026},
author = {Van Vu, S and Kundu, S and Woo, KH and Uttarotai, T and Van Doan, H},
title = {Impact of Body Weight on the Intestinal Microbiome of Cage-Cultured Oyster Pompano (Trachinotus anak).},
journal = {Animal genetics},
volume = {57},
number = {2},
pages = {e70092},
doi = {10.1002/age.70092},
pmid = {41937700},
issn = {1365-2052},
support = {106.05-2023.64//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; //Chey Institute for Advanced Studies' International Scholar Exchange Fellowship/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; *Body Weight ; Bacteria/classification/genetics ; *Ostreidae/microbiology ; },
abstract = {Oyster pompano (Trachinotus anak) is a commercially valuable marine species widely farmed in Southeast Asia, yet growth heterogeneity remains a persistent challenge in cage aquaculture. To investigate whether body weight influences the intestinal microbiota of this species, we compared the gut microbial communities of small and large T. anak using high-throughput 16S rRNA gene sequencing. The intestinal microbiota was dominated by Pseudomonadota (Proteobacteria) and Mycoplasmatota, together accounting for nearly 80% of total sequences, with additional contributions from minor phyla such as Spirochaetota, Thermodesulfo bacteriota, and Bacteroidota. While alpha- and beta-diversity analyses revealed no significant differences between groups, community composition and structure varied. Smaller fish harbored a more heterogeneous assemblage at the class level and a broader suite of core taxa, including Acinetobacter, Aeromonas, Bdellovibrio, and Comamonas. In contrast, larger fish were dominated by fewer classes, with Photobacterium and Brevinema emerging as distinctive core members. LEfSe analysis identified discriminant taxa between groups, although these trends were not statistically significant after multiple-testing correction. Network analysis highlighted striking differences in microbial interactions: smaller fish exhibited highly modular, densely connected networks with potential keystone taxa such as Paracidovorax and Ensifer, whereas larger fish displayed simpler, less structured networks indicative of reduced ecological stability. Together, these findings demonstrate that body weight is associated with subtle but ecologically meaningful shifts in microbiota composition, core membership, and interaction networks in cage-cultured T. anak. This work underscores the potential of microbiome-informed management strategies to mitigate growth variability and enhance the sustainability of marine aquaculture.},
}
@article {pmid41937731,
year = {2026},
author = {Kong, JF and Phang, HC and Wan Kamal, WHB and Ng, Y and Mohamad, S and Kee, PE and Liew, KB},
title = {Role of Probiotics in Oral Health: A Review From Microbial Balance to Clinical Applications.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010421039251206192855},
pmid = {41937731},
issn = {1873-4316},
abstract = {A diverse microbial community exists within the human oral cavity that plays an essential role in maintaining health or inducing diseases such as dental caries, periodontal disease, and halitosis. Probiotics, live microorganisms that provide health benefits when consumed in adequate amounts, have been found to be promising as a means of modulating the oral microbiome and combating these diseases. This review incorporates present knowledge about the mechanism of probiotic action, including competitive exclusion of pathogens, antimicrobial metabolite production, biofilm disruption, and immune modulation. Efficacy against pathogenic bacteria like Streptococcus mutans and Porphyromonas gingivalis has been proven by prominent probiotic groups Lactobacillus, Bifidobacterium, and Streptococcus, resulting in oral microbial homeostasis. Clinical applications of probiotics include prevention of caries, plaque reduction, and management of gingivitis and periodontitis, with research focusing on strain-specific effects. Emerging trends include precision probiotics tailored to each oral condition, postbiotics as strong alternatives (formerly "strong contenders"), and innovative delivery systems to enhance viability and colonization. The hurdles of strain specificity, regulatory gaps, and inconsistencies of clinical outcome continue. Safety concerns, while rare, represent possible risks of horizontal gene transfer and opportunistic infections in immunocompromised hosts. Future directions lie in genetic modification, new delivery methods, and standard clinical protocols to enhance probiotic function. This review emphasizes the clinical potential of probiotics as adjunctive treatments in oral medicine, with the caveat that further work is needed to overcome current challenges and enhance their therapeutic efficacy.},
}
@article {pmid41937967,
year = {2026},
author = {Hiratsuka, D and Matsuo, M and Hirota, Y},
title = {Endometrial Microbiome and Implantation: From Basic Knowledge to Clinical Medicine.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70040},
pmid = {41937967},
issn = {1445-5781},
abstract = {BACKGROUND: Recurrent implantation failure (RIF) is an infertility condition in which uterine factors remain difficult to diagnose and treat. Recent studies implicate the endometrial microbiome in implantation.<br><br>METHODS: This clinically oriented narrative review summarizes female reproductive tract microbiota and evidence on endometrial microbiome testing and management in infertility.<br><br>MAIN FINDINGS RESULTS: Vaginal dysbiosis is linked to adverse reproductive outcomes and provides a reference for interpreting upper-tract findings. Endometrial microbial signals are detectable by sequencing, but interpretation is challenged by the low-biomass environment and vulnerability to carry-over, kitome effects, and contamination. Across ART studies, a Lactobacillus-enriched endometrial profile is more often associated with favorable pregnancy-related outcomes, whereas non-Lactobacillus-dominant patterns are more frequently reported in implantation failure, although effect sizes and statistical significance vary across cohorts and depend on sampling validity and cutoff definitions. Limited nonrandomized intervention studies suggest that testing-guided targeted management (typically antibiotics with or without vaginal Lactobacillus-containing probiotics) may benefit selected patients, but protocols are heterogeneous and results remain inconsistent.<br><br>CONCLUSION: Evidence is rapidly evolving, yet observational designs and methodological variability limit causal inference. Future progress will require standardized sampling and contamination controls, outcome-anchored threshold validation, and pragmatic real-world evaluations of protocolized test-and-treat pathways using clinically meaningful endpoints.},
}
@article {pmid41938040,
year = {2026},
author = {Khalil, A and Thayer, ZM and Rivera, LM},
title = {Preterm birth, airway microbiome, and the evolutionary origins of asthma.},
journal = {Evolution, medicine, and public health},
volume = {14},
number = {1},
pages = {1-2},
pmid = {41938040},
issn = {2050-6201},
}
@article {pmid41938156,
year = {2026},
author = {Liu, YH and Huang, JR and Tao, Y and Wang, CC and Gu, CQ and Zhang, YM and Li, WJ and Jiang, HC},
title = {Aridity gradient overrides degradation in shaping the topsoil microbiome of the Tianshan wild fruit forest.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100586},
pmid = {41938156},
issn = {2666-5174},
abstract = {The Tianshan wild fruit forest, a critical relict ecosystem and biodiversity hotspot, is experiencing severe degradation, a process widely assumed to be the primary driver of negative shifts in soil microbial communities. However, in arid regions, the overarching influence of climatic aridity may supersede localized degradation effects, creating a pivotal scientific question: which factor-aridity or degradation-dominantly regulates the soil microbiome in this unique habitat? To address this, we analyzed 360 topsoil samples across degradation and aridity gradients using high-throughput sequencing. The results demonstrate that the aridity index, not degradation level, is the paramount factor shaping microbial community structure, explaining the largest proportion of variation in both bacterial (∼43%) and fungal (∼30%) communities. The ecosystem harbors an exceptionally stable core microbiome, with community assembly predominantly governed by stochastic processes. Notably, alternating wet-dry (dry sub-humid) conditions significantly enhanced the complexity and stability of microbial co-occurrence networks compared to semi-arid or humid regions. Additionally, soil microbes mediated multiple core ecological processes, with nitrogen cycling as the most abundant-dominated by Rhodoplanes, Alcaligenes, and rhizobial taxa (Bradyrhizobium, Allorhizob), among others-wherein nitrate reduction was exceptionally active in the Tianshan wild fruit forest, particularly in humid and semi-arid habitats. These findings challenge the prevailing degradation-driven paradigm, highlighting aridity as the master regulator of microbial communities. This insight is crucial for guiding conservation strategies, emphasizing that managing water availability and protecting dry sub-humid habitats are essential for maintaining the microbial stability and functional resilience of this invaluable ecosystem under climate change.},
}
@article {pmid41938217,
year = {2026},
author = {Mphande-Nyasulu, FA and Meksang, S and Noranate, N and Kongpanyakul, S and Kulalert, P and Nilchan, P and Trivijitsilp, P},
title = {Investigating Candida species and associated bacteria from vaginal swabs and smears of symptomatic and asymptomatic adult women: A cross-sectional study.},
journal = {IJID regions},
volume = {19},
number = {},
pages = {100868},
pmid = {41938217},
issn = {2772-7076},
abstract = {OBJECTIVES: Vaginal Candida infections are common among women, affecting between 75% and 80% of women in their lifetime, with a higher prevalence in women of childbearing age. This study assessed vaginal carriage of Candida species and associated bacteria in adult women.<br><br>METHODS: A total of 101 vaginal swabs and smears from symptomatic and asymptomatic adult women were analyzed for the presence of Candida sp. using culture, Gram stain, and next-generation sequencing (NGS). Morphology of selected Candida sp. was examined using scanning electron microscopy.<br><br>RESULTS: Candida colonization was observed in 39.6% (40 of 101) of the women. Candida albicans was identified in 75.0% (30 of 40) of the women, whereas the non-albicans species Nakaseomyces glabrata was observed in 7.5% (three of 40), P. kudriavzevii in 5% (two of 40), and C. tropicalis in 2.5% (one of 40). Women aged 18-25 years had the highest prevalence of colonization among all age groups, 47.5% (19 of 40). A significant difference in vaginal bacterial composition was observed among age groups 18-25 and 26-35 years (&#x3b1; 0.05 <0.038*, 95% confidence interval [CI] -0.16 to 0.99); between women positive for Candida aged 26-35 years and those aged 46-55 years (&#x3b1; 0.05 <0.016*, 95% CI -0.28 to -0.03); and between women who were Candida-positive and those who were Candida-negative (&#x3b1; 0.05 <0.016*, 95% CI 0.17 to -0.40). Among the women positive for Candida, symptomatic individuals had predominantly Gram-positive bacterial species 92.6% (23 of 25) compared with 46% (19 of 42) in asymptomatic individuals. Five bacterial species were shared between the symptomatic and asymptomatic samples. Unique budding patterns, surface modifications, and phylogenetic clusters are reported.<br><br>CONCLUSION: Vaginal Candida colonization including differences in microbiome composition according to age, disease status, and colonizing Candida species are reported. This study opens new areas of study in vaginal Candida colonization, pathogen-pathogen interaction, and microbiome analysis in more specific age brackets, away from the traditional pre-menopausal and menopausal women.},
}
@article {pmid41938356,
year = {2026},
author = {Chen, Y and Zhao, S and Ma, X and Ling, L and Du, P and Liu, X and Yao, Y and Ma, Q and Cheng, Y and Wang, Y and Wei, J and Nian, H and Lian, T},
title = {Selenium nanoparticles and glutathione synergistically enhance salt tolerance in soybean via the jasmonic acid pathway and arbutin-regulated rhizosphere microbiota.},
journal = {aBIOTECH},
volume = {7},
number = {2},
pages = {100022},
pmid = {41938356},
issn = {2662-1738},
abstract = {Soil salinity threatens agriculture worldwide. Nano-fertilizers offer a promising strategy to enhance tolerance to salinity and other stresses in crops, but their field performance is sometimes unpredictable, potentially due to complex interactions within the plant-microbe holobiont. Here, we designed chitosan-stabilized selenium nanoparticles (SeNPs@CS) as a novel nano-fertilizer. SeNPs@CS exhibited a uniform size (∼109.8 nm) and a positively charged surface (+14.7 mV), which confers good adhesion to plant tissues. Due to their good biocompatibility and small size, SeNPs@CS can be readily absorbed and utilized by plant leaves. When SeNPs@CS were combined with glutathione (GSH) to form a nanocomposite (SeG), they significantly promoted plant growth and enhanced salt tolerance in soybean (Glycine max). Multi-omics analyses revealed that SeG activates jasmonic acid (JA) pathways in the plant and remodels the root metabolic profile, leading to the enrichment of arbutin, a key signaling molecule, in the rhizosphere. This metabolic shift recruits and enriches beneficial salt-tolerant microbes, including Bacillus and Streptomyces, thereby establishing a protective microbiome. Treatment of plants with a synthetic microbial community (SynCom) composed of these elite strains, in combination with arbutin, reproduced the salt tolerance phenotype conferred by SeG treatment. Therefore, SeG improves salt tolerance in soybean via activation of the JA defense pathway and arbutin-driven recruitment of salt-tolerant rhizosphere microorganisms. Together, these two mechanisms enhance plant resilience under salt stress. This multi-kingdom synergistic mechanism for alleviating stress provides a new paradigm for developing smart agricultural inputs that target the plant holobiont to improve crop resilience.},
}
@article {pmid41938562,
year = {2026},
author = {Ye, B and Liu, R and Li, R and Roduan, MRM and Noor, WSAWM and Sairi, F},
title = {Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens).},
journal = {Veterinary world},
volume = {19},
number = {2},
pages = {864-876},
pmid = {41938562},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The gut microbiota is essential for nutrient digestion, immune function, and environmental adaptation in ruminants, particularly high-altitude species like yaks (Bos grunniens). Different husbandry practices (captive vs. free-range) can potentially alter the microbial communities and affect the yak health. However, comparative data on how these systems affect yak gut microbiomes remain limited, with most studies focusing on taxonomy rather than functional implications. This study aimed to compare gut microbiome composition, diversity, and predicted functional profiles between captive (CY) and free-range (FY) yaks using a 16S rRNA gene metabarcoding approach.<br><br>MATERIALS AND METHODS: Fecal samples were collected from healthy ~2-year-old yaks (n=5 CY, n=5 FY) in Litang County, Ganzi Prefecture, Sichuan, China, during summer. DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced on Illumina NovaSeq 6000. Bioinformatic analyses included quality filtering, Operational taxonomic units (OTU) clustering (97% similarity), taxonomic annotation (SILVA database), &#x3b1;- and &#x3b2;-diversity analysis. The microbial function was predicted using PICRUSt2 (KEGG pathways), BugBase (community phenotypes), and FAPROTAX (ecological functions). Statistical comparisan used Welch's t-tests, Wilcoxon rank-sum tests, principal coordinates analysis (PCoA), and Analysis of similarities (ANOSIM) with significance set at p < 0.05.<br><br>RESULTS: &#x3b1;-Diversity indices (e.g., Shannon p = 0.5476) showed no significant differences between CY and FY. However, &#x3b2;-diversity revealed distinct community structures (PCoA: PC1 30.52%, PC2 12.25%; ANOSIM R = 0.976, p = 0.007), with FY samples more homogeneous. At the genus level, CY were enriched in Ruminococcaceae bacterium UCG-005, Streptococcus, Escherichia-Shigella, Treponema, Christensenellaceae R-7, and Clostridium sensu stricto 1 (many fermentative or potentially opportunistic). FY showed higher abundances of Bacillus, Arthrobacter, Rhodococcus, Candidatus Saccharimonas, Prevotellaceae UCG-001, and Paenibacillus. Predicted functions indicated FY had greater capacities for carbohydrate/amino acid metabolism, DNA repair, fatty acid biosynthesis, and vitamin B pathways, while CY favored fermentation and reductive acetogenesis. BugBase highlighted higher anaerobic phenotypes in CY.<br><br>CONCLUSION: Husbandry practices profoundly influence yak gut microbiome structure and inferred metabolic potential, with free-range systems promoting, homogeneous communities suited to natural high-fiber diets while captive systems promotes fermentative and opportunistic shifts. These microbiome differences suggest opportunities for probiotic interventions to enhance yak health, productivity, and sustainability in high-altitude pastoral systems. Future metagenomic and metabolomic validation is needed.},
}
@article {pmid41938768,
year = {2026},
author = {Xue, Z and Han, Q and Han, H and Yan, L and Ma, X and Ji, P and Wang, B and Zhang, L and Wang, L and Liu, G},
title = {Mechanisms of fetal growth restriction in gestational cholestasis: role of gut microbiota and placental redox.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1815498},
pmid = {41938768},
issn = {2297-1769},
abstract = {INTRODUCTION: Intrahepatic cholestasis of pregnancy (ICP) is a cholestatic liver disorder associated with substantial fetal morbidity, including preterm birth, fetal distress, and even intrauterine demise. Although prior studies have documented structural and transcriptional alterations in the placenta during ICP, the mechanistic underpinnings linking maternal cholestasis to adverse fetal outcomes remain incompletely elucidated.<br><br>METHODS: In this study, a murine model of ICP was established by feeding pregnant C57BL/6 mice a 0.1% DDC (3,5-dicarboxylic acid-1,4-dihydrocollidine) diet from E0.5 to E18.5. We assessed fetal growth and employed multi-omics approaches, including placental transcriptome sequencing, maternal gut microbiome profiling, and serum/placental metabolome analysis.<br><br>RESULTS: Placental transcriptome sequencing revealed that ICP significantly downregulated the expression of antioxidant-related genes including Mgst1, Gstt1, Ggt1, Gpx8, Gstk1, and GSTA4 leading to reduced total antioxidant capacity in placental tissue and elevated levels of malondialdehyde (MDA), a marker of lipid peroxidation. Furthermore, ICP disrupted the maternal gut microbiota, resulting in decreased production of antioxidant microbial metabolites such as valeric acid and erythritol. This deficiency further aggravated oxidative damage in the placenta.<br><br>DISCUSSION: Collectively, our findings uncover a novel gut microbiota-placenta axis driven by cholestasis, which contributes to fetal IUGR. The maternal cholestasis induces gut dysbiosis, which diminishes the production of valeric acid and erythritol. The deficiency of these metabolites, coupled with a direct suppression of the placental Nrf2/Keap1 antioxidant signaling pathway by cholestasis, leads to placental oxidative stress. This oxidative damage impairs placental function, ultimately resulting in fetal growth restriction. Disrupting this pathogenic cycle may offer a promising therapeutic strategy for preventing or treating ICP-related reproductive disorders.},
}
@article {pmid41930959,
year = {2026},
author = {Horinouchi, M},
title = {Identification of the C9-hydrogenase for 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (9,17-DOHNA) and the 7α-dehydratase essential for initiating β-oxidation of the B-, C-, and D-rings in steroid degradation by Comamonas testosteroni TA441.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0233125},
doi = {10.1128/aem.02331-25},
pmid = {41930959},
issn = {1098-5336},
abstract = {Comamonas testosteroni TA441 is a model aerobic steroid-degrading bacterium whose sterane degradation pathway has been elucidated in the greatest detail to date. Similar pathways have been identified in many genera of bacteria, including both proteobacteria and actinobacteria, such as Mycobacterium tuberculosis. However, the genes encoding the C9-hydrogenase for 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (9,17-DOHNA, also known as HIP) and the 7α-dehydratase essential for initiating β-oxidation of the B-, C-, and D-rings had not been identified. In this study, we identified these missing genes, located adjacent to the chsE1E2H1H2ltp2 cluster involved in C17 side-chain degradation, and designated them scdB and scdH, respectively. This finding completes the elucidation of all degradation steps of 9,17-DOHNA prior to D-ring cleavage. AlphaFold models showed that ScdB and at least five hydrogenases/dehydrogenases involved in steroid degradation in TA441 share a similar dimer structures with Rossmann fold motif. In contrast, ScdH was predicted to form a homohexameric structure similar to ScdY and ScdN, involved in B-, C-, and D-ring degradation in TA441. Furthermore, AlphaFold modeling revealed that SteC, the dehydratase responsible for removing the C12β-hydroxyl group from 9,17-DOHNA derivatives, exhibits strong structural similarity to BaiE, the bile acid 7α-dehydratase of Clostridium scindens JCM 10418/VPI 12708, despite sharing only ~28% amino acid sequence identity.IMPORTANCEResearch on bacterial aerobic steroid degradation began more than 70 years ago, initially to produce intermediates for steroid drug synthesis. Recently, this field has gained renewed attention due to its implications for human health-for example, the role of cholesterol import and degradation in the persistence of Mycobacterium tuberculosis H37Rv within chronically infected lungs. Comamonas testosteroni TA441 serves as a key model organism for elucidating aerobic steroid degradation, with pathways for cleavage of the A-, B-, C-, and D-rings already well established. The functions and structures of the enzymes identified in TA441 display striking similarities to those in actinobacteria, such as M. tuberculosis. In this study, we identified two enzymes indispensable for initiating β-oxidation of the B-, C-, and D-rings, thereby filling the last remaining gaps for initiating this pathway. Our AlphaFold-based structural analysis of these enzymes not only provides new insights into the steroid metabolism of M. tuberculosis but also broadens understanding of the ecological and physiological significance of bacterial steroid degradation.},
}
@article {pmid41930960,
year = {2026},
author = {Nan, F and Song, H and Sun, M and Cui, L and Bian, Z and Yin, J and Lin, Z and Wang, Y},
title = {Hijacking competitor-derived signals: RcsB/C drives Lysobacter enzymogenes to exploit farnesol for enhanced antifungal capacity.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0030426},
doi = {10.1128/aem.00304-26},
pmid = {41930960},
issn = {1098-5336},
abstract = {Microbial antagonism is a fundamental ecological process that shapes community composition and maintains ecosystem balance. However, the molecular signals, such as cross-kingdom interactions between bacteria and fungi in natural environments, remain largely unexplored. Lysobacter enzymogenes is a widespread predatory bacterium that produces the antifungal secondary metabolite heat-stable antifungal factor (HSAF), which enables interactions with diverse fungi. Here, we investigated the interkingdom interactions between L. enzymogenes and the environmental fungus Candida krusei, both of which are widely distributed, to elucidate the bacterial-fungal communication. We found that the antagonistic effect of bacteria-fungi was significant under both contact and non-contact co-culture conditions, indicating the involvement of diffusible metabolites. Given that farnesol is a common quorum-sensing (QS) molecule in Candida, metabolite profiling combined with exogenous addition and biosynthesis inhibition experiments demonstrated that farnesol functions as a cross-kingdom signal regulating HSAF production and bacterial antagonism. Further mechanistic analysis of the intrinsic mechanism revealed that the two-component system (TCS) RcsB/C in L. enzymogenes can sense farnesol and activate the production of HSAF through the MarR family regulators, mediating the antagonistic pathway. In addition, our work identified the key amino acid residues in RcsC of L. enzymogenes responsible for recognizing farnesol. In summary, we report the bacterial TCS involved in farnesol sensing and reveal a novel bacterial-fungal antagonistic mechanism, in which L. enzymogenes "hijacks" a fungal QS molecule to enhance its antifungal capacity, uncovering a previously unrecognized strategy of cross-kingdom communication.IMPORTANCEBacteria and fungi frequently interact in shared habitats, yet the chemical cues that shape these cross-kingdom relationships remain poorly defined. Farnesol is a well-known quorum-sensing molecule in Candida, but its ecological roles beyond fungal communication are unclear. Here, we show that Lysobacter enzymogenes directly senses fungal-derived farnesol through the RcsB/C two-component system, which activates the downstream regulator MarR-2 and induces the production of the antifungal metabolite heat-stable antifungal factor (HSAF). This signal hijacking strategy allows L. enzymogenes to convert a fungal communication molecule into a cue that strengthens its antagonistic capacity. We further identify key amino acid residues in RcsC responsible for farnesol recognition, revealing the bacterial two-component system (TCS) known to detect this molecule. These findings expand the functional scope of fungal quorum-sensing signals, uncover a previously unrecognized mechanism of interkingdom antagonism, and provide insights with potential applications in microbiome-based biocontrol.},
}
@article {pmid41930968,
year = {2026},
author = {Cheng, D and Luo, Z and Ning, W and Heath, SL and Gisslen, M and Price, RW and Adekunle, R and Salman, T and Johnson, D and McKinnon, JE and Ndhlovu, LC and Hossain, R and Hu, W and Jiang, W},
title = {Systemic translocation of Staphylococcus aureus promotes autoimmunity: implications in autoantibody-mediated poor immune reconstitution from antiretroviral therapy in HIV.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0196525},
doi = {10.1128/jvi.01965-25},
pmid = {41930968},
issn = {1098-5514},
abstract = {In 2017, our group first demonstrated that autoimmunity contributes to HIV pathogenesis, even without autoimmune disease. This concept is now broadly recognized, exemplified by the role of autoimmunity in severe COVID-19. In people with HIV (PWH) on suppressive antiretroviral therapy (ART), anti-CD4 autoantibodies may impair CD4+ T-cell recovery, though the mechanisms driving their production remain unclear. Building on evidence from our group and others that Staphylococcus aureus and its peptidoglycan (PGN) promote autoimmunity, we investigated their contribution to anti-CD4 IgG in HIV. Plasma from 32 ART-naive PWH, 53 ART-treated PWH, and 32 HIV-negative controls was analyzed for IgG autoantibodies and markers of S. aureus translocation using protein array and ELISA. EcoHIV mice were injected intraperitoneally with saline, S. aureus PGN, or Bacillus subtilis PGN. PGN structures were compared by mass spectrometry. Among 87 autoantibodies, 40% were elevated in ART-naive PWH and largely normalized by ART; however, anti-CD4 IgGs remained elevated in PWH on ART. Anti-CD4 IgG levels inversely correlated with CD4+ T-cell counts in ART-treated PWH and positively with markers of S. aureus translocation. In mice, S. aureus PGN induced anti-CD4 IgGs, reduced frequency of CD4+ T cells among total gut T cells, and promoted surface IgG binding and apoptosis in CD4+ T cells. S. aureus and its PGN translocation may drive anti-CD4 autoimmunity and hinder immune recovery in PWH on suppressive ART, highlighting S. aureus colonization as a therapeutic target and supporting the development of competitive probiotic interventions.IMPORTANCECurrently, no treatment is available for improving CD4+ T-cell recovery in people with HIV (PWH) on suppressive antiretroviral therapy (ART). Up to 20% of PWH on ART fail to restore peripheral CD4+ T-cell counts to levels observed in healthy individuals, a condition associated with increased morbidity and mortality and representing a major unmet challenge in HIV clinical care. Our study demonstrates that systemic Staphylococcus aureus translocation contributes to autoimmunity and impaired immune reconstitution in a subset of PWH on suppressive ART. These findings identify a previously unrecognized mechanism of immune failure and support a novel therapeutic strategy combining probiotics with ART to enhance immune recovery and reduce HIV-associated morbidity and mortality.},
}
@article {pmid41931049,
year = {2026},
author = {Rosen, CJ and Ingelfinger, JR},
title = {GLP-1 Receptor Agonists.},
journal = {The New England journal of medicine},
volume = {394},
number = {13},
pages = {1313-1324},
doi = {10.1056/NEJMra2500106},
pmid = {41931049},
issn = {1533-4406},
mesh = {Humans ; *Cardiovascular Diseases/etiology/metabolism/prevention &amp; control ; *Diabetes Mellitus, Type 2/complications/drug therapy/metabolism ; Glucagon-Like Peptide 1/agonists/metabolism ; *Glucagon-Like Peptide-1 Receptor Agonists/adverse effects/pharmacology/therapeutic use ; Hypoglycemic Agents/adverse effects/pharmacology/therapeutic use ; Incretins/metabolism ; *Obesity/complications/drug therapy/metabolism ; *Renal Insufficiency/etiology/metabolism/prevention &amp; control ; Anti-Obesity Agents/adverse effects/pharmacology/therapeutic use ; Disease Progression ; Gastric Emptying/drug effects ; Glucagon/metabolism ; Gastrointestinal Microbiome/drug effects ; Satiety Response/drug effects ; Randomized Controlled Trials as Topic ; Medication Adherence ; },
abstract = {Glucagon-like peptide-1 (GLP-1) receptor agonists are incretin analogues that promote glucose-mediated insulin release and are used to treat type 2 diabetes mellitus and obesity. GLP-1 receptor agonists and GLP-1 and glucose-dependent insulinotropic peptide agonists have several mechanisms of action, including reduction of gastric emptying, inhibition of glucagon secretion, beneficial changes in the intestinal microbiome, and direct effects on hypothalamic nuclei to enhance satiety (which promotes weight loss). Beyond the impressive effects of GLP-1 receptor agonists on blood glucose levels and body weight, large-scale randomized, controlled trials have shown that GLP-1 receptor agonists reduce cardiovascular risk and slow progression to renal failure in persons at high risk and those with type 2 diabetes. Adverse side effects from GLP-1 receptor agonists are mostly gastrointestinal but may also include loss of muscle and bone mass. Questions remain about long-term adherence, weight regain after discontinuation of treatment, and the functional implications of the loss of muscle and bone mass. Recent and ongoing targeted studies suggest the possibility of additional uses for GLP-1 receptor agonists.},
}
@article {pmid41931118,
year = {2026},
author = {Ansari, S and Purohit, KJ and Shelke, AB and Shah, M and Nkhoma, IA and Navale, AM and Wakchaure, R},
title = {Microbiota-driven mechanisms in multisystem diseases: integrative evidence across cardiovascular, metabolic, neurological and autoimmune disorders.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {41931118},
issn = {1572-9699},
mesh = {Humans ; *Autoimmune Diseases/microbiology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; *Cardiovascular Diseases/microbiology ; *Nervous System Diseases/microbiology ; *Metabolic Diseases/microbiology ; *Microbiota ; Animals ; },
abstract = {The human microbiota represents one of the body's most influential biological systems, engaging in constant metabolic, immunological, and neuroendocrine communication with the host. Disruption of this intricate ecosystem, or dysbiosis, has emerged as a fundamental determinant in the onset and progression of numerous chronic diseases. This review consolidates contemporary evidence on how alterations in microbial composition, metabolite production, and barrier integrity contribute to pathophysiological changes across multiple organ systems. Gut-derived metabolites-including short-chain fatty acids, bile acid derivatives, trimethylamine-N-oxide, and lipopolysaccharide-serve as key mediators linking microbial imbalance to systemic inflammation, metabolic dysfunction, autoimmunity, and neurodegeneration. We outline the mechanistic pathways through which dysbiosis promotes hypertension, atherosclerosis, obesity, type 2 diabetes, Parkinson's disease, Alzheimer's disease, rheumatoid arthritis, inflammatory bowel disease, asthma, chronic obstructive pulmonary disease, urinary tract infections, and chronic kidney disease. Particular emphasis is placed on the gut-brain, gut-lung, and gut-kidney axes, which facilitate bidirectional immune and metabolic signalling between the intestine and distant tissues. Additionally, the review highlights emerging therapeutic interventions aimed at restoring microbial homeostasis, including targeted dietary strategies, probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and microbiome-directed pharmacological approaches. Collectively, the evidence positions the microbiota as a central regulator of human health and disease, offering a compelling platform for next-generation diagnostic and therapeutic innovation. Advancing mechanistic understanding of host-microbe interactions will be essential to developing personalized microbiome-based strategies capable of preventing, mitigating, or reversing disease across diverse clinical contexts.},
}
@article {pmid41931121,
year = {2026},
author = {Liu, B and Wan, SH and Zhang, YT and Lin, JH and Ke, XC and Lin, WH and Zhan, MX},
title = {Gut microbiome remodeling across hepatocellular carcinoma progression and transarterial chemoembolization is associated with therapeutic response and prognosis.},
journal = {Clinical and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10238-026-02137-z},
pmid = {41931121},
issn = {1591-9528},
support = {2023A1515012588 and 2022A1515220092//Guangdong Basic and Applied Basic Research Foundation/ ; 2022B1515020010//Guangdong Basic and Applied Basic Research Foundation/ ; 82472084//the National Natural Science Foundation of China/ ; 82272103//the National Natural Science Foundation of China/ ; 2021B1212040004//the Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment/ ; },
}
@article {pmid41931829,
year = {2026},
author = {Venkitaraman, AR},
title = {Proteostasis Deregulation by Metabolism Drives the Hallmarks of Cancer.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051424-052148},
pmid = {41931829},
issn = {1545-4509},
abstract = {Cancer cells acquire hallmark behaviors through adaptations that extend beyond genetic and epigenetic changes. Proteostasis-the biochemical network governing protein synthesis, folding, trafficking, and degradation-is a fundamental, yet underappreciated, mediator of these adaptations that merits consideration as a hallmark-enabling mechanism. Metabolic alterations impose proteotoxic stress, globally rewire protein homeostasis, and selectively modulate key oncogenic and tumor suppressive proteins. A unifying framework is proposed wherein metabolic deregulation of proteostasis operates throughout carcinogenesis: early, by enhancing accumulation of premalignant clones bearing cancer-driving somatic mutations in response to environmental and systemic metabolic stress, and later, by buffering proteotoxic stress to sustain malignant growth in hostile tissue environments. This perspective connects cancer risk with genetic background, diet, microbiome-derived metabolites, and metabolic disease, introduces metabolic bypass of tumor suppression as an alternative to classical genetic models, and highlights the metabolism-proteostasis interface as a promising target for cancer prevention and therapy.},
}
@article {pmid41931987,
year = {2026},
author = {Dang, W and Li, W and Dong, F and Huang, Y and He, S and Zhu, Y},
title = {Microbial metabolites: Bridging the gut-brain divide in ischemic stroke.},
journal = {Microbiological research},
volume = {308},
number = {},
pages = {128510},
doi = {10.1016/j.micres.2026.128510},
pmid = {41931987},
issn = {1618-0623},
abstract = {The Microbiota-Gut-Brain Axis (MGBA) has recently crystallized into a focal frontier spanning neuroscience and microbiology, illuminating the intricate reciprocity between intestinal microbes and the central nervous system. Stroke, a devastating and life-threatening cerebrovascular disorder, is now recognized to have its onset, progression, and long-term outcome intimately entwined with MGBA dynamics. Accumulating empirical literature substantiates the existence of intimate bidirectional gut-brain signaling circuits, wherein the gut microbiome functions as a central modulator. This microbial consortium not only orchestrates neuroinflammatory cascades following cerebral insult, but also bio-transforms dietary and host-derived substrates into multifunctional metabolites that exert both local and systemic bioactivity. Emerging evidence suggests that individual microbial metabolites and their secondary derivatives may serve as candidate signaling intermediaries, mediating the transduction of microbial cues into neurovascular responses. Accordingly, the present review provides a forward synthesis of how the MGBA intersects with ischemic stroke pathobiology, focusing on elucidating the therapeutic potential and strategies of gut microbial metabolites in ischemic stroke. It provides theoretical insights and translational prospects for gut-derived metabolites as therapeutic targets.},
}
@article {pmid41932005,
year = {2026},
author = {Parente, E and Pietrafesa, R and De Filippis, F and De Vivo, A and Labella, MG and Hidalgo, M and Lavanga, E and Ricciardi, A},
title = {A survey of bacterial and fungal communities of table olives.},
journal = {International journal of food microbiology},
volume = {455},
number = {},
pages = {111759},
doi = {10.1016/j.ijfoodmicro.2026.111759},
pmid = {41932005},
issn = {1879-3460},
abstract = {Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.},
}
@article {pmid41932098,
year = {2026},
author = {Zhang, M and Xiong, W and Shao, R and Wang, Z and Shen, Z and Zhou, Q and Du, G},
title = {Disrupted Salivary Fungal Community in Patients With Oral Lichen Planus.},
journal = {International dental journal},
volume = {76},
number = {3},
pages = {109546},
doi = {10.1016/j.identj.2026.109546},
pmid = {41932098},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: Oral lichen planus (OLP), a chronic inflammatory oral mucosal disorder with malignant potential, has been associated with oral microbial dysbiosis. While bacterial community alterations in OLP are well-documented, the fungal community architecture and ecological dynamics, particularly within salivary microbiota, remain poorly characterised.<br><br>METHODS: Saliva samples were collected from 30 participants and stratified into 3 cohorts: 10 healthy controls (HC), 10 reticular OLP (R-OLP) patients and 10 erosive OLP (E-OLP) patients. The fungal community profile was assessed using internal transcribed spacer (ITS) sequencing, complemented by multi-dimensional analytical approaches, including diversity metrics, co-occurrence network construction and functional prediction.<br><br>RESULTS: Significant diversity disparities distinguished fungal communities across groups. Taxonomically, Pseudozyma and Simplicillium demonstrated reduced abundance in OLP patients versus HC, while Pyronema was exclusive to OLP cohorts. Fungal ecological networks in OLP exhibited increased density compared to HC. Linear discriminant analysis effect size (LEfSe) analysis identified Pseudozyma as an HC-associated biomarker and Pyronema as an E-OLP discriminant, while predictive models highlighted Pseudozyma and Simplicillium as effective group stratifiers. FUNGuild profiling revealed predominant saprotrophic activity across all groups, with decreased pathotroph-symbiotroph guild representation in OLP patients.<br><br>CONCLUSIONS: Salivary fungal communities in OLP exhibit structural and compositional alterations. Through integrated analyses of relative abundance, random forest modelling and LEfSe, this study indicated that 3 fungal taxa may be as potential biomarkers for distinguishing OLP from HC. Among these, Pseudozyma and Simplicillium showed characteristics suggesting a possible probiotic role, while Pyronema, with its detection limited to OLP and absence in HC, may be associated with the disease.<br><br>CLINICAL RELEVANCE: The fungal profile observed in this study, comprising the potentially beneficial taxa Pseudozyma and Simplicillium as well as the OLP-linked Pyronema, offers new directions for developing noninvasive diagnostics and microbial-targeted therapies for OLP.},
}
@article {pmid41932183,
year = {2026},
author = {Liu, L and Liu, L and Li, A and Liu, Z and Xue, S and Li, J and Mao, Y},
title = {Robust gut microbiota as a key protective barrier for Ruditapes philippinarum survival following an extreme-rainfall disturbance.},
journal = {Marine environmental research},
volume = {218},
number = {},
pages = {108033},
doi = {10.1016/j.marenvres.2026.108033},
pmid = {41932183},
issn = {1879-0291},
abstract = {Gut microbiota is critical for host health, yet its role in buffering filter-feeding bivalves against acute habitat disturbance remains poorly understood. Here, the Manila clam Ruditapes philippinarum was used as a model to investigate how an extreme rainfall event reshaped microbial communities in the gut and surrounding habitat (water and sediment), with sampling conducted before and 10 and 30 days after the event. Extreme rainfall caused mass mortality and markedly disrupted host-associated microbiota. Surviving clams harbored gut microbiota with higher diversity and richness, enrichment of putatively beneficial taxa (e.g., Actinomycetota, Bacteroidota, Verrucomicrobiota, and Bacillus), reduced abundance of the opportunistic pathogen Vibrio, and increased network complexity and stability, accompanied by enrichment of functional potentials related to energy metabolism, signal transduction, and stress adaptation. Notably, gut community assembly shifted toward greater stochasticity, broader niche breadth, and reduced dispersal limitation during recovery, indicating a reassembly pattern that balances compositional stability with adaptive flexibility. Together, these results highlight gut microbiota robustness and assembly plasticity as key mechanisms linking extreme-rainfall disturbance to clam resilience, providing insights for microbiome-informed management to support sustainable bivalve aquaculture.},
}
@article {pmid41932251,
year = {2026},
author = {Huang, H and Yin, J and Xu, C and Gu, HY},
title = {The role of the gut-spinal axis in immune-metabolic coupling after spinal cord injury.},
journal = {International immunopharmacology},
volume = {178},
number = {},
pages = {116581},
doi = {10.1016/j.intimp.2026.116581},
pmid = {41932251},
issn = {1878-1705},
abstract = {Spinal cord injury (SCI), representing a devastating trauma to the central nervous system (CNS), is often accompanied by complex immune responses and metabolic dysregulation, significantly affecting patients' functional recovery and quality of life. In recent years, the gut-spinal axis, as an important pathway connecting the gut microbiome and the CNS, has emerged as a pivotal area of investigation regarding the pathological mechanisms of SCI. Changes in the gut microbiome modulate inflammatory responses and tissue repair processes after SCI by regulating immune system activation and metabolic pathways. However, the specific mechanisms by which the gut-spinal axis mediates the interplay between immune and metabolic processes after SCI have not been fully elucidated. This article summarizes the structural and functional characteristics of the gut-spinal axis, as well as the gut microbial imbalance, immune activation, and metabolic regulation induced by SCI. It focuses on how the gut-spinal axis mediates the interaction between immunity and metabolism, thereby influencing the pathological progression and repair potential of SCI. By integrating basic and clinical research findings, it aims to offer a theoretical framework for the comprehensive regulatory mechanisms of immunity and metabolism in SCI and to explore innovative therapeutic strategies targeting the gut-spinal axis.},
}
@article {pmid41932357,
year = {2026},
author = {Winston, JA and Jennings, R and Randolph, NK and Welton, M and Partridge, E and Schreeg, M and Yaxley, PE and Rudinsky, AJ},
title = {Fecal microbiota transplantation dosing regimen accelerates clinical resolution in canine parvovirus infection: a novel spectrum-of-care approach.},
journal = {Journal of the American Veterinary Medical Association},
volume = {},
number = {},
pages = {1-9},
doi = {10.2460/javma.25.11.0764},
pmid = {41932357},
issn = {1943-569X},
abstract = {OBJECTIVE: To evaluate the efficacy of a novel spectrum-of-care fecal microbiota transplant (FMT) dosing regimen as an adjunctive therapy for canine parvovirus (CPV).<br><br>METHODS: 27 client-owned dogs naturally infected with CPV were enrolled from March to November 2023 in a prospective, double-blinded, placebo-controlled clinical trial. Patients were randomized into FMT-treated (n = 19) or placebo-treated (8) groups. Along with conventional treatments, CPV-infected dogs were administered FMT (single FMT enema, then 14 days of oral lyophilized FMT capsules) or placebo (single saline enema, then 14 days of oral placebo capsules) at admission. During hospitalization, dogs were monitored daily including fecal, clinical severity, and medication scores. Feces and serum were collected at admission, day 4, day 7, day 14, and day 21 for quantification of CPV viral shedding and immune response (bead-based multiplex of cytokines/chemokines). The primary outcome variable was length of hospitalization.<br><br>RESULTS: Interim analysis revealed that placebo-treated dogs had excessive study withdrawals due to worsening clinical status when compared to FMT-treated dogs (37.5% compared to 0%, respectively), leading to ethical discontinuation of the placebo arm. Fecal microbiota transplant-treated dogs had significantly reduced hospitalization length and medications required for treatment (maximum medication score) compared to placebo-treated dogs. Fecal microbiota transplant did not reduce fecal viral shedding or elicit a host immune response.<br><br>CONCLUSIONS: This novel FMT dosing regimen (single enema FMT followed by oral capsular FMT), designed to be feasible for inpatients or outpatients, accelerated clinical recovery from CPV.<br><br>CLINICAL RELEVANCE: In-house and commercially available FMT products were effective in CPV-infected dogs, thus broadening the spectrum of care available to these patients.},
}
@article {pmid41932913,
year = {2026},
author = {Barbour, A and Bendayan, Y and Marks, C and Choi, YHK and Oveisi, M and Callaghan, M and Sun, C and Zargaran, S and Xia, M and Wood, D and Smith, L and McLean, JS and Mazzulli, T and Glogauer, M},
title = {Phosphorylated lantibiotics-producing commensals integrate into the human oral microbiome to suppress pathogens and promote microbiome homeostasis.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00976-y},
pmid = {41932913},
issn = {2055-5008},
abstract = {Commensal bacteria produce antimicrobial peptides (AMPs) to maintain microbiome homeostasis, yet the traits underlying this resilience and their translation into biotherapeutics remain understudied. Phosphorylated lantibiotics (pLANs) are a recently identified class of ribosomally synthesized and post-translationally modified peptides (RiPPs), with dual antimicrobial and pro-immune activities. In this manuscript, we explore the potential of commensals' pLANs biosynthesis as a mechanism for pathogen suppression and microbiome homeostasis. Subgingival metagenomics revealed that oral health correlates with Streptococcus salivarius enrichment and an increased prevalence of streptococcal RiPP biosynthetic gene clusters. Guided by these associations, we screened 80 S. salivarius isolates, identifying a small subset producing pLANs with potent activity against Porphyromonas gingivalis, vancomycin-resistant Enterococcus faecium, and multidrug-resistant Streptococcus pneumoniae. A representative lead strain, SALI-10, exhibited robust epithelial adhesion and a sorbitol-driven metabolic adaptation that enhances pLANs expression. In human-derived dysbiotic biofilms, SALI-10 stably engrafted, suppressed periopathogens, reduced antibiotic-resistance genes, and enriched acid-buffering pathways. In a first-in-human feasibility trial, daily oral administration of SALI-10 for one week yielded increased pLANs signals, pathogen depletion, and reduced oral neutrophil counts. Ultimately, pLANs-producing S. salivarius acts as a precision commensal to restore ecological balance, defining a mechanistically grounded and microbiota-mediated strategy to prevent oral and respiratory infections.},
}
@article {pmid41933092,
year = {2026},
author = {Han, M and Liu, X and Li, G and Li, P},
title = {Analysis of Bacterial Wilt Management Strategies From the Dynamic Perspective of Environmental Adaptation Approaches of Ralstonia solanacearum.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70335},
doi = {10.1111/1758-2229.70335},
pmid = {41933092},
issn = {1758-2229},
support = {32260652//The National Natural Science Foundation of China/ ; },
mesh = {*Ralstonia solanacearum/physiology/genetics/pathogenicity ; *Plant Diseases/microbiology/prevention &amp; control ; *Adaptation, Physiological ; Quorum Sensing ; Virulence ; Soil Microbiology ; },
abstract = {The Ralstonia solanacearum species complex (RSSC) ranks among the most destructive plant pathogens worldwide, due to its broad host range, extensive geographic distribution and remarkable environmental adaptability. Its persistence in soil and colonization of plant vascular tissues severely limits the effectiveness of conventional chemical control, posing significant challenges for disease management. This review highlights recent advances in understanding the environmental adaptation mechanisms of RSSC. Key topics include the dynamic evolution of pathogenicity, niche-specific survival strategies and virulence regulation mediated by quorum sensing, and complex interactions with surrounding microbial communities that shape its behaviour and fitness. We further provide a comprehensive assessment of current control strategies from an ecological perspective, encompassing physical, chemical, genetic, agronomic and microbial approaches, with critical evaluation of their mechanisms, potential and limitations. Meanwhile, we discuss the major challenges in bacterial wilt management and outline future directions, with an emphasis on multi-omics-informed precision breeding, microbiome engineering and intelligent integrated disease management (IDM). These emerging strategies hold promise for the sustainable and effective long-term control of bacterial wilt disease caused by RSSC.},
}
@article {pmid41933095,
year = {2026},
author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W},
title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44972-w},
pmid = {41933095},
issn = {2045-2322},
abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.},
}
@article {pmid41933198,
year = {2026},
author = {Ondreičková, K and Böhmer, M and Rusňáková, D and Kubáňová, M and Szemes, T and Pániková, L and Oxikbayev, BK and Mukasheva, D and Janiga, M},
title = {Microbial community structure across freshwater ecosystem types in a high-altitude region, Zhongar Alatau, Kazakhstan.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41933198},
issn = {1573-0972},
support = {101160008//European Union's Horizon Europe research and innovation programme/ ; AP26102759//Ministry of Education and Science of the Republic of Kazakhstan/ ; },
}
@article {pmid41933201,
year = {2026},
author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB},
title = {Unbinned contigs expand known diversity in the global microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41933201},
issn = {2058-5276},
support = {12/RC/2273-P2 (APC Microbiome)//Science Foundation Ireland (SFI)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100724//Department of Education and Training | Australian Research Council (ARC)/ ; },
abstract = {The ongoing census of microbial life is hampered by disparate sampling across Earth's habitats, challenges in isolating uncultivated organisms, limited resolution in taxonomic marker gene amplicons and incomplete recovery of metagenome-assembled genomes. Here we quantify discoverable Bacterial and Archaeal diversity in a comprehensive, curated cross-habitat dataset of 92,187 publicly available metagenomes. Clustering 502 million sequences of 130 marker genes, we predict ~705,000 Bacterial and ~27,000 Archaeal species-level clades, the vast majority of which were hidden among unbinned contigs. We estimate that ten and 145 previously undescribed Archaeal and Bacterial phyla, respectively, are discoverable in this dataset. We identify soils and aquatic environments as hotspots of discoverable lineages, but predict that undescribed taxa remain abundant across all habitats. Finally, we show that prokaryotic diversity appears to arise within common evolutionary patterns, as clade size distributions follow power laws, consistently across the Tree of Life.},
}
@article {pmid41933264,
year = {2026},
author = {Ma, Y and Li, X and Luo, Y},
title = {Microbiome-driven innovations for climate-resilient crop production.},
journal = {Nature food},
volume = {},
number = {},
pages = {},
pmid = {41933264},
issn = {2662-1355},
support = {41991335//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
}
@article {pmid41933289,
year = {2026},
author = {Lawther, K and Tapio, I and Vera-Ponce de León, A and Aho, VTE and Huws, SA and Dimonaco, NJ},
title = {A curated database of rumen ciliate protozoal 18S rRNA gene sequences for metataxonomic applications.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-026-01420-y},
pmid = {41933289},
issn = {2730-6844},
abstract = {OBJECTIVES: Protozoa are key members of the rumen microbiome playing significant roles in nutrient cycling and methane production, yet are understudied. As rumen metataxonomic studies increasingly incorporate protozoal primers, the lack of curated dedicated reference databases limits accurate classification. This dataset was developed to address that gap and support future protozoa-focused rumen microbial analyses.<br><br>DATA DESCRIPTION: The curated dataset comprises 228 rumen ciliate protozoal 18S rRNA gene sequences sourced from publicly available datasets. Sequences were processed to remove redundancy and standardise naming. The final database spans 23 families, 53 genera, and 100 species, and is suitable for use in metataxonomic pipelines, including QIIME2. It provides a valuable resource for researchers aiming to improve taxonomic resolution of protozoal communities in rumen environments.},
}
@article {pmid41933306,
year = {2026},
author = {Adamczak, M and Pokora, P and Kaczmarczyk, M and Gojowy, D and Wierzbicka-Woś, A and Cembrowska-Lech, D and Kolonko, A and Łoniewski, I and Więcek, A},
title = {Intestinal microbiome and acute transplanted kidney rejection - results of a single-center, case-control study.},
journal = {BMC nephrology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12882-026-04951-9},
pmid = {41933306},
issn = {1471-2369},
}
@article {pmid41933371,
year = {2026},
author = {Yao, T and Fan, M and Hao, Z and Jiang, Z and Li, X and Wang, S and Xu, Z},
title = {Gordonibacter-associated regulatory T cell dysfunction and S100A11-mediated neural impairment in Hirschsprung's disease: a microbiota-immune-neural axis.},
journal = {Cell &amp; bioscience},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13578-026-01562-7},
pmid = {41933371},
issn = {2045-3701},
support = {PL2024H140//Natural Science Foundation of Heilongjiang Province/ ; 24ZX008//Pediatric Special Project of the Sixth Affiliated Hospital of Harbin Medical University/ ; ZL2024H001//Key Project of the Joint Fund of the Natural Science Foundation of Heilongjiang Province/ ; },
abstract = {BACKGROUND: Hirschsprung's disease (HSCR) is a congenital disorder characterized by intestinal aganglionosis. Despite evidence linking gut microbiota and immune cells to various gastrointestinal diseases, their role in HSCR pathogenesis remains poorly understood. We investigated associations between gut microbiota composition, immune cell phenotypes, and neural impairment in HSCR patients.<br><br>RESULTS: Mendelian randomization analysis identified associations between Gordonibacter species and elevated HSCR risk (OR&#x2009;=&#x2009;2.74, 95% CI 1.42-5.28), potentially mediated through CD28&#x207a;CD39&#x207a; regulatory T cells. Multi-omics profiling revealed notable S100A11 upregulation in HSCR tissues. CD28&#x207a;CD39&#x207a; Tregs from HSCR patients exhibited functional alterations, including reduced suppressive capacity alongside elevated S100A11 production. Both CD4&#x207a; T cells and CD68&#x207a; macrophages expressed S100A11 by immunohistochemistry. S100A11 treatment activated RAGE-NF-&#x3ba;B signaling in vitro, accompanied by suppression of neural developmental markers (SOX10, RET, PHOX2B) and impaired neuronal migration. Serum S100A11 showed diagnostic potential (AUC&#x2009;=&#x2009;0.947). Microbiome profiling demonstrated differential bacterial enrichment, while antibiotic depletion experiments indicated microbiota-dependent modulation of immune-neural interactions.<br><br>CONCLUSION: Our findings link gut microbiota alterations, immune dysregulation, and neural developmental impairment in HSCR, implicating S100A11-RAGE-NF-&#x3ba;B signaling as a pathway deserving mechanistic investigation.},
}
@article {pmid41933391,
year = {2026},
author = {Liu, Y and Liu, J and Niu, D and Hu, L and Kou, F and Jiao, Y and Cao, W and Liu, Q and Fu, X and Hu, C and Tong, J and Xiong, H and Wang, Y},
title = {16S rRNA gene sequencing reveals distinct intratumoral bacterial microbiome signatures between CT indeterminate benign and early-stage malignant pulmonary lesions.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08078-1},
pmid = {41933391},
issn = {1479-5876},
}
@article {pmid41933403,
year = {2026},
author = {Dugény, E and Ceolotto, L and Franch, R and Pesce, G and Alvarez, E and Esposti, E and Mazzariol, S and Centelleghe, C},
title = {Optimizing cetacean blow collection methods under controlled conditions: implications for further non-invasive UAV-based sampling of the cetacean respiratory microbiome in the wild.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00555-8},
pmid = {41933403},
issn = {2524-4671},
support = {CN_00000033//NextGenerationEU/ ; ECS00000043//NextGenerationEU/ ; },
}
@article {pmid41933494,
year = {2026},
author = {Yang, X and Gao, S and Kong, X and Gao, F and Xu, Q},
title = {Host Filtering Overrides Environmental Heterogeneity in Shaping Sea Cucumber Gut Microbiomes.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70294},
doi = {10.1111/1462-2920.70294},
pmid = {41933494},
issn = {1462-2920},
support = {2025FY101004//Science and Technology Fundamental Resources Investigation Program/ ; 2022YFD2401305//National Key Research and Development Program of China/ ; 2025-73//Hainan Postdoctoral Scientific Research Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Sea Cucumbers/microbiology ; Ecosystem ; Phylogeny ; },
abstract = {Gut microbiomes play critical roles in host physiology and ecological contributions of sea cucumbers in tropical coral reefs. However, the relative importance of host filtering versus environmental factors in gut microbiome assembly remains poorly quantified in natural populations. Using 16S rRNA gene amplicon sequencing and sediment physicochemical analyses, this study characterized gut microbiomes of three co-occurring sea cucumber species (Holothuria atra, Holothuria edulis and Stichopus chloronotus) across heterogeneous habitats. Despite significant spatial variation in sediment properties and microbial communities, all three sea cucumber species maintained species-specific and stable gut microbiomes across sites. Although source tracking identified sediment as the primary microbial reservoir, variation partitioning revealed that host filtering far overrode environmental heterogeneity, with sediment physicochemical properties explaining a negligible fraction (< 1%) of community variation. Each host harboured distinct functional taxa, and most dominant genera showed no significant correlations with sediment properties. These results support a 'host as filter and sediment as source' pattern, indicating that host-mediated selection can filter microbes from distinct source pools to establish a conserved gut microbiome largely independent of environmental variation. By retaining microbial taxa with functional potentials, sea cucumbers may ensure consistent contributions to organic matter degradation and nutrient cycling regardless of environmental fluctuations.},
}
@article {pmid41933499,
year = {2026},
author = {Tonanzi, B and Massimi, A and Di Pippo, F and Petruccioli, M and Rossetti, S and Crognale, S},
title = {Unveiling Microbial Communities: Methodological Biases in DNA Extraction and 16S rRNA Sequencing Skew Microbial Profiles in Anaerobic Fermentation.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70297},
doi = {10.1111/1462-2920.70297},
pmid = {41933499},
issn = {1462-2920},
mesh = {*RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics/isolation &amp; purification ; Anaerobiosis ; Fermentation ; *Bacteria/genetics/classification/isolation &amp; purification ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; Phylogeny ; },
abstract = {Modern molecular analyses have revolutionized the study of microbial communities, yet DNA extraction and sequencing remain critical sources of bias. This study investigated the impact of seven different DNA extraction protocols and two 16S rRNA hypervariable regions (V1-V3 and V3-V4) on the profiling of a complex anaerobic fermentative biomass selected for medium-chain fatty acids production. Microscopic analysis established a baseline community dominated by Actinobacteria (53% ± 2%) and Firmicutes (47% ± 3%). The results demonstrate that Kit1 and Kit5 provided the highest DNA yields (up to 603 ng/μL) and the most effective recovery of these hard-to-lyse phyla, although they introduced a slight taxonomic bias toward Actinobacteria. In contrast, protocols relying on intensive chemical lysis without robust mechanical disruption (Kit4) significantly underestimated total bacterial abundance and showed the lowest purity. 16S rRNA gene sequencing revealed that the V3-V4 region provided higher alpha-diversity and a more balanced representation of the community core compared to V1-V3, which was more susceptible to extraction-related variability and overrepresented the genus Olsenella. Our multi methodological approach reveals significant biases introduced by both extraction technique and 16S rRNA gene region. This evidence highlights that protocol optimization is mandatory for achieving an accurate and comprehensive characterization of microbial ecosystems.},
}
@article {pmid41933506,
year = {2026},
author = {Qiu, CW and Zhang, S and Gao, ZF and Chen, ZH and Zhang, C and Ali, MA and Wu, F},
title = {First Tetraploa Genome and Multi-Omics Analysis Reveal Key Plant-Microbe-Soil Interactions for Salt Tolerance and Yield Improvement of Wheat.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70663},
pmid = {41933506},
issn = {1467-7652},
support = {32161143035//National Natural Science Foundation of China/ ; BP0618021//the 111 Project of China/ ; FT210100366//Australian Research Council/ ; WSU2303-001RTX//Grains Research and Development Corporation/ ; },
abstract = {Salinity is a major threat to global agricultural productivity of staple crops such as wheat. Although microbial-based solutions hold promise for alleviating salinity stress, practical implementation is hindered by insufficient mechanistic characterization of bioinoculants and their interactions with plants. Here, we assembled the first complete reference genome of a halotolerant strain within the genus Tetraploa-the endophytic fungus Tetraploa sp. E00680. This novel genomic resource serves as a foundation for exploring previously uncharacterised salt tolerance mechanisms in this potential fungal inoculant. Our research demonstrates that E00680 enhances wheat yield under both controlled and field saline conditions. We found that E00680 systematically modulates the plant-microbe-soil interactions by optimizing rhizosphere microbial communities, increasing nutrient bioavailability, and triggering coordinated transcriptional and metabolic reprogramming in wheat. Notably, E00680 expands tryptophan metabolism to synergistically boost auxin biosynthesis in wheat by supplying precursors and activating relevant metabolic pathways. This cross-kingdom metabolic coupling facilitates better growth and salt tolerance in wheat plants. Our findings offer multi-omics and rhizosphere-level insights that can guide the development of microbial inoculants to enhance climate-resilient and sustainable crop production.},
}
@article {pmid41933614,
year = {2026},
author = {Abdollahi, S and Vajhadin, F and Rafiei, A and Tamrin, SH and Daniel, SD and Banoei, MM and Zarin, B and Sen, A and Kim, K and Sanati-Nezhad, A},
title = {On-Chip modeling of drug-gut interactions in Oral drug delivery.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115864},
doi = {10.1016/j.addr.2026.115864},
pmid = {41933614},
issn = {1872-8294},
abstract = {The gastrointestinal tract is a dynamic ecosystem where biophysical forces, enzymatic gradients, and microbial metabolism converge to govern the fate of orally administered therapeutics. These multifactorial interactions-spanning shear stress, mucus transport, and microbial metabolism-collectively shape absorption, transformation, and therapeutic response. Such complexity drives the wide interindividual variability in oral pharmacokinetics and pharmacodynamics, challenging predictive modeling and formulation design. Capturing these intertwined processes requires experimental systems that bridge the physiological fidelity of human tissue with the analytical control of engineered models. Microphysiological Gut-on-a-Chip (GoC) platforms have emerged as promising tools that reconstruct human intestinal architecture and function with high precision. These devices integrate living epithelia, peristaltic motion, oxygen and nutrient gradients, immune and microbial co-cultures, and on-chip sensing within precisely engineered microenvironments. They enable direct observation and quantification of luminal-mesenchymal communication, barrier regulation, and metabolite exchange under physiologically relevant flow. This review delineates how GoC technology is advancing oral drug delivery by bridging biology, microengineering, and pharmacology. We summarize advances across three therapeutic domains-small-molecule drugs, macromolecular and biopharmaceutical agents, and microbiome-interacting therapeutics-highlighting how GoCs now recapitulate absorption, enzymatic metabolism, immune modulation, and microbial transformation in human-relevant contexts. By merging organ-level physiology with analytical precision, GoCs establish a unified platform for predicting oral bioavailability and systemic exposure. As these systems evolve toward sensor-integrated, multi-omics, and AI-enabled designs, they are poised to become the mechanistic backbone of next-generation preclinical drug discovery and personalized oral therapeutics.},
}
@article {pmid41933765,
year = {2026},
author = {He, Y and Wang, Z and Xu, Z and Wang, H and Yuan, L and Xu, X and Deng, W},
title = {Regulatory effects of natural polysaccharides on skin wound repair through modulation of immune-microbiome interactions.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {151732},
doi = {10.1016/j.ijbiomac.2026.151732},
pmid = {41933765},
issn = {1879-0003},
abstract = {Chronic non-healing wounds pose a significant clinical challenge, driven by dysregulation of the "inflammation-immune-microbiome" triad. Traditional "debridement-anti-infection-coverage" approaches fail to break the vicious cycle of dysbiosis and immune dysfunction. Leveraging structural diversity and bioactivity, natural polysaccharides provide a versatile platform for multi-targeted intervention. This review systematically explores the mechanisms through which polysaccharides modulate the wound immune microenvironment, restructure microbial communities, and facilitate barrier repair. This interaction enables precise regulation of macrophage polarization, particularly the promotion of the M2 phenotype, as well as neutrophil function and adaptive immunity, thereby alleviating chronic inflammation. Moreover, polysaccharides utilize a variety of mechanisms to impact the microbiome, including direct antimicrobial effects through electrostatic interactions and prebiotic support that promotes the colonization and metabolism of beneficial bacteria. This review also explores advancements in intelligent delivery systems, such as microenvironment-responsive hydrogels, discusses challenges in clinical translation, and considers future directions that incorporate single-cell multi-omics, microbiota-based personalization, organ-on-a-chip models, and phage-polysaccharide synergistic therapies. This work offers a theoretical foundation and translational perspective for the development of next-generation polysaccharide-based strategies for chronic wound management.},
}
@article {pmid41933826,
year = {2026},
author = {Ma, J and Zhang, H and Liang, S and Feng, X and Xia, Z and Li, H and Zou, S and Li, D},
title = {The health threat of wild animals by Rank I ARGs from habitat soils: Metagenomic and metabolomic evidence.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {398},
number = {},
pages = {128041},
doi = {10.1016/j.envpol.2026.128041},
pmid = {41933826},
issn = {1873-6424},
abstract = {Human disturbance (HD) leads to the enrichment of antibiotic resistance genes (ARGs), posing a threat to the health of wild animals. However, not all ARGs necessarily endanger wild animals' health. Therefore, this study used the golden snub-nosed monkeys (Rhinopithecus roxellana) as a sentinel species, and employed metagenomics to investigate the impact of high-risk ARGs (Rank Ⅰ ARGs) from habitats on wild animals' health. Subsequently, we studied the expression of metabolites within the metabolic network harboring homologous functional genes based on metabolomics. The results indicated that only 0.034% of ARGs in the habitat soils were classified as Rank I ARGs. HD not only increased the accessibility, mobility, pathogenicity and availability of Rank I ARGs in the soils of wild animals' habitats, thereby elevating the health risks to wild animals. Especially, the energy metabolism and carbohydrate metabolism functions of the gut microbiome were disrupted in wild animals. Multiple factors influence the health of wild animals posed by Rank I ARGs under HD: primarily, the strong correlation between ARGs and MGEs; the indirect impact of the content of AP in the soil; the increased proportion of the host bacteria Enterobacter; and the rise in the potential host bacteria of Rank I ARGs. We suggested that the use of aminoglycoside, glycopeptide, and peptide antibiotics should be strictly controlled in nature reserves, coupled with enhanced monitoring of soil nutrients, particularly available phosphorus.},
}
@article {pmid41933853,
year = {2026},
author = {Rao, X and Zhou, R and Li, W and Chai, X and Zhang, H},
title = {Pulmonary Microbiota is a Hidden Link between Lung Cancer Development and Microenvironment: Potential for Future Immune Therapeutic Strategies.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105308},
doi = {10.1016/j.critrevonc.2026.105308},
pmid = {41933853},
issn = {1879-0461},
abstract = {Lung, as a vital interface with the external environment, hosts a diverse microbiota that plays a significant role in lung cancer development. The dual role of pulmonary microbiota is characterized by its potential to trigger chronic inflammation(precursor of cancer), and its ability to stimulate anti-tumor immune responses. In lung cancer patients, the pulmonary microbiota often exhibits reduced bacterial diversity and over representation of pathogenic bacteria. Distinct pathological types of lung cancer, and clinical stage of lung cancer were correlates with variations in microbial diversity. Particular focus on its influence on the immune microenvironment have also been delved. Including immune cells, inflammatory signaling pathways, microbiota-metabolic interactions, and modulation of the programmed cell death protein 1(PD-1)/ programmed death-ligand 1 (PD-L1) checkpoint, which is crucial for tumor immune evasion. Understanding these interactions is essential for optimizing lung cancer immunotherapy strategies. For instance, antibiotics may reduce the efficacy of immune checkpoint inhibitors (ICIs), especially in lung cancer patients with high PD-L1 expression or EGFR-mutant NSCLC. Additionally, new therapeutic interventions, such as microbiome-targeted therapies or probiotics, are suggested to enhance the efficacy of ICIs. By uniquely integrating clinical correlations with mechanistic insights on immune microenvironment, this may render pulmonary microbiota to be potential therapeutic strategies for future immunotherapy treatments.},
}
@article {pmid41934012,
year = {2026},
author = {Moraïs, S and Mizrahi, I},
title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.005},
pmid = {41934012},
issn = {1878-4380},
abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.},
}
@article {pmid41934098,
year = {2026},
author = {Sweeney, CJ and Bottoms, M and Hutcheson, K and Schulz, L},
title = {Dose response OECD 216 studies for agrochemicals.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjag057},
pmid = {41934098},
issn = {1551-3793},
abstract = {The nitrogen transformation test, as described by Organisation for Economic Co-operation and Development (OECD) test guideline 216, forms the basis of the current European risk assessment to assess the impacts of pesticides on the soil microbiome. This guideline contains both a two-dose threshold approach and a dose response study design, for use with agrochemicals and non-agrochemicals respectively. Recent proposals have suggested the use of a dose response study design for agrochemical risk assessment. However, differences in the principles underpinning the threshold and dose response study protocols including the method of endpoint calculation, study length and interpretation of stimulatory versus inhibitory responses, necessitate careful consideration of how to appropriately perform and interpret dose response OECD 216 studies for pesticides. Our study explores these considerations, through the conduct of dose response OECD 216 nitrogen transformation tests on four agrochemicals (dicyandiamide, nitrapyrin, dinoseb acetate and a fludioxonil metabolite). A comparison of four potential methods for endpoint calculation revealed this has little impact on the ecotoxicological inference derived from dose response OECD 216 studies. Hormetic responses were present for two of the four compounds tested, and for these compounds, the system had not reached a steady state over the 28-day study period. Test extensions beyond the 28-day test period defined in the dose response study may therefore need to be considered, as is currently implemented in the two-dose threshold approach. Furthermore, as dose response studies allow for consideration of the full ecotoxicological response over a range of concentrations, we suggest that dose response OECD 216 studies for agrochemicals should focus on inhibitory and not stimulatory responses. Finally, our work has shown that dose response OECD 216 studies are possible for agrochemicals, and their use offers a sensible approach to improving the European soil microbial risk assessment.},
}
@article {pmid41934196,
year = {2026},
author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ},
title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.},
journal = {Molecular nutrition &amp; food research},
volume = {70},
number = {7},
pages = {e70450},
pmid = {41934196},
issn = {1613-4133},
support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; },
mesh = {Humans ; *Diet, Mediterranean ; Male ; Female ; Adult ; Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; Middle Aged ; Olive Oil ; *Gastrointestinal Microbiome ; Feces/microbiology ; Fruit ; Vegetables ; Multiomics ; },
abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.},
}
@article {pmid41934308,
year = {2026},
author = {He, L and Zhong, Q and Zhang, X and Li, T},
title = {The effects of cetylpyridinium chloride mouthwash combined with triamcinolone acetonide on oral microbiota and the Th17/Treg balance in patients with oral lichen planus.},
journal = {Pakistan journal of pharmaceutical sciences},
volume = {39},
number = {6},
pages = {1708-1720},
doi = {10.36721/PJPS.2026.39.6.162.1},
pmid = {41934308},
issn = {1011-601X},
mesh = {Humans ; *Lichen Planus, Oral/drug therapy/immunology/microbiology ; *Mouthwashes/administration &amp; dosage/therapeutic use/adverse effects ; Female ; Male ; *T-Lymphocytes, Regulatory/drug effects/immunology ; Middle Aged ; *Th17 Cells/drug effects/immunology ; *Triamcinolone Acetonide/administration &amp; dosage/therapeutic use/adverse effects ; Adult ; *Cetylpyridinium/administration &amp; dosage/adverse effects/therapeutic use ; *Microbiota/drug effects ; Treatment Outcome ; Drug Therapy, Combination ; *Mouth/microbiology/drug effects ; *Anti-Inflammatory Agents/administration &amp; dosage ; Cytokines ; },
abstract = {BACKGROUND: Oral lichen planus (OLP) is a chronic inflammatory disease associated with oral microbiome imbalance and immune dysregulation.<br><br>OBJECTIVES: To evaluate the effects of CPC mouthwash combined with triamcinolone acetonide on oral microbiota and Th17/Treg balance in erosive OLP patients.<br><br>METHODS: This study involved 80 patients with erosive OLP from January 2023 to January 2025. They were divided into: A control group treated with triamcinolone acetonide and a combination group treated with triamcinolone acetonide plus cetylpyridinium chloride mouthwash. After 4 weeks, primary outcomes included clinical efficacy, visual analog scale (VAS) pain scores, changes in signs and erosive area, oral salivary bacteria detection rate, Th17/Treg ratio, serum adipokine chemerin and cytokine levels (IL-17, TNF-&#x3b1;, IL-10) and OHIP-14 scores. Secondary outcomes were adverse reaction incidence and recurrence rates during follow-up.<br><br>RESULTS: The combination group showed better outcomes after 4 weeks of treatment. The total effective rate was 95%, higher than the control group's 80% (P=0.022). The combination group had superior pain relief (P=0.024), better mucosal repair (P=0.002) and a significant decrease in erosive area (P=0.021). It also had lower oral detection rates of Staphylococcus and Candida albicans (P<0.05). Immunologically, the combination therapy significantly reduced serum levels of chemerin, Th17 cells, Th17/Treg ratio, IL-17 and TNF-&#x3b1; (P<0.001), while increasing Treg cells and IL-10 levels (P=0.003), indicating stronger anti-inflammatory and immune-balancing effects. The combination group showed a greater reduction in the OHIP-14 score (P < 0.001), indicating improved oral health-related quality of life. No significant difference in adverse reactions was observed (P>0.05) and all were mild. The combination group had a lower recurrence rate within 3 months post-treatment, although the difference was not statistically significant (P=0.521).<br><br>CONCLUSION: The combination of cetylpyridinium chloride mouthwash with triamcinolone acetonide effectively regulates the oral microbiota structure and restores the Th17/Treg immune balance in OLP patients.},
}
@article {pmid41934511,
year = {2026},
author = {Kumar, KS and Jeyabal, J and Yagoo, A and Vilvest, J and Vaishnika, AM},
title = {Dietary chitosan enhances gut microbial diversity and modulates beneficial and pathogenic communities in Channa striata fingerlings.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {41934511},
issn = {1572-9699},
mesh = {*Chitosan/administration &amp; dosage/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Diet ; Dietary Supplements ; *Fishes/microbiology ; Biodiversity ; Aquaculture ; },
abstract = {Dietary modulation of the gut microbiome is a promising approach for improving fish health and sustainability in aquaculture. Chitosan, a biopolymer derived from Artemia shells, has gained attention as a functional prebiotic feed additive due to its antimicrobial and immunomodulatory properties. The effects of dietary chitosan on gut microbial diversity and community composition were evaluated in Channa striata (murrel) fingerlings. Fish were fed three experimental diets: a basal diet (Exp-1), a black soldier fly larvae (BSFL)-based control diet (in which BSFL meal was used as a primary protein ingredient, with its nutritional composition considered during formulation), and a chitosan-supplemented diet (Exp-2). Gut microbiota were characterized using high-throughput 16S rRNA gene sequencing, and microbial diversity, composition, and interaction networks were analyzed. Alpha diversity analysis demonstrated that the chitosan-based diet significantly enhanced microbial richness (Chao1 = 531.62) and promoted a more balanced gut microbial structure compared to the basal diet, which showed reduced diversity and relative dominance of certain taxa previously reported to include opportunistic species. Chitosan supplementation enriched genera such as Lactobacillus, Bacteroides, and Alloprevotella, along with members of Muribaculaceae, which are commonly associated in the literature with functions such as polysaccharide degradation and short-chain fatty acid production, although functional roles cannot be conclusively assigned at the genus level. In contrast, the basal diet group showed a higher abundance of taxa including Plesiomonas and Clostridium sensu stricto, which have been reported in some contexts to include opportunistic strains. Network analysis further revealed stronger clustering and connectivity among microbial taxa under chitosan supplementation, suggesting improved microbial stability. Overall, dietary chitosan appears to influence gut microbial composition and diversity, suggesting a possible role in influencing gut microbial balance. These findings highlight its possible application as a sustainable feed additive in aquaculture, although further functional validation is required.},
}
@article {pmid41934548,
year = {2026},
author = {Cui, K and Chen, J and Kuang, M and Yang, H and Bu, Z and Xiong, X and Liu, X and Hu, Y and Wang, R and Chen, Y and Xu, T and Zhu, Y},
title = {Integrated Physiological and Omics Analyses Reveal Endophytic Streptomyces Regulates N and P Uptake, Utilization, and Crop Productivity Enhancement.},
journal = {Physiologia plantarum},
volume = {178},
number = {2},
pages = {e70858},
doi = {10.1111/ppl.70858},
pmid = {41934548},
issn = {1399-3054},
support = {ZR2024QD159//Natural Science Foundation of Shandong Province/ ; 32172497//National Natural Science Foundation of China/ ; 32400100//National Natural Science Foundation of China/ ; CSTB2023NSCQ-MSX0852//Natural Science Foundation of Chongqing City/ ; 502251012//Yuelushan Laboratory Breeding Program/ ; },
mesh = {*Streptomyces/physiology/metabolism ; *Nitrogen/metabolism ; *Phosphorus/metabolism ; Plant Roots/microbiology/metabolism ; *Endophytes/physiology/metabolism ; Rhizosphere ; *Crops, Agricultural/growth &amp; development ; Soil Microbiology ; },
abstract = {The inherent deficiency of available nitrogen (N) and phosphorus (P) in acidic soils severely limits productivity in agriculture and forestry. While plant-beneficial microorganisms offer a sustainable solution, the mechanisms by which endophytic actinobacteria regulate N and P absorption and utilization remain largely unexplored. In this study, we characterize Streptomyces sp. CoH27, an endophyte isolated from Camellia oleifera, which exhibits pronounced abilities in N fixation and insoluble P solubilization. Inoculation with CoH27 significantly promoted the growth of C. oleifera across different ages and propagation types, as evidenced by enhanced root architecture, improved photosynthetic parameters, and increased N and P absorption and utilization efficiencies. Physiological analyses revealed that CoH27 colonization upregulated the activity of key enzymes involved in organic acid synthesis and N assimilation in roots, thereby enhancing rhizosphere P mobilization and plant N utilization. Furthermore, CoH27 reshaped the rhizosphere microbiome, increasing bacterial diversity and the abundance of beneficial taxa, while reinforcing microbial networks. The driving effect of nutrient cycling was evidenced with enriched abundance of microbial genes involved in P solubilization (phnA, ppa) and N metabolism (nasA, narB, amoA, nxrA). Concurrently, transcriptomics identified the upregulation of critical transporter genes (CoPHT1;4, CoNRT2.5) and transcription factors in CoH27-inoculated roots, orchestrating improved N and P uptake and assimilation. The efficacy of CoH27 was further validated in Brassica napus L. and Capsicum annuum L., underscoring its potential as a versatile microbial inoculant to enhance sustainable crop production in acidic soils.},
}
@article {pmid41934839,
year = {2026},
author = {Dong, C and Sun, L and Liu, Z and Sun, C and Pan, D and Zhu, L and Hu, B},
title = {Seafood resistome across trophic levels: Tissue patterns, drivers, and potential dietary exposure.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141959},
doi = {10.1016/j.jhazmat.2026.141959},
pmid = {41934839},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) are recognized as emerging contaminants relevant to human exposure. They are widespread in seafood, but their distribution across trophic levels and tissues remains unclear. We analyzed 43 metagenomes covering five marine trophic levels, from seawater plankton to obligate piscivores, and examined muscle, gill, and viscera samples. Multidrug, tetracycline, bacitracin, and β-lactam genes together accounted for about 70% of total relative ARG abundance. ARG richness, diversity, and abundance increased with trophic level. In higher trophic taxa, edible muscle contributed a larger share of the total ARG signal, indicating greater relevance to dietary exposure. Procrustes and variation partitioning showed that ARG composition was mainly associated with microbial community structure and mobile genetic elements (MGEs). Contig analysis further showed co-occurrence of ARGs and MGE markers, suggesting mobility potential. A composite risk index that integrates abundance, mobility proxies, and host or pathogen association also increased with trophic position. These results show clear trophic and tissue patterns of ARGs in marine foods and support priority monitoring of high trophic taxa, edible tissues, microbiome and MGE features along seafood supply chains.},
}
@article {pmid41934858,
year = {2026},
author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F},
title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141965},
doi = {10.1016/j.jhazmat.2026.141965},
pmid = {41934858},
issn = {1873-3336},
abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.},
}
@article {pmid41934884,
year = {2026},
author = {Macpherson, CV and Daisley, BA and Drosdowech, SM and Meers, JA and Raine, NE and Allen-Vercoe, E},
title = {Anthropogenic stressors drive microbiome assembly: A global meta-analysis of bumble bees.},
journal = {The Science of the total environment},
volume = {1029},
number = {},
pages = {181748},
doi = {10.1016/j.scitotenv.2026.181748},
pmid = {41934884},
issn = {1879-1026},
abstract = {Bumble bees (Bombus spp.) play a vital role in the provision of ecosystem services that benefit humans through crop pollination and supporting natural plant biodiversity. While their ecological function is well studied, the microbial communities within their gut are only beginning to be recognized for their contributions to bee health and resilience. To better understand these communities, we conducted a meta-analysis of 814 gut samples from 15 studies across 9 countries. This analysis confirmed Snodgrassella, Lactobacillus, Bifidobacterium, Bombilactobacillus, and Gilliamella as core gut taxa, and proposed the addition of Neisseriaceae_unclassified and Orbaceae_unclassified. Human-altered environments were identified as the most influential factor shaping microbiota composition, with indoor versus outdoor rearing showing the strongest effect. Outdoor bees collectively hosted 253% more genera and exhibited higher microbial richness, connectivity, and stability. In contrast, indoor bees showed reduced diversity and the loss of multiple environmentally-associated taxa. Based on these patterns, we propose a "captivity-sensitive core" of twelve taxa, including Frischella, Apilactobacillus, Staphylococcus, and Acinetobacter. These findings establish a robust reference for the bumble bee gut microbiome and highlight how anthropogenic environments alter microbial community structure, with implications for insect pollinator health, management, and conservation.},
}
@article {pmid41934901,
year = {2026},
author = {Usmani, A and Siddiqui, MA and Kumar, D and Gowri, S and Webster, TJ and Faiyazuddin, M},
title = {Next 5 years in autoimmunity: predictive diagnostics, immune signatures, and personalized immune therapy.},
journal = {International immunopharmacology},
volume = {179},
number = {},
pages = {116530},
doi = {10.1016/j.intimp.2026.116530},
pmid = {41934901},
issn = {1878-1705},
abstract = {Autoimmune diseases are experiencing a conceptual transformation in the traditional system of phenotypical classification to a more molecularly stratified system. The next five years suggest that immunological and metabolic signals, such as autoantibody patterns, epitope-spreading patterns, and inflammatory signals of microbiome interactions, will frequently predict clinical illness making the preclinical period a critical predictive and intervention time. Simultaneously, single-cell and multi-omic profiling are being used to discover molecular endotypes and pathogenic immune programs which can more effectively explain the heterogeneity of autoimmune diseases. Such insights are also incorporated more and more with computational methods, such as digital immune modeling, to allow for individual risk assessment and disease prediction. The combination of these advancements is hastening the shift toward precision immunology, where predictive diagnostics and targeted immune-modulating therapies can be implemented sooner and more successfully. This review synthesizes the major mechanistic innovations over the past few years and describes how predictive biomarkers, molecular endotyping, and novel treatment regimens in the coming years are likely to transform the diagnosis and treatment of autoimmune diseases.},
}
@article {pmid41935031,
year = {2026},
author = {Grassi, L and Heye, F and Proesmans, K and Abatih, E and Van Daele, A and Lahousse, L and Crabbé, A},
title = {Bacteria of the lung microbiome and health biomarkers in chronic airway disease: a systematic review and meta-analysis.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00967-z},
pmid = {41935031},
issn = {2055-5008},
support = {12X6322N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {The lung microbiome is increasingly recognized as a key contributor to the development and progression of chronic airway diseases. While these conditions are typically associated with reduced microbial diversity and pathogen overgrowth, emerging evidence suggests that non-pathogenic bacteria may influence clinical outcomes. However, inconsistent findings across studies have made it difficult to determine their exact role in disease pathophysiology. To identify potentially beneficial members of the lung microbiome, we conducted a systematic review and meta-analysis of clinical studies investigating the association between non-pathogenic bacterial genera or species and clinico-pathological features in individuals with asthma, bronchiectasis, chronic obstructive pulmonary disease and cystic fibrosis. For the meta-analysis, data from different diseases were combined. Our analysis revealed that several bacteria in the lung microbiome were significantly associated with improved lung function and/or reduced airway inflammation across diseases. Although causal relationships cannot be established due to the absence of interventional studies, our findings highlight promising candidates for functional characterization and therapeutic exploration. Considerable heterogeneity in study design and reporting underscores the need for standardized methods and validation in relevant experimental models to advance our understanding of the lung microbiome in chronic airway diseases and inform the development of effective microbiome-based interventions.},
}
@article {pmid41935059,
year = {2026},
author = {Bodkhe, R and Sankaran, K and Shapira, M},
title = {Caenorhabditis elegans populations shape their microbial environment.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00975-z},
pmid = {41935059},
issn = {2055-5008},
abstract = {Nematodes represent one of the most abundant and ecologically significant taxonomic groups on earth, playing diverse roles in the cycling of organic matter. However, little is known about their effects on their microbial environment. To explore such effects, we took advantage of the bacteriovore free-living nematode Caenorhabditis elegans, which has been shown to assemble a characteristic gut microbiome from different microbial environments. Worm populations (initially germ-free) were raised in several microbially-distinct natural-like environments emulating the environment from which C. elegans are often isolated, allowing worms to go through four generations encompassing the typical boom-to-bust population growth cycle. Samples from worms, their environments, and from control environments without worms were analyzed using next-generation 16S rRNA gene sequencing. Data analysis showed that microbial diversity increased in the environment, either when worms were present or not, but that trajectories of change were different depending on the presence of worms. Importantly, the presence of worms led with time to convergence in the composition of their microbial environments, particularly affecting the abundance of members of bacterial families that are part of the C. elegans gut microbiome. Our findings reveal that C. elegans not only responds to environmental microbial changes but also shapes them, suggesting new roles for nematodes in modulating environmental microbial diversity and ecosystems.},
}
@article {pmid41935114,
year = {2026},
author = {Jia, Z and Meng, Y and Wang, W and Behm, J and Cai, FM and Mishra, S and Xia, S and Liu, S and Yang, X},
title = {Differential responses of termite gut bacterial and fungal community to tropical forest conversion.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09939-7},
pmid = {41935114},
issn = {2399-3642},
support = {41977057//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32201421//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Land-use change significantly impacts biodiversity, but its effects on the gut microbiomes of soil invertebrates remain poorly understood. We investigated how forest conversion to rubber plantations alters bacterial and fungal diversity, composition, and function in termite guts within a biodiversity hotspot Xishuangbanna, China. Our results showed that termites from natural forests harbored higher gut bacterial diversity than those from plantations, with effects varying across host species. Fungal diversity was shaped primarily by host species identity, with Odontotermes yunnanensis exhibiting the highest diversity index. While termite species solely governed bacterial community composition, both termite species and forest type shaped fungal composition. Fungal community variation correlated with local soil properties, whereas bacterial variation only associated with soil pH. Termites shared 17% of core gut bacteria (e.g., Bacillus, Pseudomonas, Mycobacterium) but 100% of fungi with the environment. Co-occurrence networks exhibited species-specific responses to forest conversion. Host species (Ancistrotermes and Odontotermes) predicted bacterial functional potential, but both forest type and host species influenced fungal functional potential. These findings demonstrate that termite gut microbiome responses to land-use change are multifaceted and taxon-specific, highlighting their role in ecosystem functional resilience under anthropogenic disturbance.},
}
@article {pmid41935132,
year = {2026},
author = {Łopucki, R and Stępień-Pyśniak, D and Wójciak, J and Pacan, M and Jurczyk, S and Kuźniar, A},
title = {Early-life gut microbiota differentiation in sympatric wild raptors.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47288-x},
pmid = {41935132},
issn = {2045-2322},
abstract = {The establishment of the gut microbiota during early life plays a crucial role in host physiology and development, yet remains poorly understood under natural conditions, particularly in wild raptors. Limited access to free-living nestlings constrains our understanding of how host species identity, parental trophic ecology (shaping dietary microbial input and nutrient availability), and environmental factors structure early-life microbiota. Here, we investigated the gut microbiota of nestlings of two sympatric raptor species, the white-tailed eagle (Haliaeetus albicilla) and the lesser spotted eagle (Clanga pomarina), which differ in parental foraging ecology (fish/waterbird vs. small mammal-based diet). Using non-invasive fecal sampling during routine ringing, we characterized gut microbiota composition and predicted functional potential, and tested the effects of host species, geographic distance between nests, and within-nest variability. Gut microbiota composition differed markedly between species, with clear separation of microbial communities and higher alpha diversity in white-tailed eagle nestlings. In contrast, geographic distance between nests had a limited influence on microbiome structure, while pronounced inter-individual and within-nest variability was observed, highlighting the importance of individual-specific and potentially stochastic processes during early microbiome assembly. Predicted functional profiles also differed between species, with enrichment of amino acid biosynthesis pathways in white-tailed eagles and carbohydrate-related pathways in lesser spotted eagles. No dysbiosis-like microbiome profiles were detected in either species, providing a baseline for future comparative studies. Overall, our findings demonstrate strong species-level differentiation in early-life gut microbiota in wild raptors, in the context of contrasting trophic ecology, while local environmental variation appears to be of secondary importance.},
}
@article {pmid41935154,
year = {2026},
author = {Pandey, K and Parmar, A and Vilas, S and Gosai, H and Mistry, H and Singh, KS and Roy, M and Dholpuria, S and Patel, RB},
title = {Weissella as a core member of the Gir cow milk microbiome: functional insights.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {41935154},
issn = {1572-9699},
mesh = {Animals ; *Milk/microbiology ; Cattle ; *Weissella/genetics/isolation &amp; purification/classification/physiology ; *Microbiota ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Female ; },
abstract = {Gir cow (Bos indicus) milk is widely valued for its nutritional quality, digestibility, and A2 β-casein content; however, the microbial determinants contributing to these attributes remain insufficiently characterized. In this study, dominant lactic acid bacteria (LAB) associated with Gir cow milk were isolated and evaluated using an integrated phenotypic and genome-based approach to elucidate their functional relevance. Raw milk samples were analyzed to isolate LAB, which were characterized through morphological, biochemical, and molecular analyses. Predominant isolates were identified as Weissella cibaria and Weissella confusa. Selected isolates exhibited strain-dependent tolerance to acidic pH, bile salts, and phenolic stress, along with auto-aggregation ability, cholesterol assimilation, and antagonistic activity against enteric pathogens. Survival under simulated gastrointestinal conditions was further validated by viable cell count analysis. Whole-genome sequencing of W. cibaria revealed a high-quality draft genome of approximately 2.43 Mb with a GC content of 44.97%, assembled into 21 contigs, encoding 2,282 protein-coding sequences, 11 rRNA genes, and 72 tRNA genes. Functional annotation indicated enrichment of genes associated with carbohydrate metabolism, stress adaptation, and membrane transport, while screening confirmed the absence of known virulence determinants and transferable antibiotic resistance genes, supporting its safety profile. The consistent predominance of Weissella spp. in Gir cow milk suggests a breed-associated microbial signature that may contribute to the functional characteristics of this indigenous dairy system. Collectively, these findings position Weissella as a promising functional component of the Gir cow milk microbiome and provide a genomic framework supporting its potential application in probiotic and functional dairy research.},
}
@article {pmid41935253,
year = {2026},
author = {Liu, K and Zhang, Z and Su, Y and Ma, X and Wang, J and Yang, Q and Nie, Q and Mo, Z and Zhou, H and Zouboulis, CC and Guo, D and Liu, Z and Yang, X},
title = {Lactobacillus-derived extracellular vesicles provide multi-target acne treatment by enriched proteins and skin microbiota protection.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04291-8},
pmid = {41935253},
issn = {1477-3155},
support = {2024YFA0918500//National Key R&amp;D Program/ ; },
abstract = {Numerous studies have highlighted the therapeutic potential of probiotics in acne. Given the complex and multifactorial nature of the disease, probiotic-based multi-target therapies may be promising. Additionally, due to their non-replicative and nanosized characteristics, probiotic-derived extracellular vesicles might provide a safer and more efficient alternative. Here, we selected three anti-acne targets-Propionibacterium acnes (P. acnes) inhibition, anti-inflammatory effects, and sebum suppression-for high-throughput screening, identifying Lactobacillus plantarum 5b4m2 with multi-target anti-acne potential. Next, we isolated 5b4m2-derived EVs (LP-EVs) and discovered that they retain the anti-acne potential of the parental bacteria while exhibiting superior skin permeability. Further studies in P. acnes-induced acne mice demonstrated that LP-EVs significantly alleviated inflammatory symptoms such as redness and swelling and effectively inhibited the colonization of P. acnes, leading to enhanced therapeutic efficacy. Then, proteomic analysis identified nine enriched proteins in LP-EVs directly associated with acne improvement, including mucus-binding protein, cell wall hydrolase, lipase, and thioredoxin. Correspondingly, pathway changes in the host were revealed by transcriptomic analysis, such as the chemokine signaling pathway, lipid metabolism, and tissue tight junctions. Moreover, LP-EVs effectively maintain the skin microbiota balance, which may also contribute to acne improvement. Collectively, our study offers a new perspective on probiotic-based multi-target strategies, which may facilitate the treatment of acne and other skin diseases in the future.},
}
@article {pmid41935274,
year = {2026},
author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S},
title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03152-y},
pmid = {41935274},
issn = {1743-422X},
abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.<br><br>METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.<br><br>RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.<br><br>CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.},
}
@article {pmid41935303,
year = {2026},
author = {He, W and Gao, M and Ren, Q and Wang, M and Zhou, S and Liu, Q and Chu, K and Qin, Y and Fan, Y and Zou, H and Cui, Y and Shu, Y and Wang, X},
title = {Causal relationship between GM, immune cells and esophageal adenocarcinoma: a mediation analysis based on MR.},
journal = {Journal of cardiothoracic surgery},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13019-026-03984-3},
pmid = {41935303},
issn = {1749-8090},
support = {LKZ2022019//Jiangsu Commission of Health/ ; LKZ2022019//Jiangsu Commission of Health/ ; LKZ2022019//Jiangsu Commission of Health/ ; 2025M782034//Supported&#xa0;by&#xa0;China&#xa0;Postdoctoral&#xa0;Science&#xa0;Foundation/ ; },
}
@article {pmid41935333,
year = {2026},
author = {Qi, X and Jin, D and Olimi, E and Chen, X and Cernava, T},
title = {What do we know about the seed microbiome?.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41935333},
issn = {2049-2618},
support = {2024YFD1501602//National Key Research and Development Program of China/ ; doi.org/10.55776/J4753//Austrian Science Fund/ ; CXTD[2025]041//Guizhou Provincial Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities (111 Program)/ ; },
mesh = {*Seeds/microbiology/growth &amp; development ; *Microbiota ; Germination ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {The seed microbiome supports plant health and increases resilience under adverse environmental conditions. Seeds are also an important vector for transgenerational transfer of the plant microbiota. Even though research over the last decade has provided valuable insights into the functional roles of seed-associated microbes, these important members of the plant microbiome remain underexplored. This review systematically highlights recently discovered key functions of the seed microbiota. It covers taxonomic composition and diversity across plant species, transmission mechanisms, functional roles in germination and seedling establishment, growth promotion, and stress resistance. The review also addresses methodological challenges and highlights critical open questions regarding assembly, spatial compartmentalization, and translation into applications. Further research into seed microbiomes has the potential to not only increase the sustainability in plant production but also to increase food security in a changing climate. Reaching such outcomes will be facilitated by mechanistic studies that will disclose the remaining secrets of plant-microbe interplay at the very first developmental stage of most plants that nowadays inhabit Earth. Video Abstract.},
}
@article {pmid41935339,
year = {2026},
author = {Castaldi, V and Wicaksono, WA and Criscuolo, MC and Gualtieri, L and Langella, E and Di Lelio, I and Monti, SM and De Filippis, F and Berg, G and Rao, R},
title = {Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00885-9},
pmid = {41935339},
issn = {2524-6372},
abstract = {BACKGROUND: Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.<br><br>RESULTS: The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log10 bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.<br><br>CONCLUSION: Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.},
}
@article {pmid41935342,
year = {2026},
author = {Herlemann, DPR and Riedinger, DJ and Fenández-Juárez, V and Delgado, LF and Andersson, AF and Pansch, C and Riemann, L and Bengtsson, MM and Gyraite, G and Reusch, TBH and Katarzyte, M and Kube, S and Martin, G and Rakowski, M and Labrenz, M},
title = {Generalist phyllosphere taxa dominate microbial communities on macrophytes across a natural salinity gradient.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00881-z},
pmid = {41935342},
issn = {2524-6372},
abstract = {BACKGROUND: Shallow coastal habitats are characterized by diverse macrophytes and often feature steep abiotic gradients, including salinity variations, which can shape the leaf- surface epi-microbiome (phyllosphere). To elucidate the effect of salinity and host identity on the phyllosphere of aquatic macrophytes in shallow water, we sampled the leaf surface microbiota across a salinity range of 6-15. Samples included the eelgrass Zostera marina, as well as the Eurasian water milfoil (Myriophyllum spicatum), muskgrass (Chara spp.), and sago pondweed (Stuckenia pectinata) in the brackish Baltic Sea during the summer of 2022. Microbial communities were characterized using 16S and 18S rRNA gene amplicon sequencing.<br><br>RESULT: As hypothesized, the phyllosphere bacterial and protist community composition was distinct from the surrounding seawater microbiome. Typically associated taxa included the genera Loktanella, Pseudorhodobacter, the methylotrophic genus Methylotenera, unclassified Synechococcales, and Rhodobacteriaceae. Protist genera such as Picochlorum were consistently detected across all macrophyte hosts, while Cocconeis, Cyclotella, Mondous and unclassified Bacillariophyceae were present in all phyllospheres except Chara spp. Both, salinity and host species significantly influenced the composition and prevalence of the microbiota, primarily through shifts in the abundance of typical phyllosphere taxa. However, only 4-11% of phyllosphere taxa were uniquely associated with a specific salinity or macrophyte host.<br><br>CONCLUSIONS: Our results demonstrate that aquatic macrophytes harbor a distinct and characteristic phyllosphere microbiome. The low proportion of host- or salinity specific taxa suggests that the most abundant members of this community are generalists, broadly adapted to the phyllosphere niche rather than being narrowly specialized. This implies that the presence of the macrophyte itself, providing a stable, nutrient-rich surface, exerts a stronger deterministic influence on the microbial community than the host identity or salinity fluctuations. Consequently, the phyllosphere appears relatively resilient to environmental variability, particularly salinity fluctuations. This highlights the robust nature of host-microbiome interactions and their importance for conservation of aquatic macrophyte ecosystems.},
}
@article {pmid41935395,
year = {2026},
author = {Theodosis-Nobelos, P and Papagiouvanni, I and Protopappas, AA and Papagiouvannis, G},
title = {Pathophysiology of CLD: Oxidative Stress and Antioxidant Mechanisms that may Limit its Progression.},
journal = {Endocrine, metabolic &amp; immune disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715303441513260220055400},
pmid = {41935395},
issn = {2212-3873},
abstract = {INTRODUCTION: Chronic liver disease (CLD) represents a progressive condition culminating in fibrosis and, ultimately, cirrhosis or hepatocellular carcinoma. A growing body of evidence implicates oxidative and nitrosative stress as key mediators in the pathogenesis of CLD.<br><br>OBJECTIVE: This review aims to summarize the role of oxidative stress in CLD progression and to highlight therapeutic strategies targeting redox imbalance and related signaling pathways.<br><br>METHODS: Relevant literature from preclinical and clinical studies was reviewed, with emphasis on mechanisms of oxidative and nitrosative stress, signaling pathways involved in fibrogenesis, and emerging therapeutic interventions targeting redox imbalance and the gut-liver axis.<br><br>RESULTS AND DISCUSSION: Reactive oxygen and nitrogen species contribute to hepatocyte damage, hepatic stellate cell activation, and extracellular matrix accumulation. Mitochondrial dysfunction, endoplasmic reticulum stress, and disrupted redox homeostasis induce tissue injury and fibrogenesis. Various signaling pathways, including Nrf2/Keap1, AMPK/SIRT1, JNK, PI3K/Akt/mTOR, and TGF-&#x3b2;/SMAD, serve as critical links between oxidative imbalance and fibrotic progression. The antifibrotic potential of antioxidants such as vitamin E, lipoic acid, berberine, and polyphenolic compounds is increasingly validated in preclinical and clinical studies. Additionally, modulation of NOX enzymes and support of endogenous defenses offer promising therapeutic avenues. The gut-liver axis and microbial dysbiosis further exacerbate redox disturbance, underscoring the systemic nature of liver injury. Probiotic and prebiotic therapies have shown hepatoprotective effects in NAFLD models.<br><br>CONCLUSION: In conclusion, targeting oxidative stress and its associated pathways represents a compelling strategy to attenuate or even reverse liver fibrosis, presenting a promising therapeutic strategy that could be integrated into clinical practice.},
}
@article {pmid41935448,
year = {2026},
author = {Hemati, S and Mohsenipour, Z},
title = {Immune exhaustion in bacterial infections: mechanisms, consequences, and therapeutic implications.},
journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases},
volume = {30},
number = {3},
pages = {105809},
doi = {10.1016/j.bjid.2026.105809},
pmid = {41935448},
issn = {1678-4391},
abstract = {T-cell exhaustion, a well-characterized phenomenon, has historically been studied in the context of viral and oncological diseases. However, its relevance to chronic bacterial infections has only recently garnered attention. This review summarizes emerging evidence suggesting that bacterial pathogens can induce immune exhaustion through a variety of mechanisms. Additionally, we explore how bacterial biofilms, immune-privileged niches, and regulatory T-cell expansion contribute to persistent immune dysfunction. The article further examines the consequences of immune exhaustion, including secondary infections, antibiotic resistance, and microbiome dysbiosis, which are often underappreciated aspects of chronic immune impairment. Therapeutic strategies targeting these exhaustion pathways, such as immune checkpoint blockade, metabolic reprogramming, and microbiome modulation, are also discussed. We emphasize the need to consider chronic bacterial infections not as static conditions but as dynamic processes that interact with and suppress the immune system. Thus, understanding the mechanisms behind immune exhaustion highlights the importance of developing therapies that restore immune function, rather than solely relying on traditional antimicrobial treatments.},
}
@article {pmid41935631,
year = {2026},
author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , },
title = {Alcohol-Related Liver Disease Disrupts Bile Acid Homeostasis and Gut Microbial Bile Acid Metabolism.},
journal = {JHEP reports : innovation in hepatology},
volume = {},
number = {},
pages = {101848},
doi = {10.1016/j.jhepr.2026.101848},
pmid = {41935631},
issn = {2589-5559},
abstract = {BACKGROUND &amp; AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.<br><br>METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n=462), alongside matched healthy controls (n=148), and validated key findings in two independent ALD cohorts (n=34 and n=52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.<br><br>RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F=69.9, p=8.6e-66) and feces (inprimis, cholic acid: F=5.5, p=1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multi-step dehydroxylation pathway (e.b. baiB) increased, whereas those in the reduction arm (baiN) were depleted. In ALD patients, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.<br><br>CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.<br><br>CLINICAL TRIAL NUMBER: GALAXY main cohort: Danish Data Protection Agency nos. 13/8204, 16/3492 and 18/22692; and Odense Patient Data Exploratory Network under study identification nos. OP_040 and OP_239 Validation cohort 1: EudraCT number 20214-001856-51 Validation cohort 2: ClinicalTrial.gov ID NCT03863730 IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive alcohol-related liver disease progression. Additionally, our study identifies specific bacterial species influencing bile acid concentrations in alcohol-related liver disease using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating alcohol-related liver disease.},
}
@article {pmid41935802,
year = {2026},
author = {Kwak, MJ and Park, B and Choi, H and Hong, W and Mun, D and Son, SH and Choi, YS and Pathiraja, D and Eor, JY and Ryu, S and Kim, JK and Whang, KY and Jeong, KC and Choi, IG and Kim, Y},
title = {Gut microbial extracellular vesicles modulate the development of metabolic dysfunction-associated steatohepatitis through the gut-liver axis.},
journal = {Pharmacological research},
volume = {227},
number = {},
pages = {108184},
doi = {10.1016/j.phrs.2026.108184},
pmid = {41935802},
issn = {1096-1186},
abstract = {Metabolic dysfunction-associated steatohepatitis (MASH) represents a growing global health challenge due to its propensity to progress to irreversible hepatic disorders, including fibrosis, cirrhosis, and carcinoma. This study aimed to investigate the role of gut microbiota in the pathogenesis of MASH. We identified Romboutsia hominis as a key contributor to MASH progression, exacerbating hepatic lipid accumulation and inflammation via the tumor necrosis factor-α (TNF-α) signaling pathway. Conversely, Akkermansia muciniphila and its extracellular vesicles (EVs) mitigated MASH by reducing hepatic lipid deposition through lipid biosynthesis-related genes downregulation. Furthermore, by integrating gut microbiota profiles and serum biomarkers using a machine learning approach, we achieved over 90% accuracy in noninvasive MASH diagnosis. These findings elucidate critical mechanisms within the gut-liver axis and suggest novel therapeutic and diagnostic strategies targeting gut microbiota and their functional EVs for MASH.},
}
@article {pmid41935870,
year = {2026},
author = {Genkel, V and Zaripova, Y and Sluchanko, A and Lebedev, E and Kuznetsova, A and Saenko, A and Pykhova, L and Sumerkina, V and Nikushkina, K and Savochkina, A and Kupriyanov, S and Shaposhnik, I and Dolgushina, A},
title = {Ultrasound-measured visceral adipose tissue thickness and carotid atherosclerosis in patients with inflammatory bowel diseases.},
journal = {Obesity research &amp; clinical practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.orcp.2026.03.001},
pmid = {41935870},
issn = {1871-403X},
abstract = {BACKGROUND AND AIM: Visceral obesity plays a pivotal role in initiating and sustaining chronic systemic inflammation through complex interactions involving adipose tissue dysfunction, insulin resistance, immune system activation, and gut microbiome composition. Visceral obesity is also hypothesized to contribute to the development and progression of extraintestinal manifestations and complications in inflammatory bowel disease (IBD). The aim was to evaluate the interrelationships between ultrasound-measured visceral and subcutaneous adipose tissue thickness with carotid artery atherosclerosis indicators in IBD patients.<br><br>METHODS AND RESULTS: The study included 90 patients with IBD aged 40-64 years. All patients underwent duplex ultrasound scanning of the carotid arteries with measurement of carotid plaque burden indicators. Ultrasound measurements of subcutaneous and visceral adipose tissue thickness (ATT) were performed: minimal subcutaneous adipose tissue thickness (mSATT), maximal preperitoneal adipose tissue thickness (mPATT), periumbilical subcutaneous adipose tissue thickness (PSATT), visceral abdominal adipose tissue thickness, peri- and pararenal adipose tissue thickness. Ultrasound-derived indicators of visceral obesity (mPATT and abdominal ATT), but not BMI or WC, were associated with an increased odds ratio for the presence of carotid plaque after adjustment for sex and age. Both mPATT and abdominal ATT demonstrated positive correlations with apoB concentration, LDL-C, sdLDL, eLDL-TG, and inverse correlations with adiponectin concentration.<br><br>CONCLUSION: In patients with IBD aged 40-64 years, visceral adipose tissue thickness measured by ultrasound and WC were associated with the carotid plaque burdens. Ultrasound-measured mPATT and abdominal ATT, but not BMI and WC, were independently associated with carotid atherosclerosis in patients with IBD.},
}
@article {pmid41936070,
year = {2026},
author = {Duan, H and Ning, Z and Sun, Z and Guo, T and Sun, Y and Figeys, D},
title = {MetaDIA: A DDA-free Database Reduction Strategy for DIA Human Gut Metaproteomics.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzag029},
pmid = {41936070},
issn = {2210-3244},
abstract = {Microbiomes, especially within the gut, are complex and may comprise hundreds of species. The identification of peptides in metaproteomics presents a substantial challenge, as it involves matching peptides to mass spectra within an enormous search space for complex and unknown samples. This poses difficulties for both the accuracy and the speed of identification. Specifically, analysis of data-independent acquisition (DIA) datasets has relied on libraries constructed from prior data-dependent acquisition (DDA) results. However, this method is resource-intensive, consumes samples, and limits identification to peptides previously identified. These limitations restrict the application of DIA in metaproteomics research. We introduced a novel strategy to reduce the search space by utilizing species abundance and functional abundance information from the microbiome to score each peptide and prioritize those most likely to be detected. Using this strategy, we have developed and optimized a workflow called MetaDIA for the analysis of microbiome data generated by DIA, which operates independently of DDA assistance. Our approach successfully created a smaller, yet sufficient database for DIA data search in metaproteomics. The results demonstrated strong consistency with the traditional DDA-based library approach at both protein and functional levels. MetaDIA is readily accessible as an open-source project hosted on GitHub (https://github.com/northomics/MetaDIA).},
}
@article {pmid41936460,
year = {2026},
author = {Calbet, A},
title = {Gut Microbiomes of Marine Zooplankton: Consequences for Host Performance, the Biological Carbon Pump, and Prokaryote Biogeography.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70271},
doi = {10.1111/1462-2920.70271},
pmid = {41936460},
issn = {1462-2920},
support = {PID2023-150548NB-I00//MICIU/AEI/10.13039/5011 00011033/ ; //ERDF/EU/ ; //Consejo Superior de Investigaciones Cient&#xed;ficas/ ; },
mesh = {Animals ; *Zooplankton/microbiology/physiology ; *Gastrointestinal Microbiome ; *Carbon/metabolism ; Bacteria/metabolism/classification/genetics ; },
abstract = {Marine zooplankton are a link between primary producers and higher trophic levels and play a pivotal role in organic matter export via diel vertical migration and faecal-pellet production. Molecular surveys have revealed each individual as a holobiont hosting dense, taxonomically structured microbiomes in the gut, on the cuticle, and within feeding structures. These microbial partners expand dietary breadth through carbohydrate-active enzymes, supply limiting vitamins, detoxify xenobiotics, and may buffer thermal and oxidative stress, thereby influencing host fitness and the fate of particulate organic carbon. Experimental studies show intact microbiomes often enhance growth or fecundity, with effects amplified under vitamin limitation or toxin exposure. In contrast, gut and pellet-associated respiration can substantially reduce the carbon content of pellets within hours to days, depending on temperature and microbial composition. Vertical migrators also transport live bacteria and viruses below the thermocline, potentially seeding mesopelagic niches and affecting remineralization patterns. Despite these influences, zooplankton holobionts remain largely absent from biogeochemical models. This minireview synthesises current understanding of microbiome assembly and plasticity, their contributions to host performance and carbon export, and their role in microbial dispersal, underscoring the need to integrate holobiont traits into Earth-system models to better predict ecosystem responses to warming and deoxygenation.},
}
@article {pmid41928315,
year = {2026},
author = {Defazio, G and Lorusso, E and De Robertis, M and Mello, T and Galli, A and Pesole, G and Fosso, B},
title = {Machine learning-based assessment of the healthy human gut mycobiota landscape using ITS1 DNA metabarcoding data.},
journal = {BioData mining},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13040-026-00532-6},
pmid = {41928315},
issn = {1756-0381},
support = {H93C22000560003//Regione Puglia/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Universit&#xe0; e della Ricerca/ ; },
abstract = {The human gut microbiome plays a critical role in maintaining host health and homeostasis, and current literature suggests a bidirectional relationship between microbiome ecology and host well-being. DNA metabarcoding has emerged as a powerful tool for investigating microbiome imbalances (i.e., dysbiosis). While the prokaryotic microbiome has been extensively studied, the fungal counterpart - or mycobiome - remains largely unexplored, despite its recognized role from the perinatal stage onward. Here, we present a comprehensive survey based on DNA metabarcoding analysis of approximately 1,500 publicly available ITS1 samples. This survey integrates conventional statistical approaches with Machine Learning (ML) methods coupled with explainable Artificial Intelligence (XAI). ML models successfully predicted host health status with accuracies exceeding 80%, and fungal genera such as Eurotium, Aureobasidium, Candida, and Cutaneotrichosporon emerged as key classification features. This study introduces a cutting-edge multiview analytical framework applied to publicly available mycobiome data, highlighting the potential of fungal community profiling as a non-invasive tool to support health diagnostics.},
}
@article {pmid41928361,
year = {2026},
author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S},
title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02392-y},
pmid = {41928361},
issn = {2049-2618},
support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; },
abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.<br><br>RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.<br><br>CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.},
}
@article {pmid41928384,
year = {2026},
author = {Valdez-Palomares, F and Noriega, LG and Reyes-Romo, D and Canizales-Quinteros, S and Nambo-Venegas, R and Salinas-Lara, C and Tovar-Palacio, A and Menjivar, M and Peña-Espinoza, B and Ortiz, G and Palacios-González, B},
title = {Human fecal transplantation from stunted children promotes metabolic dysfunction in mice fed with a high-fat and high-fructose corn syrup diet.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2651984},
doi = {10.1080/19490976.2026.2651984},
pmid = {41928384},
issn = {1949-0984},
mesh = {Animals ; Male ; *Fecal Microbiota Transplantation/adverse effects ; Mice ; Gastrointestinal Microbiome ; Humans ; Mice, Inbred C57BL ; *Diet, High-Fat/adverse effects ; *Growth Disorders/microbiology/therapy/metabolism ; Child ; *High Fructose Corn Syrup/adverse effects/administration &amp; dosage ; Bacteria/classification/isolation &amp; purification/genetics ; Feces/microbiology ; Obesity/etiology/metabolism ; *Metabolic Diseases/etiology ; },
abstract = {Stunting, or impaired child growth due to poor nutrition and infections, is characterized by a low height-for-age and affects 48%-56% of school-aged children worldwide. It is associated with later weight gain and chronic diseases. The gut microbiome in undernourished children may increase obesity risk if they are exposed to high-calorie environments. To investigate this, we assessed whether the intestinal microbiome of stunted children elevates obesity risk upon exposure to an obesogenic environment. Fecal microbiota transplantation (FMT) was performed using pooled stools from healthy (n = 6) or stunted (n = 6) school-aged children from a low-income cohort in Mexico. Eight-week-old male C57BL/6 mice underwent bowel cleansing with polyethylene glycol (PEG), followed by weekly intragastric FMT for 4 weeks. The mice were subsequently fed either a control diet (CT) or a high-fat, high-fructose corn syrup diet (HFFr, including 15% HFCS-55) for 15 weeks. Metabolic outcomes were assessed through body composition, indirect calorimetry, oral glucose tolerance test, insulin tolerance test, and histological analysis of visceral adipose tissue. The microbiota composition was evaluated by 16S rRNA V3-V4 hypervariable region sequencing, and the predicted functional capacity was analyzed using PICRUSt2. FMT from stunted children increased susceptibility to diet-induced obesity, visceral adipose tissue hypertrophy, and insulin resistance. In contrast, FMT from healthy children promoted energy expenditure and visceral adipose tissue hyperplasia, conferring a protective effect against diet-induced obesity and insulin resistance in the mice. Healthy-FMT led to sustained enrichment of Akkermansia and Parabacteroides, whereas stunting-FMT increased Proteobacteria, Veillonella, Desulfovibrionaceae, and Bifidobacterium. Microbial‒phenotypic correlations showed that Akkermansia and Parabacteroides were negatively correlated with fasting glucose, body weight, and fat mass, and positively correlated with postprandial RER, VO2, and lean mass. In conclusion, stunting-FMT recipient mice showed a higher risk of obesity and metabolic issues in an obesogenic environment. Healthy-FMT confers metabolic resilience, characterized by increased abundance of taxa such as Akkermansia and Parabacteroides, which are linked to enhanced energy expenditure, improved glucose metabolism, and favorable adipose tissue structure.},
}
@article {pmid41928387,
year = {2026},
author = {Houshyar, Y and Zhang, F and Tavakoli, P and Grimm, MC and Hold, GL},
title = {Neglected kingdoms: the gut virome, mycobiome and their role in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2653288},
doi = {10.1080/19490976.2026.2653288},
pmid = {41928387},
issn = {1949-0984},
mesh = {Humans ; *Virome ; *Mycobiome ; *Inflammatory Bowel Diseases/microbiology/therapy/virology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology/virology ; *Fungi/classification/genetics/isolation &amp; purification ; Animals ; Fecal Microbiota Transplantation ; *Viruses/classification/genetics/isolation &amp; purification ; Bacteria/genetics ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing-remitting disorder of the gastrointestinal tract characterized by immune dysregulation, epithelial barrier dysfunction, and microbial imbalance. While bacterial dysbiosis, including depletion of short-chain fatty acid (SCFA) producers and enrichment of pathobionts, is well characterized, the gut virome and mycobiome remain comparatively neglected. Both exhibit high variability and are constrained by sequencing bias, contamination, and incomplete reference databases, leaving much of the viral and fungal diversity unresolved. Emerging evidence links fungal and viral dysbiosis to IBD pathogenesis, including Candida overgrowth, loss of Saccharomyces, expansion of Caudoviricetes phages, and detection of eukaryotic viruses such as Cytomegalovirus and Epstein-Barr virus in inflamed mucosa. These alterations disrupt barrier integrity, modulate immune signaling, and interact with bacteria and archaea in cross-kingdom networks that amplify inflammation. Translationally, the virome and mycobiome are now recognized as therapeutic targets, inspiring interventions from pre/probiotics and synbiotics to precision phage therapy and microbiota-based transplantation, including fecal virome transplantation (FVT) and fecal microbiota transplantation (FMT). This review recognizes the challenges and opportunities of studying these neglected kingdoms, reframes IBD dysbiosis and highlights new directions for biomarker discovery and multikingdom microbiota-directed therapies.},
}
@article {pmid41928627,
year = {2026},
author = {Bong, SHS and Teh, KKJ and Wong, VW},
title = {Therapeutic Landscape Evolution: From Lifestyle Interventions to Precision Pharmacotherapy.},
journal = {Clinical and molecular hepatology},
volume = {},
number = {},
pages = {},
doi = {10.3350/cmh.2026.0125},
pmid = {41928627},
issn = {2287-285X},
abstract = {Steatotic liver disease (SLD) is a growing global epidemic, with metabolic dysfunction-associated steatotic liver disease (MASLD) now the most common chronic liver disease worldwide and closely linked to adverse cardiovascular outcomes. Lifestyle modification remains the cornerstone of management, with the Mediterranean diet as the preferred dietary intervention and emerging evidence supporting additional dietary and exercise strategies. Pharmacotherapy has advanced rapidly in recent years, with two U.S. Food and Drug Administration-approved options, resmetirom and semaglutide, for noncirrhotic metabolic dysfunction-associated steatohepatitis (MASH) with moderate-to-advanced fibrosis, alongside multiple agents in development targeting different disease mechanisms. In metabolic dysfunction- and alcohol-associated liver disease (MetALD), evidence remains limited, but management essentially focuses on alcohol cessation and optimization of cardiometabolic risk factors, with resmetirom, incretin-based therapies, and fibroblast growth factor (FGF)-21 analogues representing promising therapeutic agents that have yet to be fully evaluated in clinical trials. The field is increasingly moving toward a precision medicine paradigm integrating pharmacologic and lifestyle interventions, tailored to disease phenotype, genetic risk, and gut microbiome. Key challenges include heterogeneity in treatment response, assessment of alcohol intake, and real-world implementation barriers. This review summarizes current and emerging therapies and highlights the role of precision medicine in advancing individualized care across the SLD spectrum.},
}
@article {pmid41928791,
year = {2026},
author = {Bajaj, J and Sommer, A and Auch, B and Khoruts, A},
title = {Proximity-ligation metagenomics reveals disease-specific mobilome dynamics in disrupted gut ecosystems.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9142184/v1},
pmid = {41928791},
issn = {2693-5015},
abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance and virulence genes in the gut microbiome. Using proximity ligation shotgun metagenomics to resolve host-mobilome relationships, we analyzed microbiomes from two patient cohorts: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. While rCDI reflects antibiotic-driven disruption, cirrhosis-driven microbiome changes result from altered gut physiology. We found increased chromosomal determinants of antibiotic resistance in both, but plasmid-mediated amplification was more evident in rCDI.},
}
@article {pmid41928923,
year = {2026},
author = {Lesperance, DNA and Padhi, S and Macro, J and Olson, S and Stanwood, E and Kannan, K and Graveley, B and Rogina, B and Broderick, NA},
title = {Microbiome contribution to Indy longevity in Drosophila.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.25.714291},
pmid = {41928923},
issn = {2692-8205},
abstract = {UNLABELLED: Reduction in the Indy (I'm not dead yet) gene, a plasma membrane citrate transporter, in Drosophila and its homolog in worms extends lifespan by promoting metabolic homeostasis. Indy reduction delays the onset of aging-associated pathology in the fly midgut, including preservation of intestinal barrier integrity and intestinal stem cell homeostasis. Gut microbiota has broad impacts on host metabolism, health, and aging. Age-related dysbiosis impairs intestinal barrier function and drives mortality. However, the underlying mechanisms that link increased microbial load to frailty and negative effects on health remain mostly unclear. Here we show that Indy heterozygote flies have significantly lower bacterial load and increased diversity during aging compared to controls. However, the presence of the microbiome was not required for Indy lifespan extension, though removal of microbes did enhance the effects of Indy reduction on longevity, suggesting potential interactions between the microbiome and Indy . Indy down-regulation was linked to reduced expression of the JAK/STAT signaling ligands Upd3 and Upd2 in the midgut of young flies, which likely contributes to preserved intestinal stem cell homeostasis. Altogether, our results suggest that Indy reduction impacts microbiome load and composition, which preserves gut homeostasis and extends lifespan through impacts on JAK/STAT signaling pathway.<br><br>SIGNIFICANCE STATEMENT: Indy is a fly homologue of mammalian SLC13A5 (mSLC13A5) plasma membrane citrate transporter, a central metabolic regulator involved in health, longevity, and disease. Reduction of fly Indy gene activity preserves metabolic and intestinal stem cell homeostasis and extends longevity. Gut microbiota impacts host metabolism, health, and aging. Here we show that Indy reduction prevents age-associated increases in bacterial load and expression of the JAK/STAT signaling ligands Upd3, and Upd2, while maintaining microbiome diversity. These changes likely slow activation of epithelial cell turnover in the gut and contribute to downstream lifespan effects. As the role of INDY and microbiome are conserved across organisms, our study provides a framework to study underlying mechanisms of the effects of reduced Indy and the microbiome on health and longevity.},
}
@article {pmid41928970,
year = {2026},
author = {Rock, RR and Alexander, M and Noecker, C and Trepka, KR and Upadhyay, V and Ortega, EF and Ramirez, L and Siewert, L and Olson, CA and Halsey, T and Pröbstel, AK and Baranzini, SE and Turnbaugh, PJ},
title = {Female-enriched Eggerthella lenta drives neuroinflammation and IFN-γ via host receptor TLR2.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.16.711194},
pmid = {41928970},
issn = {2692-8205},
abstract = {UNLABELLED: Women are at increased risk of autoimmune diseases, including multiple sclerosis (MS); however, the degree to which sex differences in the gut microbiota impact autoimmunity remains largely unexplored. Our 27-cohort meta-analysis revealed 60 sex-associated gut bacterial species. Leveraging an independent clinical cohort, we demonstrate that female-enriched species significantly associate with MS status and clinical disability (EDSS). Top female-enriched species Eggerthella lenta drove disease in the experimental autoimmune encephalomyelitis (EAE) MS model, consistent with brain and gut lamina propria T cell infiltration and MS-associated T helper (Th) signatures. E. lenta induced intestinal Th1 and Th17 in healthy mice, independent of bacterial viability. Mechanistically, we demonstrate that TLR2 directly drives E. lenta -induced IFN-γ production in Th cells and is necessary for exacerbation of EAE. Together, we identify a causal host-microbe axis contributing to sex differences in autoimmunity and provide a framework for evaluating sex as a biological variable in human microbiome research.<br><br>HIGHLIGHTS: 27-cohort meta-analysis identifies a robust sex-signature in human gut microbiota.Female-enriched species are associated with MS risk and severity. Female-enriched Eggerthella lenta exacerbates the EAE model. E. lenta impacts neuroinflammation via toll-like receptor 2.},
}
@article {pmid41929040,
year = {2026},
author = {Patabandige, DLJ and John, J and Ortiz, M and Campbell, BJ},
title = {Environmental Gradients Shape the Hydrocarbon-Degrading Microbiome in Two Mid Atlantic Bays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.25.714183},
pmid = {41929040},
issn = {2692-8205},
abstract = {UNLABELLED: Hydrocarbons are recalcitrant organic matter that are released into the environment via natural and anthropogenic activities. We hypothesized that abiotic and biotic factors, including salinity, temperature, seasonality, microbial interactions, and functional redundancy, influence the abundance and activity of potential hydrocarbon degraders in the Delaware and Chesapeake Bays. We identified key genes in hydrocarbon degradation pathways in metagenomes, metatranscriptomes, and metagenome assembled genomes (MAGs) from these estuaries. Aerobic aromatic and alkane degradation pathways predominated in both estuaries, with higher gene abundances observed in low-salinity spring and summer samples. Hydrocarbon degrading MAG abundance were significantly structured by salinity, temperature, nitrate, and silicate concentrations. Metatranscriptomic analyses revealed consistently higher expression of aerobic alkane and aromatic degradation genes in the Delaware compared to the Chesapeake Bay, with the highest occurring under low-salinity spring conditions in the former. Catechol degradation pathways exhibited high functional redundancy, whereas the naphthalene degradation pathway showed restricted distribution. Co-expression analysis revealed that Burkholderiales displayed condition dependent metabolic coupling while Pseudomonadales integrated hydrocarbon degradation with fermentation and central metabolism, demonstrating complementary strategies that support multi-scale ecosystem resilience. In conclusion, environmental gradients and taxon-specific metabolic strategies together govern hydrocarbon degradation potential in these estuaries, with implications for predicting ecosystem responses to hydrocarbon inputs under changing conditions.<br><br>IMPORTANCE: Coastal estuaries are among the most contaminated aquatic environments on Earth, receiving continuous hydrocarbon inputs from industrial activity, urban runoff, and natural sources. Microorganisms are the primary agents of hydrocarbon breakdown in these systems yet predicting when and where this capacity is active and how resilient it is to environmental change remains a major challenge. Using paired genomic and transcriptomic data from microbial genomes across two major mid-Atlantic estuaries, we show that hydrocarbon degradation capacity is not uniformly distributed but is instead shaped by salinity, nutrients, and seasonality in pathway-specific ways. Critically, dominant degrader taxa employ fundamentally different metabolic strategies to sustain this function across fluctuating conditions, providing a form of community-level insurance against environmental disturbance. These findings advance our ability to predict microbial hydrocarbon degradation in coastal systems and inform nature-based approaches to bioremediation under increasing climate and anthropogenic pressures.},
}
@article {pmid41929113,
year = {2026},
author = {Wang, S and Guitor, AK and Valentin-Alvarado, LE and Garner, R and Zhang, P and Yan, M and Shi, LD and Schoelmerich, MC and Steininger, HM and Portik, DM and Zhang, S and Wilkinson, JE and Lynch, S and Morowitz, MJ and Hess, M and Diamond, S and Banfield, JF and Sachdeva, R},
title = {Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.27.714056},
pmid = {41929113},
issn = {2692-8205},
abstract = {DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their host's modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.},
}
@article {pmid41929228,
year = {2026},
author = {Lester, BA and Kelly, C and Henry, SN and Elias, IP and Cevenini, SE and Hendrickson, MR and Park, T and Ashley, TD and Beltz, JM and Milner, JP and Pickrell, AM and Morton, PD},
title = {Germ-free piglets display variable neuroinflammatory-like perturbations in prefrontal cortical microglia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.22.713463},
pmid = {41929228},
issn = {2692-8205},
abstract = {UNLABELLED: Communication between gut microbiota and immune cells within the brain is essential for neurotypical development. Specifically, microglia are known to play a key role in regulating and supporting neural progenitor stem cell production during brain development, and are sensitive to changes in the maternal gut microbial composition during perinatal development. Here, we employed a germ-free (GF) porcine paradigm to examine how the absence of the microbiome affects microglial dynamics during a key epoch of brain development. We utilized automated software to evaluate microglial density and morphology across three developmentally significant regions: the ventricular/subventricular zone (VZ/SVZ), the prefrontal subcortical white matter (PFCSWM), and layers II/III of the prefrontal cortex (PFCII-III). We found no significant differences in microglial morphology or density in the VZ/SVZ or PFCSWM. In contrast, the PFCII-III of P16 piglets exhibited an increase in microglia density paired with morphologies indicative of an activated/reactive functional state. Notably, these effects were identified with no overall changes in microglial density in any of the regions assessed. Transcriptomics on RNA isolated from the PFCII-III revealed a significant upregulation of genes related to neuroinflammation, in agreement with a region-specific microglial and immune response in the absence of microbial colonization during postnatal development. Together, these findings build on the limited knowledge available on how microbiota influence brain development in large animal model organisms with high similarities to human brain anatomy and developmental trajectories.<br><br>SIGNIFICANCE STATEMENT: The prefrontal cortex of porcine display unique, ramified microglia which are sensitive to germ-free conditions whereby they display alterations in morphology with a more transcriptionally reactive signature. These findings indicate that microglia are regionally sensitive to stimuli in the periphery, and studies in lissencephalic mammalian models may not be directly correlative to other higher-order species. The neuroanatomical heterogeneity of microglia across species is informative and understudied, but necessary, to draw conclusions on the array of perturbations spanning neurodevelopmental trajectories in health and disease.},
}
@article {pmid41929259,
year = {2026},
author = {Baird, AW},
title = {Coordinated regulation of colonic fluid and mucus secretion.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1757501},
pmid = {41929259},
issn = {1663-9812},
abstract = {The human colon, unlike the small intestine which is relatively sterile, contains a diverse microbiome which contributes to host metabolism. The luminal environment is constantly changing and responds to epithelial absorption and secretion which occurs as motility is regulated by longitudinal and circular smooth muscle. Mucous gels are crucial to lubrication and maintenance of an unstirred layer which separate the epithelium from the lumen. Gel-forming mucins are produced and released by goblet cells and become hydrated, although the source of water is not definitively understood. The purpose of this review is to summarize regulation of water movements across the colonic epithelium, goblet cell secretion of mucus and to consider how these distinct processes are functionally coupled.},
}
@article {pmid41929306,
year = {2026},
author = {Kramer, M and Belleau, P and Tortora, SC and Deschenes, A and Founta, K and Gurjao, C and Yueh, B and Goodwin, S and Gee, D and Subhash, S and Barbi, M and Chung, C and Ozler, K and Eskiocak, O and Izar, B and Geiger, H and Chu, TR and Goldstein, Z and Winterkorn, L and Araneo, A and Whelan, RL and Rivadeneira, D and Fox, S and Kandel, A and Ozay, F and Talabong, DJA and Lanipekun, O and Talus, H and Zeng, J and Rishi, A and Chambwe, N and Robine, N and Boyd, J and Krasnitz, A and Beyaz, S and McCombie, WR and Martello, LA},
title = {Integrative Genomic, Transcriptomic, and Microbiome Profiles of Colon Cancer by Ancestry Provide Insights into Molecular Distinctions.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.25.26349226},
pmid = {41929306},
abstract = {Colorectal cancer (CRC) incidence, tumor biology, and clinical outcomes differ by patient ancestry, yet African ancestry (AFR) populations remain underrepresented in genomic and microbiome studies. Here, we comprehensively characterized genomic, transcriptomic and microbiome features of AFR and European ancestry (EUR) colon cancer patients residing in New York City and Long Island. While confirming known drivers from other large CRC studies, our AFR to EUR comparison of somatic variation also revealed a possible enrichment of functional KRAS variants in AFR tumors. Colon cancer genomes in patients in this study also exhibit distinct patterns of DNA copy number variation, correlating with consensus molecular subtypes. Fusobacterium nucleatum-positive tumors were enriched for co-occurring oral taxa, suggesting an organized oral microbial structure within the tumor microenvironment. Our findings highlight ancestry-associated differences in somatic mutation, copy number variation, and tumor microbiome composition, underscoring the urgent need to expand AFR representation in genomic studies to uncover population-specific determinants of CRC risk and to develop treatment strategies that reflect the full diversity of patients affected by this disease.},
}
@article {pmid41929401,
year = {2026},
author = {Bokemeyer, B and Plachta-Danielzik, S and Helwig, U and Beuchert, P and Schreiber, S},
title = {Competence network inflammatory bowel diseases in Germany: 25 years of interdisciplinary and cross-sectoral research and knowledge transfer across all levels of IBD care.},
journal = {Therapeutic advances in gastroenterology},
volume = {19},
number = {},
pages = {17562848261431187},
pmid = {41929401},
issn = {1756-283X},
abstract = {The Competence Network Inflammatory Bowel Diseases (Kompetenznetz Darmerkrankungen) was established in Germany in 1999 through a 10-year funding programme by the German Ministry of Education and Research. It was created to address the growing gap between the rising prevalence and therapeutic complexity of inflammatory bowel disease (IBD) and the fragmented care structures and isolated academic initiatives of the time. The network's continuing mission is to improve care for patients with Crohn's disease and ulcerative colitis by more closely integrating clinical practice, translational science and patient involvement. This review summarises the history, governance, registries, biobanking, clinical trials, educational programmes and collaborations of the Competence Network IBD. Over the past 25 years, the Competence Network IBD has established prospective national registries (e.g. RUN-CD, RUN-UC, VEDO-IBD and FilgoColitis), developed pragmatic real-world cohorts (TARGET and GeCer) and contributed to the UMBRELLA-IBD data warehouse of the Competence Network IBD in Germany. The network played a central role in creating the German IBD DNA collection and supported the Kiel University biobank, both of which link biospecimens with longitudinal clinical data to support genetic and microbiome research. It also conducts and coordinates multicentre clinical trials and has supported the development of the German evidence- and consensus-based IBD guidelines. With more than 800 members from university centres, community practices, nursing and patient organisations, it now provides a robust platform for research and knowledge transfer across all levels of IBD care. The Competence Network IBD demonstrates how long-term interdisciplinary and cross-sectoral collaboration can improve the management of chronic inflammatory diseases. By integrating research infrastructures with education and patient involvement, the network serves as a scalable and sustainable model for national and international collaboration in IBD.},
}
@article {pmid41929449,
year = {2026},
author = {Røsland, A and Amin, H and Lie, SA and Malinovschi, A and Bunæs, DF and Bertelsen, RJ},
title = {Effect of periodontal therapy on the oral microbiome and lung function: an intervention study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1725666},
pmid = {41929449},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; Male ; *Periodontitis/therapy/microbiology ; Female ; Middle Aged ; *Mouth/microbiology ; Longitudinal Studies ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; *Lung/physiology ; Metagenomics ; Aged ; },
abstract = {INTRODUCTION: The oral cavity harbors over 700 bacterial species, and disruption of this balance can lead to periodontitis, which has been linked to systemic conditions including respiratory disease.<br><br>METHODS: In this longitudinal clinical trial, 57 never-smoking adults with stage I-II periodontitis underwent full-mouth periodontal disinfection. Airway resistance and subgingival plaque sampling (analyzed by shotgun metagenomics) was measured at baseline and six weeks after therapy.<br><br>RESULTS: Periodontal treatment significantly improved clinical periodontal parameters, and was associated with reductions in airway resistance. Microbiome analysis showed a shift from periodontitis-associated taxa, including Prevotella, Porphyromonas, and Tannerella, toward health-associated species such as Actinomyces oris, and Rothia dentocariosa. Higher airway resistance was associated with a greater relative abundance of periodontitis-associated bacteria.<br><br>DISCUSSION: Together, findings suggest that periodontal therapy promotes a healthier oral microbiome and is associated with improved lung function in non-smokers with no prior lung disease.},
}
@article {pmid41929479,
year = {2026},
author = {Pan, Y and Li, B and Liu, L and Wang, Z and Liu, X},
title = {Gut dysbiosis induces the development of asthenozoospermia through butanoate metabolism.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1760881},
pmid = {41929479},
issn = {1664-3224},
mesh = {Male ; *Dysbiosis/complications/microbiology/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Asthenozoospermia/metabolism/etiology/microbiology ; Humans ; Mice ; Case-Control Studies ; Fecal Microbiota Transplantation ; Adult ; Fatty Acids, Volatile/metabolism ; Butyrates/metabolism ; Sperm Motility ; Metabolomics ; Testis/metabolism ; },
abstract = {BACKGROUND: Asthenozoospermia is a leading cause of male infertility with a rising incidence. While gut dysbiosis is implicated in metabolic disease, its role in asthenozoospermia pathogenesis remains unclear.<br><br>MATERIALS AND METHODS: We conducted a case-control study comparing the fecal microbiomes of men with isolated asthenozoospermia (n=60) and healthy controls (n=60) using shotgun metagenomic sequencing. Causality was assessed by fecal microbiota transplantation (FMT) from patients or controls into germ-free male mice. Metabolic perturbations were profiled by untargeted serum metabolomics and targeted short-chain fatty acid (SCFA) quantification in humans, alongside untargeted testicular metabolomics and serum SCFAs in recipient mice.<br><br>RESULTS: Metagenomic analysis (LEfSe) identified species-level differences, with marked depletion of butyrate-producing taxa in asthenozoospermia, most notably the prototypical butyrate producer Faecalibacterium prausnitzii. The relative abundance of F. prausnitzii was significantly positively correlated with sperm motility and progressive motility, linking gut composition to sperm quality in asthenozoospermia. Untargeted serum metabolomics identified 39 differential metabolites; KEGG enrichment prioritized butanoate metabolism. Targeted SCFA profiling confirmed significantly lower serum butyrate in asthenozoospermia versus controls. In germ-free males, FMT with patient-derived microbiota reduced sperm motility and progressive motility and induced histopathological abnormalities, including decreased interstitial Leydig cells, loss and atrophy of select intratubular cells, and an increased proportion of abnormal seminiferous tubules. Following patient FMT, recipient mice exhibited significantly reduced serum butyrate; testicular metabolomics revealed distinct profiles with 140 key differential metabolites, again implicating butanoate metabolism. Mechanistically, reduced F. prausnitzii-derived butyrate might impair Leydig cell steroidogenesis via disrupted PPAR signaling.<br><br>CONCLUSIONS: Asthenozoospermia is associated with gut dysbiosis characterized by loss of butyrate-producing bacteria, systemic and testicular disturbances in butyrate metabolism, and microbiota-mediated transmission of impaired sperm quality. These findings implicate the gut-testis axis in asthenozoospermia pathogenesis and nominate butyrate metabolism as a potential therapeutic target.},
}
@article {pmid41929503,
year = {2026},
author = {Pisa, CM and Verrone, A and Mazuy, M and Ientile, L and Rigante, D and Esposito, S},
title = {Gut microbiota alliance to shape sceneries of familial Mediterranean fever: a scoping review detailing difference between children and adults.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1814103},
pmid = {41929503},
issn = {1664-3224},
mesh = {Humans ; *Familial Mediterranean Fever/microbiology/immunology/drug therapy ; *Gastrointestinal Microbiome/immunology ; Child ; Adult ; Dysbiosis/immunology ; Colchicine/therapeutic use ; Age Factors ; Pyrin/genetics ; },
abstract = {Familial Mediterranean fever (FMF) is the most common monogenic autoinflammatory disease worldwide and a key-model to illustrate dysregulation of innate immunity, etiologically determined by pathogenic variants in the MEFV gene, encoding pyrin, leading to uncontrolled interleukin-1β and interleukin-18 release. Despite its genetic basis, FMF shows marked clinical heterogeneity in all-aged patients, mostly in children, suggesting a role of potential environmental modifiers which are far to be exactly unraveled. Recent medical literature has increasingly illuminated the importance of gut microbiota in maintaining overall health and immune functions, and its contribution has been claimed also to explain both FMF inflammatory activity and heterogeneous disease expression. This narrative review summarizes current evidence on the interaction between gut microbiota and FMF, with a specific focus on differences between children and adults. Pediatric studies dedicated to FMF have reported intestinal dysbiosis in terms of reduced microbial diversity and depletion of short-chain fatty acid-producing bacteria, with subsequent enrichment of pro-inflammatory taxa: such alteration could modulate pyrin-inflammasome activation and contribute to systemic inflammation, disease phenotype, and response to colchicine or to other drugs specifically used in colchicine-resistant FMF. Geographic and lifestyle factors may shape intestinal microbiota composition early in life, reinforcing the relevance of gut flora and confirming its activity as a crucial tessera to determine FMF sceneries, mostly in children, and a potential target for future add-on therapeutic strategies. In addition, colchicine therapy appears to partially remodel the gut microbiome, empowering a local beneficial anti-inflammatory microbial profile.},
}
@article {pmid41929505,
year = {2026},
author = {Zhang, Y and Xiao, X and Guo, J and Lei, X and Xiong, W and Wang, S and He, Y and Lei, C and Hu, X},
title = {Multidimensional regulatory mechanisms and translational potential of epigenetic networks in the rheumatoid arthritis disease course.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1792863},
pmid = {41929505},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/genetics/immunology/metabolism ; *Epigenesis, Genetic ; MicroRNAs/genetics ; DNA Methylation ; Animals ; *Gene Regulatory Networks ; },
abstract = {Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic synovitis that may progress to irreversible joint destruction and disability, thereby substantially impairing quality of life. RA results from complex interactions among genetic predisposition, environmental exposures, and immune dysregulation; however, current therapies are not curative, and many patients continue to experience pain, morning stiffness, and recurrent inflammation. In recent years, epigenetic mechanisms have emerged as key modulators of RA heterogeneity and disease persistence. Reversible regulatory layers-including non-coding RNAs, RNA modifications, DNA methylation, histone modifications, and microbiota-host interactions-provide a conceptual framework linking environmental cues to cell-type-specific inflammatory programs. This review summarizes recent advances in the epigenetic regulation of RA and outlines six interconnected dimensions. (1) miRNA-mediated post-transcriptional regulation: dysregulated miRNAs reshape inflammatory circuits and promote synovial activation through regulatory hubs. (2) RNA m[6]A modification: aberrant m[6]A remodeling alters immune metabolism and inflammatory gene expression, thereby reinforcing pathogenic responses. (3) DNA methylation: genome-wide profiling of synovium reveals differentially methylated loci that may activate disease-relevant pathways. (4) Histone modification and chromatin remodeling: altered activity of histone-modifying enzymes (e.g., HDACs) modulates inflammatory transcriptional programs and may contribute to epigenetic memory. (5) Hypoxia-driven metabolic-epigenetic crosstalk: hypoxia-inducible factors (HIFs) coordinate metabolic adaptation and inflammatory amplification; for example, HIF-1α supports the FLSs under hypoxic conditions. (6) Microbiome-epigenome interactions: gut microbial metabolites (e.g., butyrate) regulate immune homeostasis, partly by promoting follicular regulatory T cell (TFR) differentiation and restraining inflammation. Collectively, these findings indicate that epigenetic networks exert multilevel control over RA pathogenesis and highlight translational opportunities for targeted epigenetic interventions, including RNA methylation modulators, DNA methyltransferase inhibitors, and histone deacetylase-directed strategies.},
}
@article {pmid41929571,
year = {2026},
author = {Seenivasan, R and Pachiyappan, JK and Marimuthu, A and Halagali, P and Kuppusamy, G and Nayak, PG and Tippavajhala, VK},
title = {Gut microbiota shifts in spaceflight: a case study evidence and countermeasures for microbial homeostasis.},
journal = {3 Biotech},
volume = {16},
number = {4},
pages = {152},
pmid = {41929571},
issn = {2190-572X},
abstract = {The gut microbiota is a crucial component in maintaining overall human health since it has been found to influence not only metabolism but also neurobehavioral function and immunity. The extreme conditions of space, for example, cosmic radiation, microgravity, and confinement, can severely disrupt the functioning and alter the composition of gut microbiota. In fact, this will predispose the immune system to be dysfunctional, lead to psychological and metabolic disorders that are accompanied by a decrease in the diversity of beneficial microbes and change in the pattern of metabolite production. The spaceflight analog and ground, based studies have produced important findings concerning the mechanisms and reasons for gut microbial dysbiosis in extreme conditions. Different research works have been carried out, such as dietary intervention and high fiber to support the growth of healthy microbes. Further, advanced microbial monitoring using wearable sensors to identify the microbial and proinflammatory biomarkers will mitigate dysbiosis and safeguard the crew's health for longer-duration missions. This wearable sensor will not only help monitor astronauts' microbial status continuously, but it will also provide a significant feature for designing personalized dietary plans and probiotic supplements. This article provides a comprehensive understanding of astronaut health, including disturbances to the gut microbiome during space travel, space-analogue studies conducted by many researchers to unravel mechanisms, countermeasures to stabilize the gut microbiome, and its prospects.},
}
@article {pmid41929684,
year = {2026},
author = {Chen, C and Wang, P and Tong, G and Chen, R and Shen, Y and Wu, X and Liang, W and Pu, J},
title = {The structure of rhizosphere microbial and endophytic communities of Coptis chinensis var. brevisepala: variations across different ecological niches.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1785609},
pmid = {41929684},
issn = {1664-302X},
abstract = {Coptis chinensis var. brevisepala is a valuable traditional Chinese medicinal plant, whose resources are severely depleted due to long-term overexploitation. However, the associations between its rhizosphere microbiome and habitat soil properties, as well as the composition and functions of endophytes, remain unclear. This study employed high-throughput sequencing to characterize rhizosphere microbial communities of C. chinensis var. brevisepala from four distribution sites, analyze their correlations with soil chemical properties, and explore the differences and functional traits of endophytic communities in distinct tissues (leaves, rhizomes, fibrous roots). A total of 177 core bacterial genera and 146 core fungal genera were detected in rhizosphere soils of the four sites. The dominant bacterial phyla were Proteobacteria, Acidobacteriota, and Actinobacteriota, with norank_f_Xanthobacteraceae and Bradyrhizobium as the dominant genera. The dominant fungal phyla were Ascomycota and Basidiomycota, with Paraboeremia and Saitozyma as the dominant genera. Soil chemical properties exerted significant effects on both bacterial and fungal communities in the rhizosphere, among which soil pH and total nitrogen (TN) were the key drivers shaping rhizosphere microbial communities. For endophytes, 29 bacterial phyla (596 genera) and 12 fungal phyla (653 genera) were identified, with significant differences in diversity, richness, and dominant genera across tissues; leaves harbored the highest endophytic diversity. Functional prediction indicated that endophytic fungi were dominated by saprotrophy-related functional genes, and KEGG secondary functional annotation uncovered the presence of antimicrobial-related genes. This study clarifies the rhizosphere microbiome ecological traits and tissue-specific endophytic characteristics of C. chinensis var. brevisepala, providing a scientific basis for screening beneficial microorganisms to facilitate the restoration and reconstruction of this endangered medicinal plant.},
}
@article {pmid41929693,
year = {2026},
author = {Xue, H and Zhang, M and Tang, Y and Huang, W and Yu, X and Zhang, J and Pan, M and Liu, Z},
title = {Integrated metagenomic and metabolomic profiling of spontaneous preterm birth in Chinese women.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1729476},
pmid = {41929693},
issn = {1664-302X},
abstract = {BACKGROUND: Spontaneous preterm birth (sPTB) remains a major cause of neonatal morbidity and mortality. We used integrated metagenomics and untargeted metabolomics to identify vaginal microbial and host metabolic signatures associated with sPTB in Chinese women.<br><br>METHODS: Vaginal swabs (sPTB, n&#x202f;=&#x202f;37; term, n&#x202f;=&#x202f;62) and available maternal plasma were profiled by shotgun metagenomic sequencing and UHPLC-HRMS metabolomics. Group differences in microbial diversity/taxa and metabolite features were evaluated, followed by pathway enrichment and microbiome-metabolome correlation analyses.<br><br>RESULTS: Compared with term controls, sPTB was characterized by reduced Lactobacillus dominance, higher vaginal microbial alpha diversity (p&#x202f;<&#x202f;0.05), and distinct community structure (PERMANOVA p&#x202f;<&#x202f;0.001). Metabolomic profiles of plasma and vaginal fluid differentiated sPTB from term pregnancy and highlighted decreased pantothenic acid and increased 4-pyridoxic acid, together with lipid and amino-acid perturbations. Pantothenic acid showed good discrimination (AUC&#x202f;=&#x202f;0.82), and a multi-metabolite model improved classification (AUROC&#x202f;=&#x202f;0.9544). KEGG analysis implicated vitamin B6 metabolism, pantothenate/CoA biosynthesis, and glycerophospholipid metabolism. Microbiome-metabolome integration dentified exploratory an sPTB-associated pattern in which Lactobacillus (e.g., L. crispatus) was positively correlated with pantothenic acid, while dysbiosis-/pathogen-associated taxa (including C. trachomatis) correlated with 4-pyridoxic acid.<br><br>CONCLUSION: sPTB in this Chinese cohort is associated with concurrent vaginal dysbiosis and systemic/local metabolic disturbances, supporting integrated microbiome-metabolite markers for risk stratification and potential preventive targets.},
}
@article {pmid41929779,
year = {2026},
author = {Mishra, P and Prescott, SL and Logan, AC},
title = {The gut is guilty! Will legalomics transform forensic and legal psychology?.},
journal = {Frontiers in psychology},
volume = {17},
number = {},
pages = {1739593},
pmid = {41929779},
issn = {1664-1078},
abstract = {Multiple lines of converging research are supporting the idea that gut microbes play an outsized role in human cognition and behavior. Here in this perspective article, we argue that emergent gut-brain-microbiota research, and associated advances in multi-omics technologies, are destined to be of high-level relevance to forensic and legal psychology. After summarizing neural, immune, endocrine, and metabolic channels by which gut ecosystems can modulate behavior-relevant brain states, and discussing causal inferences from microbiota-transfer and adjacent human evidence, we present auto-brewery syndrome as a bounded legal precedent for microbiome-mediated impairment. The available evidence allows for a visualized future in which legalomics-the disciplined use of microbiome and omics evidence in prevention, treatment, competency, mitigation, risk assessments, reintegration care, correctional health, and professional wellness-is in the prevue of forensic and legal psychology. Framed by neurorights, we offer a series of ideas for future directions, with possible ways to strengthen research within ethical frameworks. Using auto-brewery syndrome as an example, we argue that the legalome offers forensic and legal psychology a way to calibrate, rather than replace, biopsychosocial judgement. Microbial signatures and legalomics-reliably obtained and narrowly construed-might one day help us judge more justly.},
}
@article {pmid41929949,
year = {2026},
author = {Zhang, Q and Almanie, L and Ouyang, Y and Cheng, Z and Zhang, H},
title = {From routine periodontal therapy to Alzheimer's disease early detection: A scoping review.},
journal = {Journal of Alzheimer's disease reports},
volume = {10},
number = {},
pages = {25424823261421629},
pmid = {41929949},
issn = {2542-4823},
abstract = {An epidemiological association has been observed between periodontitis and Alzheimer's disease (AD); however, salivary and blood assays often show low specificity. Periodontal tissues and fluids, which are routinely removed and discarded during periodontal treatment, may be collected to offer matrices useful for the early detection of AD. This study aimed to map current preclinical and clinical evidence on biomarkers measured in periodontal tissues and fluids for the early detection of AD and organize them within an AD-specificity pyramid anchored to brain-relevant endpoints. Following PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses-Extension for Scoping Reviews) guidance, we searched PubMed, Scopus, and Web of Science (January 1, 2015-August 31, 2025) for preclinical and clinical studies measuring AD-relevant biomarkers in periodontal matrices. The protocol was pre-registered (OSF DOI: 10.17605/OSF.IO/EDVU9; August 20, 2025). Two reviewers extracted the data, and other two independently verified them. The findings were organized using a four-tier AD-specificity pyramid. Results: Fourteen studies met the inclusion criteria. The biomarkers from the included studies were clustered into microbiome features, molecular signals, and genetic/transcriptomic findings. Evidence ranged from Tier-1 contextual inflammation/pathogens to Tier-4 core-pathology adjacency; five studies incorporated clinical/biological anchoring, with cerebrospinal fluid amyloid-β positivity providing the most brain-relevant anchor. Periodontal matrices are practicable, high-signal sources for AD-relevant biomarkers. However, translational validation linking periodontal biomarkers to brain endpoints is needed to assess the feasibility of multi-tier and chairside panels for early AD detection as part of routine periodontal care.},
}
@article {pmid41929953,
year = {2026},
author = {Oso, TA and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Ayelaagbe, OB and Talabi, OA and Adewole, PD and Anorue, CO and Ahmed, MM and Talabi, OT and Ogaya, JB and Lucero-Prisno, DE},
title = {Microbiome alterations in Alzheimer's disease: A systematic review of current evidence and global perspectives.},
journal = {Journal of Alzheimer's disease reports},
volume = {10},
number = {},
pages = {25424823261436287},
pmid = {41929953},
issn = {2542-4823},
abstract = {BACKGROUND: Growing evidence implicates the gut-brain axis in Alzheimer's disease (AD), with gut microbiome dysbiosis proposed to modulate neuroinflammation, amyloid pathology, and cognitive decline.<br><br>OBJECTIVE: To systematically synthesize human studies (2021-2025) profiling gut microbiomes in AD; identify consistent taxonomic and functional signatures; map geographic study distribution; and highlight translational gaps.<br><br>METHODS: A PRISMA-compliant systematic review of human studies using 16S rRNA, metagenomics, metatranscriptomics, or fecal microbiota transplantation (FMT)/probiotic designs was conducted. Two reviewers screened studies and assessed quality using Joanna Briggs Institute tools. Owing to heterogeneity, findings were narratively synthesized across microbiome diversity, taxonomy, function, metabolism, oral-brain links, causality, interventions, and predictive analyses.<br><br>RESULTS: Thirty-seven studies, mainly from Asia with some from Europe, North America, and Africa, revealed consistent gut dysbiosis in AD. Findings show reduced alpha-diversity, loss of short-chain fatty acid-producing bacteria (e.g., Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory taxa (Escherichia/Shigella, Proteobacteria). Functional analyses indicate reduced butyrate synthesis, disrupted lipid and tryptophan-kynurenine metabolism, and links with apolipoprotein epsilon (&#x3b5;4) gene and cognition. Limited causal evidence arises from Mendelian randomization and small FMT trials, with randomized, longitudinal confirmation still needed.<br><br>CONCLUSIONS: Current evidence suggests a biologically plausible association between gut microbiota and AD pathogenesis, positioning microbiome-derived biomarkers and interventions as promising but still exploratory avenues. Harmonized, longitudinal, multi-omic, and geographically inclusive studies are urgently needed to clarify causal mechanisms and translate these correlational findings into validated diagnostics and therapeutics.},
}
@article {pmid41930197,
year = {2026},
author = {Wu, J and Jiang, C},
title = {The authors respond to feedback on Cancer Cell-Memory Macrophage Hybrid Theory for metastatic cancer cells.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1780597},
pmid = {41930197},
issn = {2234-943X},
abstract = {We have recently hypothesized that the hematogenous metastatic cancer cell of solid tumors is a hybrid between a primary cancer cell and a memory/trained macrophage (doi: 10.3389/fonc.2024.1412296). The hybrid cell respectively acquires mutator phenotype and overgrowth/hyperplasia property from the primary cancer cell and migratability/metastability from the memory/trained macrophage. We name this hypothesis Cancer Cell-Memory Macrophage Hybrid Theory. Since the publication of the article, a number of questions related to this Theory have been raised by colleagues in the oncology community, including intratumoral microbes and microbiomes/microbiotas, oncolytic viruses and bacteria, human papilloma virus vaccines, anti-cancer effects of γδ T-cells, and immune checkpoint inhibitors. The current article is prepared to address these issues. Additional to resolving questions like "Why metastatic cancer cells enter dormancy and can recur via stem-like self-renewal?", the Cancer Cell-Memory Macrophage Hybrid Theory distinguishes itself from other carcinogenesis and metastasis hypotheses/theories by offering answers to many puzzling clinical features including metastasis of seemingly malignant parasitic cells within the human body, intracellular microbes (including viruses, bacteria, fungi, and parasites) within cancer cells, paradoxal effects (recurrence vs. regression) of microbes on cancer, contradictory immune effects of human papilloma virus vaccines between young and adult/senior females, and immune context-dependent effects (stimulatory and inhibitory) of T-lymphocytes on cancer cells. The Theory also predicts that quantitatively and functionally dampening innate macrophages that have hybridized with cancer cells (i.e., cancer cell-memory macrophage hybrids), should be explored as a fundamental anti-cancer strategy. The Theory further forecasts how to prepare an organotropic/tumoritropic Coley's toxin-like anti-cancer microbe, which could potentially circumvent direct injection of microbial preparations into a tumor. A testable experiment that uses zebrafish larva models can potentially either validate or falsify the Theory.},
}
@article {pmid41930211,
year = {2026},
author = {Blagov, AV and Sazonova, MD and Ryzhkova, AI and Karagodin, VP and Popov, MA and Budnikov, EY and Ravani, AL and Orekhov, AN and Sazonova, MA and Arkhipenko, YV},
title = {Analysis of the use of monoclonal antibodies in the treatment of Crohn's disease.},
journal = {Antibody therapeutics},
volume = {9},
number = {2},
pages = {101-118},
pmid = {41930211},
issn = {2516-4236},
abstract = {Crohn's disease (CD) is a chronic inflammatory bowel disease with increasing global prevalence, significantly impacting patients' quality of life and healthcare costs. The introduction of monoclonal antibodies has revolutionized CD management, offering targeted therapy against specific inflammatory pathways. This review systematically analyzes the current state of monoclonal antibody therapy, including anti-TNF-α agents (infliximab, adalimumab, certolizumab pegol), anti-integrin antibodies (vedolizumab), and anti-cytokine therapies (ustekinumab, risankizumab). Despite remarkable therapeutic advances, significant limitations persist, including primary non-response (20%-40%), secondary loss of response (13%-20% annually), immunogenicity, safety concerns, and substantial economic burden. We propose evidence-based strategies to address these challenges, including therapeutic drug monitoring, combination therapy, and personalized medicine approaches. Furthermore, we identify promising novel therapeutic targets such as IL-36, IL-17C, SMAD7, TL1A, complement components, and microbiome-related factors. Targeting two or more specific targets simultaneously appears to be a promising direction of research for the development of bi- and polyspecific monoclonal antibodies capable of interfering with multiple pathological pathways in CD. The integration of advanced antibody engineering, personalized medicine, and innovative delivery systems represents the future direction for overcoming current limitations. Achieving sustained remission for all patients through safe, effective, and accessible therapeutic interventions remains the ultimate goal in CD management.},
}
@article {pmid41930263,
year = {2025},
author = {Du, YC and Wang, D and Song, YQ and Zheng, QS and Wang, L},
title = {Arbuscular mycorrhizal fungi regulate the peanut rhizosphere microbiome to alleviate salinity stress and enhance yield.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1739241},
pmid = {41930263},
issn = {1664-302X},
abstract = {Salt stress threatens peanut yield by impairing physiological performance and disrupting rhizosphere microbial community stability. To investigate how arbuscular mycorrhizal fungi (AMF) mediate plant-microbe interactions under salt stress, researchers conducted a controlled pot experiment with four treatments: non-salt control (CK), AMF inoculation (A), salt stress (S; 100 mM sodium chloride), and combined AMF inoculation under salt stress (SA), with five biological replicates in each group. Plant growth traits, yield, and rhizosphere bacterial community were assessed at different peanut growth stages. AMF inoculation significantly increased peanut biomass, chlorophyll content, and yield, both under salt and non-salt stress conditions. Salt stress significantly reduced bacterial richness and community evenness, while AMF partially restored α-diversity and reshaped bacterial community composition. Functional predictions indicated that AMF enriched nitrogen cycling pathways such as nitrate reduction and nitrogen fixation. Furthermore, AMF promoted a more complex and stable bacterial community under salt stress, characterized by enhanced synergistic effects among key taxa, including Actinobacteria, Firmicutes, and Proteobacteria. Overall, AMF inoculation enhanced plant performance and rhizosphere bacterial resistance, highlighting its potential as an effective ecological strategy for improving peanut yield in saline-alkali agricultural ecosystems.},
}
@article {pmid41930266,
year = {2026},
author = {Marter, P and Brinkmann, H and Freese, HM and Ringel, V and Bunk, B and Jarek, M and Koblížek, M and Wagner-Döbler, I and Petersen, J},
title = {The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag041},
pmid = {41930266},
issn = {2730-6151},
abstract = {Intertidal biological mats are highly dynamic ecosystems typically dominated by filamentous cyanobacteria of the genus Coleofasciculus. These primary producers play important roles in primary production, biogeochemical cycling, and coastal protection. 16S rRNA gene profiling of non-axenic cultures has recently revealed an astonishing wealth of associated bacteria. We analyzed the microbiomes of 14 non-axenic Coleofasciculus cultures from nine globally distributed marine sampling sites, representing seven distinct phylogenomic lineages. Metagenome sequencing and binning resulted in 320 metagenome-assembled genomes (MAGs) representing a broad spectrum of "uncultivated" bacterial diversity mostly belonging to Pseudomonadota, Bacteroidota and Planctomycetota. Marinovum algicola, and Roseitalea porphyridii were found in 12 of the microbiomes studied, making them the most common housemates. The complex microbiome of Coleofasciculus sp. WW12 contained seven Planctomycetota MAGs from so far undescribed species, representing inter alia a new family in the order Phycisphaerales and an MAG from a deeply branching sister lineage of all cultivated planctomycetes. The discovery of 36 proteobacterial MAGs with photosynthesis gene clusters (PGCs) and 32 MAGs with proteorhodopsin or xanthorhodopsin operons documented the coexistence with many photoheterotrophic bacteria, indicating that the cyanosphere is a hotspot of phototrophic life. The presence of a PGC-containing Myxococcales MAG (Candidatus Photomyxococcus marinus) is of special interest because it paves the way to investigate photosynthesis in Deltaproteobacteria. In a Mediterranean Coleofasciculus culture, three alphaproteobacterial MAGs were found that have both a xanthorhodopsin operon and the PGC, suggesting that dual phototrophy is not restricted to alpine lakes or glaciers, and can also be found in marine habitats.},
}
@article {pmid41930333,
year = {2026},
author = {Tan, H and Ding, Y and Gu, Z and Wang, X and Wang, J and Wei, T and Zhang, X and Pan, L and Shi, Y and Chang, S and Guo, C and Weng, J and Zheng, X and Yue, T},
title = {Microbiome-Based Clustering Identifies Glycemic Control-Related Subtypes in Youth With Recent-Onset Type 1 Diabetes.},
journal = {MedComm},
volume = {7},
number = {4},
pages = {e70705},
pmid = {41930333},
issn = {2688-2663},
abstract = {Type 1 diabetes (T1D) in children exhibits substantial heterogeneity in glycemic control, yet the biological mechanisms underlying this variation remain unclear. We aimed to explore endotype heterogeneity in youth with recent-onset T1D using unsupervised clustering based on multi-omics data, and to identify associated molecular signatures and underlying mechanisms. In a discovery cohort of 69 children and adolescents with recent-onset T1D, unsupervised clustering of fecal metagenomic profiles revealed two robust subgroups distinguished by hemoglobin A1c (HbA1c) levels. The High-HbA1c group was enriched in Bacteroidota, while the Low-HbA1c group was enriched in Firmicutes and certain Bacteroides species (Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides nordii, and Bacteroides cellulosilyticus). Metabolomics revealed significant enrichment of tryptophan-derived metabolites in the Low-HbA1c group. Bacteroides species signatures are positively correlated with tryptophan metabolite skatole. In an independent validation cohort, Bacteroides signatures discriminated individuals with good versus poor glycemic control (AUC = 0.854). Similar microbial patterns were observed in healthy children stratified by glycemic risk, indicating broader relevance of these signatures. Together, microbiome-based clustering identified glycemic control-related subtypes in T1D youth and suggested a potential role of Bacteroides and skatole in glycemic control. Mechanistic studies are warranted to confirm its role as a glycemic control-related endotype with distinct pathophysiology.},
}
@article {pmid41930403,
year = {2026},
author = {Ai, Y and Zhu, T and Gan, J},
title = {Parental autoimmune diseases and offspring's allergic disease: A systematic review and meta-analysis.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {37},
number = {4},
pages = {e70335},
pmid = {41930403},
issn = {1399-3038},
mesh = {Humans ; *Autoimmune Diseases/epidemiology ; Female ; *Hypersensitivity/epidemiology ; Asthma/epidemiology ; *Parents ; Male ; Child ; Rhinitis, Allergic/epidemiology ; },
abstract = {Epidemiological studies have reported an increased risk of allergic diseases in children born to parents with autoimmune diseases (AIDs); however, the mechanisms underlying this association remain unclear. We conducted a systematic review and meta-analysis to explore the relationship between parental AIDs and allergic diseases in offspring. EMBASE, Web of Science, and PubMed databases were searched for articles published up to December 1, 2025. AIDs in both mothers and fathers were included. Allergic outcomes included asthma, eczema, and allergic rhinitis. A random-effects model was used to synthesize the data. Twelve studies were included in the final analysis, and the methodological quality ranged from moderate to high. Maternal AIDs (of any type) were associated with an increased risk of asthma (odds ratio (OR) 1.25, 95% confidence interval (CI): 1.09-1.43), eczema (OR 1.30, 95% CI: 1.13-1.50), and allergic rhinitis (OR 1.04, 95% CI: 1.02-1.07) in offspring. Paternal AIDs were also associated with a higher risk of asthma (OR 1.16, 95% CI: 1.06-1.27) and eczema (OR 1.13, 95% CI: 1.02-1.26) in offspring. This systematic review and meta-analysis demonstrate that parental AIDs are associated with an increased risk of asthma and eczema in children. However, the available evidence is limited by potential bias in case ascertainment and inadequate adjustment for confounding factors. Larger high-quality studies are needed to confirm these findings and to elucidate the underlying genetic and microbiome-related mechanisms. Such evidence may facilitate early identification and targeted prevention or management of allergic diseases in children of parents with AIDs.},
}
@article {pmid41930490,
year = {2026},
author = {Herrera, MJ and Khanna, A and Jones, JA and Betancur-R, R and Rohner, PT},
title = {Diet Outweighs Vertical Transmission in Shaping Dung Beetle Larval Gut Microbiomes.},
journal = {Molecular ecology},
volume = {35},
number = {7},
pages = {e70336},
pmid = {41930490},
issn = {1365-294X},
support = {//University of California, San Diego/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Coleoptera/microbiology/growth &amp; development ; Larva/microbiology ; *Diet ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Cattle ; },
abstract = {The microbiome is central to host development and adaptation, yet the balance between vertical and environmental acquisition, and how hosts shape surrounding microbial communities, remains poorly understood. Dung beetles rely on microbial symbionts to extract nutrients from vertebrate dung, with part of their microbiome vertically inherited via a maternal faecal pellet. However, the relative importance of vertical versus horizontal transmission is unclear. We examined this in the gazelle dung beetle (Digitonthophagus gazella), rearing larvae on brood balls made of dung from grass-(high-quality), hay-(low-quality) or silage-fed (a novel fermentable energy-rich diet) cattle, with or without maternal microbes. We integrated measures of gut morphology with 16S rRNA amplicon sequencing to assess host development and the gut microbiome. Diet significantly influenced overall size, hindgut area, and microbiome composition. Silage-dung fed larvae had more even and taxonomically rich microbiomes, with higher microbial diversity in individuals reared with maternal microbes. Diet explained ~26% of the variation in microbial composition, while the vertical transmission of microbes only explained 3%. Vertical transmission only slightly increases microbial species richness and relative hindgut area but did not influence overall microbial diversity. The larval brood ball contributed 40%-50% of the hindgut microbiome, while maternal microbes contributed < 0.05%. These findings demonstrate that horizontal acquisition through diet is the dominant force shaping larval gut microbiomes, while vertical inheritance plays a minor but detectable role in enhancing richness and gut development. More broadly, this work reinforces the importance of examining host-microbiome-environment interactions in ecological and evolutionary contexts.},
}
@article {pmid41930642,
year = {2026},
author = {Xu, S and Guo, G and Gao, J and Fang, Z and Chai, L and Gao, Y and Liu, J and Wang, J and Siqinbateer, and Zhang, L},
title = {Systematic Identification and Characterization of Causal Risk Genes Implicated in Colorectal Cancer by Integrating GWAS, eQTL, and mQTL Data.},
journal = {Current drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113894501444884260130225445},
pmid = {41930642},
issn = {1873-5592},
abstract = {INTRODUCTION: Knowledge of the mechanisms through which common single-nucleotide polymorphisms (SNPs) modulate colorectal cancer (CRC) susceptibility is central to elucidating the molecular basis of this disease. Genome-wide association studies (GWAS) reveal noncoding SNPs influencing CRC susceptibility, yet their functional mechanisms, particularly through gene expression dysregulation, DNA methylation alterations, and interactions with gut microbiota, remain uncharacterized. Through integrative analysis, systematically exploring the effects of genetic variations on gene expression heterogeneity, DNA methylation, and gut microbiome is expected to yield potential biomarkers for early diagnosis and intervention of CRC.<br><br>METHODS: An integrative framework is developed to prioritize causal risk genes at CRC-associated GWAS loci, applying the SMR&amp;HEIDI (Summary-data-based Mendelian randomization and heterogeneity in dependent instruments) and TSMR (Two-sample Mendelian Randomisation) methods. The findings were validated via gene expression and TF binding affinity.<br><br>RESULTS: 10 tissue-specific gene-SNP pairs, 3 blood eQTL-gene pairs, 26 gene-CpG-SNP regulatory modules, and 39 microbiota-associated gene-SNP pairs are identified. A few potential regulatory influences on CRC development associated with genes and variants, such as POU5F1B and rs10797801, were identified. Moreover, the genetic variants disrupted TF binding affinity while only a few promoted the binding of transcription factors (TFs).<br><br>DISCUSSION: The data integration enabled us to prioritize genes according to different regulatory mechanisms, such as gene expression and DNA methylation, and bridge the gap between statistical associations and biological functionality.<br><br>CONCLUSION: Multi-omics integration reveals some causal risk genes and variants implicated in CRC. These findings offer novel insight into the molecular mechanisms underlying CRC susceptibility and provide valuable clues for diagnosis and therapeutic intervention strategies.},
}
@article {pmid41930694,
year = {2026},
author = {Yuhan, W and Zhiru, C and Yu, D and Ruiqing, Z and Guangtao, P and Jie, X},
title = {Research Progress on the Synergistic Role of Gut Microbiota and Exosomal miRNAs in the Treatment of Androgenetic Alopecia.},
journal = {Current topics in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115680266424195251211072643},
pmid = {41930694},
issn = {1873-4294},
abstract = {INTRODUCTION: Androgenetic alopecia (AGA), a widespread condition marked by the gradual shrinkage of hair follicles, involves complex pathogenic mechanisms. Recently, a growing body of research has begun to uncover the influence of gut microbial communities and exosomederived microRNAs (miRNAs) in hair follicle regulation. Although current findings remain preliminary, they point toward a potential interplay between intestinal microbiota and exosomal signaling pathways, which may offer novel therapeutic avenues. This review seeks to dissect the biological contributions of gut microbiota and exosomal miRNAs to the onset and progression of AGA, aiming to inform future clinical approaches through an integrative perspective.<br><br>METHODS: We performed a comprehensive literature search (2018-2025) in PubMed, Web of Science, and CNKI. Studies were selected based on predefined criteria focusing on gut microbiota, exosomal miRNAs, and their roles in AGA pathogenesis.<br><br>RESULTS: Gut microbiota contribute to hair follicle health by modulating host immune responses, metabolic pathways, and the skin microbiome, thereby enhancing follicular stem cell activity. Exosomes, as key mediators of intercellular communication, transport miRNAs that play essential roles in regulating the hair growth cycle. These miRNAs can counteract follicular miniaturization by targeting specific suppressor molecules.<br><br>DISCUSSION: The gut microbiota may influence the composition and functional properties of exosomes, thereby exerting indirect regulatory effects on hair follicle dynamics. These findings provide new insights into potential therapeutic strategies for AGA.<br><br>CONCLUSION: Gut microbiota and exosomal miRNAs may synergistically influence the progression of AGA through interconnected metabolic, immune, and microbial skin axes. Targeted modulation of the "microbiota-miRNA axis" could represent a novel, multidimensional approach for AGA treatment. Nevertheless, the precise molecular crosstalk and signaling cascades underlying these phenomena remain largely unresolved, warranting more targeted experimental investigations.},
}
@article {pmid41930951,
year = {2026},
author = {Everett, BA and Prindle, A},
title = {AexB is an aromatic amino acid exporter that functions as a metabolic safety valve.},
journal = {mBio},
volume = {},
number = {},
pages = {e0023126},
doi = {10.1128/mbio.00231-26},
pmid = {41930951},
issn = {2150-7511},
abstract = {UNLABELLED: Aromatic amino acids-tryptophan, tyrosine, phenylalanine, and histidine-are essential for bacterial growth and are among the most energetically expensive metabolites to synthesize. Despite this cost, it has been recently shown that bacteria possess exporters for these amino acids. Here, we identify aexB (formerly yvjA) as a gene encoding a novel aromatic amino acid exporter in Bacillus subtilis. Using a transposon-based screen, we found that aexB overexpression confers resistance to the toxic tryptophan analog 5-fluorotryptophan. Additional analog screens revealed that AexB also promotes tolerance to toxic derivatives of tyrosine, phenylalanine, and histidine but not non-aromatic amino acids. LC-MS analysis showed that AexB specifically exports aromatic amino acids, and co-culture assays confirmed that overexpression of aexB can support the growth of aromatic amino acid auxotrophs. Furthermore, overexpression of aexB impaired growth when intracellular tryptophan was limiting. On the other hand, deletion of aexB exacerbated growth defects under excess tryptophan conditions, likely due to feedback inhibition of aromatic amino acid synthesis pathways. Our findings reveal that AexB is an aromatic amino acid exporter that functions as a metabolic safety valve.<br><br>IMPORTANCE: Identification and characterization of amino acid exporters is a broadly relevant topic. Amino acid synthesis is energetically costly, and thus functional relevance for their export is unintuitive. Identification of the molecular components that allow export may offer new engineering opportunities to improve biomanufacturing and metabolic engineering. Characterization of these exporters may also provide a more complete understanding of the human microbiome where amino acids, especially tryptophan, have been established as nodes of crosstalk between host and microbiota.},
}
@article {pmid41930957,
year = {2026},
author = {Benucci, GMN and Garcia-Barreda, S and Sanchez, S and Marco, P and De Miguel, AM and Le Tacon, F and Marozzi, G and Baciarelli Failini, L and Eslick, H and Elliott, TF and Deveau, A and Murat, C and Donnini, D and Bonito, G},
title = {Mycorrhizal competition release and microbial dynamics in native and non-native Tuber melanosporum habitats.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0022526},
doi = {10.1128/aem.00225-26},
pmid = {41930957},
issn = {1098-5336},
abstract = {Truffles in the genus Tuber (Pezizales) are among the few ectomycorrhizal taxa successfully cultivated worldwide. Australia has recently become one of the top producers of Tuber melanosporum, a high-valued black truffle native to Europe. Truffle co-introductions in the Southern Hemisphere with their Northern Hemisphere plant symbionts are hypothesized to benefit from reduced ectomycorrhizal competition and natural enemies. In this study, we tested whether T. melanosporum in Australia experiences competition release by sampling soils and truffles across France, Spain, Italy, and Australia. Fungal and prokaryotic communities in truffle plantations were assessed in native (European) and non-native (Australian) habitats through ITS and 16S rDNA amplicon sequencing from soil and truffles. Community composition was primarily structured by site of origin and secondarily by presence of brûlé, vegetation-free area induced by truffle production of plant-growth inhibiting compounds, with significant interactions indicating site-dependent brûlé effects. European soils showed higher fungal richness outside the brûlé, with higher evenness overall and for ectomycorrhizal fungi only outside brûlé. T. melanosporum showed higher abundance in Australia, with significant differences restricted to outside the brûlé. Overall, ectomycorrhizal fungi in European soils had more than four times the taxa and higher diversity compared to Australian soils. Among the main competitors, Tomentella, Inocybe, and Trichophaea co-dominated in Europe, versus Scleroderma, Hebeloma, and Tarzetta in Australia. Despite differences in soil microbiomes, bacterial communities within T. melanosporum truffle ascocarps were strikingly similar across sites and continents and were dominated by Bradyrhizobium. Despite high site-level variation, our results support the competition release hypothesis, with reduced enemies benefiting T. melanosporum colonization outside the brûlé in Australia.IMPORTANCEThis study provides the first cross-hemisphere analysis of the truffle microbiome, comparing native and non-native soils and truffles from Europe and Australia. We demonstrate that the remarkable success of Tuber melanosporum cultivation in Australia is compatible with ecological release from competitors, which favors its development outside the brûlé. At the same time, we reveal striking cross-hemispheric similarities in truffle-associated bacterial communities, consistently dominated by Bradyrhizobium. These findings highlight both the novelty and transcontinental relevance of our work, offering new perspectives on fungal ecology and truffle cultivation.},
}
@article {pmid41927455,
year = {2026},
author = {Seo, JI and Koh, A and Lim, S and Yoo, HH},
title = {The 3M roles of the gut microbiome in pharmacotherapy for diabetes: mediator, modifier, and marker.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2025.12.006},
pmid = {41927455},
issn = {1879-3061},
abstract = {The rising global prevalence of type 2 diabetes mellitus (T2DM) presents major challenges to healthcare systems; thus, more effective treatment strategies are urgently needed. In this context, the growing recognition of the gut microbiome's role in T2DM pharmacotherapy has shifted attention toward integrating microbiome-derived mechanisms to optimize drug response. This review proposes a structured '3M' framework that classifies the gut microbiome's roles in T2DM pharmacotherapy into three translational categories: mediator of drug action, modifier of therapeutic response, and marker for predicting efficacy or intolerance, based on recent clinical and mechanistic insights. Together, these insights support a translational framework that may guide the integration of microbiome-informed strategies into future T2DM pharmacotherapy.},
}
@article {pmid41927536,
year = {2026},
author = {Dong, Y and Wang, M and Zhou, X and Wang, P and Yan, K and Wang, S and Zhong, JC and Li, H and Zhao, L and Li, B and Li, J},
title = {Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations.},
journal = {Nutrition &amp; diabetes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41387-026-00418-w},
pmid = {41927536},
issn = {2044-4052},
abstract = {BACKGROUND: Several studies have investigated the association between the gut microbiota and type 2 diabetes mellitus (T2D) in various populations. Nonetheless, noises specific to individual cohorts might distort the microbial dysbiosis characteristics and result in inconsistent findings across studies. Thus, we aimed to identify the universal features of perturbed gut microbiota across diverse populations.<br><br>METHODS: A total of 433 fecal shotgun metagenomic sequences were analyzed to profile and compare the gut microbiome shifts between patients with T2D and healthy controls from cohorts in Europe and Asia.<br><br>RESULTS: Based on cross-cohort integrative analysis, patients with T2D showed significantly higher microbial alpha diversity, and distinctive microbial structures compared to healthy individuals. By excluding bacteria exhibiting divergent directional changes, consistent characteristics with ten T2D-enriched bacteria, such as Clostridium bolteae and Clostridium citroniae and eight T2D-depleted bacteria, including Streptococcus thermophiles and Haemophilus parainfluenzae were revealed across populations. Particularly, these reliable bacterial markers, which were robust against demographic variation, distinguished patients with T2D from healthy controls with high accuracy (AUCs&#x2009;>&#x2009;0.8) in both European and Asian cohorts. Correlation analysis demonstrated that T2D-enriched and T2D-depleted bacteria, respectively, formed their own mutualistic networks that were negatively linked to each other. Moreover, T2D-enriched bacteria were dramatically positively associated with fasting blood glucose and glycated hemoglobin. Functionally, 10 KEGG pathways with consistent directional changes across European, Asian, and combined cohorts were identified. Specifically, the Nucleotide excision repair pathway was markedly downregulated in patients with T2D, while the AGE-RAGE signaling pathway in diabetic complications was consistently enriched in patients with T2D across cohorts.<br><br>CONCLUSIONS: Our results elucidated reproducible profiles of gut commensal bacteria in patients with T2D, which are robust across populations. Identifying the universal gut microbiome signatures of T2D in heterogeneous cohorts offers valuable insights for understanding disease development and is crucial for prevention and diagnosis across diverse populations.},
}
@article {pmid41927585,
year = {2026},
author = {Song, J and Tang, S and Guo, Y and Hong, C and Song, T},
title = {The gut-heart dialogue: an epigenetic perspective on myocardial infarction.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00974-0},
pmid = {41927585},
issn = {2055-5008},
support = {No. 20250602055RC//Jilin Province Science and Technology Department/ ; },
abstract = {Myocardial infarction (MI) remains a leading cause of global mortality, with adverse cardiac remodeling and heart failure presenting persistent metabolic and clinical challenges. While traditional pharmacotherapies have improved outcomes, there is an urgent need to elucidate how lifestyle and nutritional factors influence disease progression. Emerging evidence underscores the critical interplay between natural bioactive compounds (e.g., dietary fibers, polyphenols), the gut microbiota, and host metabolic regulation. This review systematically clarifies the "gut microbiota-epigenetic axis" as a pivotal mechanism linking nature-derived bioactives to cardiac repair. We delineate how the gut microbiota transforms specific bioactives into functional metabolites, such as short-chain fatty acids (SCFAs) from fibers and urolithin A from ellagitannins, which act as potent epigenetic modulators. These microbial metabolites remodel the epigenetic landscape of the host heart via histone modification and DNA methylation, thereby regulating gene networks governing inflammation, energy metabolism, and fibrosis. Synthesizing evidence from in vivo animal studies and clinical observations, we explore therapeutic strategies centered on natural bioactives, including high-fiber dietary interventions and polyphenol supplementation, alongside probiotics and postbiotics. By integrating the metabolic potential of the gut microbiome with epigenetic regulation, this review offers novel insights into how natural bioactive compounds can be leveraged for precision prevention and therapeutic strategies in myocardial infarction.},
}
@article {pmid41927589,
year = {2026},
author = {Jiang, P and Liang, Z and Kovacevic, V and Shi, J and Milicevic, N and Wang, F and Liu, L and Liu, Y and Jiang, Y and Han, M and Lin, X and Petronić, &#x10c; and Stanojevic, N and Wang, L and Wang, S and Cheng, H and Li, J and Chen, R and Zhang, Y and Li, Y and Li, J and Fang, X and Yue, Z and Xue, C and Yin, P and Chen, H},
title = {The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71145-0},
pmid = {41927589},
issn = {2041-1723},
abstract = {Microorganisms in extreme environments represent a promising source of novel metabolites, yet their global diversity and biosynthetic potential remain underexplored. Here, we reconstruct 78,213 bacterial and archaeal genomes from 2293 publicly available metagenomes and 3214 microbial isolates to establish a unified database, the Extreme Environment Microbiome Catalog (EEMC). The EEMC expands known global phylogenetic diversity, encompassing 32,715 representative species and nearly 4 billion non-redundant genes, 63.00% and 19.21% of which are previously unannotated, respectively. It also comprises 163,693 biosynthetic gene clusters, grouped into 64,733 gene cluster families, 58.68% of which are classified as novel, underscoring the functional diversity of microbial communities across various extreme habitats. We further develop protein large language models to predict genome-encoded candidate antimicrobial peptides (cAMPs) from the EEMC, identifying 3032 non-toxic candidates. Of 100 synthesized peptides, 84% demonstrate antibacterial activity, and all 50 tested cAMPs exhibit low cytotoxicity. Notably, six of the most potent cAMPs show significant efficacy against multidrug-resistant, Gram-negative pathogens in vitro, indicating their biomedical potential. Together, our study establishes the EEMC as a foundational resource for uncovering novel microbial lineages and biosynthetic capabilities, highlighting its substantial potential for drug discovery and laying the foundation for future advances in biotechnology and biomedicine.},
}
@article {pmid41927609,
year = {2026},
author = {Duffy, EP and Sterrett, JD and Hale, LH and Ward, JO and Saba, LM and Frank, DN and Bachtell, RK and Ehringer, MA},
title = {Oxycodone self-administration and genetic background exert community-specific effects in the gut microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41666-1},
pmid = {41927609},
issn = {2045-2322},
}
@article {pmid41927721,
year = {2026},
author = {Nakamaru, K and Ito, T and Shimogama, T and Shijimaya, T and Tahara, T and Yamazaki, J and Orino, A and Masuda, M and Nakayama, S and Ikeura, T and Naganuma, M},
title = {Distinct difference of pancreatic tissue-specific microbiome in autoimmune pancreatitis and pancreatic ductal adenocarcinoma.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44821-w},
pmid = {41927721},
issn = {2045-2322},
support = {22K16032//JSPS KAKENHI Grant-in-Aid for Young Scientists/ ; },
abstract = {Autoimmune pancreatitis (AIP) is a form of chronic pancreatitis that may be difficult to distinguish from pancreatic ductal adenocarcinoma (PDAC). Emerging evidence suggests the substantial involvement of gut microbiome dysbiosis in various disorders, including pancreatic diseases. This study investigates the differences in pancreatic tissue-specific microbiomes between AIP and PDAC. Pancreatic tissues were obtained from patients with type 1 AIP (n = 17) or PDAC (n = 24) via ultrasound-guided tissue acquisition and subjected to 16S rRNA sequencing. The sequences were used to determine the bacterial alpha diversity and characterize the microbiome structures related to different sample groups. The pancreatic microbiome in PDAC exhibited increased bacterial alpha diversity compared to that in AIP. The abundances of 16 bacteria were significantly different between the AIP and PDAC groups, and most of them (15/16) were increased in PDAC relative to that in AIP. The bacterial index calculated using these bacteria had a favorable discriminative ability for these different groups, with an area under the curve value of 0.91. Functional analysis demonstrated that the pentose phosphate pathway, gondoate biosynthesis, and several pathways related to adenosine biosynthesis were positively associated with the bacterial index. The findings from this preliminary study indicate that pancreatic microbiome, as a new diagnostic alternative, may potentially help with the differential diagnosis of AIP and PDAC.},
}
@article {pmid41927746,
year = {2026},
author = {Akanmu, AM and Hassen, A and van Marle-Köster, E and Adejoro, FA},
title = {Dietary plant extracts reduce methane emission and modulate rumen microbial functionality in Merino lambs.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46933-9},
pmid = {41927746},
issn = {2045-2322},
support = {SRUG2204254606//National Research Foundation/ ; },
abstract = {The formation of enteric methane from ruminants represents a significant loss of dietary energy that adversely affects growth and production while also contributing to the environmental footprint of livestock production through greenhouse gas accumulation. Phytogenic feed additives rich in bioactive compounds have been proposed as sustainable alternatives to synthetic additives for improving nutrient utilisation and reducing methane. This study evaluated the effects of Moringa oleifera, Jatropha curcas, and Aloe vera extracts on growth performance, nutrient digestibility, methane production, rumen fermentation in South African Mutton Merino lambs using an in vivo feeding trial while the microbial diversity and functionality was evaluated using shotgun metagenomic sequencing. Supplementation with Moringa and Jatropha improved dry matter and crude protein digestibility (P < 0.05). Methane emission decreased in all plant extract groups, with reductions of 17% (Jatropha), 9% (Moringa), and 12% (Aloe) relative to control (P < 0.05). Ammonia nitrogen concentrations were lower in supplemented groups, particularly Moringa and Aloe (P < 0.01), while volatile fatty acids and growth performance were unaffected. Metagenomic profiling revealed Bacteroidetes as the dominant phylum and showed enrichment of genes which may be associated with protein biosynthesis and carbohydrate metabolism in Moringa and Jatropha lambs, aligning with improved digestibility and reduced methane emissions. Dietary inclusion of M. oleifera, J. curcas, and A. vera extracts reduced methane emissions and improved dry matter and crude protein digestibility without compromising growth. These results suggest that these phytogenic extracts can serve as sustainable feed additives to improve efficiency and mitigate environmental impacts in ruminant production systems.},
}
@article {pmid41927935,
year = {2026},
author = {Gao, W and Wang, X and Shi, Y and Wu, G and Zhou, M and Lin, X},
title = {Retraction Note: Predictable regulation of gut microbiome in immunotherapeutic efficacy of gastric cancer.},
journal = {Genes and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41435-026-00397-z},
pmid = {41927935},
issn = {1476-5470},
}
@article {pmid41928235,
year = {2026},
author = {Arzu, JL and Fleury, ES and Cecil, KM and Chen, A and Lanphear, BP and Yolton, K and Buckley, JP and Braun, JM and Laue, HE},
title = {Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study.},
journal = {BMC medical genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12920-026-02359-w},
pmid = {41928235},
issn = {1755-8794},
}
@article {pmid41928236,
year = {2026},
author = {Gschwendtner, S and Kovacevic, D and Gaede, KI and Herzmann, C and Overmann, J and Schloter, M and Krauss-Etschmann, S},
title = {Longitudinal dynamics and site-specific recovery of the human respiratory microbiome following smoking cessation.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03644-z},
pmid = {41928236},
issn = {1465-993X},
}
@article {pmid41920180,
year = {2026},
author = {Thomas, CE and Loroña, NC and LaBrie, SD and Curtis, KR and Yin, H and Ma, N and Randolph, TW and Qu, C and Huyghe, JR and Thomas, S and Hsu, L and Koehne, AL and Nayemi, S and Ammar, H and Kahsai, OJ and Redwood, D and Li, CI and Li, L and Peters, U and Figueiredo, JC and Thomas, TK and Phipps, AI and Hullar, MAJ},
title = {The phylum Fusobacteriota is associated with CRC-specific mortality: Results from the Translational Research Program in Cancer Differences across Populations.},
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-25-1580},
pmid = {41920180},
issn = {1538-7755},
abstract = {BACKGROUND: The microbiome is an important component of the tumor microenvironment implicated in colorectal cancer (CRC). However, its relationship with CRC-specific mortality remains unclear.<br><br>METHODS: We included 581 participants with CRC (167 African American, 176 Alaska Native, 118 Hispanic, 120 non-Hispanic White) from the Translational Research Program in Cancer Differences across Populations (TRPCDP). We sequenced the V4 region of the 16S rRNA bacterial gene using DNA extracted from formalin-fixed paraffin embedded tumors. 204 participants died of CRC and 377 did not die of CRC. Participants who died of CRC were matched to participants who did not die of CRC during follow-up by age, sex, tumor site, tumor stage, year of diagnosis, and population group. Logistic regression estimated odds ratios (ORs) and 95% confidence intervals (CIs) for associations between bacterial presence with CRC-specific mortality, adjusting for matching factors and tissue macrodissection status.<br><br>RESULTS: Individuals who died from CRC were 1.71 times as likely to have bacteria from the Fusobacteriota phylum present in their tumors (OR=1.71, 95% CI: 1.19-2.47). Associations with Fusobacteriota were strongest among African American participants (OR=2.36, 95% CI: 1.14-4.99) compared to other populations, however this different was not statistically significant (OR range = 1.05-1.38, Pinteraction = 0.697). Candidate pathways of pyruvate fermentation to acetate and lactate II and peptidoglycan biosynthesis I were associated with higher odds of CRC death.<br><br>CONCLUSIONS: Fusobacteriota was significantly associated with CRC-specific mortality with noted differences across populations.<br><br>IMPACT: This finding highlights the tumor microbiome as a candidate for further investigation into CRC outcome disparities.},
}
@article {pmid41920710,
year = {2026},
author = {Wan, Y and Alessa, HB and Guasch-Ferré, M and Tobias, DK and Lee, KH and Manson, JE and Willett, WC and Sun, Q and Hu, FB},
title = {Intake of Fiber From Different Food Sources and Type 2 Diabetes Risk: An Integrated Analysis of Epidemiological and Multiomic Data.},
journal = {Diabetes care},
volume = {},
number = {},
pages = {},
doi = {10.2337/dc25-2957},
pmid = {41920710},
issn = {1935-5548},
support = {/NH/NIH HHS/United States ; //Novo Nordisk Foundation/ ; },
abstract = {OBJECTIVE: To examine the association between fiber from various food sources and type 2 diabetes (T2D) risk, as well as the molecular profiles involved.<br><br>RESEARCH DESIGN AND METHODS: Using data from three large prospective U.S. cohorts comprising 195,222 participants observed for up to 34 years, we evaluated the association between fiber from various food sources and T2D risk. We also assessed the association between fiber intake, plasma metabolic biomarkers, and a metabolomic profile indicative of T2D risk. Additionally, we examined gut microbial features related to fiber intake and the T2D metabolomic profile.<br><br>RESULTS: During follow-up, we documented 18,369 incident T2D cases. Higher intakes of total fiber (hazard ratio [HR] comparing extreme quintiles 0.88; 95% CI 0.82, 0.94), cereal fiber (HR 0.77; 95% CI 0.73, 0.82), and fruit fiber (HR 0.82; 95% CI 0.78, 0.87) were each associated with a lower T2D risk. Greater intakes of total fiber, cereal fiber, and fruit fiber, but not vegetable fiber, were linked to more favorable plasma profiles of insulinemic, lipid, and inflammatory biomarkers and a metabolomic profile indicative of a lower T2D risk. We also identified multiple gut microbial species, such as Faecalibacterium prausnitzii, Ruminococcus lactaris, and Gemmiger formicilis, along with relevant butyric acid-producing enzymes, all of which were associated with higher fruit fiber intake and a metabolomic profile indicating a lower likelihood of T2D development.<br><br>CONCLUSIONS: Higher intakes of total, cereal, and fruit fiber are associated with a lower risk of T2D and a more favorable metabolic profile, with the gut microbiome potentially contributing to the beneficial association of fruit fiber.},
}
@article {pmid41920740,
year = {2026},
author = {Mingolelli, G and Subedi, P and Bonitatibus, S and Johnson, JJ and Henke, M},
title = {Metabolism by ex vivo cultures of human stool increases the activity of coumarin, a widespread antioxidant from herbal supplements.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117199},
doi = {10.1016/j.celrep.2026.117199},
pmid = {41920740},
issn = {2211-1247},
abstract = {Host and microbiome metabolism of bioactive compounds can alter their efficacy. Herbal supplements contain many bioactive compounds, but their metabolism by gut microbes and the effects on efficacy remain poorly understood. To gain clarity, we investigate coumarin, an antioxidant in food, cosmetics, and supplements and a scaffold for diverse bioactive compounds. In this study, we characterize coumarin metabolism by the human gut microbiome, which produces 3,4-dihydrocoumarin and melilotic acid. We characterize this pathway in the culturable microbiota from 9 stool donors with liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics and microbiome profiling. We discover that 17 microbiome species metabolize coumarin and that the E. coli gene nemA is necessary for coumarin reduction. In antioxidant assays, melilotic acid is more potent than coumarin, suggesting that this pathway may impact bioactivity, with possible contributions to supplement efficacy. Further characterization may provide insights on the metabolic fate of coumarins and contributions of the microbiome to their efficacy.},
}
@article {pmid41920780,
year = {2026},
author = {Donovan, SM},
title = {Human Milk Oligosaccharides Support Coordinated Microbiome and Immune Development and Function in Infancy.},
journal = {Annals of nutrition &amp; metabolism},
volume = {},
number = {},
pages = {1-15},
doi = {10.1159/000549867},
pmid = {41920780},
issn = {1421-9697},
abstract = {BACKGROUND: Human milk contains functional ingredients that shape the microbiome and immune development of infants. Human milk oligosaccharides (HMOs) are among the largest and most diverse components of human milk. Their heterogeneity enables unique structure-function relationships that contribute to their physiological effects. This narrative review will focus on how HMOs directly and indirectly protect the infant from pathogens and educate the immune system.<br><br>SUMMARY: Preclinical research, observational studies, and intervention trials demonstrate that HMOs provide multilayer modulation of host defense and immune development. HMOs are soluble glycans that are acetylated, sialylated, or fucosylated, which mediate their interactions with viruses and bacteria to reduce infectivity. Additionally, HMOs enhance pathogen exclusion by promoting intestinal cell maturation, mucin production, and barrier function. Moreover, HMOs directly interact with immune cells through binding to carbohydrate recognition domains. HMOs promote the growth of beneficial bacteria, particularly Bifidobacterium longum subspecies infantis, which is also immunomodulatory. Lastly, HMOs are fermented to short-chain fatty acids, which lower the pH of the intestinal lumen, providing further antimicrobial defense.<br><br>KEY MESSAGES: Breastfed infants have a reduced risk of infectious disease compared to non-breastfed infants, attributable in part to the high concentration and structural diversity of HMOs. Clinical trials using formulas supplemented with synthetic human-identical milk oligosaccharides (HiMOs) have demonstrated benefits to adaptive and innate immunity, reduced infections, increased bifidobacteria, and reduced pathogenic bacteria. These benefits are amplified in formulas containing higher concentrations and greater varieties of HiMOs. However, the clinical benefit of routinely supplementing term infant formulae with HiMOs remains unsettled due to variability across existing clinical trials. Further research in healthy infants focused on short- and long-term immune outcomes is needed.},
}
@article {pmid41920852,
year = {2026},
author = {Kim, H and Kim, S and Kimbrel, JA and Morris, MM and Mayali, X and Buie, CR},
title = {Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1014102},
doi = {10.1371/journal.pcbi.1014102},
pmid = {41920852},
issn = {1553-7358},
abstract = {Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. In this study, we introduce a new MDS-based ordination method, "F-informed MDS," which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community's response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.},
}
@article {pmid41920977,
year = {2026},
author = {Flower, S and Gruvstad Melén, A and Seidler, K},
title = {Investigating the Link between the Intestinal Microbiome and Th17/Treg Dysregulation in Hashimoto's Thyroiditis, and the Therapeutic Potential of Vitamin D.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/27697061.2026.2644894},
pmid = {41920977},
issn = {2769-707X},
abstract = {Objective:Autoimmune disease (AD) has become a leading cause of illness in the twenty-first century, with autoimmune thyroid disease at the forefront of these conditions. Hashimoto's thyroiditis (HT) shares many features with other ADs, including associations with gastrointestinal symptoms linked to intestinal dysbiosis (ID). However, the pathogenesis of HT remains incompletely understood, particularly the role of specific T cell lymphocyte activity. The primary objective of this review was to investigate links between ID and HT pathogenesis, focusing on the relationship between a specific cluster of differentiation 4 (CD4) T cell subsets including T helper 17 (Th17) and regulatory T cells (Treg). A secondary aim was to explore whether vitamin D supplementation may serve as a viable intervention in managing HT, given existing research demonstrating links between Vitamin D status, HT pathogenesis and ID. Methods:A systematic literature search was conducted in PubMed using predefined inclusion/exclusion criteria across three tranches. A search of the review literature pertaining to thyroid autoimmunity, HT and the intestinal microbiome identified 21 papers for inclusion. A mechanistic literature search covering animal, in vitro and human studies on HT, autoimmunity, ID, intestinal microbiota, intestinal permeability (IP) and Th17 yielded 43 papers. A final search of human studies examining vitamin D status or supplementation in relation to ID, IP, Th17 and interleukin (IL)-17 identified 45 relevant papers. Accepted studies were critically appraised and synthesized in a narrative analysis.Results:Evidence across the included studies suggests an association between ID and pathogenesis of HT. Increased IP and alterations in Th17/Treg balance emerged as key contributing mechanisms. Vitamin D status was also associated with immune modulation, particularly involving Th17 activity, and was strongly linked to both ID and HT pathogenesis.Conclusions:ID may play a contributory role in HT pathogenesis through immune modulation involving CD4+ T cell subsets. Vitamin D supplementation demonstrates potential as an adjunctive strategy; however, further targeted human studies are required to clarify causality and therapeutic efficacy.},
}
@article {pmid41921305,
year = {2026},
author = {Teixidó Mulet, M and Veas Rodriguez, J and Terán, E and Piñol, M and Vilardell, F and Iglesias, M and Hierro, C and Calvo, M and Matias-Guiu, X and Salud, A and Tabernero, J and Montal, R},
title = {Biomarker-guided immunotherapy in gastric cancer: current insights and future perspectives.},
journal = {Cancer treatment reviews},
volume = {145},
number = {},
pages = {103124},
doi = {10.1016/j.ctrv.2026.103124},
pmid = {41921305},
issn = {1532-1967},
abstract = {Gastric and gastroesophageal junction adenocarcinoma (GC) is a biologically challenging malignancy associated with suboptimal clinical outcomes due to limited effective treatment options. The recent incorporation of immune checkpoint inhibitors (ICIs) into therapeutic algorithms has improved the clinical prospects of subsets of GC patients. However, responses to anti-PD-1/PD-L1 agents remain highly heterogeneous, with only some patients deriving long-term benefits. This variability highlights the importance of identifying optimal biomarkers to enhance patient selection, thereby enabling tailored immunotherapy strategies. Whereas microsatellite instability has demonstrated a potent capacity for predicting immunotherapy benefits in GC, other predictive biomarkers, such as PD-L1 expression, remain suboptimal. Advances in gene expression and epigenetic profiling, liquid biopsy approaches, gut microbiome characterization, and artificial intelligence-driven multimodal algorithms applied to multi-omics or digital pathology are key drivers for the comprehensive characterization of the GC tumour microenvironment (TME), which could be used for better treatment selection. Similarly, elucidating the complex tumour-immune interplay with these technologies will be crucial for the success of novel immunotherapeutic approaches under clinical development, by evaluating alternative immune pathways alone or in combination with current actionable targets of GC. The current review aims to give an overview of the current immunotherapeutic landscape in GC, evaluate standard-of-care and emerging biomarkers of immunotherapy response, and discuss the translational potential of incorporating multi-omic and AI-derived biomarkers into biomarker-enriched clinical decision-making frameworks.},
}
@article {pmid41921320,
year = {2026},
author = {Huang, DQ and Zhou, S and Jia, Y and Yan, Y and Lu, H},
title = {Deciphering pharmaceutical resistance in sulfur-driven autotrophic denitrification: an integrated multi-omics artificial intelligence-driven structural biology approach.},
journal = {Water research},
volume = {298},
number = {},
pages = {125834},
doi = {10.1016/j.watres.2026.125834},
pmid = {41921320},
issn = {1879-2448},
abstract = {Sulfur-driven autotrophic denitrification (SdAD) is a promising low-carbon technology for nitrogen removal; however, its stability and adaptive mechanisms under pharmaceutical stress remain poorly understood. In this study, ibuprofen (IBU) was used as a representative pharmaceutical to investigate the response of an SdAD system. Throughout the 210-day operational period, the system demonstrated exceptional functional robustness, maintaining high sulfide (97.46 ± 3.18%) and inorganic nitrogen (99.17 ± 4.34%) removal efficiencies across IBU concentrations ranging from environmentally relevant levels to elevated shock loads (100-2000 μg/L). Underpinning this macroscopic stability, community-level analyses revealed that instead of succumbing to inhibition, the SdAD microbiome actively reorganized its composition and topological structure to accommodate the selective pressure. This adaptation was characterized by enhanced microbial diversity and stress-induced network modularity (particularly at 100-500 μg/L), alongside strengthened cooperative interactions between sulfur-oxidizing bacteria and denitrifiers. To unravel the specific molecular drivers of this resilience, we integrated AlphaFold-based structural modeling with machine learning-coupled molecular docking. This enabled us to resolve the three-dimensional structure of sulfide: quinone oxidoreductase (SQR) and perform the first structure-function analysis of SQR within an SdAD context under pharmaceutical stress, revealing that arginine residues serve as key interaction hotspots for IBU binding. Consistent with this binding mechanism, multi-omics data further corroborated a systemic adjustment involving the coordinated regulation of sulfur oxidation genes and the transcriptional upregulation of arginine biosynthesis pathways. Overall, these findings shed light on how the SdAD community mitigates pharmaceutical toxicity through a multi-tiered strategy involving ecological network reorganization and metabolic compensation. Methodologically, this work highlights the value of integrating artificial intelligence-driven structural biology with multi-omics analyses to decode the mechanisms of contaminant resistance in biological wastewater treatment systems.},
}
@article {pmid41921321,
year = {2026},
author = {Sudarshan, AS and Konstantinidis, KT and Pinto, AJ},
title = {Gene-centric analysis of Raskinella chloraquaticus reveals a functionally conserved taxonomic group in global drinking water distribution systems.},
journal = {Water research},
volume = {298},
number = {},
pages = {125784},
doi = {10.1016/j.watres.2026.125784},
pmid = {41921321},
issn = {1879-2448},
abstract = {A recent metagenomic survey of drinking water systems revealed that a highly prevalent and dominant uncultured bacterial genus (Raskinella) was represented globally by a single species (Raskinella chloraquaticus). R. chloraquaticus comprises of two sub-species groups, Lineages 1 and 2, the former representing a globally prevalent genomovar. The objective of this study was to perform comparative analysis of the gene content of R. chloraquaticus to characterize the gene-level diversity and determine factors shaping the diversity of this species. Pangenome analysis revealed that R. chloraquaticus possesses a core set of genes that constitute a major portion (87.74%) of the known gene content of the genome. Furthermore, most of the gene diversity of R. chloraquaticus is associated with Lineage 2 organisms, which consists of at least four distinct genomovars. Lineage 1 organisms consist of a higher proportion of identical genes than would have been expected if changes primarily occurred through random mutations and thus is potentially indicative of recombination. In contrast, Lineage 2 organisms appear to have emerged through random mutations and display stronger geographic preference. These results indicate that homologous recombination and geographic isolation likely shape the genetic repertoire of R. chloraquaticus. Further, the high level of gene conservation in R. chloraquaticus may be reflective of highly selective environment in drinking water systems. Thus, R. chloraquaticus may represent a model organism to probe selective pressures shaping the drinking water microbiome.},
}
@article {pmid41921531,
year = {2026},
author = {Li, W and Lv, M and Cheng, M and Han, Y and Yu, H and Huang, Y and Meng, D and Xu, X and Sun, L and Lu, Z and Liu, QL},
title = {Feasibility of Low-Biomass Exhaled Breath Microbiome Sequencing Using a PDC-Sampler in Febrile and Healthy Individuals.},
journal = {Journal of breath research},
volume = {},
number = {},
pages = {},
doi = {10.1088/1752-7163/ae5a51},
pmid = {41921531},
issn = {1752-7163},
abstract = {Exhaled breath is a noninvasive and repeatable biological matrix offering new opportunities for respiratory microbiome analysis, yet its extremely low microbial biomass limits current high-throughput applications. Building on our previously developed phase-change drywall cyclone sampler (PDC-sampler), which integrates condensational growth with dry-wall cyclone separation, we established a validated workflow for efficient aerosol collection and multi-omics sequencing of exhaled breath. Using this platform, exhaled breath from 15 febrile patients and 6 healthy volunteers was analyzed via shotgun metagenomic and 16S rRNA sequencing to assess microbial composition, diversity, and functional features. The PDC-sampler significantly increased microbial DNA yield, enabling stable detection of bacterial taxa dominated by Pseudomonadota, Bacillota, Bacteroidota, and Actinomycetota. Functional annotations and diversity metrics revealed distinct microbial and metabolic patterns between individuals, confirming the platform's analytical sensitivity and biological representativeness. This work experimentally validates the feasibility of exhaled breath microbiome sequencing using the PDC-sampler, providing a practical and generalizable framework for noninvasive respiratory microecology studies and future diagnostic applications.},
}
@article {pmid41921618,
year = {2026},
author = {Khajanchi, BK and Grocholl, J and Alam, M and Hasan, NA and Wang, H and Hughes, S},
title = {Colonization of Salmonella Newport and Microbiome Analyses of Bulb Onions Grown in Artificially Contaminated Soil at Lab-Scale Under a Controlled Environment.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100769},
doi = {10.1016/j.jfp.2026.100769},
pmid = {41921618},
issn = {1944-9097},
abstract = {INTRODUCTION: Several multistate Salmonella outbreaks in the United States have been linked to bulb onions. In this study we investigated the extent of Salmonella colonization on bulb onions grown in contaminated soil.<br><br>PURPOSE: The study evaluated the colonization potential and microbial community dynamics of Salmonella Newport on bulb onions grown in artificially spiked soil.<br><br>METHODS: Red bulb onions were grown from seed, and resultant seedlings were transplanted into pots containing soil. Soil surface was spiked with S. Newport at transplant and again two weeks before harvest. Three inoculum levels [10[2] (low), 10[4](medium), 10[6] (high) CFU per 200 g soil] of Salmonella Newport were investigated in triplicate, with three unspiked controls. Three independent trials were conducted using two different soil types. Microbiome analyses were performed on the bulb onions and soil from the high inoculum group in Trial 1 (field topsoil) at 0 h, 1 h, and 24 h pre-enrichment. Results Salmonella was detected in one high-inoculum bulb onion in Trial 1 (field topsoil) and in all high-inoculum onions in Trials 2 and 3 (Miracle-Gro soil). Among the medium inoculum groups, all onions in Trial 2, one in Trial 3, and none in Trial 1 were positive for Salmonella. No onions in the low inoculum group were Salmonella-positive. Microbiome analysis of control and Salmonella-spiked high inoculum field topsoil samples and associated bulb onions revealed that bacterial community composition remained stable at 0 h and 1 h pre-enrichment but underwent notable shifts after 24 h. Bacterial diversity decreased following 24 h of pre-enrichment, with increased dominance of Proteobacteria and Firmicutes. However, Salmonella spiking had minimal or no effect on microbiome dynamics. Significance These findings provide insights into the colonization capability of Salmonella Newport on bulb onions in different soil types and associated microbial community shifts after 24h pre-enrichment.},
}
@article {pmid41921761,
year = {2026},
author = {Nee, GW and Agrawal, K and Dalan, R and Kasahara, K and Xiang Darren, LY and Ali, Y and Wong, S},
title = {The oral-gut microbiome axis in diabetes mellitus: a systematic review and emerging clinical perspectives.},
journal = {Diabetes research and clinical practice},
volume = {235},
number = {},
pages = {113232},
doi = {10.1016/j.diabres.2026.113232},
pmid = {41921761},
issn = {1872-8227},
abstract = {Emerging evidence suggests that diabetes mellitus (DM) is not only a metabolic disorder but also a mucosal disease shaped by microbial interactions across body niches. This review synthesizes current evidence on the oral-gut microbiome axis in DM, focusing on microbial transmission, functional overlap, and clinical relevance. A systematic search of six databases identified studies profiling paired oral and gut microbiomes in individuals with diabetes. Across included studies, consistent findings demonstrate concurrent dysbiosis in both niches. Notably, oral-associated taxa such as Streptococcus, Prevotella, Fusobacterium, and Porphyromonas were detected in the gut, suggesting ectopic colonization and inter-niche microbial transmission. Functional analyses revealed shared disruptions in key metabolic pathways, including short-chain fatty acid production and glycine betaine metabolism, with downstream effects on inflammation and insulin resistance. These microbial alterations correlated with established clinical markers such as HbA1c, fasting glucose, and inflammatory indices. Emerging machine-learning models integrating oral and gut microbiota demonstrated promising diagnostic performance (AUC > 0.83). Collectively, these findings support a potential bidirectional oral-gut axis associated with metabolic dysregulation in DM. Despite limitations including cross-sectional design and heterogeneity, this axis represents a novel target for biomarker development and therapeutic intervention. Future longitudinal and interventional studies are required to determine causal relationships and clinical utility.},
}
@article {pmid41921818,
year = {2026},
author = {Ziade, I and McDermott, MM and O'Riordan, KJ and Cryan, JF and Schneider, E},
title = {The microbiome and eating disorders: a new framework at the interface of interoception and reward.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.03.050},
pmid = {41921818},
issn = {1873-7544},
abstract = {Accumulating evidence suggests that the gut microbiome can modulate brain and behaviour including those relevant to eating behaviours and reward signalling through the dynamic communication pathways of the microbiota-gut-brain-axis. Emerging evidence links altered gut microbial composition to disordered eating patterns, implicating the gut microbiome as a possible mechanism underlying eating disorders, as well as a potential therapeutic target for these conditions. In this review, we synthesise evidence across preclinical and clinical research to propose an integrated framework wherein the gut microbiome, interoception and reward circuits may interact to shape disordered eating behaviours. We firstly explore how microbial signals modulate homeostatic and reward feeding systems via vagal afferents, neurotransmitter modulation and immune-neural pathways, and how these signals converge in brain regions implicated in reward systems and interoception. Particular attention is given to how these interactions may occur in under- and over-eating phenotypes of disordered eating. The therapeutic potential of microbiota-targeted interventions to modulate eating disorder-induced dysregulations in interoception and reward signalling is discussed. Combined evidence suggests a paradigm shift in the etiological considerations of eating disorders is warranted taking into account dysregulations of gut microbiota and its effects on reward processing and interoceptive signalling. Specifically, we propose that EDs are underpinned by dysregulations of gut microbiota, reward processing and interoceptive signalling, rather than neurobehaviour alone. The novel, integrated, and transdiagnostic framework posited in this review could represent a conceptual shift in the aetiological understanding of eating disorders with the potential to derive new neurobiological targets for intervention.},
}
@article {pmid41921920,
year = {2026},
author = {Yang, MT and Qin, Y and Xu, C and Leng, X and Li, XM and Hou, QY and Sun, YZ and Zhao, Q and Liu, S and Tang, LY and Ma, H and Chen, BN and Zhang, XX and Li, ZY and Ni, HB},
title = {Virulence and antimicrobial resistance profiling of Klebsiella pneumoniae isolated from foxes in northern China.},
journal = {Microbial pathogenesis},
volume = {215},
number = {},
pages = {108476},
doi = {10.1016/j.micpath.2026.108476},
pmid = {41921920},
issn = {1096-1208},
abstract = {Klebsiella pneumoniae is a significant opportunistic pathogen in animal farming. To investigate the occurrence of K. pneumoniae and associated antimicrobial resistance risk in foxes, this study collected 350 fecal samples from foxes across five northern Chinese provinces. A total of 163 K. pneumoniae isolates were recovered (isolation rate: 46.57%), and all isolates were classified as multidrug-resistant (MDR). All isolates were resistant to azithromycin and sulfisoxazole, with high resistance to enrofloxacin (98.16%), ciprofloxacin (87.12%), and tetracycline (70.55%). Resistance to tigecycline and polymyxin B was lower. Notably, all isolates were susceptible to meropenem. Antimicrobial resistance gene (ARG) analysis revealed high carriage rates of tet(E), aac(3)-IIa, and qnrS, alongside the colistin resistance genes mcr-1 and mcr-8. Whole-genome sequencing of 66 isolates revealed substantial genetic diversity: 45 sequence types (STs) were identified among 64 typeable isolates, with ST35 and ST603 being the most common (5/64, 7.81% each), and lineages previously reported in human clinical settings (e.g., ST307 and ST15) were also detected; however, no direct cross-host transmission was evaluated in this study. Capsular types KL22 (10/64, 15.63%) was the most common. Metagenomic analysis further showed that the fox gut microbiome harbored diverse ARGs, with 29 ARGs detected in both K. pneumoniae isolates and fox gut resistome datasets (descriptive overlap). Among these, 20 genes (e.g., blaCTX-M-55 and aac(3)-IIa) were located on predicted plasmids or transposons, suggesting potential mobility rather than confirmed transfer. Conjugation assays provided limited proof-of-concept evidence for plasmid-mediated transfer of tet(A) and tet(E). Collectively, these findings suggest that farmed foxes may serve as potential reservoirs of MDR K. pneumoniae and transferable resistance determinants, supporting the need for continued surveillance and prudent antibiotic use within a One Health framework.},
}
@article {pmid41922110,
year = {2026},
author = {Bhat, A and Chaudhary, S and Kumari, A and Sharma, S and Sarin, SK and Maras, JS},
title = {Aspirin reprograms platelet signaling and the intrahepatic microbiome to suppress RyR2-driven inflammation and fibrosis in preclinical chronic liver disease.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {198},
number = {},
pages = {119296},
doi = {10.1016/j.biopha.2026.119296},
pmid = {41922110},
issn = {1950-6007},
abstract = {Platelet deactivation by aspirin possibly helps in regression of liver fibrosis, though the mechanisms are unclear. We administered aspirin in a murine model of liver fibrosis and studied molecular signatures associated with fibrosis regression; both in vivo (murine model/ patients) and in vitro. Increase in intrahepatic PF4, p-selectin, PDGFR-β levels (platelet activation) correlated with increase in liver fibrosis (p < 0.05, r[2]>0.3). Aspirin reduced the number and activation of intrahepatic platelets, inflammation and fibrosis (p < 0.05). Platelet deactivation using aspirin in murine model increased autophagy, glutathione, energy metabolism and decreased arachidonic acid and butanoate metabolism (p < 0.05). Aspirin modulated liver microenvironment and showed decrease in intrahepatic immune cell activation (blood transcription module) which correlated with histidine and tryptophan metabolism (r2 > 0.5, p < 0.05). The intrahepatic microbiome post-aspirin showed increased abundance of Firmicutes (Ruminococcaceae, Lachnospiraceae, and Clostridiaceae) and improved functionality (p < 0.05). Aspirin caused decreased expression of Ryanodine-receptor-2 (RyR2), Arginase-1 and Kynurenine-3-monooxygenase, which correlate with reduction in α-SMA and degree of hepatic fibrosis (r2 > 0.75; p < 0.05). In addition, pan specific blocking of RyR2 by carvedilol/flecainide markedly inhibited HSC activation and proliferation in-vitro by reducing Ca[2+] overload, ER/mitochondrial stress (p < 0.05). Further, RyR2 blockade in HSCs reduced its activation by activated platelet secretome or TGFβ1 (p < 0.05). CONCLUSIONS: Platelet deactivation using aspirin regresses hepatic fibrosis by decreasing intrahepatic platelet accumulation/activation, inflammation and modulation of intrahepatic microbiome. Induction of RyR2 is critical for fibrosis development and pharmacological inhibition of RyR2 could ameliorate liver fibrosis.},
}
@article {pmid41922261,
year = {2026},
author = {Adebayo, AA and Babalola, OO},
title = {Rhizosphere Microbiome as an Underexplored Resource for Agroecosystem Sustainability: Insights From the Carrot Root Zone.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70325},
pmid = {41922261},
issn = {1758-2229},
support = {CRP/ZAF22-93//International Centre for Genetic Engineering and Biotechnology/ ; },
mesh = {*Daucus carota/microbiology/growth &amp; development ; *Rhizosphere ; *Plant Roots/microbiology ; *Microbiota ; *Soil Microbiology ; Agriculture ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {Rhizosphere microbiome is critical for nutrient turnover, pathogen suppression, and stress modulation, forming the basis of microbial products relevant to agriculture. However, microbial communities associated with carrot root zone remain relatively underexplored, with limited studies focused beyond descriptive surveys. Here, we synthesise existing information on the structural, functional, and ecological dynamics of the carrot rhizomicrobiome, highlighting its emerging yet underdeveloped mechanistic profiling. Existing literature indicates that carrot-associated microbes may play a role in nutrient mobilisation, growth promotion, and antagonism. The early proof-of-concept works demonstrate that the microbes may gain potential applications in biofertilizers, biostimulants, and biocontrol agents. While these functions are strongly influenced by soil properties, genotype, and management, only a few carrot-specific isolates/consortia have been multi-environmentally validated. The limited progress partly reflects the overall underrepresentation of vegetables in microbiome-based studies, compared to other major crops. We explored the key characteristics, economic, and agricultural significance of the carrot rhizosphere, highlighting its richness with beneficial microorganisms. Among the gaps identified are inadequate functional-level and field trial, and insufficient multi-omics integration, which currently limit biotechnological translation. Addressing these gaps through targeted isolation, mechanistic functional and field validation could position carrot rhizosphere microbiome as a valuable yet underexplored resource for enhancing agroecosystem sustainability.},
}
@article {pmid41922263,
year = {2026},
author = {Hosogaya, N and Fukui, S and Takazono, T and Fukushima, K and Morio, R and Irifune, S and Morimoto, S and Nakada, N and Yoshida, M and Takeda, K and Ide, S and Iwanaga, N and Nemoto, K and Izumikawa, K and Yatera, K and Yanagihara, K and Mukae, H},
title = {Hypoalbuminemia and reduced sputum microbiome diversity associated with antibiotic treatment failure in nursing and healthcare-associated pneumonia.},
journal = {Drug discoveries &amp; therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.5582/ddt.2026.01005},
pmid = {41922263},
issn = {1881-784X},
abstract = {Nursing and healthcare-associated pneumonia (NHCAP) pose significant challenges in older populations, yet factors predicting antibiotic treatment failure remain elusive. This exploratory secondary analysis of a multicenter phase IV trial aimed to identify the clinical and microbiome predictors of treatment failure in patients with NHCAP treated with lascufloxacin. Among the 56 evaluable patients (median age 86 years; cured n = 44, not cured n = 12), paired sputum and tongue samples were analyzed using 16S ribosomal RNA gene clone library sequencing. Alpha diversity was assessed using the Shannon index, Simpson index, observed richness, and Pielou's evenness, whereas beta diversity was calculated using Bray-Curtis dissimilarity and visualized by principal coordinate analysis. Serum albumin was significantly lower in not cured patients (3.0 vs. 3.5 g/dL, p = 0.0497) and emerged as the strongest predictor of treatment failure in univariate logistic regression (odds ratio 0.18, 95% confidence interval 0.05-0.73, p = 0.016). Sputum Pielou's evenness showed a comparable predictive ability (odds ratio 0.010, p = 0.047). The overall microbiome community composition did not differ according to the outcome. Notably, patients with hypoalbuminemia (< 2.85 g/dL) exhibited significantly reduced sputum alpha diversity (Shannon p = 0.034, Simpson p = 0.025, Pielou's evenness p = 0.010). A simple risk stratification combining hypoalbuminemia and denture use identified a high-risk subgroup with markedly elevated treatment failure rates (75.0% vs. 12.5%, p = 0.001). These findings suggest an interconnected pathophysiology linking nutritional status and respiratory microbiome stability in patients with NHCAP. Nutritional status and oral health may be modifiable targets for improving treatment outcomes in high-risk patients.},
}
@article {pmid41922553,
year = {2026},
author = {Cloud, RE and Irwin, P and Muturi, EJ and Cáceres, CE},
title = {Characterizing the Microbiome and Prevalence of Wolbachia in Culex pipiens Complex and Culex restuans Mosquitoes in the Midwest United States.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02750-1},
pmid = {41922553},
issn = {1432-184X},
support = {DEB - 1754115//National Science Foundation/ ; DEB - 1754115//National Science Foundation/ ; DBI - 2022049//Genomics and Eco-evolution of Multi-scale Symbioses Institute/ ; },
}
@article {pmid41922622,
year = {2026},
author = {Chan, E and Chan, WH and Kerr, G and Archer, SK and Jardé, T and Engel, RM and Gould, JA and Amarasinghe, SL and Rutten, EL and D'Adamo, GL and Gulliver, EL and Gearing, LJ and Forster, SC and Giles, EM and Abud, HE},
title = {Patient-derived intestinal organoids as a model for site-specific mucosal bacterial interactions in paediatric inflammatory bowel disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46184-8},
pmid = {41922622},
issn = {2045-2322},
support = {1188689//National Health and Medical Research Council of Australia/ ; 1188689//National Health and Medical Research Council of Australia/ ; },
abstract = {Inflammatory bowel disease (IBD) is secondary to an abnormal immune response to the microbiota. To study this, models of host-microbe interactions that represent mucosal bacterial communities and inter-patient diversity are required. Human intestinal organoids (HIOs) are an established model to investigate epithelial responses. Here, we describe a technique of culturing bacteria directly from the sites of inflammation in IBD, while simultaneously sampling host tissue. We generated HIOs from a cohort of newly diagnosed paediatric IBD patients, without confounding treatments or comorbidities, and explored their response to site-specific bacteria. A unique biobank of matched HIOs and cultured mucosa-attached bacteria was established from 27 paediatric patients. Transcriptional profiling revealed differential gene expression between control and IBD-derived organoids. We used microinjection to introduce bacteria to the apical surface of the epithelium, to determine the effect of bacteria on host epithelial cells. We measured survival and growth of bacteria within the HIOs and tested several related bacterial isolates for their impact on the epithelium. An isolate from a control patient stimulated inflammatory signalling pathways but this was not observed in response to a closely related isolate originating from an IBD patient. This study demonstrates the feasibility of isolating bacteria and generating organoids from the same biopsy tissue, to explore personalised host-microbe interactions. The microinjections, while labour-intensive, demonstrate that closely related bacteria can induce very different epithelial responses, with downstream implications for immune response. This highlights the importance of understanding host-microbe interactions in a strain- and site-specific manner and developing techniques for personalised microbiome-based therapeutics.},
}
@article {pmid41922662,
year = {2026},
author = {Liu, B and Huang, X and Chang, C and Wan, X and Liu, M and Li, R and Li, J and Li, Q and Tao, Y},
title = {Toward microbiome-assisted remediation: Vanadium-titanium magnetite mining reshapes cropland soil chemistry and rhizosphere microbiomes.},
journal = {Crop health},
volume = {4},
number = {1},
pages = {},
pmid = {41922662},
issn = {2948-1945},
support = {2024NSFSC1202//Natural Science Foundation of Sichuan Province/ ; 25FTZLCL0012//Open Projects of the Sichuan Provincial Key Laboratory for Critical Strategic Materials of Vanadium and Titanium/ ; TYNSYS-2023-Z-03//Open Projects of the Sichuan Provincial University Key Laboratory for Solar Energy Technology Integration and Application Promotion/ ; Z3785//the start-up funds provided by Chengdu University/ ; },
abstract = {Vanadium-titanium magnetite (VTM) mining can modify cropland soils and root-associated microbiomes with implications for crop health. However, how crop rhizosphere microbiomes reorganize under VTM-derived stress-particularly when bacteria and fungi are considered together-remains poorly understood. In the Hongge district (Panzhihua, China), we sampled bulk soils and rhizospheres of lettuce, rapeseed, and pea from croplands within the VTM mining influence zone (mining-impacted fields) and paired croplands outside the zone (reference fields). We measured soil chemistry and profiled bacterial and fungal communities using 16S rRNA and ITS amplicon sequencing, respectively. Mining-impacted soils generally showed a VTM geochemical imprint, neutral-alkaline pH, and reduced plant-available P and K. Bray-Curtis-based ordinations indicated a clear separation between mining-impacted and reference rhizospheres, and taxonomic profiles suggested host-dependent reassembly of both bacterial and fungal communities. Putative functional profiling suggested a shift toward stress-accommodation processes, and fungal guild assignments tended to tilt toward saprotrophic/endophytic categories. Mantel analyses identified pH as one of the strongest correlates of community turnover, whereas structural equation modeling was consistent with nutrient availability (available N/P/K composite) explaining a substantial portion of the VTM effect; the composite total-metal-load axis (Fe/V/Ti/Zn) showed limited explanatory power, especially for fungi. Together, these field-based, two-kingdom signals link VTM-altered soil chemistry to rhizosphere restructuring in edible crops and provide actionable indicators for crop health management.},
}
@article {pmid41922722,
year = {2026},
author = {Neufert, C and Neurath, MF},
title = {Pathophysiology of colitis-associated colorectal cancer.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
pmid = {41922722},
issn = {1759-5053},
abstract = {Colitis-associated colorectal cancer (caCRC) is a subset of lower gastrointestinal tract malignancies that occurs in patients with inflammatory bowel disease (IBD), such as ulcerative colitis and Crohn's disease. The global prevalence of IBD is increasing, putting more individuals at risk of developing caCRC. The pathophysiological mechanisms that underlie the initiation and growth of caCRC remain to be fully elucidated. Nevertheless, studies have provided novel insights into the pathophysiology of caCRC, underscoring the distinguishing characteristics of caCRC compared with sporadic forms of CRC. In this Review, we describe the key mechanisms that drive caCRC. Starting from a clinical perspective and highlighting key features of the tumour epithelium, we discuss typical caCRC-related characteristics among subtypes of CRC, with a particular focus on the role of stromal cells in the tumour microenvironment. In addition, we review the contributions of immune cells to tumour control versus tumour promotion, and how signals from the gut microbiome might influence tumour development in caCRC. We also discuss various aspects of the pathophysiological heterogeneity of caCRC. Finally, we outline potential implications for therapy, and how these findings could be translated into future strategies of personalized medicine targeting caCRC.},
}
@article {pmid41922727,
year = {2026},
author = {Klinhom, S and Kunasol, C and Sriwichaiin, S and Kerdphoo, S and Chattipakorn, N and Chattipakorn, SC and Thitaram, C},
title = {Development of gut microbiota composition in captive Asian elephants: a year-long analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46586-8},
pmid = {41922727},
issn = {2045-2322},
support = {59/2565//The CMU Presidential Scholarship and Chiang Mai University/ ; N42A660301//The Distinguished Research Professor Grant from the National Research Council of Thailand/ ; RSA6280095//Thailand Research Fund/ ; },
abstract = {The establishment of gut microbiota is vital for the health and development of elephant calves, especially during their first year of life. This study investigates the transformation of the gut microbiome in captive Asian elephant calves, focusing the influence of maternal milk and subsequent dietary transitions on microbial colonization. A single meconium was collected at birth, followed by monthly fresh fecal samples during the first year. Mothers' fecal samples were also collected when calves reached three months of age. Gut microbiota profiling was conducted using 16 S rRNA gene sequencing. Meconium exhibited a diverse microbiota with moderate richness at birth. Richness subsequently declined in the monthly fecal samples, reaching its lowest point by three months of age. Firmicutes, Actinobacteriota, and Bacteroidota were the dominant bacterial phyla throughout the first year. A major shift was observed around 7 to 8 months of age with emergence of the archaeal genus Methanobrevibacter from phylum Euryarchaeota, which subsequently declined by 11 to 12 months. By this age, the calf microbial community had become more similar to that of adult elephants; however, species richness and diversity remained lower, indicating that microbial maturation was still ongoing. These findings advance our understanding of gut microbiota development in elephant calves and underscore the critical role of dietary management in promoting gut health and survival, providing essential data for captive conservation and management strategies.},
}
@article {pmid41922879,
year = {2026},
author = {Dou, S and Shen, J and Wang, C and Ma, G and Fu, G and Fu, L and Cong, B and Li, S},
title = {Forensic analysis of environmental and skin microbiome differences in college dormitories based on 16 S rRNA.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {41922879},
issn = {1437-1596},
support = {82572154//National Natural Science Foundation of China/ ; 30705010060//HeBei Medical University Postdoctoral Fund/ ; },
}
@article {pmid41923122,
year = {2026},
author = {Li, M and Cui, J and Qu, R and Liu, R and Sun, Y and Li, P and Liu, J and Low, A and Huang, X and Gan, F and Xu, ZZ},
title = {Porphyromonas gingivalis induces intestinal inflammation through gingipain-dependent gut microbiome dysbiosis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02389-7},
pmid = {41923122},
issn = {2049-2618},
support = {2025AHGXZK40069//Natural Science Foundation of Education Department of Anhui Province/ ; },
abstract = {BACKGROUND: Porphyromonas gingivalis (Pg), a key pathogen in periodontitis, is implicated in various systemic diseases such as pancreatic cancer and Alzheimer's disease. However, as a periodontal pathogen that can directly enter the lower gastrointestinal tract via saliva, its potential impact on the gut microbiome, intestinal inflammation, and its underlying mechanisms remains largely elusive.<br><br>RESULTS: Here, we observed that oral administration of Pg exacerbates intestinal inflammation in mice by inducing gut microbiome dysbiosis, increasing Th17 cells and the release of pro-inflammatory cytokines. Inhibition of Th17 activity with GSK805 or an anti-IL-17A blocking antibody mitigated this inflammatory response, highlighting the mediating role of Th17 cells. Gingipains, the virulence factors of Pg, played a crucial role in this process. Sequential knockout of gingipain genes revealed a gradual reduction in inflammatory phenotypes, with statistically significant alleviation observed when all three gingipain genes were deleted. Co-housing experiments showed that gut microbiota remodeling effectively protected against Th17-driven inflammatory response. Furthermore, immunization with inactivated Pg effectively prevented gut microbiome dysbiosis and Th17 cell-mediated inflammation.<br><br>CONCLUSION: Our findings suggest that Pg may exacerbate intestinal inflammation, potentially via its gingipain virulence proteases, which are linked to gut microbiota dysbiosis and enhanced Th17-mediated immune responses. These results suggest that gingipains could be promising targets for further investigation in Pg-associated intestinal disorders. Video Abstract.},
}
@article {pmid41923148,
year = {2026},
author = {Mogouong Tambue, J and Yager, C and Bushley, KE},
title = {Associations between phloem microbiota and metabolomes in three North American ash species (Fraxinus spp.) susceptible to emerald ash borer (Agrilus planipennis).},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00884-w},
pmid = {41923148},
issn = {2524-6372},
support = {DEB 2030036//National Science Foundation/ ; },
abstract = {BACKGROUND: Microorganisms play crucial roles in the survival and fitness of their plant and insects hosts, including invasive species. The emerald ash borer (Agrilus planipennis, Fairmaire; EAB) is an invasive insect from Asia. It represents a significant threat to North American forest ecosystems, causing widespread mortality in susceptible native ash (Fraxinus) species. While previous studies have shown differences in specific plant defense metabolites between susceptible North American ash species and their more resistant Asian counterparts, widely targeted metabolite profiles and their interactions with phloem microbiota in response to EAB infestation has thus far received little attention. This study aimed to profile microbial communities associated with ash phloem and EAB larval guts and their relationship to ash phloem metabolites in three native susceptible North American ash species: F. pennsylvanica (green ash), F. nigra (black ash) and F. americana (white ash).<br><br>RESULTS: Using metabarcoding to characterize the microbial communities associated with the larval gut and host tree phloem and widely targeted metabolomics to establish the first global metabolomic profile of phloem in these ash species, we examined interspecies differences in profiles and associations of ash phloem microbiota and metabolites in relation to EAB infestation. Multivariate analysis revealed that fungal communities were distinct in all ash species, while F. pennsylvanica (green ash) harbored bacterial communities distinct from black ash. Only black ash showed a phloem profile significantly associated with EAB attack symptoms and had the largest number of differentially abundant bacterial taxa. In contrast, larval gut bacterial communities from green ash were distinct from those in other ash species. Green ash displayed a distinct global metabolite profile from the other two species and had the highest number of differentially regulated metabolites, while black ash had the least. Green and white ash shared a strong upregulation of terpenoid compounds, several of which were among compounds significantly associated with microbial communities in green ash phloem or the EAB larval gut.<br><br>CONCLUSIONS: Our results provide the first comparative analysis of phloem-associated microbial communities and metabolomes across three susceptible North American ash species and their response to EAB. We found that microbiota and metabolites in green ash showed a distinct response to EAB infestation from the other ash species and we identified specific metabolites exhibiting significant correlations with microbial communities in ash phloem or the EAB larval gut. These findings contribute novel insights into interspecies variability in host-associated microbial communities and metabolomes and their response to an invasive insect.},
}
@article {pmid41923164,
year = {2026},
author = {Kiplimo, D and Sánchez, AM and Ramakrishnan, DK and Wicaksono, WA and Mwirichia, R and Teixidó, N and Berg, G and Abdelfattah, A},
title = {Phenotypic resistance profiles and resistome variations between endophytic and epiphytic bacteria in apple fruits.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00880-0},
pmid = {41923164},
issn = {2524-6372},
support = {PID2020-117607RR-I00 (ENVIRONAPPLE)//University of Lleida and IRTA predoctoral UdL-IRTA Sponsored Fellowship 2021, Spanish 'Agencia Estatal de Investigaci&#xf3;n' (AEI), European Regional Development Fund (ERDF), 2021 SGR 01477 grant and the CERCA Programme from the 'Generalitat de Catalunya'/ ; },
abstract = {BACKGROUND: In recent years, there has been increasing concerns about antibiotic resistance. Although studies have investigated resistance in food-associated bacteria, fresh produce microbes remain underexplored as potential hub of resistance genes capable for horizontal transfer to human via consumption. To this end, we tested the antibiotic resistance profiles of bacterial isolates recovered from Golden Reinders and Mandy apple cultivars. We aimed to investigate the effects of orchard-cultivar combinations and microbial lifestyle on the antibiotic resistance profiles. The apples (Golden Reinders and Mandy) were sampled from four separate orchards (EEL-Lleida, Esterri, Fruits-de-Ponent and Gotarta) in Spain. We used combination of culture-dependent and whole genome sequencing approaches to analyse the antibiotic resistance profiles.<br><br>RESULTS: A total of 516 bacterial isolates were screened for susceptibility against seven different classes of antibiotics. Results showed that 272 isolates were resistant to at least one antibiotic. From those, 203 were epiphytes and 95 classified as endophytes (isolated from surface-sterilized apple peels), whereas 26 isolates were shared between the groups. The resistance profiles varied across the antibiotics, with over 50% of the isolates exhibiting resistance to tetracycline, quinolones and cephalosporins. In contrast, none of the isolates showed resistance to imipenem. Whole genome sequencing (WGS) was performed on 18 isolates, however, only 10 genomes passed quality-control thresholds and were included in subsequent resistome analyses. We found ARGs encoding resistance to 14 main antibiotic classes, with the majority of the confirmed resistances attributed to multidrug resistance (MDR). Only few target-specific ARGs were annotated, including (Rif)iri (rifampicin), lnu(A) (lincomycin) and FosD (Fosfomycin). Pantoea agglomerans possessed higher number of ARGs, while Staphylococcus arlettae exhibited notable prevalence of plasmid-encoded ARGs.<br><br>CONCLUSION: Overall, the study highlights the prevalence of antibiotic resistance in apple microbiomes. The presence of multidrug-resistance (MDR) genes further underscores the persistent threat of 'antibiotic resistance', underlining the necessity for deeper insight into antibiotic resistance within food chain.},
}
@article {pmid41923171,
year = {2026},
author = {Delgadillo-Ordoñez, N and Schwarzenberg, A and Zhang, H and Beenham, L and Bensaddek, D and Raimundo, I and Terraneo, T and Benzoni, F and Peixoto, RS},
title = {Coral color morphs exhibit distinct microbial and proteomic profiles linked to stress and immune mechanisms in a changing ocean.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02391-z},
pmid = {41923171},
issn = {2049-2618},
abstract = {BACKGROUND: Coral phenotypic plasticity facilitates acclimation and adaptation to environmental variability. Coral species often display a variety of color morphs, yet key biological and ecological implications of such phenotypic variation remain underexplored. Here, we present the first proteomic and untargeted lipidomic and metabolomic survey to explore the biological characteristics and potential ecological significance of different color morphs (pink and brown) of healthy Pocillopora verrucosa sampled along a latitudinal gradient.<br><br>RESULTS: Our multi-omic approach elucidated distinct mechanisms associated with these dominant color morphs. We discovered bacterial indicators specific to each morph: putative pathogens such as Salmonella, Escherichia-Shigella, and carotenoid-producing Gemmatimonas were notably associated with the pink morph, whereas the brown morph was associated with potentially beneficial bacteria, such as Lysobacter, Acinetobacter, and Endozoicomonas. Despite these microbiome differences, the lipidome and metabolome of P. verrucosa were surprisingly homogeneous across colors and locations, suggesting similar metabolic performances during summer conditions. Key polar and apolar lipid classes, such as fatty acids, glycerophosphocholines, and retinoids, were prevalent. Notably, our proteomic analysis revealed morph-specific expressions, with pink morphs exhibiting enhanced levels of GFP-like proteins, Ankyrin, and the enzyme pullulanase, suggesting novel putative&#xa0;protective roles. In contrast, the brown morphs showed a higher abundance of heat shock proteins, indicating putative differential stress response capabilities.<br><br>CONCLUSION: This comprehensive study provides the first proteomic survey of P. verrucosa and identifies key physiological pathways and trade-offs linked to color morphs, which can further contribute to enhancing our understanding of coral resilience in the face of climate change.<br><br>SIGNIFICANCE STATEMENT: Understanding the phenotypic plasticity of corals is crucial for uncovering mechanisms of resilience in warming oceans, yet the biological significance of coral color morphs still needs to be explored. Using an innovative multi-omic approach (proteomics, lipidomics, and metabolomics), we provide the first comprehensive analysis of differences between pink and brown morphs of Pocillopora verrucosa. Our data reveal key taxa, potentially pathogenic or beneficial, associated with each morph, and suggest different strategies for each color morph to cope with heat stress, either expressing proteins involved in UV protection and heterotrophic activity or enhanced levels of heat stress resilience and DNA repair. These findings offer insights into the phenotypic plasticity of coral color morphs and their differential responses to climate change. Video Abstract.},
}
@article {pmid41923274,
year = {2026},
author = {Slaughter, M and Sung, CH and Suchodolski, JS and Pilla, R and Torres, C and Lappin, MR},
title = {EXPRESS: Oral administration of Enterococcus lactis strain SF68 speeds the recovery of amoxicillin-clavulanate-induced dysbiosis in cats.},
journal = {Journal of feline medicine and surgery},
volume = {},
number = {},
pages = {1098612X261441923},
doi = {10.1177/1098612X261441923},
pmid = {41923274},
issn = {1532-2750},
abstract = {OBJECTIVES: In a previous study, Torres-Henderson et al. (2017), the probiotic Enterococcus lactis strain SF68 was clinically shown to lessen amoxicillin-clavulanate associated diarrhea. The cause or mechanism as to why this clinical benefit occurred, however, was unknown. The cause or mechanism as to why this clinical benefit occurred, however, was not apparent in that study. Since the completion of that work, a new feline dysbiosis index (DI) has been developed and new information concerning the microbiome and bile acid metabolism has been published. The objective of this study was to assess changes in the feline DI and fecal bile acid metabolism to explain how this probiotic lessened amoxicillin-clavulanate-associated diarrhea.<br><br>METHODS: Prospective, randomized, placebo-controlled, double-blinded study. 27 healthy, young, adult, purpose-bred cats were used for a previous study. Cats were randomized into the probiotic (13 cats) or placebo (14 cats) group. Each cat received amoxicillin-clavulanate for 7 days at a standard dose and either the probiotic or placebo for 14 days. Fecal samples from all cats were obtained at baseline, day 7 and day 14. All samples were frozen at -80&#xb0;C until assessed. Targeted qPCR assays were then used to determine the fecal feline DI and unconjugated fecal bile acid concentrations were measured at each time point.<br><br>RESULTS: An antibiotic-induced shift in fecal microbiota and unconjugated bile acids was observed, with the probiotic group showing normalization of the feline DI and increased secondary bile acids on Day 14 compared to the placebo group (P = 0.0322).<br><br>CONCLUSIONS AND RELEVANCE: The probiotic E. lactis strain SF68 lessened amoxicillin-clavulanate-associated clinical signs of disease at least in part from the positive effects on the selected microbiota and bile acid metabolism. These findings support supplementing this probiotic to cats that have a clinical need for amoxicillin-clavulanate treatment.},
}
@article {pmid41923440,
year = {2026},
author = {Wang, P and Liu, X and Sun, W and Dong, X and Tan, J and Chen, M and He, J and Ali, A and Wu, L and Shao, K},
title = {Network Pharmacology Combined With Gut Microbiome and Serum Metabolomics Reveals the Therapeutic Mechanisms of Hydroxysafflor Yellow A in Diabetic Kidney Disease.},
journal = {Journal of diabetes research},
volume = {2026},
number = {1},
pages = {e2131566},
pmid = {41923440},
issn = {2314-6753},
support = {SH2023073//Zhenjiang Science and Technology Innovation Fund (Key R&amp;D Program-Social Development) Project/ ; YK2024116//Scientific Research Project of Yancheng Municipal Health Commission/ ; MS2022126//Project of Jiangsu Provincial Science and Technology Development Plan for Traditional Chinese Medicine/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Diabetic Nephropathies/drug therapy/metabolism/blood/microbiology ; Metabolomics ; *Chalcone/analogs &amp; derivatives/pharmacology/therapeutic use ; *Quinones/pharmacology/therapeutic use ; Male ; Mice ; Oxidative Stress/drug effects ; *Network Pharmacology ; Kidney/drug effects/metabolism ; *Diabetes Mellitus, Experimental/drug therapy/metabolism/complications ; Mice, Inbred C57BL ; },
abstract = {Diabetic kidney disease (DKD) is a severe complication of diabetes, primarily driven by chronic inflammation, oxidative stress, and gut microbiota dysbiosis. Hydroxysafflor yellow A (HSY), a bioactive compound derived from Carthamus tinctorius L., demonstrates promising renoprotective effects. However, its mechanisms, especially through modulation of the gut-kidney axis, remain poorly understood. This study employed a combination of network pharmacology, a high-fat diet/streptozotocin-induced type 2 diabetic mouse model, 16S rRNA sequencing, and serum metabolomics to explore the therapeutic mechanisms of HSY. Renal function, oxidative stress, inflammation, and gut microbiota composition were evaluated. HSY significantly alleviated renal injury by reducing blood glucose, creatinine, and urea nitrogen levels (p < 0.05), while enhancing renal antioxidant enzyme activity (GSH, SOD, CAT). Inflammatory markers (TNF-α, IL-1β) and AGE-RAGE signaling were suppressed. Analysis of the gut microbiota revealed that HSY enriched SCFA-producing genera (e.g., Lactobacillus, Alloprevotella) and decreased the abundance of Schaedlerella. Serum metabolomics further indicated that HSY modulated riboflavin metabolism, linoleic acid metabolism, and steroid hormone biosynthesis, thereby linking microbial metabolites to renal protection. Spearman correlation analysis revealed strong associations between specific gut microbiota (e.g., Prevotella) and serum metabolites (e.g., eicosapentaenoic acid). HSY mitigates DKD by targeting AGE-RAGE-mediated inflammation, oxidative stress, and gut microbiota dysbiosis while correcting metabolic disturbances. This study offers a novel multi-omics approach to understanding HSY's renoprotective effects, highlighting its potential as a therapeutic agent for DKD.},
}
@article {pmid41923466,
year = {2026},
author = {King, Z and Buckley, HL and Lear, G and Seale, B and Lee, KC and Schwendenmann, L and Lacap-Bugler, DC},
title = {Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70324},
pmid = {41923466},
issn = {1758-2229},
support = {C09X1817//New Zealand's Biological Heritage/ ; //Ministry of Business, Innovation and Employment/ ; },
mesh = {*Phytophthora/genetics/isolation &amp; purification ; *Soil Microbiology ; New Zealand ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Forests ; *Microbiota ; Plant Diseases/microbiology/parasitology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Nucleic Acid Amplification Techniques ; Phylogeny ; },
abstract = {Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, while also comparing detection and community-profiling methods. Soils from 60 kauri trees across three sites in the Waitākere Ranges, New Zealand, were analysed using loop-mediated isothermal amplification (LAMP) for pathogen detection, and 16S rRNA gene/ITS gene amplicon sequencing alongside shotgun metagenomics for community characterisation. LAMP detected P. agathidicida in 39/60 samples, while shotgun sequencing detected Phytophthora-associated DNA at low abundance across all samples. Microbial community structure and functional potential showed weak association with pathogen presence, though differential abundance testing identified several genera enriched in pathogen-detected soils, including taxa previously linked to disease suppression. Amplicon and shotgun profiles indicated broadly comparable patterns at higher taxonomic and functional levels, while differences between approaches emerged primarily at finer taxonomic resolution. Importantly, functional predictions from PICRUSt2 closely matched shotgun-derived profiles at broader scales, indicating its suitability as a cost-effective tool for broad-scale monitoring. These findings suggest limited direct pathogen effects on microbial communities and highlight how integrating molecular approaches provides complementary insights into soil microbiome-pathogen interactions.},
}
@article {pmid41923582,
year = {2026},
author = {Menezes, GA and Sekar, P and Akhter, A and Tayade, KD and Fathima, S and Hussain, ZFZ and Nigam, A},
title = {Gut Microbiota and Dyslipidemia in Type 2 Diabetes: A Pilot Study of 16S rRNA Profiles and Predicted Functional Shifts.},
journal = {Journal of diabetes research},
volume = {2026},
number = {1},
pages = {e9317962},
pmid = {41923582},
issn = {2314-6753},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology/complications/blood ; Pilot Projects ; Middle Aged ; *Dyslipidemias/microbiology/blood ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Adult ; Bacteria/genetics/classification ; },
abstract = {Hyperlipidemia is a major, modifiable driver of global cardiovascular risk. The intestinal microbiota, comprising bacteria, archaea, fungi, and viruses, modulates lipid metabolism through bile acid transformation, energy harvest, and inflammatory signaling. This study profiled the gut microbiota of 15 adults with type 2 diabetes mellitus (T2DM) and explored associations with fasting lipid measures using 16S rRNA gene sequencing (V3-V4 region) on the Illumina MiSeq platform and PICRUSt2 functional prediction. Overall α-diversity was reduced, and community composition was dominated by Firmicutes and Actinobacteria with relative depletion of Bacteroidetes. At lower taxonomic ranks, enrichment of Prevotella copri, Collinsella spp., Ruminococcus spp., and selected Bifidobacterium spp. was observed, alongside depletion of short-chain fatty acid (SCFA)-linked taxa, including Akkermansia muciniphila, Lactobacillus plantarum, and members of the Bacteroides and Parabacteroides lineages. Exploratory within-cohort trends indicated that higher triglycerides (TGs) and lower HDL-C tended to co-occur with increased Collinsella and clostridial signals and reduced SCFA-associated taxa. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog functions suggested shifts in lipid, carbohydrate, and secondary bile acid metabolism, consistent with a metabolically activated and proinflammatory intestinal milieu. In this single-arm cohort of adults with T2DM, a low-diversity, Firmicutes/Actinobacteria-weighted microbiome with depletion of SCFA-linked taxa paralleled an atherogenic lipid profile, supporting an association between gut microbial dysbiosis and lipid abnormalities in adults with T2DM. These findings suggest the potential of microbiota-informed adjuncts, including dietary fermentable fiber, targeted probiotics and next-generation biotherapeutics, and bile-acid-modulating strategies as supportive approaches to lipid management in T2DM. This was a pilot, single-arm, exploratory study without a nondiabetic control group, and findings should be interpreted as hypothesis-generating. Nevertheless, the cross-sectional design, small sample size, and 16S-based taxonomic resolution limit causal interpretation. Larger, longitudinal studies integrating shotgun metagenomics and metabolomics are needed to confirm these associations, validate biomarkers, and elucidate mechanistic pathways that could guide precision interventions for diabetic dyslipidemia.},
}
@article {pmid41923586,
year = {2026},
author = {Oh, Y and Lee, H and Jang, S},
title = {Emerging synthetic biology-assisted technologies for overcoming antibiotic resistance: CRISPR-Cas, bacteriophage, microbiome, and metabolic engineering-based solutions.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {3},
pages = {e2512002},
doi = {10.71150/jm.2512002},
pmid = {41923586},
issn = {1976-3794},
support = {//National Research Foundation of Korea/ ; RS-2025-02214910//Ministry of Science and ICT/ ; //Incheon National University/ ; },
mesh = {*CRISPR-Cas Systems ; *Synthetic Biology/methods ; *Bacteriophages/genetics ; *Metabolic Engineering/methods ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; *Bacteria/drug effects/genetics ; Humans ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; },
abstract = {Antibiotic resistance has become a critical global health challenge due to the decreased efficacy of existing antibiotics and the emergence of multidrug-resistant pathogens. In particular, the rapid horizontal transfer of resistance genes and the diverse mechanisms by which bacteria acquire resistance have significantly undermined the effectiveness of conventional therapeutic strategies, revealing fundamental limitations in current infectious disease management. In this context, synthetic biology provides a promising framework to overcome the limitations of conventional antibiotics by integrating engineering principles with bioengineering approaches, thereby enabling precise and programmable control of biological processes. These synthetic biology-based approaches offer substantial potential for developing sustainable and highly specific antimicrobial strategies. This review comprehensively examines recent advances in synthetic biology-assisted antimicrobial strategies, including CRISPR-Cas systems, bacteriophage engineering, microbiome engineering, and metabolic engineering-driven antibiotic discovery. Collectively, these approaches represent a precision antimicrobial paradigm that enables selective targeting of resistant bacteria while preserving microbiome homeostasis. These strategies also provide new directions for limiting resistance dissemination and guiding the development of next-generation therapeutics.},
}
@article {pmid41923590,
year = {2026},
author = {Liu, Z and Hui, C and Zhang, G and Yang, H and Wang, Y and Shi, Y and Wang, C and Liu, Y and Gao, X and Wen, Y},
title = {Tanshinones from Salvia miltiorrhiza alleviate ulcerative colitis via reprogramming the gut microbiota-metabolite axis.},
journal = {Acta biochimica et biophysica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.3724/abbs.2026054},
pmid = {41923590},
issn = {1745-7270},
abstract = {The anti-inflammatory properties of the traditional herb Salvia miltiorrhiza Bunge are well-established, yet its precise mechanism of action in ulcerative colitis (UC) remains unclear. Herein, we evaluate the therapeutic potential of four major tanshinones-tanshinone IIA (Tan IIA), miltirone, neocryptotanshinone, and dihydrotanshinone I-in a murine dextran sulfate sodium (DSS)-induced colitis model. Our results show that tanshinones effectively alleviate disease severity, suppress systemic and local inflammation, and restore intestinal barrier integrity. Integrated multi-omics analysis reveals that the therapeutic efficacy originates from a comprehensive reprogramming of the gut microbiota-metabolite axis. Specifically, tanshinones reverse colitis-associated dysbiosis and rectify metabolic disturbances in linoleic acid metabolism, bile acid biosynthesis, and amino acid utilization. Correlation network analysis identifies key functional modules linking beneficial microbes (e. g., Akkermansia) to anti-inflammatory lipid mediators and associating pathobionts (e . g., Desulfovibrio) with disrupted bile acid metabolism. Notably, supplementation with Akkermansia muciniphila synergizes with Tan IIA to amplify barrier restoration and metabolic normalization. Our findings establish that tanshinones ameliorate UC through microbiota-driven metabolic reprogramming, wherein the restructured microbial community actively shapes a therapeutic metabolic output. This work elucidates a metabolite-mediated mechanism of action and positions tanshinones as promising microbiome-targeting therapeutics for inflammatory bowel disease.},
}
@article {pmid41923636,
year = {2026},
author = {Xiong, C and Delgado-Baquerizo, M and Liang, J and Wang, J and Yan, Z and Jensen, SO and Gao, M and Sáez-Sandino, T and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK},
title = {Soil microbial diversity associates with lower prevalence of human bacterial pathogens across global soils.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.011},
pmid = {41923636},
issn = {1934-6069},
abstract = {Soil-inhabiting pathogens threaten human health, but their biogeography and associations with soil biodiversity remain poorly understood. Here, we present global patterns of dominant human bacterial pathogens by integrating 1,602 soil metagenomes from 59 countries across continents. We show that dominant human pathogens are more prevalent (i.e., relative abundance) in wet (tropical and temperate) ecosystems and are particularly abundant in cropland soils. We find a global negative association between soil microbiome diversity and pathogen prevalence. We further reveal a significant and positive correlation between the abundance of dominant human pathogens and both disease virulence and global patterns of mortality associated with infectious diseases. Many dominant pathogens are likely to increase their proportion under global change scenarios. Our work provides a global atlas of dominant soil-inhabiting human pathogens and reveals their biogeography and ecology. These findings can guide the development of effective surveillance and risk management strategies to reduce outbreaks and pandemics.},
}
@article {pmid41923890,
year = {2026},
author = {Willis, DN and Dubberke, ER and Hayashi, RJ and Tarr, PI and Haslam, DB and Hink, T and Luo, J and Tao, Y and Padhye, A and Hall, EM and Storch, GA},
title = {Clostridioides difficile Colonization and Infection in Pediatric Oncology and Stem Cell Transplant Patients.},
journal = {Open forum infectious diseases},
volume = {13},
number = {4},
pages = {ofag149},
pmid = {41923890},
issn = {2328-8957},
abstract = {BACKGROUND: Pediatric oncology and hematopoietic stem cell transplant (HSCT) patients have elevated risk for Clostridioides difficile infection (CDI), which can prolong hospitalization and delay chemotherapy. Colonization is an important prelude to symptomatic CDI. We sought to characterize colonization status in these patients.<br><br>METHODS: We retrospectively studied 276 stools longitudinally collected over 34 months from 32 HSCT and 12 oncology patients treated at a single tertiary center. Specimens were cultured for C difficile and compared by whole genome sequencing. The fecal microbiome was characterized by 16S rRNA gene sequencing.<br><br>RESULTS: Baseline cultures were positive in 16 (50%) HSCT patients and 2 (12%) oncology. On subsequent samples, 64% of patients who were initially negative acquired colonization: 8 of 15 (53%) HSCT and 8 of 10 (80%) oncology. Nine clonal strains and 25 multilocus sequence types were identified by whole genome sequencing, with 4 clones found in both cohorts. Nine patients had different strains at different time points. Seven clonal strains were found in multiple patients. Seven (15.9%) patients had symptomatic CDI. C difficile-positive stools had greater microbial diversity than negative stools in both the oncology cohort (Simpson diversity index, 0.07; 95% CI, .01-.14; P = .03) and the HSCT cohort (0.15; 95% CI, .07-.24; P < .001).<br><br>CONCLUSIONS: C difficile acquisition and colonization are common in pediatric oncology and HSCT patients. The high prevalence of clonally related strains in multiple patients suggests that asymptomatic patients may be important reservoirs of this pathogen and lead to symptomatic CDI in some patients. Gut microbial composition may influence the risk of colonization.},
}
@article {pmid41924284,
year = {2026},
author = {Tao, YL and Wu, XX and Wang, JR and Liu, M and Liu, YN and Lian, YQ and Liang, ZY and Zhu, SF},
title = {The microbiome: regulating anti-tumor immunity.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1781872},
pmid = {41924284},
issn = {1664-3224},
mesh = {Humans ; *Neoplasms/immunology/microbiology/therapy ; Animals ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Tumor Microenvironment/immunology ; },
abstract = {Microorganisms distributed throughout the human body have always been a complex ecosystem that has long coexisted with other organisms. They are involved in essential key links, such as nutrient absorption, energy regulation, metabolism, toxin clearance, and immune regulation. With a deeper understanding of the microbiome, many studies have shown that the microbiome is also actively involved in the occurrence and development of tumors. The core mechanism of dysregulated microorganisms and their derivatives in the treatment response and toxicity management of tumors is the regulation of the immune function. This article explores the evolution of the microbiome and its impact on the immune function during tumor progression, and focuses on analyzing cutting-edge treatment strategies targeting the microbiome, as well as future research directions and challenges in clinical translation.},
}
@article {pmid41924305,
year = {2026},
author = {Kerff, F and Mühlematter, C and Adamov, A and Fast, D and Plüss, S and Zimmermann, P and Kurth, S and Bokulich, NA},
title = {The gut microbiota and sleep in infants: a focus on diurnal rhythmicity patterns.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2649096},
pmid = {41924305},
issn = {2993-3935},
abstract = {Emerging evidence supports a bidirectional relationship between the gut microbiome and sleep, which is partly mediated by the microbiota‒gut‒brain axis. Infancy is a critical window for the establishment of both the gut microbiome and sleep regulation, which we hypothesize to be linked across both short (diurnal) and long (monthly) time scales. In this longitudinal study, we investigated associations between gut microbiota development and sleep patterns in 20 infants at 2, 4, and 6 months of age (n = 163 samples). Infants were continuously monitored across 48-h sampling periods. The gut microbiota profiles were characterized using 16S rRNA gene sequencing; gut melatonin concentrations were measured; sleep data were collected via wearable actimetry, 24-h parent-reported sleep diaries, and the Brief Infant Sleep Questionnaire; and parenting style and behavioral development were assessed. In some infants, bacterial diversity followed diurnal rhythmic patterns. While bacterial rhythmicity was not significantly associated with sleep rhythmicity, infants with higher microbial alpha diversity showed more robust sleep patterns. Infant age emerged as the strongest predictor of gut microbial diversity and melatonin levels. Our findings suggest that gut microbial establishment may support the maturation of sleep‒wake rhythms in early infancy. Further research is needed to elucidate mechanistic roles of the gut microbiome in sleep development.},
}
@article {pmid41924306,
year = {2026},
author = {Batacan, R and Rao, A and Bajagai, YS and Stanley, D and Briskey, D},
title = {Oleoylethanolamide supplementation enriches Akkermansia muciniphila and modulates intestinal barrier function in adults with obesity: A randomized, double-blind, placebo-controlled trial.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2622259},
pmid = {41924306},
issn = {2993-3935},
abstract = {Targeted modulation of the gut microbiome represents a promising nutritional strategy to support metabolic and intestinal health in overweight and obese adults. Oleoylethanolamide (OEA) is an endogenous lipid mediator that regulates satiety, lipid metabolism, and inflammation, but its effects on the human microbiome are not well defined. In this randomized, double-blind, placebo-controlled trial, 57 adults with obesity (BMI 30-40 kg/m[2]) received either 300 mg of TRPTI, providing 250 mg/day of OEA (n = 28), or placebo (n = 29) for 12 weeks. Outcomes included shotgun metagenomics, microbiome profiling, intestinal barrier and inflammatory biomarkers, and safety measures. OEA was safe and well-tolerated with no adverse changes in clinical biomarkers. Although overall microbial diversity remained stable, OEA induced selective, health-relevant compositional shifts. Notably, Faecalibacterium prausnitzii and Akkermansia muciniphila were enriched. These changes coincided with functional host benefits, including increased occludin at Week 12 and interleukin-2 at Week 6, while reducing interleukin-1β, consistent with improved epithelial barrier dynamics and reduced inflammation. Functional pathway analysis suggested enhanced microbial metabolic and redox capacity. These findings indicate OEA supplementation selectively enriches beneficial gut bacteria - particularly A. muciniphila, while improving gut barrier biomarkers and immune function without disrupting microbiome stability. These findings position OEA as a safe, targeted microbiome-modulating ingredient with potential applications for supporting gut and metabolic health.},
}
@article {pmid41924307,
year = {2026},
author = {Bhagavata Srinivasan, SP and Kendig, MD and Hasebe, K and Kaakoush, NO and Morris, MJ and Leigh, SJ},
title = {Cafeteria diet exposure, and not weight gain propensity, impacts gut microbiota of rats - a within laboratory meta-analysis.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2649442},
pmid = {41924307},
issn = {2993-3935},
abstract = {Preclinical studies have implicated the microbiota in body weight control, but its translation to humans remains uncertain, partly owing to methodological variability in assessing the relationship between diet-induced obesity and microbiota composition. We performed an internal meta-analysis to determine whether the propensity for diet-induced obesity, defined by relative weight gain due to a high-fat, high-sugar "cafeteria" diet, is associated with changes in microbiota composition. We collated fecal microbiome data from 12 studies using our validated model of diet-induced obesity (208 male and 74 female Sprague-Dawley rats; 3.5-13 weeks of chow (control) or cafeteria diet) and determined whether the alpha diversity and composition of the gut microbiota differed between obese-prone and obese-resistant rats. We found consistent effects of cafeteria diet exposure on the microbiota, with marked changes in overall composition, and reduced microbial richness and evenness. Furthermore, specific obesity-associated microbial genera, such as Bacteroides and Blautia, were enriched by the cafeteria diet. Critically, alpha diversity measures and the gut microbiota composition did not differ between obese-prone and obese-resistant rats in either diet group. Our findings suggest that while the microbiota is substantially altered by cafeteria diet intake, these changes appear unrelated to individual susceptibility to weight gain, highlighting the role of additional host factors in modulating diet-induced obesity.},
}
@article {pmid41924422,
year = {2026},
author = {Nazarova, V and Kamzayeva, N and Ukybassova, T and Kozhakhmetov, S and Kushugulova, A},
title = {Systems analysis of the HPV-microbiome-biofilm triad.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1767224},
pmid = {41924422},
issn = {2235-2988},
mesh = {*Biofilms/growth &amp; development ; Humans ; *Microbiota ; Female ; *Papillomavirus Infections/microbiology/virology/immunology ; Dysbiosis/microbiology ; *Papillomaviridae/physiology ; Vagina/microbiology/virology ; Uterine Cervical Neoplasms/virology/microbiology ; },
abstract = {BACKGROUND: Human papillomavirus (HPV) remains the leading cause of cervical cancer worldwide, however, its pathogenesis cannot be sufficiently explained by viral factors alone. Accumulating evidence highlights the critical role of cervicovaginal microbiome composition and biofilm formation in shaping viral persistence, epithelial barrier disruption and carcinogenic progression.<br><br>METHODS: This systems-based integrative synthesis analyzed peer-reviewed literature published between January 2000 and July 2025, retrieved from PubMed and Google Scholar with additional records identified through backward citation screening. The collected data were synthesized to construct a conceptual model of the HPV-microbiome-biofilm triad and to evaluate its clinical and biological implications.<br><br>RESULTS: The analysis indicates that depletion of Lactobacillus-dominated communities and expansion of anaerobic taxa, particularly Gardnerella vaginalis, are associated with biofilm development, chronic inflammation and immune modulation. These interrelated processes form self-reinforcing feedback loops that promote HPV persistence and reduce therapeutic efficacy. Microbiome dysbiosis and biofilm formation were further linked to impaired epithelial integrity, altered cytokine signaling pathways and clinically relevant phenotypes including immune escape, metabolic shifts and treatment non-responsiveness.<br><br>DISCUSSION: This systems perspective challenges reductionist pathogen-centered models and emphasizes the importance of integrating microbiome profiling and biofilm dynamics into cervical cancer risk stratification and therapeutic strategies. The coupled interactions between microbial communities, host immunity and viral persistence underscore the cervicovaginal ecosystem as an active regulator of disease progression rather than a passive bystander. Incorporating ecosystem-based parameters into clinical decision-making may enhance prognostic assessment and improve treatment outcomes, particularly in low- and middle-income countries where high HPV prevalence coincides with increased microbiome vulnerability.<br><br>https://www.crd.york.ac.uk/PROSPERO/, identifier CRD420251208178.},
}
@article {pmid41924474,
year = {2026},
author = {Li, M and Dai, L and Yang, Y and Chen, S and Ma, J and Feng, P},
title = {Jinzhi and fecal microbiota transplantation: a comparative review of historical and modern microbial therapeutics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1700764},
pmid = {41924474},
issn = {1664-302X},
abstract = {Since its formal introduction in 1958, fecal microbiota transplantation (FMT) has gained prominence. However, challenges remain in standardizing protocols and optimizing efficacy. This review provides a systematic comparison between the historical practice of Jinzhi and modern FMT, focusing on their preparation methodologies. We hypothesize that specific, underexplored features of Jinzhi preparation could inform and refine current FMT practices. Specifically, we propose that the utilization of adolescent donors, underground low-temperature fermentation, and the careful consideration of seasonal timing, all integral to Jinzhi's traditional protocol, may offer novel insights and testable hypotheses for enhancing microbial diversity, functionality, and therapeutic stability in FMT. By bridging this ancient wisdom with modern microbiome science, we aim to outline a novel and actionable framework for developing the next generation of microbiota-based therapeutics, urging future research to empirically test these historically inspired hypotheses.},
}
@article {pmid41924483,
year = {2026},
author = {Niu, Y and Wang, C and Kuang, Y and Ma, X and Nan, S and Zhang, P and Lu, Q and Qi, Y and Nie, C and Wu, Y and Zhang, W},
title = {Multi-omics insights into triticale silage as a sustainable alternative to corn silage in heifer diets.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761287},
pmid = {41924483},
issn = {1664-302X},
abstract = {BACKGROUND: Intensive ruminant production systems rely heavily on corn silage (CS) as a primary forage source; however, its resource-intensive cultivation and environmental constraints necessitate the development of sustainable alternatives.<br><br>METHODS: In a 90-day feeding trial, 24 growing heifers were assigned to diets in which CS was replaced by triticale silage (TS) at 0, 25, 50%, or 100% (DM basis). Growth performance, rumen fermentation, ruminal fatty acid (FA) profiles, and integrated rumen microbiome-metabolome interactions were evaluated.<br><br>RESULTS: A 25% substitution (TS25) as the optimal level, maintaining growth performance comparable to the control while achieving the lowest feed cost of gain. TS25 improved rumen fermentation (lower A: P and high total VFA), promoted more efficient nitrogen utilization (higher MCP with lower ammonia N), and enriched functionally relevant bacteria associated with fiber degradation and fermentation (e.g., Ruminococcus, Prevotella, and Rikenellaceae_RC9_gut_group). Consistently, TS inclusion shifted ruminal lipid metabolism, increasing UFA proportions and elevating PUFA (TS25 and TS50 increased PUFA by 15.2 and 23.7% vs. control), alongside metabolomic signals indicating upregulation of linoleic acid metabolism and aromatic amino acid biosynthesis pathways. In contrast, TS substitution &#x2265;50% reduced DMI and ADG, impairing feed utilization.<br><br>CONCLUSION: Partial replacement of CS with TS at 25% provides a practical, data-supported strategy to improve economic efficiency while maintaining productivity and promoting favorable rumen microbial-metabolic features. This feeding approach may be applicable in water-limited or double-cropping regions, where TS can enhance forage system sustainability without compromising heifer growth.},
}
@article {pmid41924563,
year = {2026},
author = {Santoyo, G and Kumar, A and Orozco-Mosqueda, MDC and de Oliveira Mendes, G},
title = {Editorial: Role of endophytic/symbiotic fungi in plant growth promotion and disease suppression.},
journal = {Frontiers in fungal biology},
volume = {7},
number = {},
pages = {1820241},
pmid = {41924563},
issn = {2673-6128},
}
@article {pmid41924635,
year = {2026},
author = {Graspeuntner, S and Lupatsii, M and Hamala, N and Masuch, A and Depenbusch, M and Pfeffer, I and Schultze-Mosgau, A and Eggersmann, TK and Rupp, J and Griesinger, G},
title = {Vaginal microbial community state types fail to predict IVF outcomes, whereas Ureaplasma parvum and Lactobacillus iners are negative predictors of implantation, clinical pregnancy, and live birth.},
journal = {Human reproduction open},
volume = {2026},
number = {2},
pages = {hoag018},
pmid = {41924635},
issn = {2399-3529},
abstract = {STUDY QUESTION: Are previously proposed vaginal microbial community state types (CSTs) valid predictors of IVF success, or do alternative microbial signatures provide stronger associations?<br><br>SUMMARY ANSWER: Previously proposed CSTs as predictors of implantation, clinical pregnancy, and live birth were not confirmed, while an interaction between Ureaplasma parvum and Lactobacillus iners emerged as a strong negative predictor.<br><br>WHAT IS KNOWN ALREADY: Infertility affects 17% of the global population. Only one-third of treatment cycles of assisted reproductive technologies result in embryo implantation, and even fewer lead to clinical pregnancy or live births. While early findings have spurred the development of microbiome-based tests for success prediction, evidence on supporting their reliability remains inconclusive.<br><br>STUDY DESIGN SIZE DURATION: This prospective, single-centre study aimed to validate existing, and identify better, microbial predictors of infertility treatment outcomes. A cohort of 266 infertile female patients (age 18-45&#x2009;years) undergoing a frozen-thawed embryo transfer cycle in an anovulatory regimen (i.e. a cycle with transfer of an embryo following a previous oocyte retrieval, fertilization, and freezing of embryos) was recruited for the study within&#xa0;a timeframe from May 2017 to March 2019.<br><br>The female, infertile patients, aged 18-45&#x2009;years, were undergoing routine care. Vaginal swabs were taken prior to embryo transfer and subjected to DNA isolation for 16S-based microbiota analysis. Extended demographic and treatment data were recorded. Clinical outcomes were defined as: (i) implantation, confirmed by a positive hCG test, (ii) clinical pregnancy, and (iii) live birth (defined as the birth of a viable infant). Sequencing data were processed in mothur following established pipelines, and microbial composition (taxonomy) as well as microbial diversity (dissimilarity analyses) were determined using the open-source software R. A prediction model for implantation success was built using binary logistic regression based on abundance of putatively predictive microbial taxa.<br><br>This study suggests that vaginal microbial CSTs, alpha-diversity, and the ratio of dominant Lactobacillus species do not correlate in statistical terms or in a clinically meaningful manner with implantation and clinical pregnancy (as a surrogate for endometrial receptivity) or with live birth (as a surrogate for ongoing pregnancy viability). However, Ureaplasma parvum and Lactobacillus iners abundances were identified as negative predictors of embryo implantation, clinical pregnancy, and live birth. A subset of women colonized by these taxa experienced drastically reduced embryo implantation and completely failed to achieve clinical pregnancy or give birth to live offspring, suggesting a potential role of these organisms in implantation failure and reproductive outcome, independent of other influencing factors such as age, oestradiol levels, endometrial thickness etc.<br><br>LARGE SCALE DATA: The raw sequencing data used for this manuscript are publicly available at the European Nucleotide Archive under accession number PRJEB107113.<br><br>This study is a single-centre study warranting further validation cohorts. Given the variable nature of the vaginal microbiota, sample sizes need to be enlarged for better refinement of the analyses. Further, the underlying mechanistical basis of our findings is yet elusive and clinical translation has yet to be established.<br><br>While this novel association warrants confirmation, the results caution against reliance on previously suggested CSTs as predictors, and highlight the need for refined, reproducible microbiome-based diagnostics in reproductive medicine.<br><br>Financial support was received from the University of L&#xfc;beck and the German Center of Infection Research. M.L., A.M., I.P., M.D., and J.R. declare no conflicts of interest. S.G. discloses personal fees from Organon outside the submitted work. T.K.E. discloses honoraria from Ferring; travel support from Ferring, Merck, Theramex, and Gedeon-Richter; and receipt of equipment/materials/laboratory analyses (to institution) from Arthrex, Besins, Merck, and Abbott outside the submitted work. N.H. discloses personal fees from Gedeon Richter, Ferring, and Merck. G.G. reports that his institution received grants or contracts from Besins, Merck, Abbott, Ferring, and Theramex. He has received personal consulting fees, support for travel fees and meeting attendance, and honoraria for lectures or educational events from Organon, Ferring, Merck, Gedeon-Richter, Theramex, Abbott, ReproNovo, Igyxos, OxoLife, Philipps, ReprodWissen, PregLem, Guerbet, Roche, IBSA, and Besins. He also received support for travel and meeting attendance from Merck, Organon, Ferring, Theramex, Gedeon-Richter, and Abbott. Additionally, he holds unpaid leadership positions as a member of the ESHRE Working Group on RIF, the ESHRE Working Group on clinical KPI, and the ESHRE guideline development group on ovarian stimulation. A.S.-M. reports consulting fees and speaker's fees from Merck, Theramex, and Gedeon-Richter as well as travel support from Merck, Theramex, Gedeon-Richter, IBSA, Ferring, and MSD.},
}
@article {pmid41924822,
year = {2026},
author = {Gamage, MAGNDMA and Dissanayake, WMN and Yi, YJ},
title = {Response of the mTOR signaling pathway to the reproductive dysfunction of dysbiosis-induced male mice.},
journal = {Reproductive biology},
volume = {26},
number = {2},
pages = {101213},
doi = {10.1016/j.repbio.2026.101213},
pmid = {41924822},
issn = {2300-732X},
abstract = {The mammalian target of rapamycin (mTOR) signaling pathway plays a key role in coordinating several cellular activities in response to environmental signals, thereby influencing metabolism and reproduction. This study aimed to determine the role of mTOR signaling pathway in testicular dysfunction caused by intestinal microbiome imbalance. An antibiotic mixture containing ampicillin, neomycin sulfate, vancomycin, and metronidazole was administered orally to mice for four weeks, and subsequently serum, and tissues were obtained following sacrifice. Glucose, cholesterol, and sex hormone levels were measured in the serum, and real-time PCR was performed using extracts of the ileum and testis to determine the expression of genes associated with pro-inflammatory cytokines, mTOR signals and testosterone synthesis. The levels of glucose and sex hormones in the serum of antibiotic-induced dysbiosis (WD) mice were significantly decreased, while the cholesterol levels were elevated (p < 0.05). The mRNA expression of IL-1β, IL-6 and TNF-α significantly increased in the testis of the WD group (p < 0.05 &amp; p < 0.01), while testosterone synthesis, such as the expression of 3β-HSD and P450scc decreased (p < 0.05). Immunofluorescence revealed the localization of mTOR in the mid-piece and tail of the epididymal spermatozoa. The mRNA expression of mTOR signaling pathway, including Mtor, Raptor, p53, PI3K, Akt1, P70s6k, and Rheb, was significantly upregulated in the testis of the WD group (p < 0.05). Consequently, antibiotic-induced dysbiosis in male mice led to increased secretion of pro-inflammatory cytokines in the testis, decreased serum sex hormone levels, and impaired sperm quality, all of which could be associated with altered regulation of the mTOR signaling pathway.},
}
@article {pmid41925161,
year = {2026},
author = {Bergemann, CM and Jameson, LE and Kenny-Ganzert, IW and Huayta, J and Castellano-Escuder, P and Sarkar, A and Ilkayeva, OR and Sherwood, DR and Hirschey, MD and Meyer, JN},
title = {Caenorhabditis elegans fed native gut microbiota have altered bioenergetic pathway utilization impacting mitochondrial function and susceptibility to pollutants.},
journal = {Environmental science. Processes &amp; impacts},
volume = {},
number = {},
pages = {},
pmid = {41925161},
issn = {2050-7895},
support = {P42 ES010356/ES/NIEHS NIH HHS/United States ; R01 ES034270/ES/NIEHS NIH HHS/United States ; R35 GM118049/GM/NIGMS NIH HHS/United States ; T32 ES021432/ES/NIEHS NIH HHS/United States ; },
abstract = {The gut microbiome can influence host health by facilitating digestion, immune function, and xenobiotic metabolism. Microbial metabolites can influence mitochondrial function by shifting bioenergetic pathways, potentially altering sensitivity to mitochondrial toxicants. However, mechanisms through which the gut microbiota can alter mitochondrial function and susceptibility to mitochondrial toxicity are not well characterized. We used the model organism Caenorhabditis elegans and the microbiome kit CeMbio, a characterized collection of native gut commensals, to explore the interactions between gut microbiota, mitochondrial function, and chemical susceptibility. C. elegans grown on selected bacterial strains had varying levels of steady-state whole-body ATP, with an ∼3 fold difference between the highest and lowest strains, as well as 2- and 3-fold changes in antioxidant and mitochondrial unfolded protein gene induction. Further, C. elegans grown on selected bacterial strains showed differential sensitivity to short-term exposure to chemicals that inhibit mitochondrial electron transport chain Complexes I, II, and V, and fatty acid oxidation. To test mechanistically how microbiome-mediated sensitivities could result in chemical susceptibility, we carried out follow-up experiments using the Complex I inhibitor rotenone. We found that C. elegans grown on BIGb0170 (Sphingobacterium multivorum) had much higher lethality after 24- and 48-hour exposures than when grown on MYb10 (Acinetobacter guillouiae), MYb11 (Pseudomonas lurida), and OP50 (Escherichia coli) strains. Metabolomic analysis revealed that C. elegans grown on BIGb0170 had lower amounts of triglycerides and acylcarnitines. ATP levels were partially rescued by supplementing BIGb0170 with pyruvate. This work suggests that BIGb0170 can impact mitochondrial function through changes in metabolite abundance, which can increase sensitivity to the Complex I inhibitor rotenone.},
}
@article {pmid41925202,
year = {2026},
author = {Leibovitzh, H and Krongauz, D and Schlesinger, Y and Cohen, NA and Hirsch, A and Ron, Y and Thurm, T and Godneva, A and Weinberger, A and Segal, E and Maharshak, N},
title = {Phage-display immunoprecipitation sequencing reveals distinct antibody signatures against bacterial flagellins associated with treatment response in Crohn's disease.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000001030},
pmid = {41925202},
issn = {2155-384X},
abstract = {OBJECTIVES: Enhanced immune response against bacterial flagellins among patients with Crohn's disease (CD) is associated with aggressive disease course. However, its association with response to biologic treatment is unknown. We aimed to assess whether treatment response among patients with CD is associated with antibody reaction to bacterial flagellins and related microbial alterations.<br><br>METHODS: Thirty-nine patients with active CD (Harvey-Bradshaw Index [HBI]>4 or fecal calprotectin [FCP]>150&#x3bc;g/g) commencing biologic treatment were included. Serum and stool samples were collected at baseline and during treatment at weeks 14, 22 and 52. Serum samples were analyzed using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq) and fecal samples by DNA shotgun metagenomic sequencing.<br><br>RESULTS: Using PhIP-Seq analysis, only the anti-flagellin antibodies library showed consistently attenuated antibody responses against bacterial flagellins in patients achieving remission (HBI&#x2264;4 and FCP&#x2264;150) versus non-remission at all time points (p<0.05). Of the 55 anti-flagellin antibodies analyzed, 15 showed consistent >1.5-fold over-representation in non-remission samples, with high conservation of amino-acid sequences and targeting of Clostridiales, Lachnospiraceae, or Roseburia species. Remission was associated with increased abundance of flagellin-target taxa including Roseburia intestinalis and decreased Ruminococcus_B gnavus and pathways involved in cellular oxidative stress, while non-remission showed increased Bacteroides species and pathways involved in 5-aminoimidazole ribonucleotide and semi-essential amino acids biosynthesis (q<0.05).<br><br>CONCLUSIONS: PhIP-Seq revealed that biologic treatment response in patients with CD associates with consistently decreased antibody responses against specific bacterial flagellins with conserved sequences. These findings identify potential biomarkers and therapeutic targets for improving treatment outcomes.},
}
@article {pmid41925227,
year = {2026},
author = {Deng, F and Han, Y and Peng, Y and Xu, Z and Yang, J and He, J and Li, D and Dong, G and Zhang, P and Jiang, H and Chai, J and Wang, C and Zhao, J and Li, Y},
title = {Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag068},
pmid = {41925227},
issn = {1751-7370},
abstract = {Giant pandas possess a carnivore-like gastrointestinal tract yet subsist on bamboo, and their gut communities contain few canonical cellulolytic taxa. We investigated how fiber processing proceeds in this setting by building a species-resolved reference and linking community features to cellular transcriptional profiles and isolate phenotypes. Using culturomics and PacBio HiFi metagenomics, we assembled a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes). Community profiling across 142 samples resolved three enterotypes dominated by Escherichia coli (ET-Ecoli), Clostridium SGBP116 (ET-Clos), and Streptococcus alactolyticus (ET-StreA), with ET-Ecoli enriched for tricarboxylic-acid and respiratory-chain modules and showing higher abundance of an endo-β-1,4-glucanase marker. Droplet-based microbial single-cell RNA-seq from four samples (16 659 cells) assigned a substantial share of cellulase-associated transcripts (GH1/GH3/GH5/GH9) in situ to Escherichia and revealed within-species heterogeneity: E. coli subpopulations segregated into respiration-enriched versus three-carbon/anaerobic-like programs, with cellulase/LPMO-linked transcripts concentrated in the former. Guided by these associations, panda-derived E. coli isolates assayed under defined atmospheres showed oxygen-dependent cellulolytic readouts in vitro. Although in vivo oxygen levels were not measured, the convergence of species-resolved community signatures, single-cell attribution and isolate phenotypes indicates that E. coli can contribute to cellulose processing under microoxic conditions in this cohort. The Pbac v2 resource and the integrated workflow (culturomics + HiFi metagenomes, multi-omics, microbial scRNA-seq) provide a template for species-level assignment of microbiome functions in hosts with unconventional diet-physiology combinations.},
}
@article {pmid41925420,
year = {2026},
author = {Leroy, S and Roméo, B and Belaid, A and Brest, P and Marquette, CH and Vouret-Craviari, V and Hofman, V and Hofman, P and Mograbi, B},
title = {Harnessing the lung microbiome for precision management of fibrotic lung disease.},
journal = {Trends in molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmed.2026.02.002},
pmid = {41925420},
issn = {1471-499X},
abstract = {Interstitial lung diseases, particularly idiopathic pulmonary fibrosis (IPF), have dismal prognoses, with a median survival of 3-5 years, owing to a lack of early biomarkers or effective treatments. This review highlights the lung microbiome as a key biological factor in IPF pathogenesis and a promising therapeutic target. Elevated burdens of pathogenic bacteria, including Streptococcus and Staphylococcus, in bronchoalveolar lavage fluid correlate with accelerated progression and higher mortality. These bacteria release toxins and activate Th17-driven inflammation, providing mechanistic links to alveolar injury and fibrosis. Host genetics and systemic factors, including oral-gut-lung interactions, further shape disease progression. Although antibiotic trials have been unsuccessful, embracing the microbiome as an active participant in IPF may open unprecedented opportunities for personalized interventions.},
}
@article {pmid41925447,
year = {2026},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {The rhizosphere microbiome as a decentralized immune system.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.006},
pmid = {41925447},
issn = {1878-4380},
abstract = {Plant immunity should be reconsidered beyond the boundaries of the plant genome. We propose that the rhizosphere microbiome may function analogously to a decentralized immune system, contributing adaptive defenselike properties and memory effects. In this forum article, we discuss how this perspective reframes immunity as an emergent property of plant-microbiome interactions, shifting the focus from a solitary host toward an integrated holobiont.},
}
@article {pmid41925964,
year = {2026},
author = {Oriquat, G and H, M and Maharana, L and Dhyani, A and Al-Hasnaawei, S and Singh-Chauhan, A and Arora, V and Sharma, J and Sadeghi-Samarjan, R},
title = {The Gut Microbiome in Amyotrophic Lateral Sclerosis: Emerging Mechanisms and Therapeutic Potential.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {41925964},
issn = {1559-1182},
mesh = {*Amyotrophic Lateral Sclerosis/microbiology/therapy ; Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Dysbiosis ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder marked by progressive loss of motor neurons and a median survival of 2 to 3 years after symptom onset. Despite advances in genetics, particularly the identification of mutations in C9ORF72, SOD1, and TDP 43, substantial variability in disease onset and progression remains unexplained. Mounting evidence points to the gut microbiome as a potential modifier of ALS biology. Microbial communities within the intestine influence systemic and central immune responses, energy metabolism, and the bioavailability of nutrients and therapeutic agents. Animal studies reveal that dysbiosis contributes to intestinal barrier dysfunction, immune activation, and altered metabolite production, while supplementation with beneficial metabolites such as butyrate or nicotinamide can delay disease progression and extend survival. Human studies, though inconsistent in their findings, consistently identify microbial imbalances and loss of diversity in subsets of patients. The gut-brain axis provides a plausible framework for these effects, as microbial products can signal through endocrine, neural, and immune pathways to influence central nervous system function. Beyond motor decline, microbiota alterations may also contribute to non-motor symptoms such as depression, anxiety, and gastrointestinal dysfunction, further shaping quality of life. While methodological variability complicates interpretation, integration of microbiome research with host genomics and metabolomics offers a path toward precision medicine. Targeting microbial composition and function may ultimately represent a novel therapeutic approach capable of modifying both disease biology and patient outcomes in ALS.},
}
@article {pmid41926038,
year = {2026},
author = {Haykal, D and Flament, F and Balooch, G and Mora, P and Kovylkina, N and Calixto, LS and Mercurio, DG and Sachdev, M and Sundaram, H},
title = {Integrative Dermatology for Longevity: The Synergy of Topical and Internal Approaches.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {41926038},
issn = {2193-8210},
abstract = {Skin aging reflects both intrinsic biological decline and extrinsic influences collectively known as the skin exposome, including ultraviolet (UV) radiation, air pollution, psychosocial stress, fatigue, sleep disruption, and suboptimal lifestyle behaviors. These factors contribute to cumulative molecular and structural damage, positioning the skin as both a visible marker of whole-body aging and a target for longevity strategies. This review examines the validity of an integrative "In and Out" approach, combining topical treatments, such as retinoids, peptides, antioxidants, and exosome-based formulations, with internal nutraceuticals including NAD[+] precursors, collagen peptides, polyphenols, and microbiome modulators. By targeting key hallmarks of aging, oxidative stress, inflammation, and epigenetic changes, this dual-modality model has the potential to promote skin regeneration, enhance aesthetic and functional outcomes, and contribute to broader health span optimization. Emerging tools such as skin aging clocks, biomarker-driven personalization, and artificial intelligence (AI)-guided interventions further strengthen this paradigm, establishing a scientifically grounded, preventive, and personalized framework that redefines the role of dermatology in the context of longevity. Personalized strategies that integrate diagnostic tools, lifestyle coaching, and tracking technologies allow for adaptive, dynamic strategies both internally and externally.},
}
@article {pmid41926198,
year = {2026},
author = {Grotzinger, H and Martínez-García, M and Miller, EC and Stelzer, IA and Collado, MC and Jacobs, EG},
title = {The Maternal Brain in Context: Systemic Physiological Changes Across Pregnancy.},
journal = {Annual review of neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-neuro-102124-043515},
pmid = {41926198},
issn = {1545-4126},
abstract = {During pregnancy, the maternal body undergoes profound, coordinated physiological adaptations to support the developing fetus, including major shifts in immune regulation and dramatic changes in the vascular system. Accompanying these peripheral adaptations, recent longitudinal studies in humans point to significant remodeling of the nervous system, occurring in lockstep with increases in gonadal hormone production. To understand the neural adaptations tied to pregnancy and the postpartum period, a holistic approach is essential-one that accounts for changes across multiple peripheral systems. In this review, we consider the impact of the endocrine, cardiovascular, microbiome, and immune systems on the maternal brain. By adopting this integrative approach, we aim to better understand the biological pathways that shape the maternal brain during normative pregnancies and those marked by adverse events.},
}
@article {pmid41926522,
year = {2026},
author = {Chen, Y and Zhou, D and Tu, Y and Wang, Y},
title = {Analysis of the Impact of Preterm Premature Rupture of Membranes (PPROM) on Maternal and Infant Outcomes and Countermeasures.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {534571},
pmid = {41926522},
issn = {1179-1411},
abstract = {OBJECTIVE: This study aimed to analyze the risk factors for Preterm Premature Rupture of Membranes (PPROM) and evaluate the impact of the timing of antibiotic administration on maternal and neonatal outcomes.<br><br>METHODS: A retrospective cohort study was conducted involving 480 pregnant women (240 with PPROM and 240 without PPROM) hospitalized between January 2021 and December 2022. Maternal data, genital microbiome profiles, and pregnancy outcomes were collected and compared. Within the PPROM group, patients were subdivided into an Early Treatment group (received intravenous cefuroxime sodium within 12&#xa0;hours of membrane rupture, n=120) and a Late Treatment group (received antibiotics after 12&#xa0;hours, n=120). Statistical analyses were performed using SPSS 22.0.<br><br>RESULTS: Genital infections (73.8% vs 20.4%, p<0.001) and gestational diabetes mellitus (GDM; 53.3% vs 22.9%, p<0.001) were significantly more prevalent in the PPROM group and were identified as independent risk factors (Genital infections: OR=3.895; GDM: OR=11.166). The PPROM group had worse outcomes, including a higher cesarean section rate (39.2% vs 25.8%, p=0.002) and higher incidences of neonatal asphyxia (4.2% vs 0.4%, p=0.006) and sepsis (2.5% vs 0%, p=0.040). Compared to the Late Treatment group, the Early Treatment group demonstrated significantly lower rates of intrauterine infection (1.67% vs 7.50%, p<0.05), cesarean section (30.0% vs 48.3%, p<0.05), neonatal asphyxia (0.83% vs 7.50%, p<0.01), and neonatal sepsis (0% vs 5.00%, p<0.05).<br><br>CONCLUSION: Genital tract infections and GDM are significant risk factors for PPROM. Early administration of antibiotics within 12&#xa0;hours of membrane rupture is associated with substantially improved maternal and neonatal outcomes, underscoring its critical importance in clinical management.},
}
@article {pmid41926667,
year = {2026},
author = {Chen, Y and Duan, R and Zhang, C and Li, G and Ji, X and Zhang, Q and Pei, F and Wang, K and Duan, L},
title = {Maternal Preconception Antibiotic Exposure Disrupts Microbial Succession: A Transgenerational Risk for Offspring Gut Mucosal Immaturity and Colitis Susceptibility.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e16931},
doi = {10.1002/advs.202516931},
pmid = {41926667},
issn = {2198-3844},
support = {2021YFA1301300//National Key R&amp;D Program of China/ ; 82470578//National Natural Science Foundation of China/ ; 7254451//Beijing Natural Science Foundation/ ; },
abstract = {The early-life microbiome plays a pivotal role in host development and lifelong health. Maternal factors are increasingly recognized as crucial in shaping offspring microbiome. However, how maternal preconception perturbations affects offspring health remain unclear. Thus, we combined animal and clinical data to elucidate whether preconception microbial perturbations disrupt microbial succession and increase offspring susceptibility to colitis. In animals, preconception antibiotic exposure induced long-lasting disruptions in offspring microbial ecology, through enhanced maternal-offspring microbial transmission, altered microbial developmental trajectories, and increased selective pressures during microbial community assembly. Ultimately, these alterations resulted in persistent gut mucosal immaturity and heightened susceptibility to colitis in adulthood. Complementary clinical studies revealed concordant alterations in gut microbiome and metabolome of children with inflammatory bowel disease (IBD) and their seemingly healthy mothers, characterized by pro-inflammatory taxa and metabolites. Notably, mothers of IBD children reported significantly higher antibiotic exposure than controls, which was also associated with enhanced maternal-offspring microbial transmission and increased selective pressures during microbial community assembly. Our findings reveal a potential intergenerational mechanism in which preconception perturbations are associated with disrupted microbial succession, transgenerational propagation of gut mucosal immaturity, and susceptibility to colitis. These results underscore the importance of judicious antibiotic use during the often-overlooked preconception period.},
}
@article {pmid41926670,
year = {2026},
author = {Chen, F and Yu, Y and Cai, X and Lin, J and Liang, R and Kang, R and Tang, D and Liu, J},
title = {Immune Checkpoint Inhibitors and Immunomodulators for Cancer Immunotherapy: Insights Into Resistance and Therapeutic Strategies.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e21355},
doi = {10.1002/advs.202521355},
pmid = {41926670},
issn = {2198-3844},
support = {32500653//National Natural Science Foundation of China/ ; 20261A031076//Guangzhou Health Science and Technology Young Talents Cultivation Program/ ; 2025M782596//China Postdoctoral Science Foundation/ ; GZC20251317//Postdoctoral Fellowship Program of China Postdoctoral Science Foundation/ ; 2024A03J0895//Guangzhou Municipal Science and Technology Bureau/ ; },
abstract = {Cancer immunotherapy has redefined cancer treatment. However, the molecular and cellular basis of immune evasion and therapeutic resistance remains incompletely understood. Early immune checkpoint inhibitors have delivered significant clinical benefit, but their efficacy and durability remain limited in many patients. These limitations have driven the exploration of next-generation immune checkpoints and additional regulatory pathways that shape tumor-immune interactions. Recent advances have broadened the immune checkpoint landscape and revealed new targets. These targets operate within interconnected networks shaped by tumor-intrinsic alterations, microenvironmental cues, the microbiome, and neuroimmune crosstalk. The application of emerging technologies has enabled high-resolution dissection of immune-tumor dynamics, providing a technological foundation for improving clinical outcomes through precise patient stratification and intervention. Furthermore, distinct regulated cell deaths, including apoptosis, ferroptosis, pyroptosis, necroptosis, and alkaliptosis, are increasingly recognized as critical modulators of antitumor immunity. Harnessing these mechanisms offers a rational path toward designing targeted and controllable therapeutic strategies that enhance the efficacy and durability of cancer immunotherapy.},
}
@article {pmid41926812,
year = {2026},
author = {Santana, DAD and Rolinski, F and Trombetta, LG and Göhringer, RMD and Lipinski, LC and Weber, SH and Sotomaior, CS and Ollhoff, RD},
title = {Humic acid supplementation modulates ruminal and fecal microbial communities in lamb.},
journal = {Research in veterinary science},
volume = {205},
number = {},
pages = {106166},
doi = {10.1016/j.rvsc.2026.106166},
pmid = {41926812},
issn = {1532-2661},
abstract = {The gastrointestinal microbiome affects the health and productivity of animals. Modifying these traits with additives may enhance their effects, making it a relevant strategy. This study investigated the effects of humic acids (HA) on the ruminal and fecal microbiomes of lambs and its potential adherence to ruminal mucosa. Twenty weaned Hampshire Down crossbred lambs aged 102.1 ± 6.6 days with an average body weight of 24.2 ± 3.5 kg were randomly allocated into two groups. Control group was fed a basal diet without HA, and treatment group was fed a basal diet with commercial HA at a dose of 500 mg/kg BW/day for 56 days. At the end of the experiment, ruminal and fecal samples were analyzed using 16S rRNA gene sequencing, and ruminal mucosal tissue from the slaughtered lambs was evaluated using histology and scanning electron microscopy (SEM). The addition of HA to the feed of lambs increased the relative abundance of the genus Bifidobacterium and decreased the genus Lachnospiraceae CAG-127 in the ruminal microbiome of lambs. Furthermore, an increase in the relative abundance of the genera Acutalibacteraceae UBA5905 and Lachnospiraceae VUNI01, along with a reduction in the order Campylobacterales and the genus Acutalibacteraceae CAG-180 was observed in the fecal microbiome. HA was not found in the ruminal mucosa of lambs, as determined by histology or SEM. HA supplementation modulated the ruminal and fecal microbiomes of lambs by reducing harmful and increasing beneficial bacteria, highlighting its potential as a functional feed additive to support ovine gut health.},
}
@article {pmid41926825,
year = {2026},
author = {Ali Ahmad, F and Salam, DA},
title = {Microbial community dynamics and functional potential in response to organic micropollutants in river sediments.},
journal = {Marine pollution bulletin},
volume = {229},
number = {},
pages = {119679},
doi = {10.1016/j.marpolbul.2026.119679},
pmid = {41926825},
issn = {1879-3363},
abstract = {Freshwater river sediments are increasingly exposed to complex mixtures of anthropogenic contaminants, yet the ecological repercussions on indigenous microbial communities -the main drivers of biogeochemical cycling- remain poorly understood. Previous investigations have focused primarily on contaminant occurrence, with no integrated assessment linking sediment contamination to microbial community structure and function. The objective of this study is to characterize the microbiome of the Upper Litani River Basin and to determine how chronic inputs of pharmaceuticals and aromatic hydrocarbons influence taxonomic composition, diversity, and predicted metabolic functions. 54 sediment samples were collected across nine locations during consecutive wet and dry seasons. Target organic micropollutants were quantified in the river sediments using validated analytical methods, and spatiotemporal patterns in microbial composition and metabolic functional potential were determined using amplicon sequencing. Across all samples, 45 phyla were identified, with Pseudomonadota, Bacillota, and Actinomycetota consistently being the dominant taxa. At the genus level, microbial communities were dominated by Acinetobacter, Exiguobacterium, Proteiniclasticum, Planococcus, and Clostridium sensu stricto. Variations in microbial community structure were correlated with the occurrence and concentrations of specific organic micropollutants detected in the sediments, namely with the pharmaceuticals ibuprofen, clomipramine and atenolol, as well as the hydrocarbons o-xylene and toluene. Functional predictions revealed a microbiome highly oriented toward chemoheterotrophic metabolism, underscoring the community's response to persistent organic enrichment. Collectively, these results demonstrate that pollutant concentrations and chemical profiles act as a major ecological force that shapes sediment microbial community dynamics and metabolic function in impacted freshwater ecosystems.},
}
@article {pmid41926978,
year = {2026},
author = {Masson, L and Radzey, N and Abrahams, AG and Ngcapu, S and McKinnon, L and Jaspan, HB},
title = {The vaginal microbiome and HIV acquisition risk.},
journal = {The lancet. HIV},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2352-3018(26)00032-9},
pmid = {41926978},
issn = {2352-3018},
abstract = {Non-optimal vaginal bacteriomes, vulvovaginal candidiasis, and sexually transmitted infections have been associated with increased risk of HIV acquisition in multiple clinical studies. However, there are still major gaps in our understanding of the role of the vaginal microbiome in HIV acquisition risk and non-bacterial components of the vaginal microbiome are not well characterised. Additionally, the functional interactions between the vaginal microbiome and its host that can result in increased risk of HIV acquisition are not fully understood. Better vaginal microbiome diagnostics and therapeutics feasible for implementation in settings with insufficient financial, human, and infrastructural resources are needed, and the effects of vaginal microbiome interventions on HIV risk need to be clinically evaluated. Progress is being made towards effective interventions through advanced omics technologies and improved in-vitro models that more accurately represent the complexity of the female genital tract. However, continued research and investments are needed to address this important women's health issue.},
}
@article {pmid41927358,
year = {2026},
author = {Cummings, LC and Freedman, SD},
title = {Increased gastrointestinal cancer risk in cystic fibrosis: Screening, prevention, and future directions.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.03.024},
pmid = {41927358},
issn = {1873-5010},
abstract = {The marked improvement in life expectancy from advances in treatment for cystic fibrosis has focused attention on diseases of aging. Cystic fibrosis (CF) is associated with increased risk for digestive system malignancies, including colorectal cancer and pancreaticobiliary cancers. Although risk factors for gastrointestinal malignancy include solid organ transplant and older age, people with CF may present with cancer at a younger age than the general population. Potential mechanisms for increased digestive cancer susceptibility include the underlying genetic defect, dietary patterns, or alterations in the gut microbiome. The impact of cystic fibrosis transmembrane regulator modulator therapies on gastrointestinal cancer risk remains unclear. Our review summarizes the previously published consensus screening recommendations for colorectal cancer, which endorsed starting colonoscopy at age 30 in patients with history of transplant and at age 40 in patients without a transplant. Recent work evaluating the use of non invasive testing for colorectal cancer is reviewed. We propose screening practices for non-colorectal cancers based on the limited evidence to date. We discuss potential preventative approaches and conclude with future directions to improve our ability to address this growing problem. Future work should focus on a greater understanding of the underlying mechanisms of pathogenesis at a molecular level, clinical risk factors for gastrointestinal malignancies at a population level, and preventative strategies.},
}
@article {pmid41927378,
year = {2026},
author = {Cai, Z and Han, C},
title = {Letter to the Editor re: "Age-related changes in the urinary microbiome of healthy Japanese children".},
journal = {Journal of pediatric urology},
volume = {},
number = {},
pages = {105884},
doi = {10.1016/j.jpurol.2026.105884},
pmid = {41927378},
issn = {1873-4898},
}
@article {pmid41742032,
year = {2026},
author = {Zhang, J and Dai, Y and Mustafa, A and Li, L and Li, Y and Sun, T and Chen, M and Yang, H and Ma, J},
title = {Terracing influences soil microbial assembly in citrus orchards: stochastic processes dominate community dynamics in a karst sloping land.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41742032},
issn = {1471-2180},
support = {GUIKE AB22080071//Guangxi Key Research and Development Program/ ; AA20161002//Science and Technology Major Project of Guangxi/ ; },
abstract = {BACKGROUND: Terracing is a key soil conservation practice in karst citrus orchards, yet its long-term effects on rhizosphere microbial community assembly remain poorly understood, especially the relative influence of deterministic (e.g., environmental filtering) versus stochastic processes (e.g., dispersal limitation).<br><br>RESULTS: We investigated rhizosphere soil microbial communities along a terrace chronosequence (0&#x2013;12&#xa0;years) in the Lijiang River Basin using MiSeq sequencing and metabolomics, with null model analysis employed to assess community assembly processes. Terrace age did not significantly affect microbial &#x3b1;-diversity, but was associated with subtle changes in community composition: Proteobacteria, a copiotrophic group, decreased slightly, while Chloroflexi, an oligotrophic group, increased modestly. These shifts suggest a weak trend toward lower soil nutrient availability rather than a clear successional reorganization. Microbial diversity and structure were significantly correlated with soil stoichiometric ratios and available phosphorus (p&#x2009;<&#x2009;0.05). Terracing also affected microbial network complexity and potential function. Potential functional profiling and metabolome data revealed that L-glutamine, a key nitrogen source, was negatively correlated with potential catabolic nitrate reduction (p&#x2009;<&#x2009;0.05). This relationship was most pronounced at the Y5 phase (peak diversity/network complexity), suggesting accelerated L-glutamine utilization tightly coupled with enhanced potential for dissimilatory nitrate reduction to maximize nitrogen-use efficiency during the successional climax. Notably, stochastic processes explained over 96% of the microbial assembly. Bacterial communities were primarily driven by homogenizing dispersal, while fungal communities followed undominated processes.<br><br>CONCLUSION: The prominence of stochasticity in our results complements current understanding of agricultural microbiome assembly, particularly emphasizing its vital role in fragile karst environments. We propose that optimizing terrace rotation intervals (e.g., every 5-year) could be a practical strategy to enhance nitrogen-cycling efficiency and support sustainable nutrient management in karst citrus cultivation.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04811-4.},
}
@article {pmid41749104,
year = {2026},
author = {Baz, L},
title = {Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41749104},
issn = {1471-2164},
abstract = {BACKGROUND: Archaea are a major domain of life that inhabit diverse and often extreme environments, contributing to biogeochemical cycles and participating in nutrient cycling within plant rhizospheric soils. This study applies metagenomic whole-genome shotgun sequencing to characterize the archaeal component of the rhizospheric microbiome associated with the wild plant species Moringa oleifera in Saudi Arabia.<br><br>RESULTS: Based on KEGG-annotated enzymes, Thaumarchaeota and Euryarchaeota emerged as the predominant archaeal phyla in the rhizosphere, with higher abundance than in bulk soil. The most abundant archaeal enzymes were assigned to metabolic pathways related to nitrogen and sulfur metabolism, carbon transformations, and responses to oxidative stress, indicating a putative contribution to nutrient turnover and stress-related functions. Network analysis further identified archaeal chemotaxis-related regulators and two-component sensor kinases linked to the root&#x2013;soil interface. Key enzymes detected included urease, glutamine synthetase, thiosulfate sulfurtransferase, and catalase-peroxidase.<br><br>CONCLUSIONS: These findings suggest that archaeal communities form a distinct functional module within the M. oleifera rhizosphere, potentially influencing soil nutrient dynamics and plant performance. The chief limitation is reliance on DNA-based metagenomic data from a single site and time point, without multi-omics or detailed soil characterization, restricting temporal and ecological generalization. Nonetheless, the dataset provides a genome-scale view of archaeal functional potential and offers testable directions for future experimental and process-oriented studies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12700-3.},
}
@article {pmid41896654,
year = {2026},
author = {Li, Y and Fu, W and Xiang, Z and Zhao, M and Xie, X and Guo, W and Zhou, Y and Zheng, M and Yang, J},
title = {Characteristics of gut microbiota and metabolites in patients with metabolic dysfunction-associated steatotic liver disease and colorectal adenoma.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41896654},
issn = {2045-2322},
support = {2021J0252//Scientific Research Fund Project of Yunnan Provincial Department of Education/ ; 2025J0270//Scientific Research Fund Project of Yunnan Provincial Department of Education/ ; 2024B010//Innovation Fund for Postgraduate Education of Kunming Medical University/ ; 202501AY070001-088//Science and Technology Plan Project of Yunnan Provincial Department of Science and Technology/ ; 82160106//National Natural Science Foundation of China/ ; },
abstract = {UNLABELLED: Metabolic dysfunction-associated steatotic liver disease (MASLD) has become one of the most prevalent chronic liver conditions worldwide, with its incidence steadily rising. However, the underlying mechanisms linking MASLD to colorectal adenoma remain unclear, and the role of gut microbiota and metabolites in this association requires further investigation. This study aims to characterise the gut microbiota and metabolites in patients with MASLD and colorectal adenoma. A cohort of 58 MASLD patients was enrolled and stratified into two groups based on colorectal adenoma status: the MASLD with colorectal adenoma group (M-CA group, n = 30) and the MASLD without colorectal adenoma group (M-NCA group, n = 28). The gut microbial ecosystem in the M-CA group showed significant dysregulation, evidenced by a decreased Gut Microbiome Health Index (GMHI) and significantly increased Microbiome Dysbiosis Index (MDI). Linear Discriminant Analysis Effect Size (LEfSe) identified 75 differentially abundant microbial taxa between groups, with Bacteroides vulgatus, Bacteroides ovatus, uncultured bacterium of norank genus of Muribaculaceae family, Muribaculaceae, and norank of Muribaculaceae family being significantly enriched in the M-CA group, representing potential microbial biomarkers for this cohort. Partial Least Squares Discriminant Analysis (PLS-DA) screened 116 differential metabolites. When combined with Random Forest (RF), Support Vector Machine (SVM) and Least Absolute Shrinkage and Selection Operator (LASSO) machine learning algorithms, 16 significantly identified biomarkers were discovered. The joint analysis of both omics revealed that variations in differential metabolite levels were associated with changes in specific microbiota abundances. Kyoto encyclopedia of genes and genomes (KEGG) functional prediction analysis indicated that the coordinated alterations in metabolites and microbiota may collectively influence multiple metabolic pathways, including lipid metabolism, xenobiotics biodegradation and metabolism, amino acid metabolism, carbohydrate metabolism, biosynthesis of other secondary metabolites and nucleotide metabolism. This study revealed that patients with MASLD and colorectal adenoma exhibited significant alterations in the gut microbiota composition and metabolic profile, indicating potential impacts on associated metabolic pathways. These findings provided novel insights and a foundation for future research into potential intervention strategies for this clinical complication.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-45782-w.},
}
@article {pmid41915463,
year = {2026},
author = {Yasavoli-Sharahi, H and Shahbazi, R and Alsadi, N and Sahebi, NB and Cuenin, C and Cahais, V and Chung, FF and Herceg, Z and Matar, C},
title = {Lentinula edodes Cultured Extract Intake at Puberty Mitigates Inflammatory Signals at the Mammary Glands by the Involvement of Epigenetic Mechanisms in BALB/c Mice.},
journal = {The breast journal},
volume = {2026},
number = {1},
pages = {e2122220},
doi = {10.1155/tbj/2122220},
pmid = {41915463},
issn = {1524-4741},
support = {532223-18//Natural Sciences and Engineering Research Council of Canada/ ; 2019-01497//AHCC Research Association, and New Frontiers in Research Fund-Exploration (NFRF/ ; //University of Ottawa/ ; },
mesh = {Animals ; Female ; Mice ; Mice, Inbred BALB C ; *Epigenesis, Genetic/drug effects ; DNA Methylation/drug effects ; *Mammary Glands, Animal/drug effects/metabolism ; Lipopolysaccharides ; *Shiitake Mushrooms/chemistry ; Sexual Maturation ; MicroRNAs/metabolism ; *Inflammation ; },
abstract = {Exposure to immune stress or lipopolysaccharide (LPS) during critical developmental stages like puberty may lead to gut microbiome dysbiosis and epigenetic dysregulation in mammary glands, affecting gene expression and potentially elevating breast cancer susceptibility in adulthood. Although LPS's adverse impacts on intestinal and brain functions are well-documented, its effects on mammary glands remain underexplored. Using an immunocompetent BALB/c mouse model, we administered an acute LPS dose (1.5 mg/kg body weight) during puberty. The study evaluated the long-term consequences of LPS exposure alone and combined with AHCC (Lentinula edodes cultured extract, 2 g/kg body weight/day) on DNA methylation patterns, cytokine profiles, and microRNA expression in mammary glands at 9 weeks of age. Analyses included DNA methylation sequencing, multiplex immunoassays, quantitative PCR, and image processing. Pubertal LPS exposure produced persistent molecular dysregulation in mammary glands, including differential DNA methylation (> 5% change vs. control; FDR-adjusted p < 0.05), elevated inflammatory mediators, and altered microRNA expression. Differentially methylated regions were enriched in regulatory features, with decreased methylation at transcription start sites, promoters, and 5' UTRs of genes implicated in mammary development and oncogenic signaling (including Vav3, Pdgfa, Pdgfc, Jag2, Hras, Ksr1, Il2rb, Il17b, and Il17rb) in the LPS group, whereas the AHCC + LPS group exhibited a shift toward hypermethylation at these loci (approximately 5%-10% decrease). Inflammatory profiling showed increased IL-17A/F (∼2-fold vs. control; p < 0.05), while microRNA analyses indicated reduced let-7a/c (∼30% vs. control; p < 0.05). Notably, miR-130a and miR-34a increased ∼1.5-fold across all treatment groups relative to control. Pubertal LPS exposure induces enduring epigenetic and inflammatory changes in mammary glands that may heighten breast cancer risk. AHCC's mitigating role indicates potential for dietary interventions to counteract these effects.},
}
@article {pmid41915473,
year = {2026},
author = {Zhao, Y and Li, J and Han, K and Chen, L and Zhuang, Q and Li, S and Hua, M and Li, N and Yue, J and Gu, C and Rong, C and Yang, D and Deng, Z and Huang, J and He, L and Zeng, H and Yu, Z and Chen, C},
title = {Phage-related symbiosis and antagonism shape gut ecosystem dynamics in Lachnospiraceae and Bacteroidaceae.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117166},
doi = {10.1016/j.celrep.2026.117166},
pmid = {41915473},
issn = {2211-1247},
abstract = {The human gut microbiota is shaped by intricate, yet poorly resolved interactions among bacteria, as well as their relationship to bacteriophages. However, resolving this complex interaction and dynamics has been limited by the challenges in genome recovery and functional characterization. We develop culture-enriched metagenomic co-barcoding sequencing (cMECOS), obtain 5,006 high- or medium-quality (HMQ) metagenome-assembled genomes (MAGs) and reconstruct bacteria-phage interaction networks via CRISPR spacer mapping. This framework uncovers two ecologically distinct, inter-specific bacterial networks: a Lachnospiraceae-dominated community associates with temperate phages and is characterized by metabolic cross-feeding and a Bacteroidaceae-dominated community linked to virulent phages and marked by resource competition. Both network architectures are disrupted in both inflammatory bowel disease (IBD) and obesity (OB), underscoring their role in ecosystem stability. Our work establishes cMECOS as a powerful platform for deciphering complex microbiome interactions and identifies phage-related bacterial networks as critical regulators of gut homeostasis, providing a foundation for phage-informed therapeutic development.},
}
@article {pmid41915616,
year = {2026},
author = {Wei, Y and Ji, X and Mao, Y and Liu, Y and Li, Y},
title = {Gut Microbiome, Immune Cells, and Heart Failure: A Multi-Omics Mendelian Randomization Study.},
journal = {Cardiology},
volume = {},
number = {},
pages = {1-14},
doi = {10.1159/000550655},
pmid = {41915616},
issn = {1421-9751},
abstract = {INTRODUCTION: The global burden of heart failure is escalating, marked by persistently rising prevalence, incidence, and mortality. The emerging hypothesis that the gut microbiome, as a modifiable factor, influences HF pathogenesis through immune modulation.<br><br>METHODS: To examine the causal relationship, we conducted two-sample Mendelian randomization (MR) analyses using summary genetic data, which was obtained from genome-wide association studies (GWASs) of gut microbial taxa, immune cells, and HF. Single-cell RNA sequencing data and single-nucleus RNA sequencing from chronic heart failure and healthy samples were extracted for investigation. Expression quantitative trait loci (eQTL) MR analysis was used to integrate HF GWAS with eQTL from heart to confirm potential genes. We performed functional enrichment analysis to enrich their functions.<br><br>RESULTS: The analysis revealed that genus Blautia (p = 0.0287), genus Corynebactrium (p = 0.022), genus Demequina (p = 0.0064), genus Enterococcus (p = 0.0307), genus Eubacterium (p = 0.0234), genus F0482 (p = 0.0107), genus Leclercia (p = 0.0026), genus Prevotellamassilia (p = 0.0444), and genus Ruminococcus were causally linked to a higher risk of HF, while genus CAG-125 (p = 0.0443), genus CAG-245 (p = 0.0116), genus Fournierella (p = 0.0326), genus Roseibacillus (p = 0.028) protective factors for HF. Among differential microflora, genus Leclercia was significantly related to higher level of HVEM on terminally differentiated CD4+T-cell count (p = 0.0058). Moreover, HF patients underwent obviously increased NK/T cells. We identified positive association of EIF3A, RPL5, SLC25A51, HERC5, SUSD3, ZNF292, ZNF655, and DNAJC9 with increased risk of HF, whereas the expression of RMC1, CAMK2G, RPS26, ATP5PO displayed protective effect against HF by eQTL MR analysis; they were mainly enriched in myc-Targets-V1, IFN-&#x3b3;-response, IFN-&#x3b1;-response, PI3K/AKT/mTOR signaling, TGF-beta signaling, allograft rejection, notch signaling pathways, angiogenesis, epithelial mesenchymal transition, UV-response-DN, hedgehog signaling, myogenesis.<br><br>CONCLUSION: Our multi-omics MR study uncovered the causality of gut microbiome on immune cells and HF. Genus Leclercia-related changes in T cells may present as a viable focus for HF. This offers new insights into mechanisms and therapy of gut microbiome-mediated HF.},
}
@article {pmid41915730,
year = {2026},
author = {Negahban, M and Msaada, K},
title = {Beyond the crop: the role of medicinal and aromatic plants in soil carbon sequestration and nitrogen cycling.},
journal = {International journal of environmental health research},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/09603123.2026.2653197},
pmid = {41915730},
issn = {1369-1619},
abstract = {Medicinal and aromatic plants (MAPs) play a critical yet underexplored role in enhancing soil functionality through their unique phytochemical interactions and ecological adaptability. This review synthesizes current research on how MAPs influence soil carbon sequestration and nitrogen cycling, positioning them as multifunctional agents in sustainable agroecosystems. Unlike conventional crops, MAPs release complex secondary metabolites, such as flavonoids, alkaloids, terpenoids, and phenolics, which modulate microbial diversity, enzymatic activity, and nutrient transformation. These compounds shape the rhizosphere microbial communities, facilitate nitrogen fixation and mineralization, and contribute to soil organic matter (SOM) stabilization through rhizosphere priming and humus formation. Integrated approaches, such as intercropping, agroforestry, and organic amendments, enhance these benefits, while mitigating allelopathic effects and improving carbon and nitrogen fluxes. This review further explores technological innovations including remote sensing (RS), biochar applications, and nanotechnology, which support MAP-based climate-resilient agriculture. Case studies across diverse geographies demonstrate MAPs' potential to restore degraded soils, reduce greenhouse gas emissions, and improve phytochemical yields. Overall, MAPs offer a promising model for regenerative, low-input farming systems that align ecological integrity with economic viability. By actively engineering the soil environment, MAPs emerge not only as botanical resources but also as ecological catalysts in the transition to sustainable agriculture.},
}
@article {pmid41916054,
year = {2026},
author = {Pongmanee, K and Rassmidatta, K and Lee, TY and Lin, JS and Chaosap, C and Adeyemi, KD and Ruangpanit, Y},
title = {Influence of synbiotic supplementation on performance, fecal consistency, cecal microbiome, and egg quality of hens during late laying phase.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106851},
doi = {10.1016/j.psj.2026.106851},
pmid = {41916054},
issn = {1525-3171},
abstract = {Hens in the late laying phase often experience age-related physiological constraints that may reduce production efficiency, eggshell quality, and welfare. This study evaluated the effects of dietary synbiotic supplementation on laying performance, egg quality, fecal characteristics, and the cecal microbiome of late-phase laying hens. A total of 240 Lohmann Brown hens (50 weeks old) were distributed into 20 replicates and randomly assigned to a corn-soybean control diet or the same diet supplemented with 100 mg/kg synbiotic (SYNLAC Prime®) for 22 weeks. Synbiotic supplementation did not affect egg production or egg mass but significantly reduced feed intake (P = 0.036). It also improved eggshell quality by decreasing the proportion of cracked eggs (P = 0.014) and increasing eggshell weight (P = 0.049) and shell thickness (P = 0.031). Fecal score and moisture content were not affected; however, synbiotic-fed hens showed lower fecal ammonia concentration (P = 0.033). Synbiotic supplementation increased both alpha and beta microbial diversity in the cecum. While microbial composition at higher taxonomic levels was largely unchanged, the relative abundances of Ruminococcaceae and Lachnospiraceae increased, whereas those of Bacteroidaceae and Clostridiaceae decreased. At the genus level, synbiotic supplementation increased Faecalibacterium, Ruminococcus, and Lactobacillus, while reducing Bacteroides and Alistipes. Functional prediction analysis indicated that synbiotic supplementation upregulated 12 cecal metabolic pathways and downregulated two pathways. Overall, synbiotic supplementation improved eggshell quality, promoted beneficial gut microbial populations, and reduced fecal ammonia emissions, suggesting its potential as a dietary strategy to support productivity and gut health in hens during the late laying phase.},
}
@article {pmid41916081,
year = {2026},
author = {Machado, P and Mazahery, H and Black, LJ and Tremlett, H and Daly, A and Pham, NM and Tessema, GA and Zhu, F and Banwell, B and Bar-Or, A and Marrie, RA and Bernstein, CN and Mirza, AI and Yeh, EA and Waubant, E and O'Mahony, J and Dunlop, E and , },
title = {Higher ultra-processed food consumption is associated with higher likelihood of paediatric-onset multiple sclerosis.},
journal = {Multiple sclerosis and related disorders},
volume = {109},
number = {},
pages = {107159},
doi = {10.1016/j.msard.2026.107159},
pmid = {41916081},
issn = {2211-0356},
abstract = {BACKGROUND: Diets are increasingly dominated by ultra-processed foods, which have been linked to several chronic diseases. Emerging evidence suggests an association between ultra-processed food consumption and inflammatory diseases, including multiple sclerosis (MS).<br><br>OBJECTIVE: To assess associations between consumption of ultra-processed foods and paediatric-onset MS (PoMS).<br><br>METHODS: We used data from the microbiome sub-study of the Canadian Pediatric Demyelinating Disease Network Study for PoMS cases (symptom onset aged <18 years) and unaffected controls. Data on consumption of ultra-processed foods (defined within the Nova system) were derived from dietary intake data collected using the Block Kids Food Screener. Dietary contribution of ultra-processed foods (% of total grams consumed per day) was estimated. Logistic regression models were used to examine associations between ultra-processed food consumption (continuous and tertiles) and likelihood of PoMS. Models were adjusted for age at dietary data collection, sex, race, region of residence, and total energy intake.<br><br>RESULTS: Dietary data were collected from PoMS participants (females=57, males=23) aged 5-28 years and controls (females=30, males=16) aged 8-26 years. Each additional 10% in ultra-processed food consumption was associated with a 35% higher odds of being a PoMS participant (adjusted odds ratio [aOR]=1.35, 95% CI 1.05, 1.73). Participants in the highest (versus lowest) tertile for ultra-processed food consumption had over five times higher odds of being a PoMS participant (aOR=5.30, 95% CI 1.36, 20.70).<br><br>CONCLUSION: Participants with PoMS reported greater consumption of ultra-processed foods compared to unaffected peers. More comprehensive longitudinal dietary histories are required to better understand this observation.},
}
@article {pmid41916092,
year = {2026},
author = {Qiu, C and Jie, W and Qian, Y and Lu, X and Chen, Y and Si, M},
title = {Ageing of the Oral Mucosa: Mechanisms and Consequences.},
journal = {International dental journal},
volume = {76},
number = {3},
pages = {109482},
doi = {10.1016/j.identj.2026.109482},
pmid = {41916092},
issn = {1875-595X},
abstract = {Oral mucosal ageing represents a fundamental reprogramming of the tissue microenvironment, a dynamic process that underlies the functional decline and heightened disease susceptibility observed in the elderly. This review synthesises current evidence to reconceptualise oral mucosal ageing as an active reprogramming of the tissue microenvironment, delineating the interplay between structural, molecular, and immunological changes, and exploring how these alterations drive functional decline and increase susceptibility to age-related oral diseases. Through a comprehensive analysis of experimental and clinical studies from human and animal models, we demonstrate that the ageing process fundamentally transforms the oral mucosa. Key findings include structural changes such as epithelial atrophy, extracellular matrix remodelling, and salivary gland degeneration, driven molecularly by genomic instability, accumulation of proinflammatory senescent cells, stem cell exhaustion, and dysregulated stress responses. These are compounded by an immunological state of 'inflammaging' and functional decline in innate and adaptive immunity, further exacerbated by shifts in the oral microbiome. Collectively, these deficits lead to impaired regeneration, diminished sensory function, and reduced salivary secretion, creating a permissive landscape for chronic oral diseases. In conclusion, oral mucosal ageing is a dynamic process of microenvironmental reprogramming driven by cellular senescence, immunosenescence, and structural decay. This actively underpins the heightened vulnerability to oral disease in the elderly, providing a mechanistic foundation for developing targeted interventions to preserve oral health in ageing populations.},
}
@article {pmid41916240,
year = {2026},
author = {Wen, S and Liu, J and Lin, B and Li, N and Diao, X},
title = {Aging enhances the ecological toxicity of polyethylene microplastics to marine medaka larvae (Oryzias melastigma).},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129493},
doi = {10.1016/j.jenvman.2026.129493},
pmid = {41916240},
issn = {1095-8630},
abstract = {Microplastics (MPs), widely distributed in marine environments, pose urgent ecological risks as emerging contaminants. However, current ecological risk assessments are largely based on the commercially produced MPs, which poorly represent in natural settings. Here, we simulated the natural aging of polyethylene MPs (PE-MPs) using ultraviolet radiation (UV) and Fenton reactions, characterized the resultant physicochemical changes, and assessed their ecological toxicity in marine medaka larvae over a 30-day exposure experiment. Short-term aging via UV and Fenton reactions primarily altered the physical properties of PE, including surface morphology, hydrophobicity, and Zeta potential. Both original and aged PE induced intestinal damage and oxidative stress in the larvae, indicating that aged PE retains its toxicity. In contrast, aged PE significantly altered the microbial community structure in the fish intestines: Roseibacillus was significantly enriched in the UV-aged polyethylene (UVPE) exposure group, while Ruegeria and Pseudomonas were enriched in the Fenton-aged polyethylene (FPE) exposure group. Functional predictions of the intestinal microbial communities indicated that exposure to FPE resulted in the upregulation of metabolism-related functions, whereas exposure to UVPE significantly downregulated similar functions. Such upregulation likely reflects microbiome reprogramming under stress rather than improved health. Overall, our study demonstrated that aged PE exhibited pronounced toxicity to marine fish and their larvae by altering gut microbiota, and thus significantly impacting energy metabolism and nutrient absorption, leading to detrimental effects on their growth and development. These findings further underscore the enhanced ecological toxicity effects of aged MPs on marine organisms, highlighting the need for better assessments of the adverse impacts of MPs in marine environments.},
}
@article {pmid41916289,
year = {2026},
author = {Chen, S and Wang, Y and Chen, B and Hou, X and Liu, S and He, S and Qi, J and Peng, Z and Pan, H and Liang, C and Wei, G and Jiao, S},
title = {Diversity-triggered 2-naphthoic acid exudation recruits keystone microbial taxa to promote soybean drought tolerance.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.002},
pmid = {41916289},
issn = {1934-6069},
abstract = {Rhizosphere microbiomes are essential for plant growth and stress tolerance, yet how microbial diversity shapes drought resilience in soybean remains unclear. Here, we demonstrate that high rhizosphere microbial diversity, generated via dilution-to-extinction manipulation of soil microbiome diversity, improves soybean performance under drought. Integrated metabolomic and transcriptomic analyses identify 2-naphthoic acid as a diversity-induced root exudate that accumulates exclusively under drought. This metabolite selectively recruits Sinorhizobium CS204 via chemotaxis and ATP-binding cassette (ABC) transporter-mediated uptake, as confirmed by in vitro substrate utilization assays and targeted mutant construction. Molecular docking and microscale thermophoresis reveal direct interactions between this metabolite and nitrogen-cycling proteins, enhancing denitrification and nitrogen fixation of S.CS204. Co-application of 2-naphthoic acid and S.CS204 significantly improves plant nutrient acquisition and photosynthesis under drought. Collectively, our study underscores the pivotal role of rhizosphere microbial diversity in triggering the exudation of root metabolites to recruit keystone taxa, establishing microbe-plant synergies that bolster drought tolerance.},
}
@article {pmid41916309,
year = {2026},
author = {Cichy, A and Dewan, A and He, Z and Fitzgerald, C and Ratkowski, M and Krasewicz, J and Ozarkar, V and Kaye, S and Teng, T and Zhang, J and Feinstein, P and Bozza, T},
title = {A microbiome-derived olfactory signal regulates inter-male aggression and social dominance in mice.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.03.009},
pmid = {41916309},
issn = {1879-0445},
abstract = {Many species use microbiome-derived metabolites as chemosensory cues, yet the chemicals involved and the sensory pathways that detect and process them remain poorly understood. Trimethylamine (TMA) is a volatile metabolite that is produced by the gut microbiome and selectively accumulated in the urine of sexually mature male mice. Here, we show that TMA regulates inter-male aggression and social dominance by activating trace amine-associated receptor 5 (TAAR5) in the main olfactory system. In wild-type mice, early aggressive behavior during male-male encounters strongly predicts eventual social status: dominant males initiate more attacks, whereas subordinate males display more defensive behaviors. Deletion of TAAR5 eliminated this asymmetry, with dominant and subordinate mice showing similar levels of aggressive and defensive behaviors. Strikingly, restoring TAAR5 expression in olfactory sensory neurons (OSNs) rescued the behavioral asymmetry, indicating that this effect is mediated by the main olfactory system and arguing against contributions from proposed TAAR5 expression in the brain. Finally, pharmacological suppression of microbial TMA production reduced inter-male aggression, and this effect was reversed by painting treated males with TMA, showing that microbiome-derived TMA is the key volatile ligand for TAAR5 in this context. Taken together, our findings identify TMA as a critical olfactory cue that signals the presence of sexually mature males and facilitates social hierarchy formation. More broadly, our results demonstrate that a microbiome-derived metabolite can shape mammalian social interactions through the main olfactory system and uncover a previously unrecognized role for the TAAR family in regulating social behavior.},
}
@article {pmid41916434,
year = {2026},
author = {Iachizzi, M and Zajac, N and Ruiz, JL and Güller, T and Rabin, R and Schalbetter, S and de Cillis, F and Moccia, MD and Cattaneo, A and Cryan, JF and Richetto, J},
title = {Probiotic treatment rescues behavioral deficits and gut microbial abnormalities induced by preconceptional stress in mothers and offspring.},
journal = {Brain, behavior, and immunity},
volume = {136},
number = {},
pages = {106571},
doi = {10.1016/j.bbi.2026.106571},
pmid = {41916434},
issn = {1090-2139},
abstract = {Depression and anxiety during pregnancy are major public health concerns with lasting consequences for mother and child. Although the gut microbiome contributes to stress and mood regulation, its role in preconceptional stress and transgenerational outcomes remains unclear. Here, we examined behavioral, microbial, and thalamic transcriptional effects of preconceptional social isolation rearing (SIR) in female mice and tested whether maternal probiotic supplementation mitigates these alterations. SIR females displayed increased anxiety-like and social-avoidant behavior, reduced gut microbial diversity, depletion of Odoribacter, Tuzzerella, and Alloprevotella, and enrichment of Bacteroides and Lachnospiraceae. A multispecies probiotic (Lactobacillus rhamnosus HN001, L. acidophilus La-14, Bifidobacterium lactis HN019) reversed these behavioral and microbial changes. Adult offspring of SIR dams showed sex-dependent behavioral deficits and microbial alterations partly reflecting maternal patterns. Prenatal SIR was associated with reduced thalamic Bdnf expression in offspring and altered Grin2a/2b selectively in males. In contrast, prenatal probiotic exposure exerted broader transcriptional effects and restored Bdnf levels in SIR offspring. SIR-induced increases in Lachnospiraceae were transmitted to offspring, whereas reductions in Ruminococcaceae were normalized by maternal probiotic treatment. Predicted functional profiling indicated sex-dependent modulation of microbial pathways related to tryptophan and central carbon metabolism. These findings demonstrate enduring transgenerational effects of preconceptional stress on the gut-brain axis and support maternal probiotic supplementation as a potential strategy to mitigate stress-induced dysregulation.},
}
@article {pmid41916460,
year = {2026},
author = {Asiri, F and Kishk, M and Karam, H and Al-Muhanna, K and Al-Najdi, F and Al-Enezi, A and Al-Khalifah, N and Hejji, AB and Al-Salameen, F and Al-Salem, SM},
title = {Innovative soil seeding with waste-derived microbial inoculums: Enhancing plastic biodegradation and Revealing microbiome shifts.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134523},
doi = {10.1016/j.biortech.2026.134523},
pmid = {41916460},
issn = {1873-2976},
abstract = {Plastic waste accumulation in terrestrial ecosystems poses a global environmental challenge, demanding sustainable alternatives to conventional disposal. Aerobic biodegradation is promising, yet most studies rely on composting systems, often overlooking different polymer types and how seeding soil with waste-derived inoculums affect polymer breakdown. This study developed an innovative soil-seeding approach using microbe-rich inoculums derived from real waste streams: compost (Comp.), activated sludge (AS), plastic-contaminated soil (PCS), and oil-contaminated soil (OCS) to enhance biodegradation of starch, compostable bioplastic (CBP), and the mineralization of linear low-density polyethylene (LLDPE). Biodegradation was evaluated under controlled soil conditions, and microbial community responses were characterized through metataxonomic profiling. Starch exhibited the highest biodegradation (71-100%), followed by CBP (31-56%) and LLDPE mineralization (12-22%). OCS and PCS significantly enhanced CBP and LLDPE degradation, respectively, corresponding to differences in organic content and carbon-to-nitrogen ratios. Shifts in microbial composition revealed polymer-specific microbial drivers, including Bacilli (Bacillaceae, Paenibacillus) and Chaetomium for starch, and Actinobacteriota, Acidimicrobiia, Mycobacterium, and Nocardioides for CBP, particularly in OCS. LLDPE degradation remained low but was modestly improved in Comp- and PCS-amended soils. Overall, this study demonstrates that targeted soil-seeding with waste-derived inoculums can substantially influence polymer degradation and microbial succession, providing a practical strategy to accelerate biodegradation in natural soils and informing future sustainable plastic-management approaches.},
}
@article {pmid41916675,
year = {2026},
author = {Boven, A and Vranken, H and Vlieghe, E and Boleij, A and Fall, K and Engstrand, L and Brusselaers, N},
title = {Commonly prescribed drugs as risk factors for Clostridioides difficile infections: a Swedish population-based case-control study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337629},
pmid = {41916675},
issn = {1468-3288},
abstract = {BACKGROUND: Clostridioides difficile infections (CDIs) are associated with antibiotic use, although the link with other drugs remains underexplored.<br><br>OBJECTIVES: To investigate the association between antibiotic and non-antibiotic drugs with microbiome-modulating activity on new occurrences of CDI.<br><br>DESIGN: We conducted a Swedish population-based case-control study from 2006 to 2019 including 42&#x2009;921 cases matched with 355&#x2009;159 population controls on age and sex, obtained from multiple linked Swedish registries. The effect of antibiotic and non-antibiotic use within 30 days from the index date on CDI occurrence was estimated using multivariable conditional logistic regression additionally with a lasso penalty. Models were adjusted for age and sex by design and for Charlson Comorbidity Index and concomitant drug use, providing adjusted ORs (aORs) with 95% CIs.<br><br>RESULTS: Antibiotics with the greatest CDI risk were lincosamides (aOR=31.4, 95% CI 27.9 to 35.3), combinations of penicillins (aOR=19.8, 95% CI 15.9 to 24.5), sulfonamides and trimethoprim, and cephalosporins, though no association for tetracyclines. Among non-antibiotic drugs, we found decreased risks of CDI for lipid-modifiers (aOR=0.8, 95% CI 0.8 to 0.8) and aspirin (aOR=0.8, 95% CI 0.7 to 0.8) and increased risks for antidiarrhoeals (aOR=7.3, 95% CI 6.8 to 7.8), corticosteroids (aOR=2.4, 95% CI 2.3 to 2.5), proton-pump inhibitors (PPIs) (aOR=1.8, 95% CI 1.7 to 1.8), nervous system drugs, constipation drugs, histamine H2-receptor antagonists, antidepressants, and beta blockers, but no significant risk for non-steroidal anti-inflammatory drugs.<br><br>CONCLUSIONS: We found varying effects of antibiotics on CDI, providing evidence for ongoing efforts in prudent prescribing decisions and antimicrobial stewardship. We confirmed PPI as a main risk factor for CDI and provided new evidence for other non-antibiotic drugs as potentially important risk factors considering their high prescription prevalence.},
}
@article {pmid41916943,
year = {2026},
author = {Sailesh, SS},
title = {Association between soft drink consumption and depression mediated by gut microbiome: a perspective.},
journal = {East Asian archives of psychiatry : official journal of the Hong Kong College of Psychiatrists = Dong Ya jing shen ke xue zhi : Xianggang jing shen ke yi xue yuan qi kan},
volume = {36},
number = {1},
pages = {56-59},
doi = {10.12809/eaap25136},
pmid = {41916943},
issn = {2224-7041},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Carbonated Beverages/adverse effects ; *Depression/etiology/epidemiology/microbiology ; *Sugar-Sweetened Beverages/adverse effects ; Female ; },
abstract = {This perspective synthesises current evidence on the association between soft drink consumption and depression, with emphasis on the gut microbiome as a potential mediating mechanism. PubMed, Scopus, and Google Scholar were searched using the following terms: 'soft drinks', 'sugar-sweetened beverages', 'carbonated beverages', 'soda', 'depression', 'depressive symptoms', 'mental health', 'gut microbiome', 'microbiota', and 'gut-brain axis'. Peer-reviewed original articles published in English between January 2000 and October 2025 were included if they involved human participants of any age (sample size ≥50 for observational studies), assessed soft drink or sugar-sweetened beverage consumption, and measured depression diagnosis, depressive symptoms, or depression severity. Associations between soft drink consumption and increased depression risk were consistently shown across multiple study designs and populations. Evidence for artificially sweetened beverages was less consistent and suggested potentially distinct, non-sugar-related pathways. A multicentre cohort study of 932 participants revealed that soft drink consumption predicted the major depressive disorder diagnosis (odds ratio = 1.081), with stronger effects in women (odds ratio = 1.167). Eggerthella partially mediated the soft drink-depression association, explaining approximately 4% of the association. Soft drink consumption is associated with increased depression risk through multiple biological pathways involving inflammation, metabolic dysregulation, and gut microbiome alterations. Modest effect sizes suggest the involvement of multiple interconnected mechanisms. Public health interventions to limit sugar-sweetened beverage consumption are recommended to improve physical and mental health. Healthcare providers should consider dietary assessment and counselling as part of depression prevention and treatment strategies.},
}
@article {pmid41917102,
year = {2026},
author = {Roy, M and Han, D and Lee, D and Kang, B and Choi, K},
title = {Cultivation system and plant health influence root-associated bacterial community structure and interaction networks in strawberry.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45642-7},
pmid = {41917102},
issn = {2045-2322},
support = {(RS-2023-00251252 and 2020R1A6A1A03047729)//National Research Foundation of Korea/ ; (RS-2025-02613089)//Rural Development Administration/ ; },
abstract = {Strawberry is cultivated in both soil-based field and substrate-based soilless hydroponic systems, yet how cultivation context shapes root-associated bacterial communities and their interaction architecture remains unclear. We compared root-associated bacterial communities from field root-associated soil and hydroponic root-adhering substrate under asymptomatic and symptomatic conditions using 16S rRNA gene amplicon sequencing. Cultivation system was the primary driver of community structure, clearly separating field and hydroponic samples. Field communities were enriched in Firmicutes and Actinobacteria, such as Bacillaceae and Nocardioidaceae, whereas hydroponic communities showed higher relative abundances of Proteobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia, including Chitinophagaceae and Sphingomonadaceae. Differential abundance and Random Forest analyses revealed consistent enrichment of Bacillus-associated ASVs in field samples, whereas asymptomatic and symptomatic communities showed greater compositional differentiation in hydroponic than in field samples.. Co-occurrence network analysis further demonstrated that hydroponic communities contained more taxa and interactions but exhibited lower density and clustering compared to field communities, indicating reduced structural cohesion. These findings demonstrate that cultivation system strongly influences both the composition and structural organization of strawberry root-associated bacterial communities, with implications for microbiome-informed disease management in intensive production systems.},
}
@article {pmid41917200,
year = {2026},
author = {Lee, YH and Lin, WJ and Tsai, MT and Lan, B and Chu, YL and Yang, JI and Sun, SJ},
title = {Context-dependent indirect effects mediate ecological transitions between parasitism and mutualism.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09945-9},
pmid = {41917200},
issn = {2399-3642},
support = {Academic Research-Career Development Project (Sprout Research Projects; 114L7869)//National Taiwan University (NTU)/ ; },
abstract = {Symbiotic interactions frequently shift along a mutualism-parasitism continuum, altering host fitness, population dynamics, and microbial community structure with ecological context. Here, we integrate field surveys, reciprocal breeding experiments, feeding assays, and microbiome profiling to dissect interactions between phoretic mite (Poecilochirus carabi), nematode (Rhomborhabditis regina), and their burying beetle host (Nicrophorus nepalensis) during reproduction. We show that high nematode densities reduce beetle offspring survival during metamorphosis, but co-occurring mites mitigate these costs by preying on nematodes and suppressing vertical transmission, thereby enhancing beetle fitness. Both mites and nematodes are equally effective at suppressing bacterial loads on carrion, but mites drive greater shifts in carcass microbiome composition. Carcasses exposed to both symbionts display the most pronounced shifts in bacterial communities, suggesting that inter-symbiont interactions have cascading effects on host-associated microbiota. Intriguingly, in the absence of nematodes, mites impose fitness costs on their beetle hosts. These results demonstrate that the net effects of mites on beetle fitness emerge largely through indirect, density-dependent interactions with nematodes and microbial competitors. By integrating macro-symbiont and microbiome perspectives, our study highlights how phoresy extends beyond passive dispersal to actively restructure host-symbiont networks, highlighting the overlooked potential of indirect effects in driving context-dependent mutualism within multisymbiotic systems.},
}
@article {pmid41917642,
year = {2026},
author = {Gao, J and Ren, X and Hu, Y and Li, G and Yang, T and Xiao, J},
title = {New Trends and Challenges in Academic Research on Adolescent Growth and Development.},
journal = {Advances in experimental medicine and biology},
volume = {1505},
number = {},
pages = {411-420},
pmid = {41917642},
issn = {0065-2598},
mesh = {Humans ; Adolescent ; *Adolescent Development/physiology ; *Adolescent Health/trends ; Gastrointestinal Microbiome/physiology ; Epigenesis, Genetic ; *Biomedical Research/trends ; },
abstract = {Adolescence is a critical period for physical and psychological growth and development when individuals undergo a burst growth in physical size, hormonal re-adjustment, and brain development. In recent years, research studies have changed from descriptive growth charts toward focusing on the roles of multiple factors that affect adolescent health, including epigenetic regulators, genetic traits, social stressors, and gut microbiota. Compared to traditional factors like nutrition and hormones, environmental factors, personalized genomics, social media exposure, and gut-microbiome, etc. are increasing recognized as novel critical regulators of adolescent health. Currently, the goal of academic research in adolescence is to understand the interactions and underlying mechanisms of these factors and to develop targeted interventions for addressing adolescent health issues. Therefore, this chapter mainly discusses the new trends, key challenges, and translational research potential in these rapidly advancing field of adolescent growth and development.},
}
@article {pmid41917750,
year = {2026},
author = {Yeh, GY and Wayne, PM and Mehta, D},
title = {Inside the Gut-Mind Connection: Mind-Body Medicine Meets the Microbiome Revolution.},
journal = {Journal of integrative and complementary medicine},
volume = {},
number = {},
pages = {27683605261438880},
doi = {10.1177/27683605261438880},
pmid = {41917750},
issn = {2768-3613},
}
@article {pmid41917988,
year = {2026},
author = {Liu, M and Li, S and Cui, Y and Zhu, X and Wang, Z and Sun, H and Li, D and Liu, B and Shi, Y},
title = {Tryptophan metabolism mediated by the gut microbiota inhibits pyroptosis via the AhR signaling pathway to maintain intestinal epithelial homeostasis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02408-7},
pmid = {41917988},
issn = {2049-2618},
support = {CARS-34//Modern Agro-industry Technology Research System of China/ ; No. 244200510010//Science and Technology Innovation Leading Talent in Central Plains/ ; },
abstract = {BACKGROUND: The intestinal epithelial barrier protects the gut from pathogen invasion as well as exposure to food antigens and toxins. Increasing evidence has linked the gut microbiota to the function of the intestinal epithelial barrier. Fecal microbiota transplantation (FMT) can treat various intestinal diseases by reshaping the gut microbiota. However, the mechanisms by which FMT exerts its effects across different gastrointestinal conditions remain unclear. Moreover, its limitations are significant, including issues related to donor selection, the complexity of the microbiome, potential infection risks, inconsistent clinical responses, and ethical and legal considerations. Therefore, exploring the microbes and metabolites that mediate the effects of FMT as a replacement for traditional FMT is of great importance. In this study, we aim to investigate the gut microbiota and its metabolites to support the therapeutic role of FMT in intestinal barrier damage and elucidate its potential molecular mechanisms.<br><br>RESULTS: Our findings indicate that FMT prevents Lipopolysaccharide (LPS)-induced pyroptosis and damage to the colonic epithelial barrier. Mechanistically, FMT treatment reprograms the composition of gut microbiota, increasing the relative abundance of Lactobacillus reuteri and the levels of tryptophan metabolites (ILA, IAld, and IAA) in the colon, thereby inhibiting pyroptosis and protecting the intestinal epithelial barrier. Importantly, the AhR/NLRP3 axis is essential for the pyroptosis-inhibitory effects of Lactobacillus reuteri and its tryptophan metabolites.<br><br>CONCLUSIONS: Our results provide the first evidence that targeting the regulation of Lactobacillus reuteri and tryptophan metabolism is a promising strategy for inhibiting pyroptosis and improving intestinal epithelial homeostasis.},
}
@article {pmid41918066,
year = {2026},
author = {Singh, N and DuBrock, HM and Prisco, SZ and Dai, Z and Zheng, Q and Fallon, MB and Thenappan, T and Ventetuolo, CE and Jose, A},
title = {The Importance of Liver-Lung Communication in Pulmonary Vascular Diseases.},
journal = {Comprehensive Physiology},
volume = {16},
number = {2},
pages = {e70140},
pmid = {41918066},
issn = {2040-4603},
support = {HL134625/HL/NHLBI NIH HHS/United States ; HL141268/HL/NHLBI NIH HHS/United States ; HL174007/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; HL158596/HL/NHLBI NIH HHS/United States ; HL162794/HL/NHLBI NIH HHS/United States ; HL170096/HL/NHLBI NIH HHS/United States ; HL169509/HL/NHLBI NIH HHS/United States ; HL16497/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; },
mesh = {Humans ; *Lung/physiology/physiopathology ; *Liver/physiology/physiopathology ; Animals ; Hepatopulmonary Syndrome/physiopathology ; *Lung Diseases/physiopathology ; Gastrointestinal Microbiome/physiology ; Hypertension, Pulmonary/physiopathology ; },
abstract = {In normal health, the liver and lungs enjoy a close anatomic, physiologic, and functional relationship. In the context of pulmonary vascular disease, however, there is accumulating evidence that the interplay between the gut microbiome, hepatic system, and pulmonary vasculature (so-called "gut-liver-lung" axis) plays an important role in driving disease pathogenesis and determining clinical outcomes. Despite recognizing the importance of the gut-liver-lung axis in pulmonary vascular disease however, little is known about the clinical characteristics, circulating factors, and physiologic pathways that mediate this important axis of communication. In this clinical and translationally focused review, we provide an overview of liver-lung communication in normal physiology, and contrast this with gut-liver-lung derangements in pulmonary arterial hypertension, portopulmonary hypertension, and hepatopulmonary syndrome. We conclude with identifying key gaps in knowledge that will need to be addressed in order to manipulate the gut-liver-lung axis to prevent worsening pulmonary vascular disease, develop novel therapeutics, and improve patient outcomes.},
}
@article {pmid41918094,
year = {2026},
author = {Liu, Y and Liu, W and Pu, J and Wang, Y and Kang, Z and Zheng, H and Chang, W and Zheng, X and Yang, Q and Xu, H and Feng, Z and Dong, K and Li, J},
title = {Compositional disparities and potential pathogenic mechanisms of the ocular microbiome in cataract patients: insights from high-throughput sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05009-4},
pmid = {41918094},
issn = {1471-2180},
support = {2023L118//Science and Technology Innovation Program for Higher Education Institutions of Shanxi Province/ ; 2024149//Laboratory Special Project of the Health Commission of Shanxi Province/ ; B202201//Doctoral Fund Project of Shanxi Eye Hospital/ ; 2024NITFID303//Independent Research Program of the National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases/ ; },
}
@article {pmid41918359,
year = {2026},
author = {Fairfield, H and Reagan, MR},
title = {Fiber: A New Myeloma Prevention Approach with Abundant Positive Effects.},
journal = {Cancer discovery},
volume = {16},
number = {4},
pages = {623-625},
doi = {10.1158/2159-8290.CD-26-0152},
pmid = {41918359},
issn = {2159-8290},
mesh = {Humans ; *Multiple Myeloma/prevention &amp; control/diet therapy ; *Dietary Fiber/administration &amp; dosage/therapeutic use ; Quality of Life ; Obesity/diet therapy/complications ; },
abstract = {In a recent study by Shah, Cogrossi, and colleagues, patients with overweight/obesity and pre-myeloma diseases (monoclonal gammopathy of undetermined significance or smoldering myeloma) were mailed 12 weeks of high-fiber meals, provided with nutritional counseling, and required to track their food intake and weight. The intervention was well tolerated and improved quality of life, metabolic health, gut microbiome composition, and immune system function while supporting stable or improved multiple myeloma disease trajectories. See related article by Shah et al., p. 697.},
}
@article {pmid41918498,
year = {2026},
author = {Belhedi, M and Sghaier-Hammami, B and Hammami, SBM and Ben Slema, S and De Bellis, P and Somma, S and Nafati, H and Hibar, K and Abi Saad, C and Moretti, A and Masiello, M},
title = {Microbial biodiversity in Tunisian olive grove soils: a reservoir of phytopathogenic fungi and potential beneficial microorganisms.},
journal = {Frontiers in fungal biology},
volume = {7},
number = {},
pages = {1770745},
pmid = {41918498},
issn = {2673-6128},
abstract = {INTRODUCTION: Intercropping in olive orchards increases the risk of soil-borne fungal infections, particularly when associated crops are susceptible to the same pathogens. This study aimed to identify soil-borne microorganisms colonizing the roots and rhizosphere of olive trees in Tunisia intercropped with Solanaceae plants and to evaluate co-occurring bacterial communities for their potential to mitigate wilt disease and promote plant health.<br><br>MATERIAL AND METHODS: Endophytic fungi and bacteria were isolated from olive soils and roots collected from three olive orchards subjected to different intercropping systems. Fungal strains were molecularly identified at the species level using Internal Transcribed Spacer (ITS) and translation elongation factor 1-&#x3b1; (TEF1) gene sequencing, while bacterial strains were characterized by rep-PCR profiling and 16S rDNA sequencing. The pathogenicity of selected Fusarium strains was assessed by in vitro inoculation of detached olive leaves, olive twigs, and tomato seedlings. Antagonistic activity of bacterial strains against selected Fusarium species was evaluated using dual-culture assays, and bacteria-fungi interactions were further investigated by scanning electron microscopy (SEM).<br><br>RESULTS AND DISCUSSION: A total of 83 fungal and 40 bacterial strains were isolated. The fungal community was dominated by Fusarium species (62%), followed by Phoma (13%) and Alternaria (10%) species, while Verticillium dahliae was not detected at any site. The prevalence and virulence of Fusarium varied among olive groves, with the highest incidence observed at Sidi Bou Ali, where olive trees were intercropped with tomato, and the lowest at Kairouan, where potato intercropping was less frequent. Pathogenicity assays showed that 12 out of 15 of the tested Fusarium strains caused symptoms on both olive tissues and tomato seedlings. Bacterial communities were dominated by Bacillus species and Priestia megaterium. Bacillus species were particularly abundant at the site with the highest Fusarium pressure. The in vitro assay showed that several bacteria exhibited antagonistic activity against pathogenic fungi, with growth inhibition ranging from 8% to 68%, including volatile organic compound-mediated effects. SEM analyses revealed that Bacillus amyloliquefaciens inhibited fungal growth through biofilm formation and hyphal alteration.},
}
@article {pmid41918618,
year = {2026},
author = {Her, TK and Pszczolkowski, VL and Chung, G and Woollett, LA and Alejandro, EU},
title = {Multiparity as a Key Variable in Metabolism and Pregnancy Research.},
journal = {Current opinion in physiology},
volume = {47},
number = {},
pages = {},
pmid = {41918618},
issn = {2468-8673},
support = {R01 DK136237/DK/NIDDK NIH HHS/United States ; },
abstract = {Parity is defined as the total number of pregnancies reaching ≥20 weeks of gestation. It is an important variable to consider in any metabolic studies involving maternal or offspring health, as multiparity has been identified as a potential driver of numerous aspects of reproduction, maternal-fetal programming, and the health of both maternal and offspring. Currently, it is understood that multiparity may increase the risk of maternal pregnancy complications, such as preeclampsia and gestational diabetes mellitus (GDM), which can have subsequent long-term effects on both the maternal and offspring. Although there are some differences in data between rodents and humans, multiparity has been shown to disrupt glucose homeostasis, decrease pancreatic beta-cell proliferation, alter cardiac hemodynamics, and change the composition of the gut microbiome. In this review, we discuss what is known in the current literature about the impact of multiparity on pregnancy outcomes, maternal health, and offspring health.},
}
@article {pmid41918694,
year = {2026},
author = {Zheng, W and Liang, Y and Li, J},
title = {The neonatal lung microbiome: a dynamic determinant of respiratory health, disease, and novel therapeutics.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1770578},
pmid = {41918694},
issn = {2296-2360},
abstract = {The neonatal lung, once considered sterile, is now recognized to harbor a dynamic and complex microbiome that plays a critical role in respiratory health and disease. This review synthesizes current evidence on the composition, development, and functional impact of the lung microbiome in neonates, with a focus on its involvement in key respiratory disorders such as bronchopulmonary dysplasia, respiratory syncytial virus infection, neonatal acute respiratory distress syndrome, cystic fibrosis, and asthma predisposition. We place particular emphasis on the bidirectional communication along the gut-lung axis as a central mechanism, wherein intestinal microbiota and their metabolites modulate pulmonary immunity and inflammation. Emerging multi-omics studies that integrate microbial data with host metabolomic and immune profiles are highlighted for their role in deciphering disease-specific dysbiotic signatures and mechanistic pathways. Critically, this review advances the discussion beyond association by evaluating the translational potential of the microbiome as both a diagnostic biomarker and a therapeutic target. We provide a critical appraisal of innovative microbiome-targeted strategies-including probiotics, postbiotics, phage therapy, and bacterial lysates-and discuss the unique challenges and future directions for translating these approaches into safe, effective clinical interventions for vulnerable neonates. By bridging foundational science with clinical implications, this work aims to inform the development of novel, ecology-informed therapeutics to prevent and mitigate neonatal respiratory diseases.},
}
@article {pmid41918737,
year = {2026},
author = {Edwards, JS and De Paris, K},
title = {Inflammation at the maternal-fetal interface: a perspective on interacting risk factors for preterm birth in sub-Saharan African women living with HIV.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1741921},
pmid = {41918737},
issn = {1664-3224},
mesh = {Humans ; Female ; Pregnancy ; *HIV Infections/immunology/drug therapy/complications/epidemiology/virology ; *Premature Birth/immunology/epidemiology/etiology ; Risk Factors ; Africa South of the Sahara/epidemiology ; *Inflammation/immunology ; Vagina/microbiology/immunology ; *Pregnancy Complications, Infectious/immunology/virology ; Microbiota/immunology ; Macrophages/immunology ; Infant, Newborn ; *Maternal-Fetal Exchange/immunology ; },
abstract = {Globally, approximately 10% of all babies are born prematurely. The vast majority of preterm births, defined as birth <37 weeks of gestation, occur in low- and middle-income countries (LMICs) in Asia and Africa. Furthermore, premature birth has become the leading cause of death in infants under the age of 5 years. Thus, to improve maternal and infant health outcomes, better diagnostics and intervention strategies are urgently needed. However, the multifactorial etiology of preterm birth provides a major obstacle in achieving this goal. A common factor to many adverse birth outcomes, including preterm birth, is aberrant immune activation at the maternal-fetal interface. The specific cause of immune activation, however, remains unknown. Both HIV and an anaerobe-rich vaginal microbiota have been independently identified as risk factors for preterm birth, and both factors also promote inflammation and immune activation at mucosal sites. The interplay of HIV and microbiota is widely acknowledged, although mostly in the context of the intestinal microbiome. This review will highlight how the regulatory function of macrophages at the maternal-fetal interface can be altered in response to HIV and antiretroviral therapy and to changes in vaginal microbiota. We proceed to discuss interactions between the various factors and propose a dual-hit model in which macrophages act as mediators of inflammation at the maternal-fetal interface in response to specific vaginal commensals and HIV infection in sub-Saharan African women with preterm birth outcomes.},
}
@article {pmid41918738,
year = {2026},
author = {Lee, AR and Yang, SW and Lee, SY and Jeon, SB and Kang, HY and Choi, JW and Park, JH and Park, JH and Son, SB and Jeong, Y and Lee, JH and Kim, W and Cho, ML},
title = {Mitochondrial transplantation ameliorates experimental autoimmune encephalomyelitis by modulating the Th17/Treg balance and restoring metabolic homeostasis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1698136},
pmid = {41918738},
issn = {1664-3224},
mesh = {*Encephalomyelitis, Autoimmune, Experimental/therapy/immunology/metabolism/pathology ; Animals ; *Th17 Cells/immunology/metabolism ; *Mitochondria/transplantation/metabolism ; *T-Lymphocytes, Regulatory/immunology/metabolism ; Mice ; Humans ; Female ; Homeostasis ; Multiple Sclerosis/immunology/therapy/metabolism ; Oxidative Stress ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Spinal Cord/pathology/immunology/metabolism ; Disease Models, Animal ; Reactive Oxygen Species/metabolism ; },
abstract = {INTRODUCTION: Mitochondrial dysfunction has been increasingly implicated in the pathogenesis of multiple sclerosis (MS), contributing to oxidative stress, immune dysregulation, and neurodegeneration. Current therapies primarily target inflammation but do not adequately address mitochondrial impairment or progressive tissue damage. This study aimed to evaluate the therapeutic potential of mitochondrial transplantation in experimental autoimmune encephalomyelitis (EAE), a murine model of MS, by investigating its effects on immune modulation, mitochondrial function, and tissue integrity.<br><br>METHODS: EAE was induced in mice using myelin oligodendrocyte glycoprotein. Isolated mitochondria were administered intravenously, and clinical progression, spinal cord histology, immune cell populations, mitochondrial activity, fibrosis, and gut microbiota composition were assessed. Additionally, human peripheral blood mononuclear cells (PBMCs) from MS patients were co-cultured with mitochondria to examine ATP production, reactive oxygen species levels, and T cell differentiation.<br><br>RESULTS: Mitochondrial transplantation significantly reduced EAE severity, spinal cord inflammation, demyelination, and fibrosis. Treated mice showed increased regulatory T (Treg) cells, reduced T helper 17 (Th17) cells, improved mitochondrial biogenesis, and decreased oxidative stress. Gut microbiome analysis revealed beneficial compositional changes. In human PBMCs, mitochondrial transfer enhanced ATP synthesis, suppressed mitochondrial ROS, and promoted Treg differentiation while inhibiting pro-inflammatory cytokines.<br><br>DISCUSSION: Our findings suggest that mitochondrial transplantation restores mitochondrial function, rebalances immune responses, and mitigates neuroinflammation and fibrosis in EAE. This approach offers a novel therapeutic strategy for MS by addressing both metabolic and immunological drivers of disease progression.},
}
@article {pmid41918743,
year = {2026},
author = {Schröder Alvarez, L and Conejeros, I and Espinosa, G and Salinas-Varas, C and Ott, B and Weigel, M and Imirzalioglu, C and Fritzenwanker, M and Windhorst, AC and Hain, T and Taubert, A and Hermosilla, C and Wagenlehner, F},
title = {Presence of neutrophil extracellular traps (NETs) in different types of human urinary tract infections (UTI). A pilot study.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1745166},
pmid = {41918743},
issn = {1664-3224},
mesh = {Humans ; *Extracellular Traps/immunology/metabolism ; Female ; Pilot Projects ; Male ; *Urinary Tract Infections/immunology/microbiology/urine ; Middle Aged ; Adult ; *Neutrophils/immunology/metabolism ; Aged ; Biomarkers ; Pyelonephritis/immunology/urine ; Bacteriuria/immunology ; },
abstract = {INTRODUCTION: Activated polymorphonuclear neutrophils (PMN) release neutrophil extracellular traps (NETs) composed of a web-like DNA core, concomitant with nuclear histones, granular peptides and enzymes. NETs in human urine and their potential role in human urinary tract infections (UTI) pathogenesis is still understudied. This pilot study aimed to analyze presence of NETs in urine samples of patients with different types of UTI.<br><br>METHODS: Urine and blood samples were collected from three cohorts: group (A) included females (n = 24) with cystitis (n = 10), pyelonephritis (n = 6), and asymptomatic bacteriuria (n = 8); group (B) composed of males with catheter-associated UTI (n = 20) and a control group (C) consisting of healthy patients of mixed gender (n = 20). NETs in urine samples were confirmed by immunofluorescence-based detection of neutrophil elastase and citrullinated histone. The presence of granular enzymes (myeloperoxidase, cathelicidin), calprotectin (subunits S100A8, S100A9) and CD15[+] PMN were detected by ELISA, western blot and flow cytometry, respectively. To study potential associations of NETs with the respective UTI microbiome, bacterial spectrum of each urine sample was estimated by 16S rRNA gene analysis.<br><br>RESULTS AND DISCUSSION: On average, 23.29% &#xb1; 16.89% of PMN forming NETs were detected in group A [subgroups cystitis (27.72% &#xb1; 17.88%), pyelonephritis (22.75% &#xb1; 12.91%), asymptomatic bacteriuria (18.17% &#xb1; 17.14%)] and 30.63% &#xb1; 17.88% in group B, with no differences observed between UTI groups, including patients with asymptomatic bacteriuria. For the control group (group C), a low incidence of NET-releasing cells was observed (0.32% &#xb1; 1.42%), resulting in a significant difference (p < 0.05) when compared to all UTI groups studied. Furthermore, different NET-phenotypes [i. e. spread NETs (sprNETs), diffuse NETs (diffNETs) and aggregated NETs (aggNETs)] were detected in both UTI groups. The presence of NET-associated proteins was confirmed in all UTI groups, but absent in the control samples. Microbiome analyses revealed a reduced microbial variability within UTI samples with the predominance of the bacterial family Enterobacteriaceae. Overall, PMN-derived NETs were consistently found in all UTI samples, suggesting a role of NETs in diverse UTI pathologies. Future studies should investigate its utility as an inflammatory biomarker in clinical human UTI.},
}
@article {pmid41918843,
year = {2026},
author = {Huang, Q and Liang, Z and Cui, Y and Diao, J and Zhou, T and Shi, L and Deng, Z and Wang, R and Yuan, H and Chen, K and Du, Y and Chen, A and Chen, J and Xiao, W},
title = {Uremic Clearance Granules Regulate Immune Equilibrium via Gut Microbiome to Alleviate Chronic Renal Failure.},
journal = {Biomaterials research},
volume = {30},
number = {},
pages = {0342},
pmid = {41918843},
issn = {1226-4601},
abstract = {Chronic renal failure (CRF) is the common end point of various chronic kidney diseases, and there is currently no specific drug for CRF. Effectively halting its progression remains a clinical challenge. Gut microbiota disorders are a key factor influencing immune dysfunction in chronic kidney disease patients. Intervening in gut microbiota to improve immune regulatory function in patients could serve as a new strategy for treating CRF with Traditional Chinese Medicine. Uremic Clearance Granules (UCG), a Traditional Chinese Medicine formulation, effectively attenuate CRF progression, but their active components and mechanisms remain undefined. This study investigates how UCG mitigate CRF via coordinated regulation of gut microbiota, metabolites, and the T helper 17 cells / regulatory T cell axis. Using an adenine-induced CRF mouse model, we combined gut microbiota depletion, fecal microbiota transplantation, 16S rRNA sequencing, and metabolomics to delineate the gut-kidney interactions underlying UCG efficacy. Flow cytometry quantified immune cell profiles in blood, and microbial intervention experiments verified the therapeutic role of Bifidobacterium animalis (B. animalis). In this study, we found that UCG treatment alleviated renal injury, reduced intestinal permeability, and up-regulated intestinal barrier markers. Microbiota depletion and fecal microbiota transplantation demonstrated that UCG's renoprotective effects depend on gut microbial modulation. Specifically, UCG ameliorates CRF through gut-kidney axis remodeling by enhancing B. animalis abundance and sophocarpine, thereby rebalancing T helper 17/regulatory T immunity and preserving renal function. These findings identify a microbiota-dependent immunometabolic mechanism for UCG and highlight a potential therapeutic strategy for CRF via the drug-microbiota axis.},
}
@article {pmid41918857,
year = {2026},
author = {Erözden, AA and Tavşanlı, N and Demirel, G and Sanli, NO and Çalışkan, M and Arıkan, M},
title = {MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20990},
pmid = {41918857},
issn = {2167-8359},
mesh = {*Peptides/genetics/pharmacology ; *Antineoplastic Agents/pharmacology ; *Metagenome ; Humans ; *Genome, Microbial ; *Software ; High-Throughput Nucleotide Sequencing ; Algorithms ; Computational Biology/methods ; },
abstract = {BACKGROUND: Anticancer peptides (ACPs) are increasingly recognized as promising therapeutic candidates due to their ability to selectively target cancer cells. However, the systematic discovery of novel ACPs, particularly from high-throughput sequencing datasets, remains hindered by technical and methodological limitations. Current prediction frameworks require pre-extracted peptide sequences, involve manual preprocessing, and yield variable results, which restricts their applicability for large-scale, data-driven discovery.<br><br>METHODS: To address these limitations, we developed MetaPepticon, a modular, end-to-end pipeline for the discovery of ACP candidates from diverse sequencing inputs, including raw genomic, metagenomic, transcriptomic, and metatranscriptomic reads, as well as assembled contigs and peptide sequences. MetaPepticon automates quality control, filtering, assembly, small open reading frame prediction, ACP classification using multiple predictive algorithms, and in silico toxicity filtering.<br><br>RESULTS: MetaPepticon enables scalable and reproducible ACP prediction from raw sequences through integration of multiple predictors within a configurable agreement framework. Applied to 41,171 microbial genomes and 4,072,884 peptides, MetaPepticon identified 10,725 moderate-agreement ACP candidates, including 4,590 novel, non-toxic peptides. MetaPepticon expands the practical applicability of existing ACP prediction methods to high-throughput sequencing data and is freely available at: https://github.com/arikanlab/MetaPepticon.},
}
@article {pmid41918873,
year = {2026},
author = {Duan, Y and Yang, M and Li, M and Sun, Y and Liu, S},
title = {Microbiome and metabolite signatures for cirrhosis to HCC risk stratification: progress, controversies, and gaps.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1793213},
pmid = {41918873},
issn = {2235-2988},
mesh = {Humans ; *Carcinoma, Hepatocellular/microbiology/metabolism/pathology/etiology ; *Liver Cirrhosis/microbiology/metabolism/complications/pathology ; *Gastrointestinal Microbiome ; *Liver Neoplasms/microbiology/metabolism/pathology/etiology ; Fatty Acids, Volatile/metabolism ; Risk Assessment ; Disease Progression ; Dysbiosis ; Bile Acids and Salts/metabolism ; },
abstract = {The progression from cirrhosis to hepatocellular carcinoma (HCC) is a key outcome in the management of chronic liver disease. This process has a long incubation period and significant individual differences, making early warning still difficult. Clinical follow-up mainly relies on imaging examinations and alpha fetoprotein, but the ability to identify high risk precancerous states is limited. The imbalance of gut microbiota and its metabolites may occur earlier than the visible stage of tumors. They can affect barrier integrity, chronic inflammation, immune surveillance, and metabolic homeostasis through the gut liver axis, and participate in the formation of a pro tumor microenvironment. Therefore, such changes may provide more upstream risk stratification clues for the population with cirrhosis. This article summarizes previous research evidence and summarizes the common microbiome and metabolite characteristics of cirrhosis and high-risk populations, including a decrease in short chain fatty acid (SCFA) related symbiotic bacteria, an increase in inflammation related bacteria, bile acid spectrum shift, and other intestinal derived metabolite abnormalities. This article also outlines the key mechanisms that these features may correspond to, such as barrier damage and microbial translocation, immune suppression, etc. There are still significant uncertainties at present. The effect of SCFA is context dependent. Different etiologies, diets, medications, and complications can lead to significant confounding and affect cross cohort consistency. Subsequent research requires longitudinal cohort validation and the promotion of multi omics integration and the construction of interpretable predictive models to support clinical translation.},
}
@article {pmid41918874,
year = {2026},
author = {Su, X and Yang, J and Le, Z and Xiao, J and Zhao, D},
title = {Integrative multi-omics analysis reveals probiotic-induced microbiota shifts in women with gestational diabetes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1782744},
pmid = {41918874},
issn = {2235-2988},
mesh = {Humans ; Female ; *Probiotics/administration &amp; dosage ; *Diabetes, Gestational/microbiology ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; Adult ; Metabolomics/methods ; Metagenomics ; Multiomics ; },
abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a common pregnancy disorder. It is associated with impaired glucose tolerance and insulin resistance, increasing the potential risks for both maternal and fetal complications. GDM is associated with an increased risk of type 2 diabetes later in life. Management is a big issue in maternal health. New work has underscored the role of the gut microbiota in metabolism and immune function. This indicates that probiotics might exert their mode of action through modulating the microbiota and controlling metabolism.<br><br>METHODS: This study employs a multi-omics strategy to assess the impact of probiotic administration on gut microbiota composition, metabolomic profiles, and host gene expression in GDM women. Women with GDM received probiotics for 8 weeks. Metagenomic sequencing quantified alterations of gut microbiota composition and LC-MS provided untargeted metabolomics in serum and urine. Gene expression was analyzed by qRT-PCR in reference to other physiological factors such as insulin signaling, inflammation, oxidative stress, and gut barrier. Data integration was performed using Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and network analysis, then pathway enrichment analysis was conducted with KEGG and MetaboAnalyst.<br><br>RESULTS: The supplementation of probiotics resulted in a significant change of gut microbiota (Lactobacillus 7.6-fold; Bifidobacterium 6.4-fold). Escherichia/Shigella was reduced. The amounts of short-chain fatty acids (SCFAs), especially butyrate and acetate, were increased 3.1 fold and 2.5 fold, respectively. In a gene expression assessment, the insulin receptor and AKT increased 2.5- and 1.9-fold higher, respectively, indicating greater insulin sensitivity. Levels of TNF-&#x3b1; and IL-6 decreased; however, genes related to gut barrier function (ZO-1, CLDN1) increased.<br><br>DISCUSSION: The administration of probiotic has a great impact on gut microbiome, metabolic activity, and host gene expression in women with GDM. Our data indicate that probiotics may represent a non-invasive and safe treatment for gestational diabetes through enhancing insulin sensitivity, anti-inflammatory environment, and gut health status. Larger confirmatory studies are needed to corroborate these findings and augment future clinical application of probiotics in GDM patients.},
}
@article {pmid41918946,
year = {2026},
author = {Hsiao, CC and Chen, CH and Liu, CS and Wang, JY and Lin, CY and Yang, KD and Lee, CH and Lin, TT and Lin, CJ and Tsai, YG},
title = {Airway microbial dysbiosis and oxidative mitochondrial DNA damage in the development of bronchopulmonary dysplasia.},
journal = {ERJ open research},
volume = {12},
number = {2},
pages = {},
pmid = {41918946},
issn = {2312-0541},
abstract = {BACKGROUND: This study investigated the association between airway microbiome composition, oxidative mitochondrial DNA (mtDNA) damage and the development of bronchopulmonary dysplasia (BPD) in preterm infants.<br><br>METHODS: A prospective cohort study enrolled 82 very low birth weight preterm infants (<32&#x2005;weeks' gestation). Tracheal aspirates (TA) were collected at birth and on postnatal day 28. Airway microbial diversity and composition were assessed using 16S rRNA sequencing. Oxidative mtDNA damage was measured using 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in TA samples. We used PICRUSt2-based metagenome predictions from 16S rRNA gene sequencing of TA samples, with functional pathway annotations based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: Infants who developed BPD (n=25) had lower gestational age, birth weight and prolonged ventilatory support (p<0.05). Oxidative mtDNA damage was significantly higher in infants with BPD, particularly in moderate-to-severe cases (p<0.05). BPD was associated with reduced microbial alpha diversity and distinct beta diversity clustering. Infants with BPD exhibited higher relative abundance of Proteobacteria and lower relative abundance of Firmicutes, with enrichment of Stenotrophomonas, Acinetobacter and Serratia (p<0.05). By day 28, KEGG-based functional predictions revealed enrichment in microbial pathways related to bacterial motility proteins, circadian rhythm signalling pathway, MAPK signalling pathway and &#x3b1;-linolenic acid metabolism. Proteobacteria abundance correlated positively with oxidative mtDNA damage (r=0.49, p<0.01).<br><br>CONCLUSIONS: Airway microbial dysbiosis and oxidative mtDNA damage are strongly associated with BPD severity. Targeting oxidative stress and microbiome modulation may offer potential strategies for BPD prevention and management.},
}
@article {pmid41918963,
year = {2026},
author = {Athithan, P and Ishaq, SL and Allen-Vercoe, E and O'Doherty, KC},
title = {Microbes first into the life rafts: preserving microbiomes to secure health in degrading ecosystems.},
journal = {Sustainable microbiology},
volume = {},
number = {},
pages = {},
pmid = {41918963},
issn = {2755-1970},
support = {R15 DK133826/DK/NIDDK NIH HHS/United States ; },
abstract = {All organisms on the planet intrinsically rely on microbial ecosystems, and there are increasing calls from research communities to consider microbiota when administering personal or public health, ecosystem health, and the use of microbiota in personal or environmental health remediation, such as reducing the impacts of climate change, or protecting at-risk habitats which host rare microbiota. Through our collective work on the integral nature of microbiomes to host and environmental health, on health policy, and on the development of research and policy agendas, we have previously developed the concept of 'microbiome stewardship' and guidelines to promote consideration of microbial communities broadly or in specific scenarios. The practicality of stewarding one versus many microbiota is highly contextual, and will require different strategies for different scales of conservation. Here, we provide scientific arguments for the need for microbial stewardship, examples of possible solutions scaled to different ecological challenges or conservation goals, discourse on the logistical challenges which have been cited by research communities, and opportunities to use cutting-edge microbiome concepts and technology to implement large-scale interventions.},
}
@article {pmid41918966,
year = {2026},
author = {Jiang, W and Liu, J and Chen, A and Zhao, T and Xu, Z and Xu, L and Du, Y and Guan, X and Ding, J and Liu, Y and Sun, D},
title = {Antimicrobial Peptides as Novel Ecological Approaches to Caries Prevention.},
journal = {Drug design, development and therapy},
volume = {20},
number = {},
pages = {592732},
pmid = {41918966},
issn = {1177-8881},
mesh = {*Dental Caries/prevention &amp; control/microbiology ; Humans ; *Antimicrobial Peptides/pharmacology/chemistry ; Biofilms/drug effects ; Microbiota/drug effects ; *Anti-Bacterial Agents/pharmacology/chemistry ; },
abstract = {Antimicrobial strategies have consistently been a central theme in caries prevention research. Due to their potent antibacterial properties and the potential for multifunctionality through sequence modification, antimicrobial peptides (AMPs) are emerging as promising candidates for anticaries therapeutics. Traditional investigations primarily focused on the broad-spectrum bactericidal efficacy of AMPs to eradicate cariogenic bacteria; however, this approach may inadvertently harm the beneficial oral microbiome. With advancing knowledge of oral microecology, the focus has progressively shifted towards ecological approaches. These strategies aim to selectively modulate cariogenic populations or the disease-associated microbiota while preserving microbial diversity and maintaining ecological balance, as demonstrated in multispecies biofilm models and sequencing-based microbiome analyses. Current innovations include targeting specific pathogens, regulating virulence factors, utilizing bio-responsive mechanisms within the cariogenic microenvironment, and disrupting dental plaque biofilms. This article reviews the current progress and limitations of antimicrobial peptide-based ecological approaches to caries control and offers valuable insights for the future design and optimization of antimicrobial peptides with microecology regulating effects or other promising functions aiding caries prevention.},
}
@article {pmid41918983,
year = {2026},
author = {Weingarden, AR},
title = {Strengths and limitations of in vitro and animal models to advance understanding of human diet‒microbiome interactions.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2636336},
pmid = {41918983},
issn = {2993-3935},
abstract = {The gut microbiome is a critical mediator of human health. As the intestinal microbiota is far more metabolically diverse than humans, it plays a significant role in the digestion of food, particularly food components that are nutritionally inaccessible to the human host. While no system can fully recapitulate the in vivo interactions of food, the host, and the gut microbiome in the human body, in vitro and animal model tools are critical for studying these complex relationships. Here, we review many of the common in vitro and animal models used to manipulate and study how the gut microbiome affects and is affected by diet. We focus on colonic fermentation systems, with or without small intestinal contribution, bioreactors with both microbial and host epithelial cell components, and animal models that have been developed to study these relationships. We will review the limitations of these systems while also discussing new innovations that seek to address these limitations.},
}
@article {pmid41918985,
year = {2026},
author = {Keskey, R and Meltzer, R and Toni, T and Hyoju, S and Cohn, E and Cao, J and Benjamin, A and Lam, A and Zaborin, A and Zaborina, O and Alverdy, J},
title = {Microbiota-accessible carbohydrates enhance gut microbiota stability and antibiotic resilience through production of quorum sensing molecule AI-2.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2646055},
pmid = {41918985},
issn = {2993-3935},
abstract = {Dietary fiber and fat shape the gut microbiota and human health, yet their role in modulating the response of the microbiota to antibiotics remains underexplored. We hypothesized that dietary fiber, independent of fat content, mitigates antibiotic-induced weight loss and diarrhea in a microbiota-dependent manner. Mice were fed refined diets varying in fat and fiber contents for 6 weeks, compared to a standard plant-based chow diet. Following antibiotic administration, fiber consumption independent of fat reduced diarrhea and weight loss. High-fiber diets increased Bacteroidetes and decreased Firmicutes and Proteobacteria prior to antibiotic exposure, all of which correlated with elevated cecal short-chain fatty acids (SCFAs). Fermentable fiber increased AI-2 quorum-sensing pathway activity and improved Firmicutes resiliency to antibiotics. Supplementation with AI-2 reduced antibiotic-induced weight loss in mice fed high-fat, low-fiber diets. These findings suggest that fermentable fiber alters the gut microbiota composition and function, enhancing microbial resiliency and host tolerance to antibiotics. Dietary supplementation with microbiota-accessible fiber increased AI-2 production, stabilized Firmicutes populations, and attenuated antibiotic-associated weight loss, independent of dietary fat content.},
}
@article {pmid41919041,
year = {2026},
author = {Bizzarri, E and Proietti, S and Falconieri, GS and Caruso, C and Bertini, L},
title = {Exploring the molecular landscape of environmental responses in the Antarctic plant Colobanthus quitensis: insights from metatranscriptomic analysis.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1774223},
pmid = {41919041},
issn = {1664-462X},
abstract = {INTRODUCTION: The harsh environmental conditions of Antarctica significantly influence plant responses, impacting both defence mechanisms and developmental processes. Moreover, plant-associated microbial communities further modulate physiological functions, creating a complex network of interactions. This study aimed to investigate how local environmental conditions and plant-associated microbiota shape the transcriptomic landscape of the Antarctic plant Colobanthus quitensis.<br><br>MATERIALS AND METHODS: A comparative metatranscriptomic analysis was conducted on plants collected from three sites spanning a coastal-to-inland gradient of increasing climatic severity to investigate both the functional roles of differentially expressed plant genes and taxonomic profiling of the associated microbial community. In addition, the content of photosynthetic and protective pigments was quantified biochemically to assess whether environmental conditions influence the photosynthetic pathway.<br><br>RESULTS AND DISCUSSION: The results suggested that Site 2 (Puchalski Station) represents a particularly favourable microenvironment that optimises the physiological performance of C. quitensis, supporting enhanced homeostasis and the activation of multiple stress-response strategies. Furthermore, distinct variations in microbial community composition were observed across the sites, underscoring the interplay between local environment and plant-associated microbiota.<br><br>CONCLUSIONS: These findings highlight the sensitivity of C. quitensis to minor environmental changes and suggest that its associated microbiome could serve as an early-warning system for ecological change in Antarctica.},
}
@article {pmid41919346,
year = {2025},
author = {Berretta, A and Schwab, C},
title = {Fermentation-driven interactions of gut microbes with their environment.},
journal = {Essays in biochemistry},
volume = {69},
number = {6},
pages = {},
doi = {10.1042/EBC20253057},
pmid = {41919346},
issn = {1744-1358},
mesh = {*Fermentation ; *Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Butyrates/metabolism ; },
abstract = {The gut microbiome has gained a lot of attention in recent decades due to the multitude of interactions it has with the host. One of the main ways the microbiota communicates with the host is through the fermentation of dietary or host-derived nutrients. Fermentation of carbohydrates and amino acids yields structurally and compositionally different metabolites that have distinct functionality within the gut microbial community but also in the interaction with the host. The most abundant fermentation metabolites are the short-chain carboxylic acids acetate, butyrate, and propionate. While important contributions to host health have been attributed to these three, there are other compounds formed by fermentation whose relevance in the gut becomes increasingly recognized. In this essay, we will present how gut physiological properties relate to microbial fermentation capacity. We will introduce the diversity of fermentation pathways and relate functionality to the intrinsic properties of fermentation-derived metabolites. Finally, we will present strategies to restore disrupted fermentation activity.},
}
@article {pmid41919524,
year = {2026},
author = {Jain, A},
title = {Advances in New Approach Methodologies for Assessing ADME Properties of Nano-formulations.},
journal = {Xenobiotica; the fate of foreign compounds in biological systems},
volume = {},
number = {},
pages = {1-36},
doi = {10.1080/00498254.2026.2653145},
pmid = {41919524},
issn = {1366-5928},
abstract = {Conventional animal models face ethical concerns and scientific limitations, as interspecies differences often fail to capture the unique pharmacokinetics of nanomaterials.This review highlights advances in Non-Animal Models, including organoid-based systems that replicate human tissue structure, microfluidic organ-on-chip platforms that mimic dynamic physiology, and computational approaches such as physiologically based pharmacokinetic (PBPK) modelling, molecular dynamics, and machine learning.Innovations such as vascularized organoids, multi-organ chip networks, and artificial intelligence-driven refinement are evaluated for their potential to improve predictive accuracy.Remaining challenges, including scalability, standardisation, and incorporation of immune and microbiome components, are critically discussed.By integrating technological advances with regulatory perspectives, this review underscores New Approach Methodologies as a transformative pathway toward more ethical, human-relevant, and predictive nanomedicine development.},
}
@article {pmid41919539,
year = {2026},
author = {Liu, J and Sun, Y and Wu, J and Tang, S and Ding, G},
title = {[Comparative analysis of microbial communities in different oral ecological niches of preschool children].},
journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology},
volume = {44},
number = {2},
pages = {197-205},
doi = {10.7518/hxkq.2025.2025285},
pmid = {41919539},
issn = {2618-0456},
mesh = {Humans ; Child, Preschool ; *Microbiota ; Child ; *Mouth Mucosa/microbiology ; RNA, Ribosomal, 16S/genetics ; *Tongue/microbiology ; *Bacteria/classification/genetics ; *Tooth/microbiology ; *Dental Plaque/microbiology ; Male ; Mouth/microbiology ; },
abstract = {OBJECTIVES: This study aims to investigate the structural differences, dominant bacterial genera, and potential functions of microbial communities in different oral ecological niches (dorsal tongue, tooth surface, and buccal mucosa) of preschool children to clarify the influence of local microenvironments on microbial colonization and provide a theoretical basis for the microbiota-targeted regulation of pediatric oral diseases.<br><br>METHODS: A total of 105 plaque samples were collected from the dorsal tongue, tooth surface, and buccal mucosa of 35 healthy preschool children (aged 4-6 years). High-throughput sequencing of the 16S rRNA gene was performed to analyze the microbial community structure and alpha/beta diversity. Principal coordinate analysis, UPGMA clustering, and LEfSe analysis were used to identify niche-specific dominant genera. PICRUSt2 was applied to predict the potential metabolic functional profiles across niches.<br><br>RESULTS: Spatial hete-rogeneity in microbial composition and structure was observed across the three oral niches. Species richness was significantly higher on the tooth surface and buccal mucosa than on the dorsal tongue. The dominant phyla included Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Fusobacteria, and Patescibacteria. At the genus level, Actinomyces and Corynebacterium were enriched on the tooth surface, Veillonella was enriched on the dorsal tongue, and Streptococcus was predominant on the buccal mucosa. Beta diversity and clustering analyses confirmed distinct microbial community structures among the niches. LEfSe analysis identified several niche-specific genera. PICRUSt2 functional prediction revealed significant differences in amino acid metabolism, carbohydrate metabolism, cell motility, translation, signal transduction, immune system, infectious disea-ses, and membrane transport (P<0.05).<br><br>CONCLUSIONS: The dorsal tongue, tooth surface, and buccal mucosa in preschool children harbor distinct microbial communities with different taxonomic composition, diversity, and functional potential. The findings suggest that local microenvironmental factors shape oral microbiota and may contribute to the early onset of oral diseases. This study provides foundational data and theoretical insights for early microbiome-based risk assessment and personalized oral health interventions in children.},
}
@article {pmid41919541,
year = {2026},
author = {Xu, Y and Wang, S and Zhou, J},
title = {[Oral homeostasis imbalance under hypoxia].},
journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology},
volume = {44},
number = {2},
pages = {215-223},
doi = {10.7518/hxkq.2026.2025427},
pmid = {41919541},
issn = {2618-0456},
mesh = {*Homeostasis ; Humans ; *Hypoxia/physiopathology ; Mouth Mucosa/physiopathology ; Microbiota ; Salivary Glands/physiopathology ; Bone Remodeling ; },
abstract = {Hypoxia disrupts oral homeostasis through multiple interconnected pathways, including interference with tooth germ development, impairment of salivary gland function and salivary buffering capacity, compromise of the oral mucosal barrier, imbalance in jawbone and alveolar bone remodeling, and alterations in the diversity and functionality of the oral microbiome. These disturbances collectively contribute to the onset and progression of oral diseases. Moreover, disruption of oral homeostasis may, in turn, affect systemic homeostasis, increasing the risk of disorders in other organ systems through mechanisms involving inflammatory mediator release and microbial translocation. Here, we systematically review the effects and underlying mechanisms of hypoxia exposure on oral homeostasis, and further explore the interconnections between hypoxia-induced oral dysregulation and systemic homeostatic imbalance. This review aims to provide a comprehensive understanding of the regulatory networks linking oral and systemic homeostasis under hypoxia, thereby offering potential insights for maintaining homeostatic balance.},
}
@article {pmid41919563,
year = {2026},
author = {Afridi, R and Ibrahim, M and Yaqoob, M and Ahmad, W},
title = {Synergistic Effect of Glyphosate and Polyethylene Microplastics on Culturable Gut Microbiota Alterations in Zebrafish.},
journal = {Environmental toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1002/tox.70091},
pmid = {41919563},
issn = {1522-7278},
abstract = {The coexistence of emerging pollutants, that is, microplastics (MPs) and pesticides poses significant threat to aquatic organisms. This study investigated the combined effects of polyethylene microplastics (PE-MPs) and glyphosate on the gut microbiome of zebrafish. Following a 21-day exposure, 16S rRNA sequencing revealed that co-exposure caused the most significant disruption, surpassing the individual effects of each stressor. Co-exposure resulted in the lowest alpha diversity and a distinct microbial community structure, characterized by the depletion of A. veronii and a marked enrichment of opportunistic pathogens like A. hydrophila. Clear separation of all exposed groups from controls, with the co-exposure group forming the most distinct cluster was observed in non-metric multi-dimensional scale analysis. Specifically, a higher number of ASVs were differentially abundant in the co-exposure group compared to the individual exposures. In the MPs group, Aeromonas species were markedly replaced by Enterobacter species. Glyphosate significantly enriched A. hydrophila species in the gut. Treatment-specific clustering, with Enterobacter species associated with MPs, and A. hydrophila with glyphosate and co-exposure groups were observed in Heatmap analysis. The findings indicate that microplastics not only act as direct stressors but also as glyphosate carriers, leading to amplified, non-additive shifts in the gut microbiome and posing a heightened ecological risk.},
}
@article {pmid41919917,
year = {2026},
author = {Mall, A and Rode, KJ and Marx, CJ},
title = {Evolution uncovers a general tradeoff between recovery after heat shock and growth at elevated temperatures.},
journal = {mBio},
volume = {},
number = {},
pages = {e0330525},
doi = {10.1128/mbio.03305-25},
pmid = {41919917},
issn = {2150-7511},
abstract = {Fitness tradeoffs between different environments enable the maintenance of microbial diversity. While the importance of tradeoffs is clear, it has been surprisingly difficult to predict which traits they will occur between and at how granular a level. For example, it is unclear whether performance between a constant versus pulsed exposure of the same stress tends to be positively correlated, independent of each other, or negatively correlated. Empirically, it has been shown that a critical feature structuring microbial communities is temperature. However, the compatibility between strategies to deal with different forms of heat stress is unclear. For instance, are strains that grow well at higher temperatures also stronger at withstanding heat shock? To understand how environmental microbes can adapt to better deal with heat stress, we performed an evolution experiment using a dominant phyllosphere microbe Methylobacterium extorquens in a regime of intermittent heat shock. We identified the genetic basis of adaptation, discovering a large number of loci capable of mediating adaptation to heat shock, many of which had not been previously linked to heat stress. Despite the genetic divergence among evolved isolates, we discovered a general tradeoff between heat shock resistance and growth at consistently elevated temperatures. We found this tradeoff was not limited to evolved isolates, but also represented across a sample of environmentally isolated Methylobacterium strains. These findings indicate a generic conflict between strategies to deal with heat shock recovery and growth at elevated temperatures, suggesting even variation in intensities of a stressor can drive diversity in microbial strategies.IMPORTANCEOne of the key forces shaping the microbial diversity in nature is temperature. However, temperature in ecological settings is variable, and it is unknown if strategies to deal with different intensities of high temperature are compatible or not. Using evolution experiments, we identify the genetic basis of adaptation to heat shock in Methylobacterium extorquens, a dominant member of the phyllosphere microbiome. We discover a number of genetic targets where beneficial mutations improve heat shock resistance, most of which have not been implicated with heat stress before. For both the evolved isolates and a set of environmentally isolated Methylobacterium strains, we discover a general tradeoff between recovery after heat shock and growth at elevated temperatures. While the strategies to deal with increasing temperatures have garnered significant interest, our results suggest that even different intensities of heat stress can select for distinct and incompatible strategies and can drive microbial diversification in ecological settings.},
}
@article {pmid41919968,
year = {2026},
author = {Zhou, C and Wang, S and Zhao, H and Wang, S and Jiang, L and Yu, C},
title = {Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0039226},
doi = {10.1128/aem.00392-26},
pmid = {41919968},
issn = {1098-5336},
abstract = {Oil reservoir microorganisms represent a vast and largely unexplored reservoir of biological diversity and functional potential, yet comprehensive studies on their genomic and metabolic characteristics remain limited. To address this gap, we collected 101 metagenomic sequencing samples from 13 distinct oilfields across China. Through extensive de novo assembly and binning processes, we successfully reconstructed 3,057 medium and high-quality metagenome-assembled genomes (MAGs), providing an unprecedented genomic resource for reservoir microbiome research. Strikingly, 73.77% of these MAGs correspond to novel taxa at the species level, highlighting the significant unexplored microbial diversity in these environments. Detailed genomic analysis revealed that MAGs classified under the class Planctomycetia exhibited notably larger genome sizes, primarily driven by the expansion of specific gene families, suggesting adaptive evolutionary strategies in hydrocarbon-rich environments. Furthermore, we identified 68 genes implicated in anaerobic alkane biodegradation pathways, with samples from the Shengli oilfield demonstrating particularly enhanced biodegradation potential, indicating site-specific functional adaptations. Beyond biodegradation, our study uncovered three MAGs assigned to the genus Tistrella, which harbored a remarkable abundance of biosynthetic gene clusters (BGCs) for secondary metabolites. Additionally, 14 candidate antimicrobial peptides (cAMPs) were detected, signifying the potential for novel bioactive compound discovery. Critically, both the Tistrella MAGs and cAMPs were identified for the first time within petroleum reservoir ecosystems, underscoring the unique biotechnological value of these environments. This research not only expands our understanding of oil reservoir microbial communities but also emphasizes their substantial implications for industrial applications, including bioremediation, antimicrobial development, and sustainable resource management.IMPORTANCEThis study provides a groundbreaking genomic exploration of oil reservoir microbiomes across 13 Chinese oilfields, reconstructing 3,057 medium and high-quality metagenome-assembled genomes (MAGs). Remarkably, 73.77% of these MAGs represent novel species, revealing vast unexplored microbial diversity. We observed genome expansion in Planctomycetia lineages and identified 68 genes involved in anaerobic alkane degradation, with heightened biodegradation potential in Shengli oilfield samples. Crucially, we discovered three Tistrella MAGs rich in biosynthetic gene clusters (BGCs) for secondary metabolites and 14 candidate antimicrobial peptides (cAMPs), both reported for the first time in petroleum reservoirs. These findings highlight the immense biotechnological potential of reservoir microbiomes, offering new pathways for bioremediation strategies in oil-contaminated environments and novel sources for antimicrobial discovery. This work underscores the critical need for continued investigation into these unique ecosystems to harness their functional capabilities for energy sustainability and pharmaceutical innovation.},
}
@article {pmid41920102,
year = {2026},
author = {Bruyere, D and Delahaye, T and Nikkels, A and Herfs, M},
title = {Pathophysiology of cutaneous commensal human papillomaviruses.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.02.011},
pmid = {41920102},
issn = {1523-1747},
abstract = {Cutaneous human papillomaviruses (HPVs), particularly those of the β-genus, have traditionally been viewed as harmless constituents of the skin microbiome. However, a debate has emerged over the past few years regarding their possible contribution to cancer development. In immunocompetent hosts, commensal β-HPVs may contribute to immune education and cutaneous homeostasis. In contrast, under immunosuppression, their increased viral load (combined with UV-induced DNA damage) can promote early oncogenic events and facilitate cancer initiation, through a "hit-and-run" mechanism. This context-dependent behavior defines β-HPVs as dynamic modulators of skin health, capable of exerting protective or pathogenic effects within the cutaneous ecosystem depending on host and environmental factors.},
}
@article {pmid41731377,
year = {2026},
author = {Diouf, AM and Mbaye, AL and Deh, M and Lahlali, R and Elhoumaizi, MA and Rchiad, Z and Barakate, M},
title = {Comparative metagenomic analysis of bacterial and fungal communities associated with bayoud-resistant and susceptible date palm cultivars in the Zagora oasis-Morocco.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41731377},
issn = {1471-2180},
abstract = {BACKGROUND: Fusarium oxysporum f. sp. albedinis (Foa) is a destructive soil-borne fungal pathogen responsible for bayoud disease, which threatens date palm cultivation in North Africa. This disease has caused significant agricultural losses, particularly in Morocco, where the Zagora oasis is a key region for date palm production. Within this oasis, two cultivars—Black Bousthammi and Jihel—are mainly cultivated and exhibit complete resistance and high susceptibility to Foa, respectively. Thus, this study aimed to identify and compare the bacterial and fungal communities associated with the two cultivars and understand their assemblage regarding the disease resistance or susceptibility. Moreover, we explored the influence of each cultivar on the composition and structure of its root-associated microbiome and examined its relationship with the microbial populations present in the surrounding bulk soil, to better understand the recruitment dynamics that shape the microbiome in the roots.<br><br>RESULTS: The results revealed significant differences in microbiome composition between the bulk soil and roots of the two date palm cultivars, and between the microbiome of the resistant and susceptible cultivars as well. Moreover, we observed that date palm cultivars had a greater effect on bacterial community composition than on fungal population. Interestingly, the susceptible cultivar exhibited a higher enrichment of several beneficial genera, such as Pseudomonas, Lysinibacillus, Actinomadura, Halomonas, Kocuria, Serratia, Phyllobacterium, Bacillus, Streptomyces, and Trichoderma.<br><br>CONCLUSION: The presence of these beneficial genera, known for their antagonistic activity against phytopathogens, may reflect a recruitment pattern associated with pathogen pressure in the susceptible cultivar. This study is the first to compare the microbial communities between a bayoud-resistant and susceptible cultivar and provides insights into the potential role of the root microbiome when plants are under pathogen pressure. This reinforces the need to further elucidate the genetic and biological mechanisms that trigger microbiome assembly, which could be a key step in developing effective methods to manage the bayoud disease.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04837-8.},
}
@article {pmid41909894,
year = {2025},
author = {Hensen, T and Ahmad, S and Kastenmüller, G and Kraaij, R and Ghanbari, M and Ikram, A and Kaddurah-Daouk, R and Thiele, I},
title = {In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer's disease.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2443171},
pmid = {41909894},
issn = {2993-3935},
support = {RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; },
abstract = {The gut microbiome has become increasingly recognized for its role in the pathogenesis of Alzheimer's disease (AD) and is thought to influence AD pathogenesis via metabolic crosstalk with the host. However, mechanistic pathways connecting the gut microbiome to AD pathogenesis remain unknown. To explore potential mechanistic pathways in AD pathogenesis, we created host-microbiome whole-body metabolic models personalized with 16S rRNA microbiome data and predicted emergent metabolic contributions of gut microbiomes. We analyzed 63 metabolites in blood with previously known links with AD. These in silico predictions were then associated with major risk factors for AD in a cohort of 1,065 aging non-AD individuals and subsequently used to inform targeted analyses on serum metabolomics. Our analysis identified increased host-microbial production of L-arginine in older individuals. Lower production of deoxycholate correlated with the neuroprotective APOE E2 allele and it decreased with higher global cognition. Serum metabolomics from the same individuals of cholesterol products and bile acid metabolism corroborated the modeling predictions, suggesting a potential link between the APOE genotype and cognitive health. In conclusion, this study associated metabolic gut microbiome influences on human metabolism with risk factors for AD and identified cholesterol and bile acid metabolism to potentially link with AD pathogenesis.},
}
@article {pmid41909897,
year = {2025},
author = {Gitton-Quent, O and Sola, M and Maziers, N and Hiol, A and Dechamp, N and Le Chatelier, E and Touvier, M and Galan, P and David, A and Morabito, C and Famechon, A and Quinquis, B and Mariadassou, M and Veiga, P and Dore, J and Berland, M and Deschasaux-Tanguy, M},
title = {Alterations in gut microbiota characteristics along a type 2 diabetes risk gradient linked with family history.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2527766},
pmid = {41909897},
issn = {2993-3935},
abstract = {Type 2 diabetes (T2D) is a major global health issue, with growing evidence linking it to gut microbiome changes. However, whether these alterations precede T2D onset and act as predictors, risk factors, or contributors remains unclear. This study analyzed the gut microbiota of 192 individuals from the French NutriNet-Santé cohort, divided into four groups: non-T2D adults with no (n = 47), one (n = 48), or two (n = 51) T2D-affected parents, and T2D-affected adults (n = 46). A progressive microbiota shift was observed in non-T2D groups based on parental history, converging toward the T2D profile. Changes included altered enterotype distribution, increased oral-associated species, disrupted ecological networks, and a shift in Gram-positive-to-negative ratios. Notably, Prevotella copri abundance increased, alongside bacteria potentially enhancing branched-chain amino acid (BCAA), lipopolysaccharide (LPS), and acetate production. Diet also influenced microbiota patterns, with sweet product intake, vitamin levels, and copper/zinc ratios playing roles. A gradual microbiome transition from non-diabetic to T2D participants underscores its association with family history-based risk. While these shifts may reflect or drive T2D progression, further studies are needed to confirm these findings and explore their potential for preventive strategies.},
}
@article {pmid41909899,
year = {2025},
author = {Rozenberga, M and Saksis, R and Elbere, I and Birzniece, L and Briviba, M and Konrade, I and Klovins, J},
title = {Tracking the origin of bacterial DNA in blood: Indication of localized and sporadic transfer from other body sites.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2482771},
pmid = {41909899},
issn = {2993-3935},
abstract = {Recent studies propose the existence of a blood microbiome, but its composition, origin, and dynamics remain largely unresolved. In this pilot study, we analyzed the bacterial DNA present in the blood of 10 volunteers by comparing the taxonomic profiles of 16S rRNA gene sequences from skin, vaginal, oral, and fecal samples. After applying stringent decontamination protocols, we detected bacterial DNA in all blood samples, predominantly from the Pseudomonas genus. A key finding was the identification of 32 unique Amplicon Sequence Variants (ASVs) that were identical between blood and a single body site within individual participants, with no overlap between multiple body sites or across different participants. This participant-specific overlap suggests a true biological origin of bacterial DNA in blood, likely stemming from localized bacterial migration, such as from the skin. Additionally, 27.4% of the ASVs in blood were found in other body sites, with the highest overlap observed in skin samples. Furthermore, 25.3% of blood ASVs persisted after three months, suggesting a consistent pattern in the bacterial DNA composition detected in blood over time. These findings deepen our understanding of the blood microbiome and provide a basis for future research linking blood microbiota to health and disease phenotypes.},
}
@article {pmid41909901,
year = {2025},
author = {Teo, Y and Lavrinienko, A and Albertos Torres, D and Asare, PT and Ruder, A and Dominguez-Bello, MG and Egli, A and Bokulich, NA and Vonaesch, P},
title = {Evaluating long-term stool preservation methods for maximizing the recovery of viable human fecal microbiota.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2594958},
pmid = {41909901},
issn = {2993-3935},
abstract = {UNLABELLED: The gut microbiome plays a fundamental role in human health, prompting efforts to catalog and preserve its diversity across human populations. While DNA sequencing dominates microbiome research, cultivation remains essential for mechanistic studies and therapeutic development. However, best practices for long-term stool preservation remain limited. Here, we compared the stability of eight cryopreservation treatments for maintaining viable stool microbiota over a 1-y storage period at -80 °C (freezer) or at -196 °C (liquid nitrogen) using samples from infants, children, and adults. Combining cultivation on six media with 16S rRNA sequencing, we show that ultralow-temperature cryopreservation has a minimal impact on microbiota diversity compared to fresh cultures. Standard glycerol preservation and simple snap-freezing performed comparably to more complex and costly protocols, with all cultured samples retaining donor-specific microbiota profiles after long-term cryopreservation. The lack of strong treatment-specific effects on microbiota composition suggests a shared microbial response to freeze‒thaw stress favoring taxa with broad environmental tolerance. Our findings offer practical, low-cost strategies for stool biobanking.<br><br>IMPORTANCE: The cultivation of bacterial taxa from complex communities, such as those in fecal samples, is essential for mechanistic studies and the development of microbiota-based therapeutics, including defined consortia and individual probiotic strains. Such cultivation efforts typically rely on previously stored samples; however, systematic knowledge regarding long-term preservation strategies that ensure the viability and regrowth of constituent bacterial taxa remains limited. In this study, we systematically evaluated 16 distinct cryopreservation conditions to assess their efficacy in maintaining bacterial viability. Our results show that conventional glycerol-based preservation and simple snap-freezing are comparable in performance to more elaborate and cost-intensive protocols. Moreover, we identified the duration of sample transport prior to freezing as a critical determinant of post-thaw bacterial recovery. These findings provide valuable data on the relative effectiveness of various preservation methods and support the use of low-cost, easily implementable strategies that are particularly suitable for application in resource-limited settings.},
}
@article {pmid41909902,
year = {2025},
author = {Andalib, KMS and Rodosy, FB and Habib, A},
title = {The living medicine inside us: in vitro therapeutic prospects of human gut bacteria.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2480093},
pmid = {41909902},
issn = {2993-3935},
abstract = {Gut microbial metabolism is intimately coupled to host health and disease. Recent knowledge on potential health benefits of gut microbiome lays the groundwork for development of novel therapeutic strategies. But how microbiota-derived metabolites impact on host-microbiome crosstalk remains untapped from therapeutic perspectives. In this study, six gut bacteria sourced from a fecal pool of forty healthy donors were cultured in three distinct growth media. Subsequently, the bacteria were identified through 16S rRNA gene sequencing and subjected to metabolite extraction to evaluate their anti-microbial, anti-oxidant and anti-thrombotic potential. Findings reveal strong anti-oxidant activities in the metabolic-extracts from all the isolates. Metabolites derived from Lactobacillus rhamnosus, Priestia flexa and Bacillus subtiilis inhibited the growth of clinically pathogenic strains Escherichia coli ATCC-8739, Salmonella typhi ATCC-1408 and Staphylococcus aureus ATCC-6538. Escherichia fergusonii originated metabolites demonstrated the highest efficacy in lysing blood clots compared to streptokinase. Additionally, extracts from all the isolates exhibited significant ability to delay coagulation time, competing with standard warfarin. Thus, the findings of our early-stage study provide novel insights into metabolomic functions of gut microbiota. This study underscores the significance of exploring these active metabolites for prospective therapeutic and clinical exploration at the intersection of drug discovery and live bio-therapeutics.},
}
@article {pmid41909904,
year = {2025},
author = {Ramakrishnan, M and Cross, TL and Organski, AC and Saiprasad, SM and Simpson, AMR and Tancredi, DJ and Van Haute, MJ and Christensen, CM and Lewis, ZT and Auchtung, TA and Walter, J and Hutkins, R and Savaiano, DA},
title = {Two-week supplementation of Bifidobacterium adolescentis iVS-1 reduces symptoms associated with lactose intolerance in lactose maldigesters.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2508199},
pmid = {41909904},
issn = {2993-3935},
abstract = {Probiotic supplements containing high β-galactosidase-producing bacteria may aid in the management of lactose intolerance. We previously isolated a strain of Bifidobacterium adolescentis, iVS-1, from the fecal sample of a human donor after consumption of galactooligosaccharides (GOS), a prebiotic derived from lactose. Therefore, it was hypothesized that iVS-1 might reduce symptoms associated with lactose maldigestion. Compared to other probiotic strains, iVS-1 had high β-galactosidase activity and reduced gas formation by fecal communities during in vitro fermentations of lactose or milk. A randomized placebo-controlled clinical trial was then conducted with 21 lactose maldigesters, randomized to receive either B. adolescentis iVS-1 (n = 11) or placebo (n = 10) daily for 2 weeks. Compared to the two-week run-in period, iVS-1 abundance was higher both at the end of the treatment period (p = 0.0005) and after the 2-week post-treatment period (p = 0.045). The iVS-1 group reported less overall daily symptoms during the treatment period when compared to placebo (p = 0.032) and had significant improvement for fecal urgency (p = 0.033) and diarrhea (p = 0.006). The metabolism of lactose, reduction of gas, and improvement of multiple gastrointestinal symptoms suggest that B. adolescentis iVS-1 may be an effective treatment for lactose intolerance. Trial Registration: The trial is registered at ClinicalTrials.gov (https://clinicaltrials.gov/study/NCT05668468).},
}
@article {pmid41909905,
year = {2025},
author = {Chakraborty, J and Lanchenba Singh, N and Kumar Das, B},
title = {Gut microbiome and lung cancer: mechanisms, interactions, and dietary interventions.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2501313},
pmid = {41909905},
issn = {2993-3935},
abstract = {Lung cancer continues to claim countless lives globally. Several studies have shown that the gut microbiome is vital in maintaining healthy lung function through the gut-lung axis. A comparison between the gut microflora of healthy volunteers and lung cancer patients revealed that changes in the composition of gut microflora occur in lung cancer patients. The gut microflora may contribute to lung cancer by influencing immune reactions, inflammatory pathways, bacterial metabolites modulating host metabolism, microbiome dysbiosis, genotoxicity, virulence, and bacteria-induced epigenetic alterations. Thus, it may be assumed that maintaining a healthy gut microflora could help prevent lung cancer. Nutraceuticals are specialized products designed to support health and address specific nutritional needs. They contain ingredients like vitamins, minerals, probiotics, polyphenols, and herbs to reduce the risk or impact of certain illnesses. Nutraceuticals, including probiotics and polyphenols, play a role in preventing and treating various cancers, including lung cancer, by modulating the gut microbiome. This review examines the link between the gut microbiome and lung cancer, how it contributes to cancer development, and the impact of dietary interventions - particularly probiotics, polyphenols, and dietary fibers - on lung cancer prevention and treatment.},
}
@article {pmid41909906,
year = {2025},
author = {Shibi Anilkumar, A and Thomas, SM and Veerabathiran, R},
title = {Gut microbial metabolites as a convergence point between autoimmunity and solid tumors.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2470805},
pmid = {41909906},
issn = {2993-3935},
abstract = {The human gut microbiome, a diverse community of trillions of microorganisms, is essential for controlling numerous bodily functions, such as metabolism, immune response, and epithelial barrier integrity. The gut microbiota comprises bacteria, viruses, fungi, and other microorganisms that affect human health, metabolic pathways, and immune responses. Dysbiosis, or the imbalance of gut microbial composition, has been linked to the pathogenesis of several ailments, including cardiovascular conditions, gastrointestinal conditions, allergies, obesity, autoimmune disorders, and tumors. The interaction between gut microbes and immune responses, mainly through Tregs cells and Th17 cells, underscores the microbiome's function in immune regulation. Furthermore, gut microbial metabolites act as signaling molecules and substrates for metabolic processes, impacting autoimmune disorders and cancer development. Recent research highlights the microbiome's potential role in cancer immunoediting, where gut microbial metabolites may either promote or suppress cancer progression by modulating inflammation and immunosuppression. This review delves into the critical functions of the gut microbiome, its influence on autoimmune disorders, and the emerging connection between gut microbial metabolites and cancer immunoediting, offering new insights into their impact on human health and disease.},
}
@article {pmid41909907,
year = {2025},
author = {Ishii, C and Suzuki, M and Murakami, S and Song, I and Soejima, Y and Kato, M and Fukuda, S},
title = {Ecologically robust gut environment associated with personalized metabolic responses in a Japanese cohort.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2574930},
pmid = {41909907},
issn = {2993-3935},
abstract = {The gut microbiota produces numerous metabolites that affect host physiology. However, the effects of daily diet on human fecal metabolome profiles and their robustness are not well understood, and examinations of intra-individual stability over multiple time points are limited. Here, we investigated the robustness of the human intestinal environment through fecal metabolome and microbiome profiling in response to daily dietary fluctuations. We analyzed 176 fecal samples from 25 healthy Japanese individuals subjected to three dietary regimens, including heterogeneous and homogeneous diets. Fecal metabolome and microbiome profiles were unique to each individual. Further in-depth analyses of seven of these individuals showed that these profiles were stable despite daily dietary fluctuations in six individuals. In addition, random forest classification successfully predicted each subject's identity based on their metabolome profile. The correlation analysis also revealed that the food-metabolite and food-microbiome relationships were highly personalized. The findings from this study suggest that individual diet prior to sample collection is unlikely to influence the fecal metabolome and microbiome data to an extent that is not representative of the individual's "normal" condition, which may lower barriers to future research on the gut environment and its implications for host health.},
}
@article {pmid41909910,
year = {2025},
author = {Batool, M and McMahon, S and Franklin, S and Ramont, C and Sahasrabhojane, P and Chang, CC and Hayase, T and Hayase, E and Blazier, JC and Jenq, R and Shelburne, S and Galloway-Peña, J},
title = {Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2570502},
pmid = {41909910},
issn = {2993-3935},
abstract = {Infection with antimicrobial-resistant (AR) pathogens is a leading cause of morbidity and mortality among patients with hematological malignancies; however, little is known about the gut microbiome dynamics in acute myeloid leukemia patients and its impact on AR infections (ARI) and/or colonization with AR pathogens (ARC). Longitudinal stool samples collected from 154 patients undergoing induction chemotherapy were analyzed using 16S rRNA sequencing, selective and differential media culturing, MALDI-TOF, and VITEK2 to identify patients with ARC or ARI and to isolate AR infectious and colonizing bacterial strains. Shotgun metagenomic sequencing of baseline stool samples revealed taxa abundances, resistome features, and KEGG pathways associated with AR-events. Baseline observed species were lower in patients with AR-events (p = 0.01). Although several baseline taxa were more abundant in AR-event patients, they were not statistically significant when they were corrected for false discovery. Functional analysis revealed that penicillin and cephalosporin biosynthesis pathways were significantly enriched in patients with ARC. In summary, identifying the baseline microbiome, resistome, and functional pathway biomarkers may forecast an increased risk of ARI and/or ARC, thereby informing antimicrobial treatment strategies in AML patients.},
}
@article {pmid41909911,
year = {2025},
author = {Shi, J and Nguyen, SM and Yu, D and Wang, L and Liu, L and Cai, H and Wu, J and Long, J and Cai, Q and Shrubsole, MJ and Zheng, W and Shu, XO},
title = {Association of physical activity with gut microbiome among low-income black American adults in the Southern Community Cohort Study.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2589861},
pmid = {41909911},
issn = {2993-3935},
abstract = {Physical activity (PA) has been suggested to influence the gut microbiome. We evaluated this association among low-income Black American adults. This study included 489 self-identified Black American participants from the Southern Community Cohort Study. PA data, including exercise/sport- and work/home-related moderate-vigorous PA (MVPA), was collected at cohort enrollment (2002-2009). Stool samples were collected between 2018 and 2021, and microbial composition was profiled using shotgun metagenomic sequencing. General linear regression models were employed to evaluate associations between PA and gut microbial α-diversity, abundance of individual species and metabolic pathways. Among all participants, MVPA measures were not associated with Shannon α-diversity (p > 0.05) and explained approximately 0.2-0.3% variation of Bray-Curtis dissimilarity. A total of 32 bacterial species, including seven Bacteroides species, two Streptococcus species, two Prevotella species, and nine microbial metabolic pathways, including D-fucofuranose biosynthesis, xyloglucan degradation, biosynthesis of L-citrulline, L-aspartate and L-asparagine biosynthesis, and urea cycle, were significantly associated with work/home-related and/or total MVPA (all false discovery rates < 0.10). In conclusion, MVPA, particularly from work and home activities, may modulate the composition and functionality of the gut microbiome among Black American adults.},
}
@article {pmid41910033,
year = {2026},
author = {Jinato, T and Sikaroodia, M and Gilleveta, PM and Dissayabutra, T and Tangkijvanich, P and Bajaj, JS and Chuaypen, N},
title = {Gut Microbiome Signatures Differ in Cirrhosis With and Without Hepatocellular Carcinoma in a Southeast Asian Cohort.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70358},
pmid = {41910033},
issn = {1440-1746},
support = {C2F//Second Century Fund/ ; RA65/039//Ratchadapiseksompotch Fund, Faculty of Medicine Chulalongkorn University/ ; HEA_FF_68_159_3000_028//Thailand Science research and Innovation Fund Chulalongkorn University/ ; FF68//Fundamental Fund 2025/ ; B36G660004//Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation/ ; },
abstract = {BACKGROUND: Gut microbiota, microbial metabolites, and inflammatory cytokines play key roles in the pathogenesis of cirrhosis and hepatocellular carcinoma (HCC); however, data from Southeast Asia are limited. This study examined microbial composition, intestinal permeability, butyrate-related gene expression, and cytokine profiles in Thai patients with cirrhosis, with and without HCC.<br><br>METHODS: This cross-sectional study included 30 healthy controls, 33 patients with cirrhosis without HCC, and 44 patients with HCC (HCC-cirr). Fecal samples were analyzed using 16S rRNA sequencing. Microbial functional profiles were predicted using KEGG Orthology-based pathway inference. Gut permeability markers (intestinal fatty acid-binding protein [I-FABP] and lipopolysaccharide-binding protein [LBP]), butyrate-associated gene (BCoAT) expression, and cytokine profiles were assessed.<br><br>RESULTS: Alpha diversity (Chao1) was significantly lower in HCC-cirr patients than in healthy controls (p&#x2009;<&#x2009;0.001) and patients with cirrhosis (p&#x2009;=&#x2009;0.008). Beta diversity also differed significantly between HCC-cirr and controls (p&#x2009;=&#x2009;0.008). Ligilactobacillus, Catenibacterium, and Alloprevotella were enriched in the cirrhosis group, whereas HCC-cirr patients showed increased Ruminococcus gnavus and reduced butyrate producers (Coprococcus, Subdoligranulum). Functional prediction suggested pathway differences between cirrhosis and HCC-cirr, including folate, sulfur, tyrosine metabolism, and steroid biosynthesis. BCoAT expression was significantly decreased in HCC (p&#x2009;=&#x2009;0.006). Plasma LBP and I-FABP were significantly elevated in HCC-cirr (p&#x2009;=&#x2009;0.033, p&#x2009;<&#x2009;0.001), with I-FABP also higher than in cirrhosis (p&#x2009;=&#x2009;0.002). Proinflammatory cytokines (GM-CSF, IL-10, IL-18, IL-1&#x3b1;, IL-7, IL-8, and M-CSF) were elevated in HCC-cirr.<br><br>CONCLUSIONS: Among the Thai cohort, HCC with cirrhosis was associated with distinct gut microbial changes, reduced BCoAT expression, increased gut permeability, and cytokine alterations, highlighting the contribution of gut dysbiosis and microbial by-products to liver disease progression.},
}
@article {pmid41910132,
year = {2026},
author = {Sáenz, JS and Yergaliyev, T and Rios-Galicia, B and Seifert, J and Camarinha-Silva, A},
title = {The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019126},
doi = {10.1128/msystems.00191-26},
pmid = {41910132},
issn = {2379-5077},
abstract = {UNLABELLED: Viral communities, especially phages, affect prokaryotic diversity and thus influence the host's metabolic processes. However, the makeup and role of the chicken gut virome remain poorly understood. To address this gap, we mined 1,458 chicken gut metagenomes and 56 viral-enriched samples to recover viral sequences and assemble a comprehensive collection of draft viral genomes. We identified 19,778 viral operational taxonomic units (vOTUs), of which 97% were dsDNA phages from the Caudoviricetes class, primarily targeting gut bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and lacked known biological functions. Additionally, the distribution of vOTUs across samples showed that the chicken virome is highly individual-specific. Yet, the viral community also exhibited strong spatial stratification along the gastrointestinal tract, with notable differences between proximal and distal regions, primarily driven by phages linked to the Lactobacillaceae family. Moreover, this study shows that the geographical region, breed, and diet drive the chicken gut viral diversity and composition. This underscores the significant novelty of the chicken gut virome and its largely unexplored functional potential, much of which would be missed if analyses were restricted to fecal samples.<br><br>IMPORTANCE: The chicken gut harbors a vast community of viruses that remain largely unexplored despite their potential to influence poultry health and productivity. By analyzing 1,514 samples from different gut regions across 15 countries, we discovered nearly 20,000 distinct viruses, most of which were previously unknown phages. The chicken virome showed strong spatial differences along the gastrointestinal tract, meaning each gut section harbors a unique viral community, underscoring that fecal samples alone miss much of the virome's diversity. We also uncovered that the geographical region, breed, and diet could drive the chicken gut viral diversity and composition. Overall, our findings greatly expand our understanding of gut virus diversity and microbiome ecology, offering a valuable foundation for developing strategies to monitor or manipulate the microbiome to improve poultry health.},
}
@article {pmid41910137,
year = {2026},
author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {Temperature modulates gut microbiome disruption and resistome enrichment in oxytetracycline-treated channel catfish (Ictalurus punctatus).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0418725},
doi = {10.1128/spectrum.04187-25},
pmid = {41910137},
issn = {2165-0497},
abstract = {UNLABELLED: Oxytetracycline (OTC) is one of the few antibiotics approved by the U.S. Food and Drug Administration for catfish aquaculture. Unfortunately, OTC resistance has been frequently detected in production environments, with the fish gut identified as a potential hotspot for resistance selection. In aquaculture systems, water temperature is a critical factor influencing fish physiology, antibiotic pharmacokinetics, and water resistome development. However, its role in modulating OTC effects on the fish gut microbiome remains underexplored. This study examined temperature-dependent microbiome and resistome responses in channel catfish (Ictalurus punctatus) when treated with OTC at 20°C, 25°C, and 30°C. Gut contents collected at treatment completion and after withdrawal were analyzed via metagenomic sequencing. In untreated fish, temperature alone shaped microbial structure and function, with the Shannon diversity increasing with temperatures and the β-diversity differing significantly across temperature groups. After OTC exposure, microbial responses were markedly temperature dependent with few taxa affected at 20°C, whereas substantial shifts occurred at 25°C and 30°C, indicating reduced microbial resilience at higher temperatures. OTC elevated total antimicrobial resistance gene (ARG) abundance, enriching tetracycline and β-lactam resistant genes consistent with co-selection. ARG-host linkages were diffuse at 20°C but consolidated within Klebsiella, Enterococcus, Enterobacter, and Paraclostridium at 25°C and 30°C. Notably, OTC-induced dysbiosis persisted through the withdrawal period. These findings demonstrate that temperature modulates both the magnitude and persistence of OTC-driven microbiome disruption and resistome enrichment, underscoring the importance of temperature-aware antibiotic management to mitigate antimicrobial resistance risks and safeguard fish health and food safety in aquaculture.<br><br>IMPORTANCE: This study reveals that water temperature critically shapes how antibiotics affect the gut microbiome and antimicrobial resistance in channel catfish. Metagenomic sequencing results showed that oxytetracycline (OTC) treatment caused minimal disruption of the microbiome at 20&#xb0;C, but induced significant community shifts and enrichment of antimicrobial resistance genes (ARGs) at 25&#xb0;C and 30&#xb0;C. Higher temperatures reduced microbial resilience, consolidating ARGs within key bacterial genera such as Klebsiella and Enterococcus. Importantly, OTC-induced microbiome changes and resistance persisted through the withdrawal period. These findings highlight temperature as a major driver of antibiotic impact in aquaculture, emphasizing the prudent use of antibiotics at different disease breakout temperatures.},
}
@article {pmid41910192,
year = {2026},
author = {Saqib, S and Latousakis, D and Virtanen, S and Kalliala, I and Holster, T and Juge, N and Salonen, A},
title = {Exploratory analyses of cervicovaginal mucus O-glycan composition and microbiota profiles in unexplained infertility.},
journal = {Glycobiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/glycob/cwag023},
pmid = {41910192},
issn = {1460-2423},
abstract = {In addition to the specific causes of infertility, two components of the vaginal ecosystem, the vaginal microbiota and the cervicovaginal mucus (CVM), may be associated to reduced fecundity and the success of infertility treatments. The aim of this study was to explore the composition of the CVM O-glycans and vaginal microbiota in women with unexplained infertility. We collected CVM and vaginal swab samples during medically induced ovulation from 19 women with unexplained infertility. Mucin O-glycosylation profiles were generated through Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-ToF) mass spectrometry and taxonomic profiles of the vaginal microbiota through 16S rRNA gene amplicon sequencing. Altogether 57 O-glycan structures were identified, dominated by core 1 and 2 structures. A significant proportion, nearly 85%, of the glycans were fucosylated and five structures dominated the profiles, accounting for >50% of the glycans observed in most samples. The vaginal microbiota of the patients was dominated by Lactobacillus crispatus (79%), followed by Lactobacillus jensenii (32%) and Lactobacillus iners (21%) and Gardnerella vaginalis (5%, single sample). PERMANOVA analysis indicated significant associations between the glycan structures and dominant taxa (q = 0.0011, R2 = 0.37). This exploratory study provides initial insights into the composition and variation of CVM O-glycans in unexplained fertility and in relation to the vaginal microbiota composition, laying a groundwork for future research.},
}
@article {pmid41910204,
year = {2026},
author = {Green, L and Marchesani, A and Joyner, JL},
title = {The Atlanta Urban Watershed Harbors Antibiotic Resistant Halotolerant Bacteria.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag084},
pmid = {41910204},
issn = {1365-2672},
abstract = {AIMS: Rapid urbanization of the Chattahoochee River has decreased the water quality with higher levels of anthropogenic bacteria from nonpoint source pollution. Introduced bacteria are variable across urban watersheds but only monitored by the abundance of fecal indicator bacteria. Staphylococcus aureus is a halotolerant, opportunistic pathogen associated with aquatic pollution, but impact on the microbial ecology is not well understood in freshwater systems. Describing the halotolerant subset of the aquatic microbiome, can expand upon the health risk of bacterial pollution.<br><br>METHODS &amp; RESULTS: Surface water samples along the Chattahoochee River were collected and halotolerant bacteria were cultured using selective agar, typical for growing Staphylococcus species. Bacteria colonies were isolated then characterized by morphology, biochemical tests, and antibiotic resistance screening. Antibiotic resistance profiles showed isolates with a high percentage of resistance to penicillin (86.2%) and novobiocin (17.2%). Biofilm formation was common with 41.4% of isolates formed moderate to strong biofilms. 16S rRNA gene sequencing identified isolates to not be Staphylococcus spp. but within two predominant groups, Bacillus spp. and Priestia spp.<br><br>CONCLUSIONS: The Priestia genus is poorly known in freshwater systems; though the combination of antibiotic resistance, biofilm formation, and spore-forming traits indicate that it has key survival characteristics. Halotolerant bacteria harbor opportunistic human pathogens and a public health risk because the bacteria have a high prevalence of antibiotic resistance and biofilm capability, which contribute to environmental persistence and reservoirs for antibiotic resistance genes. This environmental resistome is a notable and developing characteristic of the urban aquatic microbiome.},
}
@article {pmid41910238,
year = {2026},
author = {Le, NNT and Xue, S and Mu, H and Wu, J and Xi, C and Marhaba, T and Zhang, W},
title = {Soil chemistry and microbiome modulation through water irrigation containing oxygen, hydrogen, and carbon dioxide nanobubbles.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0217325},
doi = {10.1128/aem.02173-25},
pmid = {41910238},
issn = {1098-5336},
abstract = {Nanobubble technology has shown considerable promise in sustainable agriculture due to its ability to enhance seed germination, plant growth, and soil quality without leaving harmful residues. While benefits are often attributed to improved soil aeration and soil texture changes (e.g., permeability), nanobubbles may also influence soil microbiome, an essential driver of plant health and nutrient cycling. This study systematically investigated how different nanobubble types-oxygen, hydrogen, and carbon dioxide-modulate soil chemistry and microbial community structure over a 4-week period. Multivariate analyses on microbiome taxonomic composition revealed distinct microbial responses to each gas type. Oxygen and hydrogen nanobubble treatments resulted in more pronounced shifts in microbial composition and functional potential compared to carbon dioxide nanobubbles. These shifts included enrichment of bacterial taxa associated with nutrient turnover, pollutant degradation, and pathogen suppression, such as Flavobacteriaceae, Comamonadaceae, Nannocystaceae, and Blastocatellaceae. Functional predictions showed that oxygen and hydrogen nanobubbles could promote metabolic pathways related to organic compound degradation and remediation of contaminated soil. Microbial network analysis further highlighted the beneficial impacts of nanobubbles on keystone taxa, such as Flavobacteriaceae, which in turn play pivotal roles in shaping soil ecosystem functions. Together, these findings demonstrate that gas-specific nanobubble irrigation can steer soil microbiome dynamics in ways that may enhance soil fertility, resilience, and crop productivity.IMPORTANCEThis study provides new insights into how nanobubble irrigation can be used to improve soil health and agricultural sustainability. By demonstrating that oxygen and hydrogen nanobubbles selectively enrich beneficial microbial taxa linked to soil nutrient turnover, pollution degradation, and pathogen suppression, this study identifies a promising approach to enhance plant growth and soil health through new nanobubble-driven processes. The detection of keystone taxa responsive to nanobubble treatments also reveals potential microbial mechanisms underlying the interactions between nanobubbles, soil, and plant health. Together, these findings highlight nanobubble irrigation as a novel and scalable strategy for microbiome engineering that could advance sustainable crop production and environmental stewardship. Furthermore, while prior studies have primarily focused on the microbial effects of air and oxygen nanobubbles, our study systematically examined and compared the impacts of less explored nanobubble types, specifically hydrogen and carbon dioxide, demonstrating the broad versatility of nanobubbles for diverse agricultural applications.},
}
@article {pmid41910252,
year = {2026},
author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y},
title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0252325},
doi = {10.1128/aem.02523-25},
pmid = {41910252},
issn = {1098-5336},
abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.},
}
@article {pmid41910273,
year = {2026},
author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P},
title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0179025},
doi = {10.1128/msystems.01790-25},
pmid = {41910273},
issn = {2379-5077},
abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.<br><br>IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.},
}
@article {pmid41910342,
year = {2026},
author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D},
title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0085625},
doi = {10.1128/msphere.00856-25},
pmid = {41910342},
issn = {2379-5042},
abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.<br><br>IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.},
}
@article {pmid41910441,
year = {2026},
author = {Manti, M and Dimitriadis, K and Dri, E and Mavromoustakou, K and Vakka, A and Koutsopoulos, G and Tsioufis, P and Katsimichas, T and Siakavellas, S and Gazouli, M and Tsioufis, K},
title = {Transcatheter aortic valve implantation and gut microbiota: Rationale and design of the 'GUT-TAVI' cohort study.},
journal = {Science progress},
volume = {109},
number = {1},
pages = {368504261426427},
doi = {10.1177/00368504261426427},
pmid = {41910441},
issn = {2047-7163},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Transcatheter Aortic Valve Replacement/methods ; *Aortic Valve Stenosis/surgery/microbiology ; Prospective Studies ; Methylamines/blood ; Female ; Male ; Aged ; Cohort Studies ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Hemodynamics ; },
abstract = {ObjectiveAlterations in gut microbiota have been reported in patients with aortic valve stenosis (AVS), yet the impact of haemodynamic restoration following transcatheter aortic valve implantation (TAVI) on microbiota composition remains unclear. This study protocol describes a prospective cohort investigation designed to examine changes in gut microbiota and related metabolic markers after TAVI.Methods'GUT-TAVI' is a single-centre, prospective observational cohort study enrolling 40 adults with severe AVS undergoing TAVI. Stool samples will be collected at two timepoints (1 month to 1 day pre-TAVI and 3 months post-TAVI) for 16S-rRNA sequencing. Serum trimethylamine N-oxide (TMAO), standard biochemical markers, echocardiographic parameters, and dietary adherence scores will also be assessed. The primary endpoint is the change in gut microbiota composition following TAVI. Secondary analyses will examine associations between microbiota changes, haemodynamic parameters, and TMAO levels while accounting for potential confounders.ResultsAs a protocol, no results are yet available. Planned analyses include alpha- and beta-diversity comparisons, multi-variable modelling, sub-group analyses, and sensitivity analyses addressing antibiotic exposure and procedural variability.ConclusionsThis study may provide preliminary insights into how haemodynamic improvement after TAVI is associated with changes in gut microbiota and metabolic function. Findings may help inform future, larger-scale studies investigating the gut-heart axis in cardiovascular diseases.},
}
@article {pmid41910593,
year = {2026},
author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, M and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , },
title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.},
journal = {Pancreas},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPA.0000000000002618},
pmid = {41910593},
issn = {1536-4828},
abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.<br><br>OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).<br><br>METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP) and 148 recurrent acute pancreatitis (RAP). Additionally, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.<br><br>RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared to HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve - AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.<br><br>CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.},
}
@article {pmid41910796,
year = {2026},
author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D},
title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.},
journal = {Veterinary research communications},
volume = {50},
number = {3},
pages = {},
pmid = {41910796},
issn = {1573-7446},
abstract = {UNLABELLED: Shrimp aquaculture is a rapidly expanding food sector; however, its sustainability is challenged by disease outbreaks often linked to imbalances in the microbiome. Here, we characterized the microbial communities in the intestines of shrimp and pond water from three Egyptian farms (A, B, and C) using Oxford Nanopore long-read sequencing. Descriptive comparisons of relative abundance and diversity trends revealed that pond water harbored significantly higher alpha diversity than shrimp guts. In contrast, beta diversity confirmed a strong separation between host-associated and environmental microbiomes. For the observed phyla, taxonomic profiling revealed that shrimp guts were dominated by Proteobacteria, Actinomycota, and Bacillota, whereas pond water contained additional constituents, including Cyanobacteria and Bacteroidota. Pathogen-associated genera, particularly Vibrio spp. and Pseudomonas spp., were more abundant in water samples, with farm-specific variations linked to management practices such as salinity and feed protein content. Venn analysis highlighted that pond water harbored the largest pool of unique taxa, reinforcing its role as a putative reservoir for pathogens. These findings provide the first integrative microbiome baseline for Egyptian shrimp farms, underscoring the need for microbiome-informed management to mitigate the risk of pathogens.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11259-026-11113-7.},
}
@article {pmid41910822,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41910822},
issn = {1573-0972},
}
@article {pmid41910951,
year = {2026},
author = {Dasgupta, S},
title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261419483},
doi = {10.1177/15578100261419483},
pmid = {41910951},
issn = {1557-8100},
abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.},
}
@article {pmid41911313,
year = {2026},
author = {Odem, MA and Simbassa, SB and Alvarez, CF and Jeilu, O and Simar, SR and Bosserman, R and Dutta, S and Galdamez, W and Ayele, H and Hanson, BM and Proctor, DM and Krachler, AM},
title = {Shiga toxin increases intestinal transit to displace resident microbes and facilitate pathogen colonization.},
journal = {PLoS pathogens},
volume = {22},
number = {3},
pages = {e1014104},
doi = {10.1371/journal.ppat.1014104},
pmid = {41911313},
issn = {1553-7374},
abstract = {Shiga toxin (Stx)-producing Escherichia coli (STEC) is a major cause of food-borne illnesses, and disease severity correlates with the production of Shiga toxins. While clinical symptoms such as bloody diarrhea and haemolytic uremic syndrome have been attributed to Stx, its contribution to bacterial fitness is not well understood. Here, we demonstrate that Stx2 enhances STEC colonization of the zebrafish gut by facilitating the partial displacement of gut resident microbes. Infection with Stx2-producing STEC strains or direct exposure of fish to purified Stx2 induces alterations in the zebrafish microbiome structure, impacting several bacterial phyla and genera, notably Pseudomonads. We show that Stx2 is sufficient to facilitate these changes by accelerating intestinal transit, leading to increased expulsion of select gut microbes, including resident Pseudomonas species. Additionally, prokinetic drug treatment causes similar changes in gut transit and expulsion of Pseudomonas. Collectively, these findings detail a novel mode of action of Stx2 on the host, and shed light on its contribution to bacterial fitness within the host intestine.},
}
@article {pmid41911577,
year = {2026},
author = {Kaplunova, V and Alioui, H and Griguschies, T and Müller, L and Joisten-Rosenthal, V and Lautwein, T and Metzger, S and Durán, P and Loo, E},
title = {Artificial soil (ArtSoil): Recreating soil conditions in synthetic plant growth media.},
journal = {The Plant journal : for cell and molecular biology},
volume = {126},
number = {1},
pages = {e70833},
pmid = {41911577},
issn = {1365-313X},
support = {390686111//Cluster of Excellence on Plant Sciences/ ; Wolf Frommer//Alexander von Humboldt-Stiftung/ ; 391465903/GRK 2466//Deutsche Forschungsgemeinschaft/ ; 458090666//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Soil/chemistry ; *Arabidopsis/growth &amp; development ; *Culture Media/chemistry ; Soil Microbiology ; Sucrose/metabolism ; Microbiota ; Plant Development ; },
abstract = {Controlled plant growth in laboratories can be achieved by cultivating plants under sterile or axenic conditions on predefined synthetic growth media, typically supplemented with sugar. In nature, plants do not receive exogenous sugar supplies, form symbiosis with microbes, and plant growth is influenced by soil edaphic factors. Thus, physiological and multi-omic analyses of plants grown on synthetic media will differ from those of soil-grown plants due to the influence of sucrose, and the absence of microbiota and soil edaphic factors on plant growth. The rapid advances in spatial omics call for accurate characterization of plants grown under conditions similar to soil. To address the issue, we developed Artificial Soil (ArtSoil), a growth medium containing essential nutrients for plant growth, and aqueous soil extract (ASE) to maintain soil microbiomes and edaphic factors, simultaneously eliminating the need for sugar supplementation in the medium. We compared Arabidopsis thaliana grown on conventional media and on ArtSoil under various growth conditions. We showed that complex soil microbiota in ArtSoil promote plant growth without physiological side effects induced by sucrose. We demonstrate an application for ArtSoil in single-cell transcriptomics and report microbiota-induced cell-type-specificity in immune and nitrogen signaling. We tested ArtSoil with six types of ASEs to demonstrate its potential to decouple nutrient effects from microbiota in plant growth. We conclude that ArtSoil offers a more physiologically relevant alternative to conventional media for studying plant growth within a soil-like context.},
}
@article {pmid41911622,
year = {2026},
author = {Naim, A and van Staaveren, N and Leishman, EM and Nicklas, AL and Tulpan, D and Forsythe, P and Harlander, A},
title = {Preference and behavioral responses to synbiotic supplementation via drinking water in laying hens under social stress.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106860},
doi = {10.1016/j.psj.2026.106860},
pmid = {41911622},
issn = {1525-3171},
abstract = {Synbiotics (SYN) have the potential to enhance animal health, but their efficacy depends on both biological impact and voluntary intake, particularly under stress, when hydration and gut support are critical. This study presents the first investigation of SYN supplementation delivered exclusively through drinking water in laying hens, evaluating both preference and behavioral responses, particularly feather pecking, during a period of social stress induced by repeated mixing of unfamiliar birds. A total of 226 White Leghorn hens (37 weeks old) were housed in enriched floor pens with simultaneous access to color-coded SYN-enriched and plain water containers. Following a 2-week associative learning phase and 1-week washout, hens entered a 6-week preference testing period encompassing pre-stress, stress, and post-stress phases. Water consumption was measured at the group level, while individual jug visits were tracked using RFID technology. Feather pecking was measured (10 min/day) and feather damage assessed according to severity. Hens showed a clear preference for SYN-enriched water, consuming significantly more than plain water (p < 0.0001). While overall intake remained stable, SYN consumption fluctuated across stress phases, with the strongest preference pre-stress and a modest decline during stress. Although hens with higher rates of severe feather pecking (SFP) visited SYN-enriched water more frequently than hens with lower rates (p = 0.0288), suggesting a potential coping mechanism, overall, SFP rates remained stable across all phases. Notably, the level of SFP observed during the pre-stress phase was already sufficient to cause progressive plumage deterioration, which continued throughout the study. The proportion of birds with severe feather damage rose from 39.4% to 53.5%, while those with intact plumage dropped from 37.6% to 19.9% over time. Thus, SYN supplementation via drinking water is feasible and preferred by laying hens, even under stress. These findings highlight the potential of nutraceuticals delivered through drinking water to influence hen behavior; however, the progressive plumage deterioration despite stable SFP rates suggests that SYN supplementation alone may be insufficient, underscoring the need for integrated management strategies.},
}
@article {pmid41912274,
year = {2026},
author = {Dutton, CL and Goeckner, A and Goldwire, T and Grupstra, CGB and Houghtaling, D and Nonnamaker, LE and Subalusky, A},
title = {Bioreactors on the Move: How Animals Contribute to Microbial Community Coalescence and Shape Ecosystem Function.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70291},
doi = {10.1111/1462-2920.70291},
pmid = {41912274},
issn = {1462-2920},
support = {//Florida Atlantic University/ ; //University of Florida/ ; //United States National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Microbiota ; *Ecosystem ; *Bioreactors/microbiology ; Fishes/microbiology ; Oligochaeta/microbiology ; Bacteria/classification ; Soil Microbiology ; },
abstract = {Microbiome community coalescence-the mixing of separate microbial communities and their environments resulting in a novel community-represents an important but understudied ecological process at the animal-environment interface. Here, we propose that animals function as "mobile bioreactors" across landscapes, ingesting environmental microbes that undergo selective filtering within the animal gut that are then deposited back into the environment alongside the animal's native microbiota. This coalescence of animal and environmental microbiomes can significantly alter ecosystem processes including nutrient cycling, organic matter decomposition, and trophic interactions. We synthesize emerging evidence from terrestrial, freshwater, and marine ecosystems demonstrating how animal-facilitated microbial coalescence influences ecosystem functioning. Through case studies of hippos in African rivers, fish on coral reefs, and earthworms in soil, we illustrate how these coalescence events create novel microbial communities with distinct functional capabilities. We identify methodological approaches for investigating these phenomena and outline key knowledge gaps, particularly regarding the persistence of animal microbiota in environmental settings and their quantitative contribution to ecosystem processes. Here we highlight the importance of studying animal-environmental coalescence events with far reaching implications for our understanding of ecosystem processes, animal health, and environmental resilience.},
}
@article {pmid41912276,
year = {2026},
author = {Luko-Sulato, K and Sulato, ET and Osman, JR and Nolasco-Jiménez, P and Morales, D and Rezende, GS and Rodrigues, CA and Maintinguer, SI and da Cunha, AF and Rosolen, V},
title = {Soil Microbiome of Tropical Seasonal and Permanent Small Wetlands.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70306},
doi = {10.1111/1758-2229.70306},
pmid = {41912276},
issn = {1758-2229},
support = {2021/06332-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/15396-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {*Wetlands ; Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; *Microbiota ; *Archaea/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Tropical Climate ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Characterisation of the microbial communities of two small tropical wetlands under two distinct hydrological regimes (permanent and seasonal), across a rainy and dry season was performed by 16S rRNA amplicon sequencing. We identified 48 bacterial phyla across the two wetland types, seasons and depths and 83% of the bacterial sequences consistently corresponded to six phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Proteobacteria and Verrucomicrobia. The seasonal wetland presented a predominance of Chloroflexi, Nitrospirae, Actinobacteria and Acidobacteria, whereas the permanent wetland showed higher relative abundances of Planctomycetes, Bacteroidetes, Proteobacteria and Firmicutes. Archaeal communities also differed, with Crenarchaeota predominating in the seasonal and Euryarchaeota in the permanent wetland. Microbial communities showed pronounced compositional shifts across wetland type, season and depth, while maintaining stable alpha diversity, with depth was the dominant driver. Functional inference suggested that aerobic ammonia oxidation, nitrate reduction and sulphur compound respiration were the predominant putative metabolic pathways in the seasonal wetland and methanogenesis, fermentation, dark hydrogen oxidation, nitrogen fixation, photoautotrophy, ureolysis and hydrocarbon degradation in the permanent wetland. The permanent wetland exhibited sparse correlation with environmental drivers, consistent with long-term saturation and chronic nutrient limitation, while the seasonal wetland presented influence of pH, nutrients and SOC on microbial community structure.},
}
@article {pmid41912342,
year = {2026},
author = {Engelen, MPKJ and van der Meij, BS},
title = {Targeting muscle, mitochondria, and microbiome: nutritional and exercise strategies across wasting diseases and conditions.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {29},
number = {3},
pages = {211-213},
doi = {10.1097/MCO.0000000000001220},
pmid = {41912342},
issn = {1473-6519},
}
@article {pmid41912530,
year = {2026},
author = {Jiang, J and Poulsen, CS and Boulund, U and Shah, S and Trivedi, U and Bhattacharyya, M and Neumann, AU and Dai, DLY and Petersen, C and Hoskinson, C and Moraes, TJ and Mandhane, PJ and Simons, E and Azad, MB and Subbarao, P and Bønnelykke, K and Chawes, B and Turvey, SE and Sørensen, SJ and Thorsen, J and Stokholm, J},
title = {Early life bacteria and sibling exposure associate with restoration of the infant gut microbiome after cesarean section.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71185-6},
pmid = {41912530},
issn = {2041-1723},
abstract = {Long-term gut microbiome perturbation following Cesarean section (CS) delivery has been associated with an increased risk of developing childhood asthma. Whether such CS-associated microbiome composition can be modulated by environmental exposures or ecological interactions, and thereby mitigate disease risk, is unclear. In the COPSAC2010 birth cohort (N = 700), we develop a restoration score quantifying the degree to which the 1-year gut microbiome resembled that of vaginally delivered infants. We identify predictors of this restoration score in the 1-week gut microbiome. In addition, having older siblings is linked to a higher restoration score, mediated by increased abundances of restoration-associated bacteria. The restoration score, including association with delivery mode, older siblings and later asthma as well as early bacterial drivers, is successfully replicated in the independent Canadian birth cohort, CHILD. These insights suggest that specific early-life bacteria and sibling exposure may support microbiome restoration and confer protective effects against asthma risk.},
}
@article {pmid41913243,
year = {2026},
author = {Mancin, E and Casto-Rebollo, C and Maltecca, C and Ibañez-Escriche, N and Mantovani, R and Sartori, C and Tiezzi, F},
title = {Insights into pig resilience: the Microbiome-genetic connection.},
journal = {Porcine health management},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40813-026-00506-4},
pmid = {41913243},
issn = {2055-5660},
}
@article {pmid41913289,
year = {2026},
author = {Kieri, O and Narayanan, A and Jütte, BB and Svensson, P and Aleman, S and Sönnerborg, A and Ray, S and Nowak, P},
title = {Linking gut microbiome to HIV-1 reservoir size in people living with HIV.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00828-2},
pmid = {41913289},
issn = {1757-4749},
abstract = {The gut microbiome is altered during HIV-1 infection and contributes to immune dysfunction and inflammation in people living with HIV (PLWH), these changes may persist despite effective antiretroviral therapy (ART). We explored the associations between the fecal gut microbiome and blood HIV-1 reservoir size in PLWH (n = 30) on long-term ART. The intact proviral DNA assay (IPDA) and shotgun metagenomic sequencing were performed to identify microbial species and metabolic pathways associated with the size of the HIV-1 reservoir. PLWH with a smaller intact reservoir exhibited lower evenness compared to individuals with a larger intact reservoir. We found that Phocaeicola plebeius and Lachnospira sp000437735 were significantly enriched in individuals with a smaller intact reservoir and lower intact-to-total proviral ratio, respectively. We observed a negative association between Faecalibacterium prausnitzii and a positive association of Prevotella copri, with the intact proviral reservoir size. Additionally, the metabolic pathways of glycolysis and branched-chain amino acid biosynthesis were enriched in individuals with larger reservoir. HIV reservoir size in blood is associated with gut microbiome evenness, specific metabolic pathways and microbial signatures, including Lachnospira, Prevotella, and Faecalibacterium. Our findings underscore the potential role of the gut microbiome in viral persistence, raising the possibility that modulating microbial composition could influence the HIV reservoir.},
}
@article {pmid41913604,
year = {2026},
author = {Wang, HY and Li, C and Pan, YP},
title = {[Imbalance and reconstruction of periodontal homeostasis: new perspectives on the pathogenesis, prevention and treatment of periodontitis].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {4},
pages = {445-451},
doi = {10.3760/cma.j.cn112144-20251209-00499},
pmid = {41913604},
issn = {1002-0098},
support = {2023YFC2506300//National Key R&amp;D Program of China/ ; },
abstract = {Periodontal homeostasis is a dynamic equilibrium based on healthy periodontal structures, a relatively stable oral microbiome, appropriately regulated host immunity, coordinated cellular metabolism, and a functional dentition with normal occluion. This review aims to systematically elucidate the key mechanisms underlying the maintenance and disruption of periodontal homeostasis. The dysregulation of microbiota and excessive immune activation mutually reinforce each other, serving as the core driving forces for the occurrence and progression of periodontitis. On this basis, a treatment approach oriented toward "re-establishing periodontal homeostasis" is proposed. Based on microbiota remodeling and structural reconstruction, combined with host immune regulation and immunometabolic intervention, emphasizing systemic risk factor management and functional dentition reconstruction, we aim to establish a personalized, precise, and sustainable new model for periodontal prevention and treatment.},
}
@article {pmid41913620,
year = {2026},
author = {Wang, XY and Yao, YJ and Li, LL and Yan, FH},
title = {[From oral microbiome dysbiosis to renal injury: research advances in the mechanism of association between periodontitis and diabetic kidney disease].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {4},
pages = {582-588},
doi = {10.3760/cma.j.cn112144-20251112-00446},
pmid = {41913620},
issn = {1002-0098},
support = {82301100//National Natural Science Foundation of China/ ; BK20220198//Natural Science Foundation of Jiangsu Province/ ; 0224C001//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; YKK23177//Nanjing Foundation for Development of Science and Technology/ ; },
abstract = {Periodontitis, a chronic inflammatory disease driven by dysbiosis of the oral microbiome, has increasingly been recognized for its systemic impact beyond the oral cavity. Growing evidence links periodontitis to the onset and progression of diabetic kidney disease (DKD), suggesting that disturbances of oral microbial homeostasis may influence distant organs through systemic circulation or the oral-gut-kidney axis. Such interactions can trigger systemic inflammation, immune dysregulation, oxidative stress, and metabolic disturbances, thereby accelerating renal injury. This review summarizes recent advances on the potential mechanisms linking periodontitis to DKD progression and highlights the key role of oral microbial dysbiosis and related systemic effects.},
}
@article {pmid41913730,
year = {2026},
author = {Kwoji, ID and Edwards, W and Ruffell, A and Shaw, D and Denoyelle, C and Figuiredo, A and Guadano-Procesi, I and Makkimane, J and Pantzi, K and Godfrey, A and Gentekaki, E and Stensvold, CR and Kolisko, M and Tsaousis, A},
title = {BlastoDB: first release of a community-driven multi-omics and epidemiological resource for Blastocystis biology and subtyping.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {65},
pmid = {41913730},
issn = {2732-5121},
abstract = {BlastoDB (https://www.blastodb.com/) is developed as an open-access, community-driven resource dedicated to Blastocystis, one of the most common yet understudied intestinal protists. BlastoDB will offer the scientific community up-to-date, curated information on Blastocystis by integrating epidemiological data, microbiome profiles, multi-omics datasets (genomics, transcriptomics, proteomics, and metabolomics), reference sequences for subtypes, protocols, microscopy images, and related metadata. In this initial release, we describe the data model, database architecture, curation pipelines, and web interface, which together facilitate subtype classification, comparative and integrative analyses, and cross-study synthesis of epidemiological and experimental data. We outline submission and governance workflows designed to support community contributions, training activities, and sustainable curation under the " Blastocystis under One Health" COST Action (CA21105). Finally, we highlight planned extensions, including expanded metagenomic and metatranscriptomic content, automated genome quality assessments, metagenome-assembled genomes, and geospatial and analytical dashboards. BlastoDB provides a central, FAIR-aligned hub for Blastocystis data, images, and protocols, reducing technical barriers and fostering a collaborative ecosystem for studying this globally prevalent protist.},
}
@article {pmid41913906,
year = {2026},
author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Han, G and Hou, B and Meng, Y and Wang, L and Sun, Y},
title = {Gut-Brain Axis Dysregulation in Inflammatory Bowel Disease: Implications for Coagulation Abnormalities and Extraintestinal Manifestations.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {590621},
pmid = {41913906},
issn = {1178-7074},
abstract = {Inflammatory bowel disease (IBD) involves chronic intestinal inflammation driven by gut-brain axis imbalance, fostering complications through an "inflammation-neuro-coagulation" triad. Current staging systems inadequately capture the dynamics of this multidimensional network. Therefore, integrated multi-omics analyses-including metagenomics, metabolomics, and single-cell transcriptomics-are essential to construct dynamic models that monitor coagulation, microbiome, and metabolism for precise assessment of disease activity and thrombotic or bleeding risks. Interventions targeting gut-brain axis nodes, such as eliminating tissue factor-positive (TF[+]) T cells or modulating vagal activity, show potential to disrupt the inflammation-coagulation cycle, although rigorous randomized trials are still needed. Artificial intelligence (AI)-assisted systems that integrate real-time biomarker monitoring with multi-omics predictions represent a novel paradigm for managing IBD-related coagulation dysfunction. Key challenges include elucidating gut-brain-liver axis regulation of coagulation and characterizing platelet functional heterogeneity. Future efforts must prioritize ethically compliant multi-omics platforms and racially stratified risk models to advance personalized coagulation management in IBD.},
}
@article {pmid41913928,
year = {2026},
author = {Mulinde, T and Sousa, LGV and Castro, J and George, SD and Muzny, CA and Cerca, N},
title = {Evidence from a broad-range PNA probe links several Prevotella species to bacterial vaginosis.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20902},
pmid = {41913928},
issn = {2167-8359},
mesh = {Female ; Humans ; *Vaginosis, Bacterial/microbiology/diagnosis ; *Prevotella/genetics/isolation &amp; purification ; *Peptide Nucleic Acids/genetics ; Vagina/microbiology ; Sensitivity and Specificity ; Biofilms/growth &amp; development ; Adult ; },
abstract = {BACKGROUND: Bacterial vaginosis (BV) is the most prevalent vaginal infection among reproductive-age women. It is associated with multiple adverse health outcomes in women including adverse pregnancy outcomes, an increased risk of pelvic inflammatory disease, infertility, and an increased risk of HIV and other sexually transmitted infections. BV is characterized by an imbalance in the vaginal microbiota, namely a decrease in protective Lactobacillus species and an overgrowth of facultative and strict anaerobic bacteria, leading to the development of a polymicrobial biofilm. Despite extensive research, the etiology of BV remains unclear, and its pathophysiology is not fully understood. It has been hypothesized that P. bivia, in combination with Gardnerella spp., plays an important role in the early development of the BV biofilm. We previously developed a peptide nucleic acid (PNA) probe specifically targeting P. bivia to investigate its role as a potential early colonizer. However, our recent findings have raised doubts about the specificity of this association, suggesting a broader involvement of other Prevotella species in incident BV (iBV).<br><br>METHODS: A new PNA probe targeting Prevotella spp. 23S rRNA was developed compared to the existing P. bivia-specific probe. This new probe was optimized in vitro through a variation of hybridization temperatures and times. Its performance was evaluated using a collection of 28 Prevotella strains representing 24 different species and 38 non-Prevotella spp. typically found in BV in order to assess its sensitivity and specificity. Both probes were tested on vaginal swab specimens from women with and without BV to assess the bacterial count and detection of Prevotella species.<br><br>RESULTS: In vitro validation demonstrated that the new Prevotella spp. probe achieved a specificity of 100% and sensitivity of 96%. As expected, its broader detection allowed identification of a wider range of Prevotella spp. compared to the P. bivia-specific probe, which was intentionally restricted to a single species. Application to clinical specimens revealed that the new probe identified a significantly higher count of Prevotella spp. in 6/9 (66.6%) BV-positive specimens compared to the P. bivia-specific probe. In 2/9 (22.2%) healthy control specimens, greater Prevotella spp. detection was also observed.<br><br>CONCLUSIONS: Our findings suggest that the involvement of Prevotella spp. in BV extends beyond P. bivia, implicating a wider range of species which could be present in the polymicrobial BV biofilm. The broader specificity of this new Prevotella spp. probe provides a valuable tool for future research on the vaginal microbiome and the pathogenesis of BV.},
}
@article {pmid41914163,
year = {2026},
author = {Kozin, S and Kravtsov, A and Lyasota, O and Dorohova, A and Ivlev, V and Chikhirzhina, E and Moiseev, A and Nesterova, V and Babenkova, P and Popov, K and Fedulova, L and Dzhimak, S},
title = {Consumption of Water Similar to Martian Water in Terms of Deuterium Content by Mammals Leads to the Development of an Adaptation Syndrome and Activation of Protective Mechanisms Against Stress.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {1},
pages = {39086},
doi = {10.31083/FBE39086},
pmid = {41914163},
issn = {1945-0508},
support = {125011700394-5//State Task Force of the Southern Scientific Center of the Russian Academy of Sciences for 2025/ ; },
mesh = {Animals ; *Deuterium/analysis ; Rats, Wistar ; Rats ; *Adaptation, Physiological ; Male ; *Stress, Physiological ; Brain/metabolism ; *Water/chemistry ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Deuterium is unevenly distributed in natural waters, while the same applies to the content of deuterium in ice on Mars. Moreover, changes in the deuterium content of drinking water are known to affect the bodies of mammals. Thus, since plans are in place to send people to Mars in the coming years, understanding the effects of water with a Martian isotopic composition is necessary. Therefore, this study aimed to evaluate the impact of water with an increased deuterium content of 1200 ppm on the dynamics of indicators in the body of mammals.<br><br>METHODS: The study was conducted on Wistar rats. The metabolic profile of blood and the content of deuterium in it were studied in dynamics by days using nuclear magnetic resonance (NMR) spectroscopy. Additionally, the isotopic composition of brain tissue was studied in dynamics by days using isotope mass spectrometry. A further study was conducted on the functioning of the antioxidant system in blood plasma and brain tissue using PCR analysis, chemiluminescence, and biochemical analysis methods; the intestinal microbiome was also studied. The durations of the animal experiments were 31 (blood and brain study) and 38 (stress-protective activity study) days.<br><br>RESULTS: On day 23, the deuterium content in the blood plasma increased to 856 parts per million (ppm), and to 260 ppm in the brain on day 31. This increase led to an imbalance in the antioxidant/prooxidant processes. This effect was accompanied by shifts in the intensity of oxidative processes, alongside changes in enzyme activity and the expression of genes responsible for their synthesis, shifts in amino acid composition, and changes in the concentration of metabolites and microbiome molecules in the blood plasma. By the fifth and eighth days, the number of Bacteroides in the intestines had decreased by 14% and 21.8%, respectively, compared to the values measured on day zero of the experiment. Meanwhile, the population of Firmicutes-type bacteria increased by 12% and 16% on the fifth and eighth days, respectively, compared to the indicators measured on day zero of the experiment.<br><br>CONCLUSION: An increase in the concentration of deuterium in the body promotes the development of a stress reaction and the activation of compensatory mechanisms aimed at adaptation.},
}
@article {pmid41914171,
year = {2026},
author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN},
title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {1},
pages = {39439},
doi = {10.31083/FBE39439},
pmid = {41914171},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Female ; Cattle/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; },
abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.<br><br>METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.<br><br>RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).<br><br>CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.},
}
@article {pmid41914284,
year = {2026},
author = {Wang, P and Ding, L and Lang, Z and Zhang, Y and Yu, Y},
title = {Therapeutic Modulation of the Gut Microbiome in Coronary Artery Disease: Current Evidence and Future Directions.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {3},
pages = {45081},
doi = {10.31083/FBL45081},
pmid = {41914284},
issn = {2768-6698},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Coronary Artery Disease/therapy/microbiology/metabolism ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Prebiotics/administration &amp; dosage ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; Synbiotics/administration &amp; dosage ; Methylamines/metabolism ; Diet ; },
abstract = {The gut microbiome is increasingly recognized as a modifiable contributor to coronary artery disease (CAD). This narrative review integrates mechanistic and clinical evidence regarding short-chain fatty acids (SCFAs), trimethylamine-N-oxide (TMAO), and bile acids, and appraises therapeutic modulation via diet; probiotics, prebiotics, and synbiotics; fecal microbiota transplantation (FMT); and drug-microbiome interactions. SCFAs generally confer anti-inflammatory and lipid-regulatory effects, whereas bile acid signaling exhibits context-dependent metabolic actions. Findings regarding TMAO are inconsistent; in several cohorts, associations with cardiovascular risk become null or attenuated after adjustment for renal function (estimated glomerular filtration rate [eGFR]) and dietary patterns. Most interventional studies are small, use surrogate endpoints, and vary in strains and dosing, limiting certainty. Microbiome profiles differ across geographic regions, racial and ethnic groups, and dietary patterns, underscoring the need for stratified approaches. Routine FMT in CAD remains constrained by safety, feasibility, and ethical and logistical considerations. Overall, the microbiome represents a promising yet unproven therapeutic target in CAD. Future trials should standardize interventions, rigorously control for confounders, evaluate drug-microbiome interactions, and be adequately powered to detect clinical events to enable precision medicine.},
}
@article {pmid41914628,
year = {2026},
author = {Fu, Y and Long, N and Sourn, P and Li, W and He, Z and Tan, W and Yuan, J and Chen, Y and Wu, J and Wang, S and Feng, L and Wang, Z and Ding, W},
title = {Distinct vaginal microbial signatures in pregnancies complicated by antiphospholipid syndrome: depletion of Lactobacillus johnsonii and enrichment of Bifidobacterium dentium.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0388225},
doi = {10.1128/spectrum.03882-25},
pmid = {41914628},
issn = {2165-0497},
abstract = {UNLABELLED: Antiphospholipid syndrome (APS) is a systemic autoimmune disease that contributes substantially to recurrent pregnancy loss, fetal death, intrauterine growth restriction, and preeclampsia, posing major threats to maternal and fetal health. These obstetric complications exhibit clinical similarities to those resulting from vaginal dysbiosis, yet the vaginal microbiota in APS pregnancies has not been systematically investigated. In this study, we characterized the vaginal microbiome in 33 pregnant women with APS and 90 healthy controls using 16S rRNA gene sequencing. We identified a unique microbial signature in APS pregnancies that differed from the commonly observed pattern of increased microbial diversity and Lactobacillus depletion seen in classical vaginal dysbiosis. Specifically, while overall alpha diversity and Lactobacillus dominance were preserved, we observed distinct compositional restructuring characterized by selective depletion of Lactobacillus johnsonii and marked enrichment of Bifidobacterium dentium. A logistic regression model integrating the relative abundances of these microbial biomarkers demonstrated robust diagnostic performance in differentiating pregnancies with APS from healthy pregnancies, with risk scores significantly correlating with clinical parameters and pregnancy outcomes. This study demonstrates that pregnant women with APS display a distinct vaginal microbiome pattern defined by species-specific compositional restructuring rather than global dysbiosis. These microbial alterations may contribute to APS-related pregnancy morbidity, highlighting vaginal microbial signatures as promising noninvasive biomarkers for risk stratification and potential therapeutic targets in obstetric APS management.<br><br>IMPORTANCE: Antiphospholipid syndrome (APS) is an autoimmune disease that causes recurrent miscarriage, fetal death, and pregnancy complications in women of reproductive age. While coagulation dysfunction is a known contributing factor, whether APS is accompanied by vaginal microbiota alterations and their role in adverse outcomes remains unclear. We discovered that pregnant women with antiphospholipid syndrome harbor a unique vaginal microbial community: they exhibit depletion of the protective species Lactobacillus johnsonii while showing enrichment of Bifidobacterium dentium, a bacterium typically found in the gut. Unlike typical vaginal infections that display widespread microbial dysbiosis, antiphospholipid syndrome induces only selective alterations in specific bacterial species. These microbial signatures correlated with hematological parameters and adverse pregnancy histories, including prior miscarriages. Our findings suggest that monitoring vaginal microbiota could provide a simple, noninvasive approach to identify high-risk pregnancies in women with antiphospholipid syndrome and may guide novel screening strategies for pregnancy-related disorders targeting the vaginal microbiome.},
}
@article {pmid41914631,
year = {2026},
author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS},
title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0219825},
doi = {10.1128/spectrum.02198-25},
pmid = {41914631},
issn = {2165-0497},
abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.},
}
@article {pmid41914733,
year = {2026},
author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D},
title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0235725},
doi = {10.1128/aem.02357-25},
pmid = {41914733},
issn = {1098-5336},
abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.},
}
@article {pmid41914747,
year = {2026},
author = {Franklin, S and Sahasrabhojane, P and Hayase, T and Hayase, E and Chang, C-C and Senapati, J and Desikan, SP and Kadia, T and Lorenzi, PL and Jenq, RR and Shelburne, SA and Galloway-Peña, J},
title = {Short-chain fatty acid-producing microbes differentiate non-infectious and infectious neutropenic fever in leukemia.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0134325},
doi = {10.1128/msystems.01343-25},
pmid = {41914747},
issn = {2379-5077},
abstract = {UNLABELLED: Neutropenic fever (NF) is often the first sign of infection in patients with hematologic malignancies, but its cause is frequently unknown, leading to broad-spectrum antibiotic use without confirmed infections. Although research links gut microbiome disruptions to treatment-related infections, it typically examines NF as the outcome, leaving a gap in understanding how the microbiome and metabolic factors distinguish infectious from non-infectious cases. Stool samples from acute myeloid leukemia patients were analyzed to characterize gut microbiome composition and fecal metabolites at baseline and at fever onset. Machine learning models, network analyses, and functional profiling were used to differentiate infectious NF vs non-infectious NF at baseline and at fever onset. The baseline model (area under the receiver operating characteristic [AUROC] = 0.769) identified higher levels of Akkermansia, Enterobacter, Escherichia-Shigella, and Flavonifractor as predictors of infectious NF, while Collinsella, Lachnospiraceae, Coprococcus, and acetic acid were linked to non-infectious cases. At fever onset, Enterococcus was enriched in infectious NF, whereas Gemella, Butyrate, Lachnospiraceae, Ruminococcaceae, and Eisenbergiella abundances favored non-infectious NF outcomes (AUROC = 0.752). Network analyses also revealed greater functional diversity and microbiome-metabolome connectivity in non-infectious cases at fever onset. This study suggests that gut microbiota and metabolites may serve as biomarkers for distinguishing infectious from non-infectious neutropenic fever, warranting further validation in larger cohorts.<br><br>IMPORTANCE: Our study tackles the challenge of managing neutropenic fever (NF) in immunocompromised patients whose numbers have increased due to various immunodeficiencies and treatments that suppress immune function. Fever is often the only sign of a serious infection in these patients, yet there are neither clear patterns linking risk factors to infection nor biomarkers reliable for ruling out non-infectious causes. As a result, febrile patients are typically empirically treated for major pathogens, even in the absence of confirmed infections, which propagates antimicrobial resistance and gut dysbiosis. Our research utilizes gut microbiome and targeted metabolomic profiling from two cohorts of patients with acute myeloid leukemia undergoing chemotherapy and employs a machine learning framework to distinguish between infectious and non-infectious NFs at baseline and upon fever onset.},
}
@article {pmid41914795,
year = {2026},
author = {},
title = {Corrigenda to 'Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos'.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261432716},
doi = {10.1177/13872877261432716},
pmid = {41914795},
issn = {1875-8908},
}
@article {pmid41914849,
year = {2026},
author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y},
title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0035926},
doi = {10.1128/aem.00359-26},
pmid = {41914849},
issn = {1098-5336},
abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.},
}
@article {pmid41914961,
year = {2026},
author = {Maigoro, AY and Lee, JH and Heo, D-R and Yun, B-R and Lee, HI and Kwon, H-W},
title = {Spatiotemporal variation in the microbiome of Aedes vexans from Korea reveals regional markers linked to environmental risk factors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258725},
doi = {10.1128/spectrum.02587-25},
pmid = {41914961},
issn = {2165-0497},
abstract = {Aedes vexans is a widespread mosquito species known to carry West Nile virus (WNV); however, our understanding of how its microbiome changes across different regions and seasons, particularly in temperate areas such as South Korea, remains limited. In this study, we examined the microbiome of Aedes vexans collected from 16 locations over 3 consecutive summer months. Using 16S rRNA sequencing, we found that the microbiome was largely made up of Proteobacteria, but the specific genera present, like Dickeya, Spiroplasma, and members of Enterobacterales, varied depending on the location and time of collection. Dickeya, in particular, was more common in inland areas and stayed relatively stable over time, which suggests it could serve as a useful microbial marker. We also observed a significant absence of Wolbachia, a common endosymbiont in mosquitoes, which hypothesizes potential increased risk of WNV transmission. Diversity analyses showed clear differences in microbial communities by region, and we found seasonal patterns in genera like Asaia and Pseudomonas, which were correlated to mosquito abundance and local environmental conditions. These patterns held up when we looked at co-occurrence networks between microbes. Altogether, this is the first study to track Aedes vexans microbiome across both space and time in Korea, and our findings offer new insights into mosquito ecology and the potential use of bacteria in disease control strategies.IMPORTANCEUnderstanding the dynamics of the mosquito microbiome is essential for predicting disease risk and developing targeted vector control strategies. Aedes vexans, a globally distributed species and potential vector for West Nile virus (WNV), has seen a notable population increase in South Korea, yet its microbial ecology remains poorly characterized. This study provides the first comprehensive spatiotemporal analysis of Aedes vexans microbiota across Korea, identifying key microbial taxa that vary by region and season. The absence of Wolbachia, a known antiviral symbiont, and the dominance of Dickeya, a plant-associated genus with potential ecological implications, underscore the need for microbiome-informed surveillance tools. By highlighting native microbial signatures and their environmental drivers, this work lays the groundwork for microbiota-based monitoring of vector populations and opens new avenues for symbiont-based interventions in arbovirus control.},
}
@article {pmid41915085,
year = {2026},
author = {Liang, J and Zang, S and Wang, Z and Zhang, R},
title = {Cancer and aging: complex associations and therapeutic targets.},
journal = {Molecular biomedicine},
volume = {7},
number = {1},
pages = {},
pmid = {41915085},
issn = {2662-8651},
support = {No. 202303021221201//Shanxi Provincial Basic Research Program/ ; },
mesh = {Humans ; *Aging/genetics/pathology ; *Neoplasms/therapy/pathology/genetics/metabolism/etiology ; Animals ; Cellular Senescence ; Genomic Instability ; Autophagy ; Epigenesis, Genetic ; Molecular Targeted Therapy ; },
abstract = {The incidence of cancer increases markedly with aging, and the two processes share underlying molecular mechanisms. In the context of global population aging and rising cancer incidence, nine convergent hallmark axes have been identified: genomic instability, epigenetic drift, inflammation-immunity imbalance, microbiome dysbiosis, metabolic reprogramming, telomere attrition, stem cell exhaustion, cellular senescence, and autophagy dysfunction. These hallmarks constitute an integrated regulatory network that operates synergistically, antagonistically, or through bidirectional feedback across molecular, cellular, and microenvironmental levels. Genomic instability, epigenetic remodeling, chronic inflammation, microbiome dysbiosis, and metabolic reprogramming in aging often act synergistically to promote tumorigenesis, whereas telomere attrition and stem cell exhaustion primarily exert antagonistic, tumor-suppressive effects. Cellular senescence and autophagy dysfunction display context-dependent dual roles. Importantly, this network framework has direct relevance to cancer therapeutics. Although chemotherapy, radiotherapy, and immunotherapy effectively suppress tumor progression, they frequently induce therapy-induced senescence, characterized by cell-cycle arrest and a senescence-associated secretory phenotype, thereby accelerating functional decline and increasing long-term toxicities in older patients. The proposed "synergistic-antagonistic-dual" framework linking aging and cancer not only helps explain the disproportionate cancer burden in older adults but also supports a "one drug, two targets" therapeutic paradigm. Targeting these shared pathways has delayed aging phenotypes and suppressed tumorigenesis in preclinical studies and early clinical trials, highlighting the potential of integrated interventions that concurrently address aging and cancer.},
}
@article {pmid41915167,
year = {2026},
author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E},
title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02730-5},
pmid = {41915167},
issn = {1432-184X},
}
@article {pmid41915265,
year = {2026},
author = {Volk, A and Mills, M and Chae, S and Lee, J},
title = {Investigation of cyanobacteria-hosted antibiotic resistance genes in cyanoHAB-impacted drinking water sources.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41915265},
issn = {1614-7499},
abstract = {Freshwater cyanobacterial blooms (cyanoHABs) are expanding across the world, and their frequency and severity are becoming more intense due to prevalent eutrophication and a changing climate. Traditionally, the concerns about cyanoHABs have mainly focused on cyanotoxins in water. CyanoHABs are also hypothesized to play a role in the antibiotic resistome, but whether cyanobacteria host clinically relevant antibiotic resistant genes (ARGs) in the environment is largely unknown. To investigate this emerging issue, we examined whether cyanobacteria host ARGs within the broader microbiome context. We looked for the presence of cyanobacteria-hosted ARGs using shotgun metagenomic sequencing of drinking water source samples collected during the bloom season (summer and fall) from Lake Erie and Grand Lake St. Marys (GLSM). ARGs were annotated using DeepARG and Resistance Gene Identifier (RGI). Cyanobacteria were annotated to host genes conferring putative antibiotic resistance, including efflux pumps qac/EmrE, vatB, van genes, and an OXA homolog. A maximum likelihood tree with cyanobacteria and OXA reference sequences showed OXA-like homology across multiple families of cyanobacteria. Most cyanobacteria sequences clustered in a large clade with ybxI, suggesting very limited or negligible class-D beta-lactamase activity, but a small subset formed a clade with OXA-2 and OXA-46. While those hits suggest potential resistance to clinical antibiotics, overall cyanobacteria were not found to host ARGs conferring resistance to drugs of last resort in these samples. Additionally, BLAST searches of the cyanobacteria ARG contigs and coding sequences resulted in top hits for cyanobacteria, further supporting that annotated genes are likely intrinsic rather than acquired. rpoB2 and arlR ARG annotations appear to be spurious hits on housekeeping genes, which demonstrates the need to verify automated ARG annotation tool results. Selected cyanotoxins, cyanobacteria, and ARGs were also chosen for quantification. We found high levels of Microcystis in Lake Erie as well as Planktothrix and microcystin concentrations in GLSM, supporting previous trends in these water bodies. This study takes a novel approach, pairing the issues of cyanoHABs and ARGs together in two drinking water sources. In a changing climate, drinking water treatment strategies should consider the treatment and public health implications of multiple contaminants.},
}
@article {pmid41915459,
year = {2026},
author = {Gupta, RM and Ismail, HM and Siller, AF and Pesikoff, J and Devaraj, S and Balasubramanyam, A and Redondo, MJ},
title = {Impact of Body Size on Preclinical Type 1 Diabetes Development and Progression.},
journal = {Diabetes care},
volume = {},
number = {},
pages = {},
doi = {10.2337/dci25-0134},
pmid = {41915459},
issn = {1935-5548},
support = {3-SRA-2025-1738-S-B//Breakthrough Type 1 Diabetes/ ; },
abstract = {Type 1 diabetes arises from the interplay of genetic susceptibility and environmental exposures, leading to autoimmune β-cell destruction. Although disease-modifying therapies (DMTs) can delay progression to clinical (stage 3) type 1 diabetes, treatment responses remain inconsistent and transient. The marked heterogeneity of type 1 diabetes, shaped by age, sex, race/ethnicity, and genetic background, underscores the need to elucidate distinct mechanistic pathways. Among environmental contributors, obesity stands out as a compelling modifiable target. Data from The Environmental Determinants of Diabetes in the Young (TEDDY), Type 1 Diabetes TrialNet, and other longitudinal cohorts link BMI and adiposity to the onset of islet autoimmunity, progression through preclinical stages, and development of stage 3 type 1 diabetes. These associations are not uniform; heightened susceptibility to adiposity-related risk is seen among younger children, Hispanic populations, and individuals with specific HLA genotypes. Despite robust epidemiologic evidence, the biological pathways connecting elevated BMI to autoimmune β-cell destruction remain incompletely defined. Emerging data implicate a network of immunologic and metabolic disturbances, including insulin resistance, β-cell stress, chronic adipose tissue inflammation, altered adipokine signaling, and gut microbiome changes, that collectively heighten β-cell vulnerability, amplify autoreactive immune responses, and drive metabolic decompensation toward clinical disease. Elucidating these mechanisms and identifying related biomarkers are critical to advancing precision prevention. In future studies, investigators should evaluate whether modifying elevated BMI or targeting obesity-associated immunologic and metabolic pathways can alter the preclinical trajectory of type 1 diabetes. Such mechanistic understanding may help curb type 1 diabetes incidence and improve outcomes for populations most vulnerable to obesity-related risk.},
}
@article {pmid41907525,
year = {2026},
author = {González-Valdivia, C and Tong, B and Hjalmarsson, S and Guðnadóttir, U and Wagner, N and Engstrand, L and Schuppe-Koistinen, I and Fransson, E and Prast-Nielsen, S and Brusselaers, N and Hugerth, LW},
title = {The gut microbiome in early pregnancy is associated with the severity of nausea and vomiting: a nested case‒control study.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2603861},
pmid = {41907525},
issn = {2993-3935},
abstract = {Approximately 70% of all pregnancies are affected by nausea and vomiting (NVP), yet the mechanisms controlling this phenomenon are not well known. Pregnancy hormones explain a large part of this effect, mostly through human chorionic gonadotropin and fetal production of GDF15, a hormone active in the brain stem. Still, there is a wide variation in the severity of symptoms, ranging from no nausea to severe vomiting requiring hospitalization (hyperemesis gravidarum). Here, we present a nested case‒control study within the large SweMaMi cohort, wherein 337 participants with severe NVP in early pregnancy were matched 1-to-1 with moderate and mild NVP, respectively. Subjects with more severe nausea had lower richness and diversity in their fecal microbiomes. Several taxa were significantly associated with NVP score, where the most extreme are a negative correlation with Lactobacillaceae and positive correlations with Bifidobacterium dentium and Puniceicoccaceae. Finally, higher NVP score was associated with a higher abundance of bacteria encoding for the neuroactive pathways of glutamine degradation, inositol synthesis, and lactate production. In conclusion, the gut microbiota was strongly associated with NVP. Further studies with direct interventions capable of restoring the early-pregnancy gut microbiome could open up new approaches for dealing with the most common symptom of early pregnancy.},
}
@article {pmid41907632,
year = {2026},
author = {Russo, F and Tripodi, L and Caldora, F and Pandolfo, SD and Aveta, A and Nardelli, C and Imbimbo, C and Perdonà, S and Pastore, L and Castaldo, G},
title = {Identification of a weighted urinary microbial signature for bladder cancer discrimination.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1784501},
pmid = {41907632},
issn = {2234-943X},
abstract = {INTRODUCTION: Growing evidence from microbiome studies has demonstrated associations between dysbiosis and cancers, including bladder cancer (BCa). Our recent works on urobiome revealed a different microbial composition in BCa patients compared to controls. The aim of this work was to create a Weighted Composite Index (WCI) to distinguish BCa-affected patients (mBCa) from healthy controls (mHC) in a cohort of male aged over 50 years.<br><br>METHODS: Urobiome data from 51 subjects (27 mBCa and 24 mHC) were analyzed. Random Forest (RF) classifier was trained to identify genera and species which significantly contributed to discriminating between mBCa and mHC group. A weighted normalization approach was used to compute separate WCIs at genus and species levels and in-silico validation test were performed to assess the models' robustness.<br><br>RESULTS: the WCI was calculated for each patient at both genera and species levels, showing a significant difference between the two groups (p < 0.0001) in both comparisons. WCIs showed superior discriminative performances compared to any individual taxon used for the model construction. Despite the need for validation in larger independent cohorts, the in-silico validation pipeline showed a stable high sensitivity of the models.<br><br>CONCLUSIONS: Our findings identified a candidate urinary microbial signature in a biomarker discovery setting associated with bladder cancer. This hypothesis-generating approach may contribute to the identification of a non-invasive biomarker, which requires validation in larger, independent cohorts before clinical application.},
}
@article {pmid41907707,
year = {2024},
author = {Teigen, LM and Kaiser-Powers, T and Matson, M and Elkin, B and Kabage, AJ and Hamilton, M and Vaughn, BP and Sadowsky, MJ and Staley, C and Khoruts, A},
title = {Contribution of Common Sulfur-Containing Substrates to Hydrogen Sulfide Production By Human Gut Microbiota Using an In Vitro Model Standardized For Bacterial Counts.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2361246},
pmid = {41907707},
issn = {2993-3935},
abstract = {Hydrogen sulfide (H2S) produced by human gut microbiota is highly toxic and implicated in pathogenesis of gastrointestinal tract disorders. Sulfur-containing amino acid (SAA) degradation is a major contributor to its production, but SAA degradation pathways have not been extensively characterized. In vitro model systems of fecal H2S production offer a basic method to help elucidate SAA degradation pathways, but the approach is not standardized. To address this, we used fecal microbiota separated from feces and standardized for bacterial counts to measure H2S production potential in response to different substrates in healthy controls (n = 6) with repeated sampling (three samples per participant). H2S production was highest with cysteine (mean = 16.7 ppm) compared to sodium sulfate (0.7 ppm) and taurine (0.8 ppm). Sodium-sulfate-driven H2S production negatively correlated with Ruminococcus (Spearman's ρ = -0.5) and cysteine-driven H2S production negatively correlated with Firmicutes (Spearman's ρ = -0.5). These findings, using a protocol controlling for confounding variables such as bacterial counts, validate previous findings of cysteine as a primary driver of H2S production. Finally, the inclusion of samples from two patients with UC allowed for the illustration of the potential of this approach to identify functional differences in specific disease states.},
}
@article {pmid41907708,
year = {2024},
author = {Kaufman, P and O'Meara, KE and Hawrelak, J},
title = {Preventing chemotherapy-induced diarrhea and microbiota imbalances with prebiotics and probiotics in breast cancer treatment: A case report.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2379475},
pmid = {41907708},
issn = {2993-3935},
abstract = {Breast cancer (BC) is the second most common cancer in women in the United States. Of those diagnosed, 40-80% will undergo chemotherapy. Adverse effects of chemotherapy are chemotherapy-induced diarrhea (CID) and gut microbiota dysregulation. CID can lead to dehydration, metabolic acidosis, malnutrition, and gut dysbiosis. Antidiarrheal medications are the standard treatment of care; however, this has been shown to further contribute to gut dysbiosis, is not always effective in controlling diarrhea, and can lead to rebound constipation with the potential of pathogenic bacterial overgrowth. In this case report, we describe the experience of a patient-centered, personalized intervention with pre- and probiotics to preserve the microbiota and prevent CID. A 57-year-old postmenopausal female with BC undergoing adriamycin-cyclophosphamide (AC) and taxol-cyclophosphamide (TC) chemotherapies for invasive ductal carcinoma under the care of a cancer team wanted to refrain from using loperamide and instead use nutritional interventions and supplementation for preventing CID and maintaining gut health. This case report is a narrative report of the observed outcomes of one patient with BC after taking specific prebiotics and probiotics. The outcomes included the prevention of CID and other gastrointestinal adverse effects, and maintaining microbiota alpha-diversity, butyrate producing genera, and Bifidobacterium populations while inhibiting the overgrowth of Proteobacteria pathogenic bacteria.},
}
@article {pmid41907711,
year = {2024},
author = {Varshney, N and Pandey, RK and Mishra, A and Kumar, S and Jha, HC},
title = {Aurora Kinase A: Integrating Insights into Cancer, Inflammation, and Infectious Diseases.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2419069},
pmid = {41907711},
issn = {2993-3935},
abstract = {Aurora kinase A (AURKA) is crucial in regulating cell division and maintaining genomic stability, making it significant in cancer biology. This review explores AURKA's structural and functional roles, emphasizing its involvement in cell cycle progression. Beyond cancer, AURKA emerges as a multifaceted player in host cell modulation, exerting influence over inflammatory responses, cell death mechanisms, and autophagy pathways. Moreover, recent research highlights its involvement in viral and bacterial infections. Numerous viruses, for their replication and assembly, modulate host cell cycle progression. Various viruses modulated AURKA to induce viral-mediated tumor. It also emerged as a key modulator in various gut microbiome-mediated cancers. Further, it also imparts oncogenic effect by modulation in cytoplasmic and mitochondrial regions of the cell. It hampers DNA replication independent of its kinase domain. Understanding AURKA's diverse roles underscores its potential as a promising drug target, offering therapeutic avenues for various diseases. This comprehensive exploration navigates through complex landscape of AURKA biology, paving way for future investigations and therapeutic interventions.},
}
@article {pmid41907714,
year = {2024},
author = {Molinas-Vera, M and Ferreira-Sanabria, G and Peña, P and Sandoval-Espinola, WJ},
title = {The Paraguayan gut microbiome contains high abundance of the phylum Actinobacteriota and reveals the influence of health and lifestyle factors.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2332988},
pmid = {41907714},
issn = {2993-3935},
abstract = {Most gut microbiome studies are focused on populations from developed nations. However, this overlooks the role played by host genetics, lifestyle, and diet, highlighting the need to evaluate under-represented populations. Thus, we performed the first gut microbiome study from a Paraguayan cohort via 16S rRNA sequencing and PICRUSt2 analysis. We evaluated fecal samples from 60 participants from Asunción, while considering categories such as body-mass-index (BMI), sex, age, diet, lifestyle, and clinical history. Firmicutes (76.0 ± 11.6%), Actinobacteriota (10.4 ± 7.9%) and Bacteroidota (9.4 ± 11.4%) were the most abundant phyla. Similarly, the most abundant genera were Blautia (14.1 ± 7.5%), Faecalibacterium (8.07 ± 6.8%), and Bacteroides (6.7 ± 6.8%). Likewise, the most abundant microbial pathways were predicted to be involved with sugar metabolism and fermentation. Interestingly, some categories significantly impacted the gut microbiome composition and function, such as BMI (Moryella, Bifidobacterium), sex (Faecalibacterium), and others. Additionally, dysbiotic indices differed from values previously reported as homeostatic. These observations highlight the need for further studies, considering microbial species and host genetics. Thus, this work expands the knowledge of the gut microbiome from the Collective South, while contrasts found herein reinforce the need for further research with human populations traditionally understudied.},
}
@article {pmid41907715,
year = {2024},
author = {Winters, AD and Francescutti, DM and Kracht, DJ and Kuhn, DM and Angoa-Perez, M},
title = {The Effects of Ceftriaxone on Glutamate Transporter Expression and the Gut Microbiome: Implications for a Role of Antibiotic-Induced Dysbiosis in Mediating Drug Seeking and Relapse.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2393727},
pmid = {41907715},
issn = {2993-3935},
abstract = {Ceftriaxone (CTX), a beta-lactam antibiotic, is widely used in drug seeking and relapse studies due to its ability to enhance glutamate transporter (GLT-1) expression in the brain. Since increased synaptic glutamate is believed to drive drug seeking and relapse, CTX's effect on GLT-1 offers potential for treating substance abuse. However, the effect of CTX on the gut microbiome remains unexplored. Mice received CTX at 200 mg/kg per day for 4 d, and its effects on the gut microbiome were assessed. CTX led to increased striatal GLT-1 expression and induced rapid, long-lasting dysbiosis, with females showing a greater response than males. Diversity metrics were significantly altered during the acute phase of CTX treatment. Alpha diversity showed varying recovery levels depending on sex, while beta diversity indicated that CTX-treated mice remained significantly different from controls. CTX caused significant increases in Bacillota and reductions in Bacteroidota. Most taxa were rapidly reduced by CTX, but Enterococcus and Bacillales expanded significantly. Metabolomic analysis revealed significant changes in microbial pathways related to substance use disorders. These findings indicate that CTX causes immediate and persistent alterations in the gut microbiome, highlighting the importance of considering the gut microbiome as a target in substance abuse treatment.},
}
@article {pmid41907718,
year = {2024},
author = {Tannock, GW},
title = {Scoring Microbiota Function: A Proposal to Use Features of Evolutionary, Symbiotic Innovation to Recognize a "Healthy" Human Gut Microbiota.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2376543},
pmid = {41907718},
issn = {2993-3935},
abstract = {Research concerning the significance of the bacterial community of the human colon (gut microbiota or microbiome) in the etiology of diseases has depended in large part on molecular and bioinformatic tools to assemble catalogs of bacterial diversity. This article proposes that the gut microbiotas of humans are collectively a metacommunity whose functions are characteristic and consistent across all healthy humans. The pathway of evolutionary innovation in the development of the symbiosis between humans and gut microbiotas is known. Therefore, it is suggested that functional scoring of these long-lasting symbiotic innovations will reap greater benefits in delineating health or disease than can comparative taxonomic analysis. Adoption of a function-scoring approach would offer opportunities for emerging researchers, worldwide, to form multidisciplinary teams to develop essential methodologies to advance this gut microbiota research.},
}
@article {pmid41907719,
year = {2024},
author = {Dixit, K and Ahmed, A and Singh, A and Inamdar, M and Chavan, S and Bodkhe, R and Mehtab, W and Chauhan, A and Saroj, SD and Ahuja, V and Shouche, Y and Dhotre, D and Makharia, G},
title = {Site-Specific Gut Microbial Signatures in Non-Celiac Gluten Sensitivity.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2438621},
pmid = {41907719},
issn = {2993-3935},
abstract = {Gut microbiota in non-celiac gluten sensitivity (NCGS) has been poorly studied for its involvement in the disorder and site specificity. We investigated small intestinal, large intestinal and stool microbiota profiles in patients with NCGS and highly overlapping disorder irritable bowel syndrome (IBS) as well as effect of gluten-free diet (GFD) on microbiota in patients with NCGS. True NCGS patients were recruited based on serological response for anti-gliadin antibodies, 6-week gluten free diet (GFD) and symptom recurrence with gluten-rechallenge. Analyses using 16S rRNA gene amplicon and shotgun sequencing revealed community differences in core microbiome and diversity measures across sample types indicating dysbiosis mainly in mucosa-associated small intestinal microbiome of NCGS patients. Genera Elusimicrobiaum, Succinivibrio, Bacillus and Alcaligenes appeared as signatures in small intestine and stool in NCGS patients. Presence of differential taxa co-occurring at sampling sites, enabled recognition of site-specific microbial signatures. GFD led to a shift in mucosa-associated small intestinal core microbiome. Metagenome analysis revealed subtle differences in pathways for amino acid biosynthesis including L-ornithine. Mucosa-associated small intestine microbial structure was quite distinct in patients with NCGS in comparison to that with IBS.},
}
@article {pmid41907720,
year = {2024},
author = {Funahashi, K and Lee, CG and Sugitate, K and Kagata, N and Fukuda, N and Song, I and Ishii, C and Hirayama, A and Fukuda, S},
title = {Development of a Specialized Method for Simultaneous Quantification of Functional Intestinal Metabolites by GC/MS-Based Metabolomics.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2429408},
pmid = {41907720},
issn = {2993-3935},
abstract = {Intestinal metabolites produced by gut microbes play a significant role in host health. Due to their different chemical structures, they are often analyzed using multiple analyzers and methods, such as gas chromatography/mass spectrometry (GC/MS) for SCFAs and liquid chromatography/mass spectrometry (LC/MS) for bile acids (BAs), amino acids (AAs), and sugars. In this study, we aimed to develop a specialized method for the simultaneous determination of important intestinal metabolites, specifically addressing the main issue of SCFA volatilization during the dry solidification process. We discovered that these compounds can all be measured in fecal samples by GC/MS after trimethylsilyl (TMS) derivatization despite the expected volatility of SCFAs. Validating the results using SCFA standards suggested that the fecal matrix exerts a stabilizing effect. This method enabled the simultaneous quantification of 65 metabolites. For further validation in a biological context, a mouse study showed that high-MAC and high-fat diets increased SCFAs and BAs in feces, respectively, and showed a negative correlation between Alistipes and sugars, all consistent with previous studies. As a result, we successfully developed a specialized simultaneous quantification method for SCFAs, BAs, AAs, AA derivatives, and sugars in fecal samples using GC/MS-based metabolomics in conjunction with a TMS derivatization pretreatment process.},
}
@article {pmid41907847,
year = {2026},
author = {Tng, TJW and Vanan, S and Tan, EK and Zeng, L and Goh, WWB and Wong, SH and Lim, KL},
title = {Examination of shared gut microbiome signatures in aging and Parkinson's disease.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1745455},
pmid = {41907847},
issn = {1663-4365},
abstract = {Parkinson's disease (PD) is a prevalent neurodegenerative disorder that is characterized clinically by a constellation of motoric deficits including resting tremors, bradykinesia, and rigidity. In recent years, there has been increasing interest in the gut-brain axis with several studies examining the relationship between gut microbiome and PD. Although association studies have reported multidimensional microbiome changes in PD, these observed changes may be confounded by various factors, especially age. Notably, existing literature on gut microbiome tends to consider aging and PD separately. This review thus examines the gut microbiome factors associated with both aging and PD. Our comprehensive analysis of the available literature reveals significant overlaps in gut microbes that are associated with aging and PD. For example, the bacterial genera Akkermansia, and Alistipes have shown increased abundance in both conditions, while Faecalibacterium and Blautia conversely show decreased abundance. Our findings were temporally consistent with more recent studies. These shared gut microbiome signatures were identified in patients across the clinical spectrum of PD symptom severity, and may influence aging and disease pathogenesis via depletion of butyrate, a beneficial anti-inflammatory microbial metabolite, since major producers of butyrate (such as Faecalibacterium and Blautia) were constantly decreased with age (across both Asian and Western populations). Given these observations, we wish to highlight the need to consider age-related factors in understanding microbiome changes in PD; the intersection of which could reveal gut microbes and their corresponding microbial metabolites such as butyrate as potential therapeutic targets for PD.},
}
@article {pmid41907858,
year = {2026},
author = {Hashim, NT and Babiker, R and Padmanabhan, V and Islam, MS and Priya, SP and Chaitanya, NCSK and Mohammed, R and Dasnadi, SP and Ahmed, A and Gismalla, BG and Rahman, MM},
title = {Oral and cardiometabolic health through the lens of biobanks and large-scale epidemiologic research.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1774868},
pmid = {41907858},
issn = {2673-4842},
abstract = {Oral diseases and cardiometabolic disorders are among the most prevalent non-communicable conditions worldwide and share common inflammatory, metabolic, and social determinants. Over the past two decades, growing evidence has linked poor oral health-particularly periodontitis and tooth loss-to cardiometabolic outcomes such as type 2 diabetes and cardiovascular disease. However, progress in this field has long been constrained by fragmented data systems and limited availability of large-scale resources capturing both oral health exposures and cardiometabolic endpoints. Recent advances in biobank infrastructure, population-based cohorts, and electronic health record linkage have transformed this landscape, enabling robust secondary analyses at unprecedented scale. This narrative review synthesizes current evidence from major biobanks and large-scale epidemiologic datasets relevant to oral-cardiometabolic research. We describe how oral health and cardiometabolic outcomes are operationalized across data ecosystems, critically appraise the strengths and limitations of key resources, and integrate epidemiologic findings with established biological mechanisms, including chronic systemic inflammation, microbial dysbiosis, metabolic dysfunction, and vascular impairment. We further highlight the bidirectional nature of the relationship, whereby cardiometabolic disease can also exacerbate oral inflammatory conditions. Methodological challenges-such as exposure misclassification, residual confounding, and reverse causation-are discussed alongside emerging solutions, including data linkage, multi-omics integration, and advanced analytic approaches. Harnessing large-scale data sources offers a powerful opportunity to reposition oral health within cardiometabolic disease research and prevention. Strategic integration of dental and medical data has the potential to inform precision public health approaches and support more holistic models of chronic disease prevention.},
}
@article {pmid41907864,
year = {2026},
author = {Taudte, N and Liebe, L and Jänckel, N and Ramsbeck, D and Schilling, S and Potempa, J and Eick, S and Buchholz, M},
title = {Novel small molecule targeting PgQC reduces Porphyromonas gingivalis virulence.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1716188},
pmid = {41907864},
issn = {2673-4842},
abstract = {INTRODUCTION: Periodontitis, a chronic inflammatory disease affecting the periodontium, is primarily driven by dysbiosis of the oral microbiome with Porphyromonas gingivalis as a keystone pathogen. Current therapeutic approaches rely on mechanical debridement and antimicrobials, which face limitations including antibiotic resistance and microbiome disruption. Pathoblockers represent a novel therapeutic strategy that selectively targets virulence factors without bactericidal effects, potentially reducing resistance development while preserving beneficial microbiota. Here, we describe the characterization of S-0636, a novel reversible inhibitor of zinc-dependent glutaminyl cyclase (PgQC), as a compound to selectively inhibit the bacterial virulence of P. gingivalis.<br><br>METHODS: The compound's effects were assessed through enzymatic assays, bacterial growth studies, virulence factor activity measurements (gingipain activity, hemagglutination, keratinocyte invasion), selectivity testing against commensal oral bacteria, resistance development analysis over 50 passages, and cytotoxicity evaluation in human cell lines.<br><br>RESULTS: S-0636 demonstrated potent PgQC inhibition with a Ki value of 0.014&#x2005;&#x3bc;M and has successfully reduced the intracellular PgQC activity by 50% at 8&#x2005;&#x3bc;M and had no bactericidal effects. Treatment of P. gingivalis with S-0636 significantly decreased gingipain activity, impaired hemagglutination capacity, and reduced keratinocyte invasion by 76% at 62.5&#x2005;&#x3bc;M. The compound showed high selectivity, with no growth inhibition of ten tested oral commensal species at concentrations up to 0.25&#x2005;mM. Importantly, no resistance development was observed after 50 bacterial passages, and cytotoxicity remained minimal in human cell lines with >80% viability at 0.5&#x2005;mM.<br><br>DISCUSSION: In previous studies, PgQC was suggested as an enzyme responsible for pGlu-modification and stabilization of bacterial virulence factors. The current study now validates PgQC as an attractive target for pathoblocker development, demonstrating that S-0636 effectively attenuates P. gingivalis pathogenicity through selective virulence factor inhibition while preserving bacterial viability and oral microbiome integrity. The absence of resistance development and low cytotoxicity profile support the potential clinical translation of this approach for periodontal disease management, representing a promising alternative to conventional antimicrobial therapies.},
}
@article {pmid41908157,
year = {2024},
author = {Pfavayi, LT and Sibanda, EN and Baker, S and Woolhouse, M and Mduluza, T and Mutapi, F},
title = {Diversity and composition of gut protist in young rural Zimbabwean children.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1399160},
pmid = {41908157},
issn = {2813-4338},
abstract = {BACKGROUND: The human gut microbiome harbours diverse species of archaea, bacteria, fungi, protists and viruses. To date, most gut microbiome studies have focused on bacteria, neglecting other microbial communities. Consequently, less is known about the diversity and abundance of the latter. Here, we aimed to characterise the diversity and composition of protists in the gut of preschool-aged children (PSAC) in rural Zimbabwe relative to host age, sex, and schistosome infection status.<br><br>METHODS: The gut protist of 113 PSAC (1-5 years) was examined via shotgun metagenomic sequencing and analysed for diversity. Variation in protist abundance with host and environmental factors was analysed by permutational multivariate analysis of variance (PERMANOVA). To investigate how the composition of specific taxa varies across age, sex, nutritional measures and Schistosoma hematobium infection status, analysis of the composition of microbiomes (ANCOM) was used.<br><br>RESULTS: Eighty protist genera were identified, and the most abundant genera detected was Blastocystis. The prevalence of pathogenic protists was comparatively low, with 12.4% and 3.4% of the participants' gut colonised by E. histolytica and Cryptosporidium, respectively. Of all the independent variables only S. haematobium infection showed significant relationship with the structure of the gut protist, being associated with increases in Peronospora, Pseudoperonospora, Plasmopara and Blastocystis (FDR= 0.009).<br><br>SUMMARY: This study provides data on the prevalence and diversity of the gut protists in young Zimbabwean children with an emphasis on the host factors; age, sex and schistosome infection status. Our results showed no association between the host factors investigated, including anthropometric measures adjusted for age and the intestinal protist composition and structure, but S. haematobium infection status was associated with composition of specific taxa. There is a need for more studies determining how pathogenic protist interact with non-pathogenic protist in people exhibiting clinical symptoms to inform therapy and nutraceuticals.},
}
@article {pmid41908202,
year = {2026},
author = {Awashra, A and Neiroukh, H and AbuBaha, M and Shehadeh, W and Jallad, H and Emara, A and Abu-Khazneh, O and Zahran, A and Elgendy, MS and Fkheideh, T and Sawaftah, Z and Milhem, F and Hajjeh, O and Shubietah, A},
title = {The gut-heart axis in atrial fibrillation: Pathophysiology, evidence, and therapeutic potential.},
journal = {Heart rhythm O2},
volume = {7},
number = {3},
pages = {581-597},
pmid = {41908202},
issn = {2666-5018},
abstract = {BACKGROUND: Recent advances in microbiome research highlight a bidirectional relationship between gut microbiota and atrial fibrillation (AF), the most common sustained arrhythmia worldwide. Gut dysbiosis has been implicated in systemic inflammation, metabolite imbalance, bile acid signaling, and autonomic dysfunction, whereas AF itself alters microbial homeostasis through hemodynamic and neurohormonal changes.<br><br>OBJECTIVE: This review aimed to synthesize current evidence linking gut dysbiosis to AF pathogenesis, identify mechanisms underlying this interaction, and explore the therapeutic potential of microbiota-targeted interventions.<br><br>METHODS: We conducted a narrative review of preclinical, clinical, and epidemiologic studies examining the gut-heart axis in AF. Particular emphasis was placed on microbial metabolites (eg, trimethylamine N-oxide, short-chain fatty acids, indoxyl sulfate), bile acid modulation, and inflammatory signaling. Data on interventions, including diet, probiotics, pharmacologic approaches, and fecal microbiota transplantation, were integrated to assess translational potential.<br><br>RESULTS: Evidence suggests that gut-derived signals contribute to atrial remodeling through activation of the NLRP3 inflammasome, altered calcium handling, and impaired gap junction integrity. Conversely, AF promotes dysbiosis by reducing gut perfusion, altering motility, and exposing patients to polypharmacy. Microbiota-directed strategies, particularly dietary modification and probiotics, demonstrate promise in reducing arrhythmic risk, whereas early data indicate potential biomarker roles for gut microbial signatures in AF stratification. However, causality remains uncertain, given that most studies are observational with limited sample sizes.<br><br>CONCLUSION: The gut-heart axis represents a novel paradigm in AF research. Although preliminary findings support its mechanistic and therapeutic relevance, interventional studies are needed to establish causality and guide clinical application.},
}
@article {pmid41908552,
year = {2026},
author = {Yu, N and Pang, S and Li, Y and Diao, H},
title = {Integrated microbiome-metabolome analysis reveals multiorgan toxicity of 1-nitropyrene and the limited efficacy of ferroptosis inhibitor Fer-1 in rats.},
journal = {Frontiers in toxicology},
volume = {8},
number = {},
pages = {1771766},
pmid = {41908552},
issn = {2673-3080},
abstract = {INTRODUCTION: 1-Nitropyrene (1-NP), a prevalent nitro-polycyclic aromatic hydrocarbon, is increasingly recognized as a potential metabolic disruptor, yet its systemic biological effects remain insufficiently characterized.<br><br>METHODS: This study investigated the metabolic, immunological, hepatic, and microbiome alterations induced by chronic 1-NP exposure in rats and assessed whether ferroptosis inhibition via Fer-1 could mitigate these effects.<br><br>RESULTS: Although body weight was not significantly altered overall, high-dose exposure impaired growth from week 4. Exposed groups exhibited progressively elevated fasting blood glucose and impaired glucose tolerance, indicating significant disruption of glucose homeostasis. Serum biochemistry revealed dose-dependent reductions in HDL and total cholesterol, while histopathology confirmed hepatocyte ballooning, inflammation, and steatosis consistent with NAFLD-like progression. Hematological changes, including shifts in neutrophil and lymphocyte populations, suggested chronic inflammatory activation. Untargeted metabolomics identified extensive alterations in pathways related to glycolysis, tryptophan metabolism, glycerophospholipid metabolism, and ABC transporters. Gut microbiota analysis demonstrated reduced richness and significant compositional shifts, with functional predictions linking dysbiosis to xenobiotic degradation, lipid metabolism, and phosphotransferase systems. Integrated microbiome-metabolome analysis revealed coordinated disruptions in host-microbial metabolic networks. Fer-1 intervention modified specific metabolic and microbial signatures but did not substantially alleviate major toxic outcomes.<br><br>CONCLUSION: Overall, chronic 1-NP exposure causes widespread metabolic injury driven by combined effects on host metabolism, immune regulation, hepatic function, and gut microbial ecology. These findings highlight 1-NP as a potent environmental metabolic disruptor and underscore the need for further mechanistic studies to inform mitigation strategies.},
}
@article {pmid41908560,
year = {2026},
author = {Anand, S and Shete, O and Srivastava, A and Verma, A and Goswami, S and Aggarwal, S and Luthra, K and Ghosh, TS},
title = {Urinary Microbiome Dysbiosis in Children With Congenital Uropathies at Varying Risk for Urinary Tract Infections.},
journal = {Kidney international reports},
volume = {11},
number = {4},
pages = {103799},
pmid = {41908560},
issn = {2468-0249},
abstract = {INTRODUCTION: Febrile urinary tract infections (UTIs) may occur in 30% to 50% of children with vesicoureteral reflux (VUR) or posterior urethral valves (PUVs), frequently leading to renal scarring despite chemoprophylaxis. Approximately 15% of children with uretero-pelvic junction obstruction (UPJO) may develop UTIs. However, investigations that can identify at-risk children before the first episode of UTI are lacking. In this exploratory study, we investigated the preinfection urinary microbiome in Indian children with congenital anomalies of the kidney and urinary tract (CAKUT) to determine whether microbiome alterations, metabolic potential, and antibiotic resistance profiles precede UTI.<br><br>METHODS: In this prospective cohort study with follow-up, urine samples were collected from 80 children: 36 with newly diagnosed, antibiotic-na&#xef;ve CAKUT (18 UPJO, 12 VUR, 6 PUV) and 44 controls. Patients were stratified a priori into low (n = 19) and high-risk (n = 17) groups using clinically defined UTI-susceptibility criteria. V3-V4 16S ribosomal RNA sequencing was used to define urinary microbial profiles. Alpha- and beta-diversity were compared using Shannon index and permutational multivariate analysis of variance (PERMANOVA), respectively. Sliding-window and network-based analyses were used to map dysbiosis gradients. Patients were followed-up longitudinally to assess UTI incidence. Identified dysbiosis-linked microbial markers at baseline were investigated using Kaplan-Meier and Cox-proportional hazard-based analyses as predictors of UTI-risk. Metabolic functions were inferred from taxonomic data. Antibiotic resistance patterns were characterized using the Comprehensive Antibiotic Resistance Database - Resistance Gene Identifier (CARD-RGI) and the World Health Organization Access, Watch, and Reserve classification.<br><br>RESULTS: Urinary microbial alpha diversity declined significantly from controls to low-risk to high-risk groups (P = 0.002), accompanied by an increase in intragroup variability (P &#x2264; 0.005). PERMANOVA revealed distinct clustering by risk (R [2] = 0.11; P = 0.001). Dysbiosis scores inversely correlated with the first Kendall Principal Coordinates Analysis (PCoA) axis (&#x3c1; = -0.62; P < 0.001). With increasing risk of UTI, the commensal, control-associated genera declined along this axis while the facultative pathogens became dominant. Control-associated microbiomes favored short- and branched-chain fatty acid and spermidine production; high-risk microbiomes overproduced ammonia, putrescine, and cadaverine. Resistance to 18 of 22 routinely tested antibiotics was almost confined to the 31 risk-associated microbiomes (P = 0.001). During the median (interquartile range) follow-up of 564 (518-594) months, 14 of 36 children with CAKUT developed UTIs, and baseline depletion of health-associated microbial consortia correlated with reduced UTI-free survival. A panel of 10 species-level and 12 genus-level taxa were identified as health-associated markers negatively associated with future UTI-risk during follow-up investigation.<br><br>CONCLUSION: Children with CAKUT exhibit urinary microbiome dysbiosis before their first symptomatic UTI, characterized by loss of conserved health-associated taxa, metabolic imbalance, and broad-spectrum antibiotic resistance. These findings support the potential of microbiome-informed, noninvasive risk stratification and microbiome-tailored prophylaxis, while establishing the first Indian pediatric reference set for CAKUT-related UTI prevention.},
}
@article {pmid41908828,
year = {2026},
author = {Zhang, Z and Ku, A and Ji, R and Song, B},
title = {Multi-omics analysis reveals the mechanism of Huaganjian in alleviating cholestatic liver fibrosis.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1744312},
pmid = {41908828},
issn = {1663-9812},
abstract = {Huaganjian (HGJ) is a traditional Chinese medicinal formula with liver-protective effects. However, the pharmacological mechanisms of the effects of HGJ on cholestatic liver fibrosis (CLF) are yet to be clarified. To evaluate the effects of HGJ on CLF and elucidate the underlying mechanisms, C57BL/6J mice were fed a 0.1% 3, 5-diethoxycarbonyl-1, 4-dihydrocollidine (DDC) diet to induce CLF. The efficacy of HGJ was evaluated by measuring the biochemical indicators of liver function, fibrosis, and histology. The underlying mechanisms were investigated using an integrated multi-omics approach, including fecal 16S rRNA sequencing, serum metabolomics, and hepatic transcriptomic analysis. The findings were further validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Western blotting (WB). HGJ significantly alleviated liver injury, cholestasis, and fibrosis. Microbiome analysis revealed that Bifidobacterium, Turicibacter, and Clostridium_sensu_stricto_1 abundances were positively correlated with liver injury and fibrosis marker levels, and these abundances decreased following HGJ treatment. Metabolomic analysis identified 531 differential metabolites, including 299 upregulated and 232 downregulated metabolites, following HGJ intervention. Hepatic transcriptomic analysis revealed 164 differentially expressed genes, including 102 upregulated and 62 downregulated genes. Integrated multi-omics analysis revealed that HGJ alleviated CLF by modulating the glycine/serine/threonine metabolism pathway. RT-qPCR and Western blotting experiments confirmed that in this pathway, aminolevulinic acid synthase 1 levels decreased, whereas serine dehydratase and serine dehydratase-like levels increased after HGJ treatment. Overall, HGJ effectively alleviated CLF, and its mechanisms of action were closely linked to the regulation of the glycine/serine/threonine metabolism pathway.},
}
@article {pmid41908923,
year = {2025},
author = {Kurt, &#xd6; and Scanlan, PD and Gentekaki, E and Robertson, LJ and Carmena, D and Dogruman-Al, F and Tsaousis, AD},
title = {The Blastocystis-colorectal cancer hypothesis: correlation is not causation.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {379},
pmid = {41908923},
issn = {2732-5121},
abstract = {Although superficially persuasive, claims suggesting a causal link between Blastocystis and colorectal cancer (CRC) lack robust scientific support. As Blastocystis is the most common gut protist found in human populations globally, its detection in CRC patients is unsurprising and does not imply pathogenicity. Current claims championing a causal role for Blastocystis in CRC are based on speculative correlations, a single poorly controlled animal study, and inconsistent subtype associations. We argue that linking Blastocystis to CRC is premature, misleading, and may give rise to unnecessary concern in patients that are colonised by or test positive for Blastocystis. We emphasise the need for rigorously designed investigations to establish causal roles for any microorganism in disease and the importance of conclusions being based on solid evidence, particularly in matters of public health.},
}
@article {pmid41909054,
year = {2025},
author = {Hanna, M and Huang, S and Ross, M and Reyes, A and Perera, D and Surathu, A and Cregeen, SJ and Hagan, J and Pammi, M},
title = {Microbiome Signatures and Inflammatory Biomarkers in Culture-Negative Neonatal Sepsis.},
journal = {Applied microbiology (Basel, Switzerland)},
volume = {5},
number = {3},
pages = {},
pmid = {41909054},
issn = {2673-8007},
support = {R03 HD098482/HD/NICHD NIH HHS/United States ; },
abstract = {Overuse of antibiotics is a concern in 'culture-negative sepsis' but it is unclear whether this is due to infection with viruses, fungi or other microbes that are not easily cultured, or whether it results from inflammatory processes. In a prospective study, we enrolled 50 preterm neonates with culture-positive sepsis (CP), culture-negative sepsis (CN), and asymptomatic preterm controls (CO). The microbiome of stool, skin, and blood, including bacterial, viral and fungal components and serum cytokine profiles were evaluated. The microbiome alpha or beta diversity did not differ between CN and CO groups. A MaAsLin analysis revealed increased relative abundances of specific bacterial and fungal genera in stool and skin samples in the CN group compared to CO. The virome analysis identified 24 viruses from skin samples, but they were not statistically different among the three groups. The cytokine and chemokine biomarker profiles were elevated in the CP group but were not statistically different between the CN and CO groups. Although the CN group had a longer hospital stay and higher BPD rates than the controls in unadjusted analyses, these differences were not significant after adjusting for gestational age and birth weight. The CN infants demonstrated microbial shifts without systemic immune activation or significantly worse clinical outcomes, supporting the rationale for discontinuing antibiotics in the absence of positive cultures.},
}
@article {pmid41909172,
year = {2026},
author = {Bao, Y and Xu, K and Du, Y and Feng, M and Li, L and Li, L and Yan, G and Li, X},
title = {PPARγ: a key orchestrator of epidermal barrier, immune responses, and lipid metabolism in atopic dermatitis pathogenesis and therapy.},
journal = {Frontiers in allergy},
volume = {7},
number = {},
pages = {1780908},
pmid = {41909172},
issn = {2673-6101},
abstract = {Atopic dermatitis (AD) is an immune-mediated inflammatory dermatosis characterized by epidermal barrier dysfunction, immune dysregulation, and cutaneous microbial dysbiosis. Existing therapeutic modalities for AD are limited in efficacy and durability, highlighting an unmet clinical need for novel, safe, and effective treatment strategies. Peroxisome proliferator-activated receptor gamma (PPARγ), a pivotal nuclear receptor involved in metabolic and inflammatory regulation, has emerged as a promising therapeutic target for AD. Its pleiotropic mechanisms encompass the restoration of stratum corneum integrity, modulation of aberrant immunoinflammatory signaling, normalization of cutaneous lipid metabolism, and regulation of the cutaneous microbiome and neuroimmune circuitry. This review comprehensively synthesizes the mechanistic evidence linking PPARγ to AD pathogenesis and critically appraises its potential as a novel therapeutic.},
}
@article {pmid41909251,
year = {2026},
author = {Sun, F and Yuan, M and Liao, C and Sun, Y and Yu, L and Zhuo, Y and Peng, Y and Tang, X and Zeng, Q and Song, J and Tao, X and Li, Q and Chen, M and Zhang, Y},
title = {Optimizing flue-cured tobacco planting patterns: enhanced rhizosphere nutrient availability and microbial community dynamics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1735540},
pmid = {41909251},
issn = {1664-302X},
abstract = {INTRODUCTION: Continuous monoculture of flue-cured tobacco causes soil degradation and microbial dysbiosis. While crop rotation can alleviate these obstacles, how different cropping patterns regulate soil carbon (C) and nitrogen (N) metabolic functions remains unclear.<br><br>METHODS: A four-year field experiment compared tobacco monoculture (CK), tobacco-maize rotation (TM), tobacco-rice rotation (TR), and tobacco-sweet potato intercropping (TP). Soil physicochemical properties, enzyme activities, metagenomic sequencing, and microbial network analysis were integrated.<br><br>RESULTS: TR significantly improved soil health: pH (+6.6%), organic matter (+22.1%), and urease activity (+12.5%). It enriched beneficial microbes (Pseudomonadota +16.4%, Mucoromycota +327%) and upregulated C-cycle (korA +42.3%) and N-assimilation genes (amoC +460%), while suppressing denitrification (nirK). TM increased available P/K but enriched oligotrophic taxa and reduced sucrase activity. TP triggered pathogenic fungi (Olpidium +160%), depleted beneficial microbes, and broadly suppressed C/N metabolic genes (cbbL -94.5%, nirS -21.8%).<br><br>DISCUSSION: Cropping patterns differentially reshape microbial communities and metabolic functions, determining their efficacy against continuous cropping obstacles. TR establishes efficient C/N cycling with "high assimilation, low denitrification," whereas TP induces pathogenic proliferation and metabolic suppression. This provides a functional framework for designing cropping systems to enhance soil health and tobacco productivity.},
}
@article {pmid41909261,
year = {2026},
author = {Choi, J and Shim, K and Bae, GS and Jeon, E and Hwang, EH and Kim, G and Baek, SH and Hong, JJ and Kim, DS and Kim, SH and Koo, BS},
title = {Comparative analysis of gut microbiota and host phenotypic characteristics across enterotype-like clusters in cynomolgus and rhesus macaques.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1775757},
pmid = {41909261},
issn = {1664-302X},
abstract = {Microbiome has been increasingly recognized for its close association with host physiology and diseases. Due to their close genetic relatedness to humans and standardized environmental conditions, captive macaque species serve as the most evolutionarily comparable preclinical animal models for studying human microbiome research. However, the characterization of gut microbiota and host phenotypic traits within each enterotype-like cluster of macaque species remains poorly understood. We analyzed microbiome characteristics and host metadata within enterotype-like clusters of cynomolgus and rhesus macaques housed in the same facility but with different origins of birth. At the phylum level, Bacteroidota, Firmicutes, Spirochaetota, and Proteobacteria were predominantly observed in both species. Except for Fibrobacterota at the phylum level, no significant interspecies differences were observed in bacterial composition or alpha diversity across taxonomic levels. Based on a prevalence threshold of 90%, cynomolgus macaques were found to share 12.4% of genera, while rhesus macaques shared 18.2%. Based on the relative abundance patterns of the genera Prevotella 9, Rikenellaceae RC9 gut group, and Treponema, the fecal microbiome of cynomolgus macaques was classified into three enterotype-like clusters (cluster 1, cluster 2, and cluster 3) whereas that of rhesus macaques was classified into two enterotype-like clusters. Using linear mixed-effects models, we identified species-specific associations between enterotype-like clusters and host phenotypes. In cynomolgus macaques, clustering was primarily associated with hematological and selected biochemical parameters, whereas in rhesus macaques, enterotype-like clusters were limited to body weight and hemoglobin. Despite a standardized diet and shared environments, distinct clusters and pronounced microbial individuality associated with birthplace suggest that early-life colonization is a key determinant of long-term gut microbiome structure and host phenotypes in captive primates. Also, identifying enterotype-like clusters in NHPs prior to analysis is essential for accurate and relevant human microbiome modeling, since each cluster may correspond to distinct human enterotypes and phenotypic traits.},
}
@article {pmid41909266,
year = {2026},
author = {Zhu, Z and Li, X and Cui, T and Chen, Z and Liu, Y and Chen, X and Tian, Y and Mu, Y and Wu, Y and Ji, Q and Yan, S and Cheng, Y},
title = {Temporal heterogeneity of microbial ecosystems and its formation mechanisms in Moutai-flavor Baijiu fermentation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798174},
pmid = {41909266},
issn = {1664-302X},
abstract = {The influence of workshop age on Moutai-flavor Baijiu fermentation is recognized, but the mechanisms driving microbial community shifts remain unclear. Understanding how the physical environment selects for specific microbiota is crucial for optimizing new workshops. Through 16S/ITS sequencing of pit-entry fermented grains, Daqu, air, and cooling yards in 5-, 10-, 20-, and 30-year-old workshops, Lactobacillus emerged as a key discriminant genus, increasing from 15.02% (5-year) to 35.59% (30-year). SourceTracker analysis revealed the cooling yard as the primary microbial source, contributing 54.2% on average to fermented grains. CO2-TPD analysis showed a 3.6-fold reduction in cooling yard surface basicity (from 0.11 to 0.03 mmol·g[-1]) over 30 years, resulting in high abundances (>10%) of alkalotolerant bacteria (e.g., Alkalibacterium, Nesterenkonia) and low Lactobacillus (2.17%). Nesterenkonia was also a biomarker in 5-year fermented grains. This confirms cooling yard surface basicity drives microecological differences, revealing how long-term production practices domesticate microbial communities and providing a theoretical basis for new workshop adaptation.},
}
@article {pmid41909643,
year = {2026},
author = {Yao, Y and Hu, X and Li, R and Tan, Z and Yu, H and Lin, Z and Zhang, T and Habimana, O},
title = {Probiotic yeast engineers a protective biofilm environment to enhance bioremediation and seahorse health in aquaculture.},
journal = {Biofilm},
volume = {11},
number = {},
pages = {100357},
pmid = {41909643},
issn = {2590-2075},
abstract = {Sustainable animal farming via intensive aquaculture relies on a balanced microbial ecosystem that promotes animal well-being. This research explored the use of the probiotic yeast Saccharomyces boulardii to influence tank biofilm microbiomes for improving the health of lined seahorses, Hippocampus erectus. Following a severe mortality event at week 6 that affected both groups, the control group demonstrated partial recovery to 71.4% survival, whereas the probiotic group achieved a higher survival, with a final rate of 88.9% after a disease challenge. This recovery led to a notable reduction in enteritis occurrences with a significant increase in average body weight and a 3.9-fold increase in activity compared to control conditions. Shotgun metagenomic analysis indicated that the enhancements were significantly supported by a marked reorganization of the tank's biofilm community. Probiotic supplementation significantly reduced microbial diversity and selected for a beneficial consortium enriched in taxa with recognized roles in nutrient cycling, including Rhodobacterales (involved in sulfur cycling and pathogen antagonism) and Pirellulaceae (key in polysaccharide breakdown). This engineered biofilm has greater genetic potential for energy generation, glucose degradation, and inorganic ion transfer. Crucially, virulence factor genes and pathogen-associated sequences were substantially suppressed in probiotic-treated biofilms. Our research shows that S. boulardii acts as a crucial modulator, creating a protective biofilm that boosts bioremediation while decreasing pathogenic threats. This ecological approach to the application of probiotics (targeting the environmental rather than host-associated microbiome) may offer a sustainable means to promote health and resilience within aquaculture systems.},
}
@article {pmid41909648,
year = {2026},
author = {Kumar, V and Das, BK and Roy, S and Bhowal, P and Roy, A and Bruce, TJ and Galindo-Villegas, J},
title = {Exploring the host-pathogen interaction and genome analysis of multidrug-resistant bacterial pathogen Proteus penneri isolated from Labeo rohita.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1733414},
pmid = {41909648},
issn = {1664-3224},
mesh = {Animals ; *Fish Diseases/microbiology/immunology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Host-Pathogen Interactions/genetics ; *Cyprinidae/microbiology/immunology ; Phylogeny ; *Proteus Infections/microbiology/veterinary/immunology ; *Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Virulence ; Genomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Multidrug-resistant (MDR) bacterial pathogens represent an escalating challenge to sustainable aquaculture, particularly in high-value freshwater species such as Labeo rohita, a cornerstone of South Asian aquaculture. This study provides the first comprehensive integration of genomic, immunological, and microbiome analyses to characterize Proteus penneri as an emerging MDR pathogen associated with severe disease manifestations in L. rohita, including exophthalmia, ulceration, and hemorrhage. Robust identification through biochemical assays, 16S rRNA sequencing, and phylogenetic analysis confirms the clinical relevance of this isolate. Functional assays demonstrated pronounced virulence, evidenced by hemolysin activity, extensive histopathological damage, and dose-dependent mortality, underscoring its pathogenic capacity in vivo. The observed resistance to multiple frontline antibiotic classes, including tetracyclines, macrolides, and carbapenems, highlights a critical therapeutic limitation in aquaculture settings. Genomic analysis further revealed a diverse repertoire of antimicrobial resistance genes, virulence determinants (notably biofilm formation and secretion systems), and mobile genetic elements, suggesting a strong potential for persistence, adaptability, and horizontal gene transfer. Infection-associated gut microbiome disruption, marked by elevated MAR indices and enrichment of virulence-associated taxa, indicates that P. penneri not only exploits host tissues but also reshapes the microbial ecosystem in ways that may exacerbate disease severity and resistance dissemination. Concurrently, heightened serum cortisol, C3, and Hsp70 levels, along with transcriptional upregulation of key immune and stress-related genes (hsp70, nod, il6, sod, c3, and myd88), reflect an intense pro-inflammatory and physiological stress response. In silico docking analyses implicating myd88-lipopolysaccharide interactions provide mechanistic insight into potential immune-modulatory strategies employed by the pathogen. Collectively, these findings delineate a multifactorial basis for P. penneri virulence and MDR, emphasizing its significance as an emerging aquaculture pathogen. Future research should prioritize functional validation of key virulence and resistance genes, longitudinal surveillance to assess transmission dynamics and AMR spread, and experimental evaluation of alternative disease mitigation strategies, including probiotics, phage therapy, and immune-modulating interventions, to reduce antibiotic reliance and enhance fish health resilience in aquaculture systems.},
}
@article {pmid41909844,
year = {2026},
author = {Lin, B and Tong, S and Ba, C and Wang, X},
title = {Precision treatment of gastrointestinal tumours and liver disease interaction mechanisms based on multi-omics data and microbiome hubs.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1791531},
pmid = {41909844},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Neoplasms/therapy/microbiology ; *Gastrointestinal Microbiome ; *Liver Diseases/therapy/microbiology ; *Precision Medicine/methods ; Genomics/methods ; Proteomics/methods ; Metabolomics/methods ; Tumor Microenvironment ; Carcinogenesis ; Multiomics ; },
abstract = {The global prevalence of gastrointestinal tumours and the bottlenecks in their diagnosis and treatment are being systematically overcome by the multi-omics revolution: high-throughput technologies are driving the multidimensional integration of genomics-transcriptomics-proteomics-metabolomics to comprehensively decode the genetic architecture of tumours. Meanwhile, the gut microbiota, acting as a core regulatory hub, drives carcinogenesis through immune microenvironment remodelling and metabolic pathway hijacking, further facilitating proteome-metabolome multidimensional integration, comprehensively decoding tumour genetic architecture. The gut microbiota, acting as a core regulatory hub, drives carcinogenesis through immune microenvironment remodelling and metabolic pathway hijacking, while mediating a vicious cycle network linking liver disease and tumours via the gut-liver axis. This review examines the application of multi-omics technologies in gastrointestinal tumour research, summarises the role of gut microbiota in tumourigenesis and its interaction with liver disease, and envisions future interventions targeting the gut microbiome for early disease diagnosis and precision treatment.},
}
@article {pmid41909873,
year = {2026},
author = {Yu, J and Baek, H and Jaiswal, V and Park, M and Lee, HJ},
title = {Heavy metal accumulation and fecal microbiota response in black soldier fly larvae: identification of Leminorella grimontii as a potential indicator species.},
journal = {Food science and biotechnology},
volume = {35},
number = {5},
pages = {1329-1338},
pmid = {41909873},
issn = {2092-6456},
abstract = {UNLABELLED: With growing environmental concerns about marine pollution from heavy metals, black soldier fly larvae (BSFL) are gaining attention for their potential use in sustainable waste-to-feed systems. In this study, BSFL were raised on diets containing cadmium (Cd), lead (Pb), mercury (Hg), and arsenic (As) to assess their growth, metal accumulation patterns, and changes in microbiota. While Cd mainly accumulated in the larval body, Pb, Hg, and As were primarily excreted through exuviae and feces. This pattern remained consistent even when larvae were fed naturally contaminated mackerel heads. Microbiome analysis of fecal samples showed that Leminorella grimontii had a strong positive correlation with Hg and As concentrations, suggesting its potential as a microbial indicator species for heavy metal exposure. These findings support the use of BSFL in bioconversion systems and suggest L. grimontii as a new biomarker for environmental monitoring.<br><br>GRAPHICAL ABSTRACT: Scheme 1Experimental procedure and fecal microbiome results.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-026-02114-y.},
}
@article {pmid41909880,
year = {2025},
author = {Cold, F and Heintz, JE and Ghathian, KSA and Stenbøg, PA and Hansen, LH and Carstens, AB and Petersen, AM and Halkjaer, SI and Bendtsen, F and Ytting, H},
title = {Low incidence of cytolysin-positive E. faecalis and no correlation to survival in Danish patients with alcohol-associated hepatitis: A prospective cohort study.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2549729},
pmid = {41909880},
issn = {2993-3935},
abstract = {Alcohol-associated hepatitis (AH) is a severe and life-threatening form of alcohol-associated liver disease with no approved treatments for reducing long-term mortality. Cytolysin-producing E. faecalis in the gut microbiota of AH patients has been reported as highly correlated to mortality. We investigated whether we could reproduce this correlation in a cohort of Danish patients with AH. Fecal samples from 28 hospitalized patients with AH were analyzed for cytolysin-producing E. faecalis and were followed for 1 y after hospital admission. The primary endpoint was comparison of 180-d mortality in AH patients with and without cytolysin-positive fecal samples. Three of twenty-eight (10.7%) fecal samples were identified as cytolysin-positive. There were no significant differences at baseline between cytolysin-positive and -negative patients in terms of age, Glasgow Alcoholic Hepatitis Score, Charlson Comorbidity Index or biochemical variables (INR, bilirubin, albumin). There was no difference in mortality between the groups 180 d after hospital admission; one of the three (33%) cytolysin-positive patients had died compared to 9 of the 25 (36%) cytolysin-negative (p-value for difference = 1.0). We report a low incidence of cytolysin-positive E. faecalis in hospitalized Danish AH patients and no greater risk of mortality compared to cytolysin-negative AH patients.},
}
@article {pmid41909881,
year = {2025},
author = {Liu, W and An, M and Wang, Q and Liu, Y and Shang, Y and Dong, X and Ding, H and Fu, S and Han, X and Shang, H},
title = {Gut microbiome-induced metabolites promote the role of Silybin as adjunctive drug in HIV-positive immunological nonresponders.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2569789},
pmid = {41909881},
issn = {2993-3935},
abstract = {HIV-infected immunological nonresponders (INRs) endure persistent T-cell dysfunction and chronic inflammation, facing high risk of various complications and mortality, with no effective therapies available. Silybin, the principal constituent of a plant extract, possesses anti-inflammation and immunomodulatory properties. The gut microbiome has been shown to modulate the efficacy of immune therapies and drugs. We gave 54 INRs oral silybin for three months and used multi-omics to investigate the gut-related factors influencing the efficacy of silybin. Silybin raised CD4[+] T cells counts in 52% of participants and an efficacy classification model based on baseline gut microbiome and metabolites was developed. Favorable gut bacteria produced anti-inflammatory metabolites that downregulated Ras/MAPK/PI3K-Akt signaling pathways also targeted by silybin. Our findings shed light on a novel therapeutic approach for addressing immune dysfunction in HIV-positive INRs and have important implications for personalized medical strategies in the management of HIV infection.},
}
@article {pmid41909883,
year = {2025},
author = {Abubakar, D and Abdullahi, H and Ibrahim, I},
title = {Bridging Microbiomes: Exploring Oral and Gut Microbiomes in Autoimmune Thyroid Diseases- New Insights and Therapeutic Frontiers.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2452471},
pmid = {41909883},
issn = {2993-3935},
abstract = {Autoimmune thyroid diseases (AITDs) are the most common organ-specific autoimmune disorders characterized by thyroid dysfunction and immune system deficiencies. In recent decades, the role of the microbiome in autoimmune diseases has gained increasing attention, with emerging research linking gut microbiome alterations to the development of AITDs. This review summarizes current knowledge on the relationship between AITDs and the gut microbiome. Additionally, it emphasizes the role of the oral microbiome in AITDs, an area often overlooked in autoimmune research. Beyond the microbiome, the virome and mycobiome have been recognized as critical but underexplored components of the human microbiome, potentially contributing to immune dysregulation and the pathogenesis of AITDs. The review also explores modulating the microbiome for managing AITDs, including diet adjustment, the potential use of probiotics, postbiotics, symbiotics, and even fecal microbiota transplantation (FMT) to restore a balanced microbiome that may positively influence the immune system and, by extension, the course of AITDs. This review thoroughly explores the intricate relationship between AITDs, the gut, and oral microbiomes, paving the way for precision medicine applications in AITDs. Examining microbiota-thyroid interactions highlights the potential for targeted, personalized treatments and novel therapeutic therapies, guiding future therapeutic strategies for more effective and precisely tailored AITD management approaches.},
}
@article {pmid41909884,
year = {2025},
author = {Pateriya, D and Prasoodanan P K, V and Scaria, J and Sharma, VK},
title = {Landscape of flavonoid metabolism in human gut microbiome and its association with health and disease.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2520788},
pmid = {41909884},
issn = {2993-3935},
abstract = {The positive effects of dietary flavonoids on health depend on their bioavailability in the human gut, where the flavonoid-modifying enzymes (FMEs) in gut bacteria play a crucial role in flavonoid metabolism. Thus, to comprehensively examine the role of FMEs in this process, we first constructed a database of potential FMEs containing 6,865 proteins. We identified homologs of these FMEs in gut bacterial genomes and reported species that can potentially modify flavonoids but were not previously known in this context. We examined the differential abundance of FMEs in the gut microbiomes of healthy and diseased individuals from Western and non-Western populations with distinct dietary habits. The differential enrichment of key FMEs between Western and non-Western populations and between disease and healthy samples highlights differences in gut flavonoid metabolism based on diet, population, and health status. This study reveals a comprehensive landscape of flavonoid metabolism in the human gut microbiome.},
}
@article {pmid41909885,
year = {2025},
author = {Lau, RI and Wong, MCS and Lau, LHS and Lau, AYL and Mak, IWC and Lo, OSH and Chan, NN and Dai, DLK and Hau, KC},
title = {Role of gut microbiome in pathogenesis and treatment of diseases: Multidisciplinary experts' opinion of the Asian Medical Experts Academy (AMEA).},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2558575},
pmid = {41909885},
issn = {2993-3935},
abstract = {Emerging evidence suggests the role of the gut microbiome in the health and diseases of multiple organs and systems. In the past decade, an increasing trend in the use of microbiome-based therapeutics (e.g., probiotics, prebiotics, synbiotics) has been observed in Asia and globally. However, local and global clinical guidelines on the use of microbiome-based therapeutics are limited. A multidisciplinary working group has been established to foster communication between experts from diverse medical specialties on the clinical application of microbiome-based therapeutics. Through conducting an extensive review on current evidence on the importance of the gut microbiome and the potential use of microbiome-based therapeutics in health and diseases, the experts' working group identified the unmet needs related to the use of microbiome-based therapeutics in the clinical settings in Asia and global contexts. Thirteen position statements were developed, including eight statements focusing on the role of the gut microbiome in health and disease pathogenesis, as well as six statements focusing on the potential clinical applications. A list of potential indications for microbiome-based therapeutics was also proposed based on current evidence and clinical experience. This paper is intended to serve as a reference that assists healthcare professionals in improving care for patients using microbiome-based therapeutics in Asia and globally.},
}
@article {pmid41909889,
year = {2025},
author = {Lan, Z and Chen, J and Lan, S and Li, N and Yang, B and Hou, J and Yang, X},
title = {Hydrogen-rich water attenuates radiation-induced oral mucositis in mice via antioxidant and gut microbiota-stabilizing effects: a longitudinal study.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2595392},
pmid = {41909889},
issn = {2993-3935},
abstract = {Radiation-induced oral mucositis (RIOM) frequently complicates head and neck radiotherapy, leading to severe pain, compromised nutrition, and often requiring treatment modifications. Although craniofacial-only irradiation is confined to the head and neck region, it can still disrupt gut homeostasis. Mice subjected to head and neck irradiation developed marked epithelial damage in both the oral and intestinal mucosa, as evidenced by pronounced RIOM and diminished barrier integrity. Histological examination revealed substantial mucosal thinning and leukocyte infiltration in the tongue, along with reduced occludin and ZO-1 expression in colonic tissues. Supplementation with hydrogen-rich water (HW) markedly decreased the severity of oral lesions and preserved epithelial thickness, while restoring the expression of tight junction proteins in the colon. Fecal 16S rRNA sequencing showed that radiation alone provoked expansions of Streptococcus and Helicobacter, coupled with a decline in short-chain fatty acid-producing families (Lachnospiraceae, Ruminococcaceae). In contrast, HW supplementation partially reversed these microbial shifts, which correlated with reduced oral inflammatory markers. Collectively, these findings underscore an oral-gut axis whereby HW fosters mucosal healing through microbiome stabilization and decreased inflammatory stress, suggesting that HW as a promising adjunct for managing head and neck irradiation-related complications.},
}
@article {pmid41909890,
year = {2025},
author = {Park, G and Oh, S and Kim, M and Jeong, Y and Kim, G},
title = {Common microbial signatures in blood and their amplification in clinical disorders.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2473450},
pmid = {41909890},
issn = {2993-3935},
abstract = {Blood microbiome research has emerged as a significant area of study, exploring microbial signatures within the bloodstream and their potential implications for various clinical disorders. This study aimed to identify common microbial signatures in blood across cohorts and investigate how these signatures are altered in clinical conditions. We conducted a meta-analysis of 15 publicly available studies utilizing amplicon sequencing, including 687 control and 651 case individuals with various disorders from diverse geographic locations to compare their blood microbiome profiles. The results revealed that most microbes detected in the blood originated from the gut, oral cavity, and skin, with several genera such as Corynebacterium, Streptococcus, and Lactobacillus consistently identified across studies. Furthermore, we observed a significant increase in microbial diversity and abundance in individuals with clinical disorders compared to the control group. Notably, microbial genera originating from the gut and oral cavity, including Acinetobacter, Prevotella, and Clostridium sensu stricto-1, were more prevalent in disease cohorts, suggesting a potential link between the translocation of microbial signatures and disease pathology. The study underscores the importance of considering microbial signatures as potential biomarkers in clinical settings and calls for further investigation into the role of circulating microbial DNA in immune response and disease progression.},
}
@article {pmid41909891,
year = {2025},
author = {Manzoor, H and Kayani, MUR},
title = {Insights into the gut microbiome-metabolite dynamics in breast cancer.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2483446},
pmid = {41909891},
issn = {2993-3935},
abstract = {In recent years, understanding the intricate connection between gut microbiome and cancer development has gained significant attention. The gut microbiome has a key role in maintaining overall human health and modulating the body's defense mechanism against various diseases. This review examines the multifaceted association between the gut microbiome and breast cancer, providing a comprehensive overview of studies from the last two decades that investigate both anti-cancer and pro-cancer properties of gut metabolites. Compounds such as nisin, inosine, acetate, propionate, and conjugated linoleic acids have demonstrated potential as therapeutic agents against breast cancer, while others, including butyrate, lactate, certain bile acids, and secondary metabolites, exhibit dual roles, showing both anti-cancer and pro-cancer properties under different conditions, with some implicated in tumor progression. Moreover, emerging research highlights the dual roles of these metabolites in influencing the efficacy of conventional breast cancer therapies. Despite promising evidence, the molecular mechanisms underlying these opposing actions remain unclear and require further investigation. To advance our understanding, future research should prioritize elucidating these mechanisms, establishing dose-response relationships, and conducting animal and clinical studies to validate in vitro findings. This review also identifies key gaps and highlights potential directions for future research in this field.},
}
@article {pmid41909893,
year = {2025},
author = {Jorgensen, JA and Choo-Kang, C and Wang, L and Issa, L and Gilbert, JA and Ecklu-Mensah, G and Luke, A and Bedu-Addo, K and Forrester, T and Bovet, P and Lambert, EV and Rae, D and Argos, M and Kelly, TN and Sargis, RM and Dugas, LR and Dai, Y and Layden, BT},
title = {Toxic metals impact gut microbiota and metabolic risk in five African-origin populations.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2481442},
pmid = {41909893},
issn = {2993-3935},
abstract = {Underlying mechanisms by which exposures to toxic metals/metalloids impact obesity and type 2 diabetes (T2DM) risk remain largely unknown. Gut microbiota have been strongly associated with cardiometabolic risk. To assess relationships between high metal exposures, gut dysbiosis, and metabolic dysregulation, we analyzed associations among gut microbiome taxa, dichotomized metal levels (arsenic, lead, mercury, cadmium), clinical measures (BMI, fasting blood glucose, blood pressure), and diagnoses (hypertension, obesity, diabetes) in 178 African-origin adults (52% female, mean age = 43.0 ± 6.4 years) from Ghana, South Africa, Jamaica, Seychelles, and USA. High vs. low lead and arsenic levels had a significant effect on beta diversity (p < 0.05). Seventy-one taxa were associated with high lead levels: 30 with elevated BMI, 22 with T2DM, and 23 with elevated fasting blood glucose (p < 0.05); 115 taxa were associated with high arsenic levels: 32 with elevated BMI, 33 with T2DM, and 26 with elevated blood glucose (p < 0.05). Porphyrin metabolism was the most enriched metabolic pathway in taxa associated with higher lead and arsenic exposure. These data provide the first findings from African-origin adults that demonstrate the association between the gut microbiome with lead and arsenic exposure and obesity and T2DM risk.},
}
@article {pmid41900768,
year = {2026},
author = {Zhou, S and Xu, Z and Shen, J},
title = {Female Reproductive Tract Organ-on-Chips: Modeling Barrier Function and Drug Transport.},
journal = {Pharmaceutics},
volume = {18},
number = {3},
pages = {},
pmid = {41900768},
issn = {1999-4923},
support = {1U01FD007656//United States Food and Drug Administration/ ; 33040//Massachusetts Life Sciences Center/ ; },
abstract = {Female reproductive tract (FRT) disorders such as maternal conditions and gynecological cancers represent a significant global health burden. However, women's health, and particularly locally acting therapies targeting the FRT, has historically been underprioritized in drug development and translational research. Developing safe and effective therapies requires a clear understanding of drug transport across FRT barriers. Conventional in vitro culture systems and animal studies fail to recapitulate the physiological complexity of the human FRT, including stratified mucosal architecture, functional mucus barriers, microbiome interactions, as well as dynamic hormonal regulation. Recently, organ-on-chip (OoC) microfluidic platforms, integrating human cells with precisely controlled perfusion, have emerged as advanced in vitro systems capable of recreating dynamic physiological microenvironments. This review summarizes the major anatomical and physiological barriers of the FRT, including the vagina, cervix, endometrium, and placenta, and discusses critical design considerations for the development of FRT-on-chip models. We highlight the advanced OoC developed to study infection, drug permeation, hormonal responses, and maternal-fetal interface dynamics. Finally, future perspectives are outlined, including the integration of immune components, vascularization strategies, and multi-organ systems to better simulate inter-organ communication. Collectively, these advances underscore the potential of FRT-on-chip models as predictive platforms for preclinical drug screening, toxicity evaluation, and personalized medicine.},
}
@article {pmid41900770,
year = {2026},
author = {Vadlapatla, R and Shirazi, AN and Koomer, A and Weng, J and Ghilarducci, ME and Qudus, A and Parang, K},
title = {Microbiome-Responsive Hydrogels: From Biological Cues to Smart Biomaterials.},
journal = {Pharmaceutics},
volume = {18},
number = {3},
pages = {},
pmid = {41900770},
issn = {1999-4923},
abstract = {Background: Stimuli-responsive hydrogels (SRHs) are smart polymeric materials that undergo reversible physicochemical changes in response to abiotic cues and externally applied fields, enabling applications in drug delivery, wound healing, and tissue engineering. However, they exhibit limited biological specificity and do not adequately reflect the dynamic, disease-relevant complexity of native tissue microenvironments. Microbe-colonized tissues display distinctive biochemical features driven, shaped by microbial metabolism, including localized pH gradients, short-chain fatty acid production, secretion of quorum-sensing molecules, biofilm formation, and expression of specialized enzymes. These endogenous, spatiotemporally regulated signals are closely linked to host physiology and pathology but remain underutilized in hydrogel design. This review aims to highlight microbiome-responsive hydrogels (MRHs) as a strategy to address this gap. Methods: This study summarizes current engineering approaches, key microbial stimuli, and emerging biomedical applications of MRHs, with emphasis on translational and regulatory challenges. Results: Microbiome-responsive hydrogels (MRHs) address this gap by leveraging microbial metabolic and biochemical cues to induce swelling, degradation, drug release, antibacterial activity, or structural transformation. By directly coupling to microbe-derived stimuli, MRHs offer improved physiological relevance, enhanced local specificity, and new opportunities for precision therapy targeting disease-associated microbial niches. Conclusions: Despite their promise, MRHs remain an early and fragmented field, lacking standardized biological triggers, material design frameworks, and performance evaluation strategies. This review summarizes current engineering approaches, key microbial stimuli, and emerging biomedical applications, with emphasis on translational and regulatory challenges, positioning MRHs as an underexplored platform for next-generation smart biomaterials.},
}
@article {pmid41900857,
year = {2026},
author = {Shah, IM and Lebrilla, CB and German, JB and Mills, DA},
title = {Selective Human-Milk-Inspired Antimicrobial Peptides for the Treatment of Bacterial Vaginosis.},
journal = {Pharmaceutics},
volume = {18},
number = {3},
pages = {},
pmid = {41900857},
issn = {1999-4923},
support = {R43AI165105/GF/NIH HHS/United States ; },
abstract = {Background: Antimicrobial resistance (AMR) is a global healthcare threat. Traditional largely non-selective antibiotics produce side effects due to the natural host microbiome being modified creating a loss in homeostasis. In women, AMR is a cause of acute generational impact. For example, bacterial vaginosis (BV), the most common gynecological infection in reproductive-age women, is a serious public health concern due to its high rates of recurrence, secondary infections, and reproductive issues; and two currently prescribed antibiotics for BV do not fully resolve the symptoms. Objective: The strong need for innovative, potent, safe, and selective therapeutics has prompted a search for such bioactive molecules in milk. Resulting from 200 million years of evolutionary pressure, mammalian lactation not only nourishes infants, but it has also been under relentless Darwinian selective pressure to provide protection from a variety of infections. Methods: Computationally designed human-milk-inspired peptides (AMPs) were tested in standard microbicidal assays for activity against BV pathogens, and evaluated for stability and safety. Results: Several AMPs are bactericidal towards Gardnerella vaginalis, a major BV-associated pathogen, and other BV-associated pathogens. Some novel AMPs do not impact the viability of key lactobacilli linked to a healthy vaginal microbiome. These stable, membrane-acting cationic AMPs reduce inflammation during an infection assay and are safe in EpiVag organoid tissues. Conclusions: AMPs can address concerns like non-selectivity and antibiotic resistance-thereby addressing AMR. Lead AMPs from this study offer a promising solution for the development of novel therapeutics for the treatment of BV, which may reduce the burden of AMR.},
}
@article {pmid41900935,
year = {2026},
author = {Santaniello, U and Mastorino, L and Pala, V and Rosset, F and Crespi, O and Quaglino, P and Ribero, S},
title = {Pharmacomicrobiomics in Psoriasis: Microbiome-Drug Interactions Across Systemic Treatments.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {3},
pages = {},
pmid = {41900935},
issn = {2075-1729},
abstract = {Psoriasis is a chronic immune-mediated skin disease with highly variable responses to systemic therapies. Emerging evidence highlights the microbiome as a potential modulator of drug efficacy and toxicity. Gut bacteria can enzymatically metabolize drugs, such as methotrexate, altering bioavailability and therapeutic outcomes, while microbial metabolites-including short-chain fatty acids, branched-chain amino acids, and tryptophan derivatives-shape host immunity and barrier integrity, influencing drug action. Baseline microbial signatures have been linked to treatment response, potentially predicting anti-TNF or IL-17 inhibitor efficacy. Systemic therapies themselves reshape microbial communities: IL-17 blockade induces broad shifts in gut and skin microbiota, whereas cyclosporine and anti-TNF agents exert subtler effects. Small molecules such as apremilast and fumarates may reduce fungal overgrowth and influence microbial composition, whereas data on JAK/TYK2 inhibitors remain limited. Notably, current evidence exhibits a literature bias toward the gut microbiota, while the roles of the oral and skin axes remain understudied. Adjunctive microbiome-directed interventions, including probiotics and fecal microbiota transplantation, have demonstrated potential to enhance treatment outcomes by promoting anti-inflammatory taxa and restoring barrier function. Despite these promising findings, current evidence is heterogeneous, often limited by small sample sizes, short follow-up, and variable methodology. Integrating pharmacomicrobiomics data with clinical, genetic, and multi-omics profiling could enable precision medicine approaches in psoriasis, allowing therapy selection tailored to individual microbial and metabolic signatures. Future research should focus on longitudinal, multicenter studies to identify actionable microbial biomarkers, clarify mechanistic interactions between drugs, microbes, and host immunity, and evaluate microbiome-targeted adjuncts in randomized trials. Understanding the bidirectional crosstalk between systemic therapies and the microbiome may transform psoriasis management, improving efficacy, reducing adverse events, and enabling durable, personalized responses.},
}
@article {pmid41901063,
year = {2026},
author = {Nunna Sai Venkata, L and Mishra, AK and Mohanta, YK and Rustagi, S and Bahuguna, A and Tomar, A and Baek, KH and Mishra, B},
title = {The Gut Gambit: A Review of How Microbial Imbalance Fuels Metabolic Mayhem.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901063},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/metabolism ; Oxidative Stress ; *Metabolic Diseases/microbiology/metabolism ; Epigenesis, Genetic ; Probiotics ; Inflammation/microbiology ; Animals ; },
abstract = {BACKGROUND/OBJECTIVES: An imbalance in gut microbiota, known as gut dysbiosis, results in reactive oxygen species overproduction, which can cause inflammatory conditions, damage DNA, trigger immunity, and induce epigenetic modifications of crucial genes that regulate metabolic pathways. Such a condition can also weaken the resilience of the protective gut wall and elevate colon permeability, allowing toxins from the gut to reach the liver and bloodstream, contributing to oxidative damage, autoimmune diseases, and epigenetic changes linked to metabolic disorders.<br><br>METHODS: The Scopus database was exclusively searched for the literature. Relevant articles were identified using predefined keywords, including gut dysbiosis, microbiota, microbiome, oxidative stress, metabolic disorders, inflammation, and epigenetics or combinations. Gut microbiota- and diet-induced metabolic disorders, particularly obesity, insulin resistance, dyslipidemia, and hypertension, may be inherited through epigenetic pathways.<br><br>RESULTS: The evidence analyzed suggests that the gut microbiota serves as a diverse metabolic and immunological organ. Its disruption affects the production of short-chain fatty acids, bile acid metabolism, immune signaling, and the redox balance, which contributes to the development of obesity, insulin resistance, and metabolic syndrome.<br><br>CONCLUSIONS: This review highlights key epigenetic mechanisms underlying metabolic disorders and oxidative stress in the context of gut dysbiosis. Furthermore, therapeutic strategies targeting the gut microbiota, such as dietary interventions, prebiotics, probiotics, postbiotics, and fecal microbiota transplantation, hold promise for mitigating oxidative stress and inflammation associated with metabolic syndrome.},
}
@article {pmid41901066,
year = {2026},
author = {Thomas, EG and Ortutu, BF and Watson, JC and Ong, E and Blankley, KE and Meaurio Martin, A and Shankar, S and Zhang, D and Boland, DJ and Wu, CS},
title = {Purified Diets Lacking Fermentable Fiber Reduce Microbial Diversity, Alter Epithelial Transcriptome, and Exacerbate Colitis.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901066},
issn = {2072-6643},
support = {R21ES036683/ES/NIEHS NIH HHS/United States ; RP230204//Texas A&amp;M Health-Center of Excellence in Cancer Research/ ; 58-3091-1-018//Texas A&amp;M AgriLife Institute for Advancing Health Through Agriculture/ ; },
mesh = {Animals ; *Dietary Fiber/administration &amp; dosage ; Mice, Inbred C57BL ; Male ; *Gastrointestinal Microbiome ; *Transcriptome ; *Colitis/microbiology/chemically induced ; Mice ; *Intestinal Mucosa/metabolism/microbiology ; Fermentation ; Fatty Acids, Volatile/metabolism ; Colon/metabolism/microbiology ; Dextran Sulfate ; Feces/microbiology ; *Diet ; Disease Models, Animal ; },
abstract = {Background/Objectives: Dietary fibers play key roles in shaping gut microbiome and intestinal homeostasis. While purified diets offer experimental precision and reproducibility in rodent models, they omit the complex mixture of fermentable and non-fermentable fibers found in grain-based chow diets. We hypothesized that excluding fermentable fiber impairs intestinal homeostasis by reducing microbial metabolites and altering the colonic epithelial transcriptome, thereby increasing susceptibility to inflammation. Methods: Wildtype male C57BL/6 mice were maintained on either a standard grain-based chow diet or a purified low-fat diet (LFD) containing 5% non-fermentable cellulose for ten weeks. Fecal microbiomes, short-chain fatty acid (SCFA) profiles, and colonic epithelial transcriptomes were analyzed. A separate group was challenged with dextran sodium sulfate (DSS) following a five-week dietary intervention to compare colitis severity between the two diet groups. Results: Relative to mice fed the grain-based chow, those consuming the purified LFD (containing only non-fermentable cellulose) showed decreased gut microbial diversity and significantly lower SCFA levels. These changes were accompanied by marked differences in colonic epithelial cell transcriptomes. In LFD-fed mice, the top upregulated gene networks included ribosomal pathways and MHC complex protein binding, suggesting increased growth and gut inflammation. The most downregulated pathways included mineral absorption, actin and tubulin binding, and membrane organelle assembly, indicating major alterations in cellular structure and transport. LFD-fed mice also exhibited increased colonic expression of S100a9, a gut inflammation biomarker, and more severe disease symptoms when challenged with DSS compared to chow-fed mice. Conclusions: Fermentable fibers are one of the factors contributing to intestinal homeostasis and mitigating the severity of ulcerative colitis.},
}
@article {pmid41901079,
year = {2026},
author = {Cirio, S and Mantegazza, G and Salerno, C and Guglielmetti, S and Allam, A and Campus, G and Cagetti, MG},
title = {Assessing the Impact of Heyndrickxia coagulans Administered Through Sugar-Free Chewing Gum on Dental Biofilm: A Double-Blind Randomized Controlled Trial.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901079},
issn = {2072-6643},
mesh = {Humans ; *Chewing Gum ; Double-Blind Method ; *Biofilms/drug effects ; Male ; Female ; Adult ; *Dental Plaque/microbiology ; *Probiotics/administration &amp; dosage ; Middle Aged ; Young Adult ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background:Heyndrickxia coagulans has emerged as a candidate for oral health applications, and chewing gum offers a promising delivery method. This study evaluates whether H. coagulans delivered via sugar-free chewing gum can induce detectable changes in plaque microbial ecology. Methods: A randomized, double-blind, placebo-controlled clinical trial was conducted on 52 healthy adults. Participants consumed probiotic or control gum for 4 weeks. Dental plaque was collected at baseline (T0), mid-intervention (T1), end of intervention (T2), and one week post-intervention (T3). qPCR quantified H. coagulans, while 16S rRNA gene profiling assessed microbial diversity and taxonomic composition. Statistical analyses included rank-based difference-in-differences models, Wilcoxon and Mann-Whitney tests, and differential abundance inference based on negative binomial modeling. Results: Forty-four subjects completed the study. In the Intervention group, the strain was detected in 71.4% of participants at T1 and 61.9% at T2, and it persisted in 9.5% at T3. Differential abundance analysis revealed a broad depletion of taxa linked to oral dysbiosis at T2 with partial persistence at T3, along with selective enrichment of beneficial strains. Conclusions:H. coagulans delivered via chewing gum can reach the dental biofilm and induce modest, transient shifts in microbial composition. However, these biofilm ecology findings should be interpreted in the context of clinical outcomes.},
}
@article {pmid41901112,
year = {2026},
author = {Solano-Aguilar, G and Lakshman, S and Chen, C and Beshah, E and Molokin, A and Vinyard, B and Dawson, HD and Santin-Duran, M and Bruna, G and Smith, A and Urban, JF},
title = {Fruit and Vegetable Supplemented-Diet Ameliorates Dextran Sodium Sulfate (DSS)-Induced Colitis by Modulating Host Transcriptome and Gut Metagenome Response.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901112},
issn = {2072-6643},
support = {Cris 8040-51000-058-00D//United States Department of Agriculture/ ; },
mesh = {Animals ; Dextran Sulfate ; *Fruit ; *Colitis/chemically induced/prevention &amp; control/microbiology/diet therapy ; *Transcriptome ; *Gastrointestinal Microbiome ; *Dietary Supplements ; *Vegetables ; Swine ; *Metagenome ; Disease Models, Animal ; *Diet ; Colon/pathology ; },
abstract = {Background/Objectives: Dietary intake of fruits and vegetables (FVs) has been inversely associated with a lower risk of ulcerative colitis. Using a pig model, we evaluated the effect of FV supplementation on dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet (negative control), grower diet + 4% DSS (positive control), half-FV diet + DSS, or full-FV diet + DSS. FV levels matched half or full daily recommendations from the Dietary Guidelines for Americans (DGA). Clinical signs were monitored; proximal colon contents (PCs) and mucosa (PCM) were analyzed for metagenome, transcriptome and histopathology. Results: Full-FV pigs showed no diarrhea, less fecal occult blood (FOB), crypt hyperplasia, but no changes in gene expression or microbiome diversity (p < 0.05). Half-FV pigs had increased FOB, differentially expressed genes (DEGs) linked to tissue remodeling, crypt/goblet cell hyperplasia and two cases of diarrhea (p < 0.05). DSS controls showed reduced immune-related DEGs, altered microbiome, PCM erosion, FOB, and persistent diarrhea in one pig (p < 0.05). Conclusions: A three-week full-FV diet conferred protection against DSS-induced colitis, with a dose-dependent protection of intestinal tissue and gut metagenome under inflammatory challenge.},
}
@article {pmid41901128,
year = {2026},
author = {Lupu, VV and Nedelcu, AH and Borka-Balas, R and Anton, CR and Tarnita, I and Azoicai, A and Forna, L and Munteanu, D and Anton, SC and Shawais, SK and Badescu, MC and Salaru, DL and Morariu, ID and Anton, E and Petrariu, F and Lupu, A},
title = {The Gut Microbiota: An Essential Component in Understanding Pediatric Obesity: A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901128},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Pediatric Obesity/microbiology ; Child ; Dysbiosis/microbiology ; Probiotics ; },
abstract = {Background: Childhood obesity has become a major public health concern worldwide. Increasing evidence suggests that alterations in the gut microbiome may play a significant role in the development and progression of pediatric obesity. This narrative review synthesizes and analyzes recent studies investigating microbiome alterations in children with obesity, highlighting emerging insights and their potential implications for disease management. Understanding the relationship between gut microbial composition and obesity may provide new perspectives for prevention and therapeutic strategies in overweight pediatric populations. This narrative review was conducted through a search of major biomedical databases, including PubMed and Web of Science, complemented by manual screening of reference lists of relevant articles. Key findings: Children affected by obesity exhibit significant changes in gut microbiome composition, characterized by reduced microbial diversity and predominance of the Firmicutes and Bacteroidetes phyla. The balance between these two bacterial groups appears critical for maintaining gut homeostasis. Studies consistently report an increased Firmicutes-to-Bacteroidetes ratio in children with elevated body weight, suggesting that disruption of this balance may contribute to metabolic dysregulation and obesity-related pathologies. Given the essential role of the gut microbiota in nutrient metabolism and energy extraction, dysbiosis in obesity is associated with enhanced energy harvest and lipid absorption. Certain bacterial populations may promote increased caloric uptake, thereby contributing to weight gain and adiposity. Multidimensional interventions, including dietary modification and physical activity, have demonstrated the potential to reduce obesogenic microbiota patterns and restore microbial diversity. Additionally, probiotic supplementation is being investigated as a strategy to reestablish microbial homeostasis and potentially support body mass index reduction. Despite promising findings, further research is required to clarify mechanisms, establish causality, and determine the clinical effectiveness of microbiome-targeted therapies before they can be fully integrated into the management of pediatric obesity.},
}
@article {pmid41901151,
year = {2026},
author = {Green, GBH and Cox-Holmes, AN and Flowers, JT and Williams, MB and Potier, ACE and Brandom, JL and Watts, SA and Luke, R and Yu, JS and McFarland, BC},
title = {Dietary and Nutritional Strategies for Patients with Glioma: A Narrative Review of Treatment, Recovery, Immune Support, and Microbiota Modulation.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901151},
issn = {2072-6643},
support = {R01CA270750-01A1/CA/NCI NIH HHS/United States ; T32NS121721/NS/NINDS NIH HHS/United States ; },
mesh = {Humans ; *Glioma/therapy/immunology/microbiology/diet therapy ; *Gastrointestinal Microbiome ; *Brain Neoplasms/therapy/immunology/microbiology/diet therapy ; *Nutritional Support/methods ; Quality of Life ; *Diet ; Tumor Microenvironment ; Nutritional Status ; },
abstract = {This narrative review aims to explore the relationship between glioma and nutrition throughout stages of treatment and recovery. Gliomas are aggressive brain tumors that significantly impair quality of life and present treatment challenges. There has been a growing interest regarding the gut-brain axis and the microbiome, particularly their roles in modulating immune function and influencing the response to cancer treatment. This review examines how specific nutritional approaches may assist patients throughout the course of chemotherapy, radiation, immunotherapy, surgical intervention, and the recovery process. It also addresses the potential for integrative nutritional approaches to complement conventional treatment and improve clinical outcomes. Emerging evidence suggests that nutrition may influence immune function, treatment-related side effects, and the tumor microenvironment, in part through effects on the gut microbiota. Nutritional support during therapy has been linked to increased strength, decreased inflammation, and improved treatment tolerance. Dietary patterns may influence gut-brain interactions and systemic immune responses, opening the potential to improve therapeutic outcomes in glioma. In summary, nutrition may represent an important supportive component of glioma care, while microbiota-mediated and metabolic dietary strategies remain areas of active investigation. Further clinical studies are needed to determine whether specific nutritional interventions can improve survival, treatment response, or quality of life in patients with glioma.},
}
@article {pmid41901159,
year = {2026},
author = {Brăgaru, MA and Kraft, A and Moldovan, CA and Moldovan, AD and Răzvan, A and Cochior, D and Luca, A and Nica-Badea, D and Chirsanov Capanu, &#x218;E and Rusu, E},
title = {Optimizing Perioperative Nutrition in Elective Gastrointestinal Surgery: An ERAS-Focused Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901159},
issn = {2072-6643},
mesh = {Humans ; *Elective Surgical Procedures/adverse effects ; *Digestive System Surgical Procedures/adverse effects ; *Perioperative Care/methods ; *Malnutrition/prevention &amp; control ; Postoperative Complications/prevention &amp; control ; *Enhanced Recovery After Surgery ; Sarcopenia/prevention &amp; control ; *Nutritional Support/methods ; Nutritional Status ; Dietary Supplements ; },
abstract = {Background/Objectives: Perioperative malnutrition, sarcopenia, and reduced functional reserve are frequent in adults undergoing elective gastrointestinal (GI) surgery and are associated with higher postoperative morbidity and delayed recovery. Enhanced Recovery After Surgery (ERAS) pathways incorporate nutrition-focused elements, but reported effects vary across procedures, protocols, and baseline risk. This review aims to summarize and critically appraise current evidence on perioperative nutritional strategies within ERAS-focused elective GI care, including risk identification, nutritional prehabilitation (oral nutritional supplements and immunonutrition), preoperative carbohydrate loading, early postoperative feeding, and selected microbiome-directed adjuncts. Methods: This narrative literature review was informed by a focused search of PubMed/MEDLINE and Scopus (2010-early 2026), supplemented by targeted screening of relevant clinical practice guidelines and consensus statements (e.g., ESPEN). Evidence was interpreted by hierarchy (guidelines/meta-analyses, randomized trials, observational studies) and discussed with attention to heterogeneity in surgical populations, intervention definitions (composition, timing, duration), and endpoint reporting. Results: Early nutritional risk screening is consistently supported to identify malnutrition and sarcopenia and to trigger tailored optimization plans. Perioperative oral nutritional supplementation, particularly when started preoperatively and continued postoperatively, is frequently associated with improved intake and reduced infectious morbidity in malnourished or at-risk patients, though effect sizes vary. Immunonutrition shows potential benefit in selected high-risk settings but remains formulation- and timing-dependent. Carbohydrate loading is generally endorsed within ERAS and may reduce insulin resistance and improve patient comfort, while impacts on major clinical outcomes are context-dependent. Early oral/enteral feeding is feasible in many elective GI procedures and may accelerate gastrointestinal recovery without increasing major complications when implemented with structured advancement and appropriate patient selection. Probiotics/synbiotics show the most consistent signals in colorectal surgery, with strain-specific effects and important safety boundaries in immunocompromised or critically ill patients. Conclusions: Perioperative nutritional optimization is a core component of elective GI surgical care within ERAS pathways. Benefits are most reproducible in higher-risk patients and when interventions are integrated into high-compliance multidisciplinary programs. Future research should prioritize procedure-specific, risk-stratified trials with standardized interventions and clinically meaningful endpoints.},
}
@article {pmid41901182,
year = {2026},
author = {Silverstein, HR and Rizvanov, AA and Haines, DD and Mahmoud, FF and Rose, SC and Solovyeva, VV and Kitaeva, KV and Tosaki, A},
title = {The Simultaneous Prevention of Multiple Diseases: A "One Ring to Rule Them All" Framework for Redox-Driven Health and Longevity.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901182},
issn = {2072-6643},
support = {A.A.R., V.V.S. and K.V.K. were supported by the Kazan Federal University Strategic Academic Leadership Program (PRIORITY-2030)//Ministry of Science and Higher Education of the Russian Federation/ ; This study was also supported by the HUN-REN-DE//Hungarian Research Network/ ; },
mesh = {Humans ; Oxidation-Reduction ; *Longevity ; Oxidative Stress ; Antioxidants ; Dietary Supplements ; *Noncommunicable Diseases/prevention &amp; control ; Cardiovascular Diseases/prevention &amp; control ; Diet ; },
abstract = {Chronic non-communicable diseases rarely occur in isolation; cardiovascular, metabolic, neurodegenerative, malignant, and age-associated disorders share upstream drivers including oxidative stress, chronic inflammation, mitochondrial dysfunction, and metabolic imbalance. This narrative review synthesizes epidemiological, interventional, and mechanistic studies identified through targeted literature searches to examine redox biology as a shared mechanistic hub linking these conditions. We evaluate antioxidant-rich dietary patterns, selected nutraceuticals, myocardial ischemia-reperfusion injury as a clinical exemplar, rare redox-imbalance disorders as mechanistic stress models, and emerging gene-based reinforcement of endogenous antioxidant systems. Rather than proposing clinical targets, we present an integrative, hypothesis-generating framework illustrating how coordinated lifestyle-driven modulation of redox balance may simultaneously influence multiple disease trajectories. Collectively, the evidence supports a unified redox framework for multi-disease prevention for multi-disease prevention and future intervention design.},
}
@article {pmid41901189,
year = {2026},
author = {Witt, BL and Singaravelan, N and Tollefsbol, TO},
title = {Combined Effects of Withaferin A and Sodium Butyrate on NF-κB Signaling and Epigenetic Regulation in Breast Cancer Cells.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901189},
issn = {2072-6643},
support = {R01CA178441//Natrional Institutes of Health/ ; },
mesh = {Humans ; *Withanolides/pharmacology ; *Epigenesis, Genetic/drug effects ; *Signal Transduction/drug effects ; Female ; *Butyric Acid/pharmacology ; *NF-kappa B/metabolism/genetics ; Cell Line, Tumor ; *Breast Neoplasms/genetics/drug therapy/metabolism ; Cell Survival/drug effects ; Gene Expression Regulation, Neoplastic/drug effects ; MCF-7 Cells ; Triple Negative Breast Neoplasms/drug therapy/genetics ; },
abstract = {Background/Objectives: There is a clear need for more options to control the progression of breast cancer and prevent the occurrence of breast cancer in minority populations that have a higher rate of mortality due to triple-negative breast cancer (TNBC) subtypes. Prevalent nutraceuticals such as Ashwagandha (also known as the Indian Winter Cherry) have anti-inflammatory and apoptotic capabilities, as well as the ability to inhibit cancer growth. The purpose of this study is to analyze the novel combination of withaferin A (derived from the Indian Winter Cherry and known to have histone deacetylase inhibition capabilities) and sodium butyrate (a short-chain fatty acid produced from the gut microbiome and known to have DNA methyltransferase inhibition capabilities) treatment on breast cancer-derived cell lines. There is a scientific gap of possible causality of decreasing breast cancer progression when treated with sodium butyrate and withaferin A. Methods: Two in vitro cell viability assays were utilized consisting of [MTT (4,5 Dimethylthiazol-2-yl)] and the neutral red assay to analyze the impact of treatment of compounds alone and in combination on breast cancer cells for 72 h. The Highest Single Agent (HSA) combination analysis was utilized to derive combination indexes for our breast cancer cell types. Protein and gene expression was investigated for Class 1 histone deacetylases, de novo DNA methyltransferase, the p65 subunit of NF-κB, and NFκB1. Lastly, DNA methyltransferase enzymatic activity was analyzed via the Epigentek DNMT Activity/Inhibition ELISA Easy Kit. Results: Through the cell viability assay [MTT (4,5 Dimethylthiazol-2-yl)], MCF-7, MDA-MB-231, and MDA-MB-157 cells were found to have a decrease in cell viability due to combinatorial treatment with withaferin A and sodium butyrate. Western blot results depicted a decrease in protein expression levels for DNA methyltransferases due to the administration of 2.5 mM sodium butyrate and 0.2 µM withaferin A alone and in combination for breast cancer cell lines MCF-7, MDA-MB-231, and MDA-MB-157. Additionally, the combination of these two components have successfully inhibited the progression of the NFκB1 gene within analysis through the quantitative polymerase chain reaction (qPCR). Conclusions: The novel combination of withaferin A and sodium butyrate have markedly reduced the progression of breast cancer-derived cell lines for cell viability, epigenetic DNMT gene expression, as well as inhibiting NFκB1 signaling on the gene expression level.},
}
@article {pmid41901191,
year = {2026},
author = {Di Maio, G and Tafuri, MG and Casillo, M and Messina, A and Allocca, S and Villano, I and Moscatelli, F and Monda, A and La Marra, M and Monda, V},
title = {Physiological Regulation of Nutritional and Metabolic Biomarkers in Obesity: Implications for Precision Nutrition.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901191},
issn = {2072-6643},
mesh = {Humans ; *Biomarkers/blood/metabolism ; *Obesity/metabolism/physiopathology ; *Precision Medicine ; *Nutritional Status ; Adipokines/blood ; Gastrointestinal Microbiome ; Insulin Resistance ; },
abstract = {Obesity represents a heterogeneous metabolic disorder characterized by substantial interindividual variation in inflammatory status, insulin sensitivity, and cardiometabolic risk. Traditional anthropometric measures fail to capture this metabolic diversity, limiting risk stratification and personalized intervention strategies. This review critically examines nutritional and metabolic biomarkers that reflect the physiological dysregulation underlying obesity, including adipokines (leptin, adiponectin, resistin), inflammatory markers (C-reactive protein, interleukin-6, TNF-α), insulin resistance indices (HOMA-IR, fasting insulin, HbA1c), and lipid metabolism indicators (LDL cholesterol, triglycerides, HDL cholesterol, and liver enzymes such as ALT and GGT). Among these, elevated CRP, reduced adiponectin, and increased HOMA-IR have demonstrated the strongest clinical utility for early metabolic risk identification. We further evaluate emerging biomarkers-including circulating microRNAs, gut microbiota-derived metabolites (short-chain fatty acids, TMAO, lipopolysaccharides), and bile acid profiles-which offer additional mechanistic insight into diet-microbiome-host interactions. We systematically assess the mechanistic basis, clinical relevance, and nutritional modulation of each biomarker class, emphasizing how dietary composition-particularly fatty acid quality, fiber intake, and overall dietary patterns such as the Mediterranean diet-influences biomarker profiles and metabolic outcomes. Furthermore, we explore how biomarker-based phenotyping enables precision nutrition approaches by identifying individuals most likely to benefit from specific dietary interventions. Integration of multi-biomarker panels with clinical and genetic data holds promise for advancing from population-based dietary guidelines toward individualized nutrition strategies that optimize metabolic health and prevent obesity-related complications. Future research should prioritize validating biomarker-guided intervention frameworks, establishing standardized thresholds across diverse populations, and developing clinically implementable tools for personalized nutritional medicine.},
}
@article {pmid41901195,
year = {2026},
author = {Xiong, H and Ji, S and Ding, Q and Zhou, Y and Yao, X and Zhu, Y},
title = {The Impact of Seasonal and Meteorological Factors on Microorganisms Present in Knee Joint Effusions Among Patients with Rheumatoid Arthritis.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {3},
pages = {},
pmid = {41901195},
issn = {1424-8247},
support = {the Macau Science and Technology Development Fund (FDCT (0012/2021/AMJ, 003/2022/ALC,0092/2022/A2, 0144/2022/A3)).The National Natural Science Foundation of China (No. 81973320,No.82160869). Shenzhen-HongKong-Macao Science and Technology Fund (Category C://the Macau Science and Technology Development Fund&#x3001;The National Natural Science Foundation of China&#x3001;Shenzhen-HongKong-Macao Science and Technology Fund&#x3001;University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention/ ; },
abstract = {Background/Objectives: Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by persistent synovial inflammation and vascular abnormalities. Emerging evidence suggests that dysbiosis of the microbiome contributes to the pathogenesis of this disease, while seasonal and meteorological variations represent significant factors influencing microbial community dynamics. However, the specific pathological mechanisms mediated by microbial populations within knee joint effusions of RA patients remain poorly elucidated. The present study employs 16S rRNA high-throughput sequencing technology to characterize seasonal variation patterns affecting microbial communities in knee joint effusions of RA patients and to investigate the relationship between microbial community structures and climatic lag effects. Methods: Microbial communities in knee joint effusion samples obtained from RA patients were analyzed using 16S rRNA high-throughput sequencing methodologies. A Distributed Lag Non-linear Model (DLNM) was applied to quantify the delayed effects of climatic variables on microbial community composition. The correlation patterns between meteorological parameters and community structure were elucidated through the integration of ridge regression and redundancy analysis (RDA). Preliminary identification of potential biomarkers was conducted using random forest algorithms. Results: According to research findings, the microbial composition of knee joint effusions in RA patients shows seasonal fluctuation patterns that are compatible with those seen in RA patients, even though there is no discernible seasonal change in β-diversity. Compared with samples obtained during other seasons, spring specimens exhibited significantly elevated relative abundances of both beneficial microorganisms and opportunistic pathogenic taxa. Random forest modeling identified Escherichia-Shigella and Curtobacterium as preliminary candidate biomarkers; however, external validation is required to establish their specificity as disease indicators. Further analysis revealed that although short-term meteorological fluctuations exert minimal influence on overall microbial diversity, specific alterations in mean wind speed (MWS) and relative humidity (RH) drive compositional changes in the microbial community, manifested as rapid responses from dominant bacterial taxa and compensatory buffering effects from rare taxa. Conclusions: This study suggests that the synovial cavity microbiota in RA patients may exhibit seasonal variation patterns that are statistically associated with environmental parameters, particularly humidity and temperature. Due to the inherent limitations of the cross-sectional study design, the preliminary candidate biomarkers identified herein require validation through external cohorts. Additional investigations incorporating healthy controls and osteoarthritis (OA) cohorts are necessary to confirm specificity and to elucidate the therapeutic potential of these microbial targets for RA microbiome interventions. Currently, insufficient evidence exists to establish causal relationships among microbial populations, joint pathology, and climatic factors. Longitudinal cohort studies are imperative to validate the temporal dynamics and clinical significance of these associations.},
}
@article {pmid41901248,
year = {2026},
author = {Xue, X and Zhang, F and Wang, H and Guo, M and Qin, W and Yang, Y and Huo, Z and Li, X and Han, Q and Li, X},
title = {Si-Wu-Tang Targets Microbiota Homeostasis and Intestinal Mucosal Barriers to Provide Protection Against MASLD by Favoring P. goldsteinii-like Taxa Colonization.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {3},
pages = {},
pmid = {41901248},
issn = {1424-8247},
support = {ZYGXQNJSKYCXNLZCXM-H4//Scientific Research Innovation Capability Support Project for Young Faculty/ ; 2022YFC3502100//National Key Research and Development Program on Modernization of Traditional Chinese Medicine/ ; 2023-JYB-JBZD-046//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Objective: This study examined the pharmacological mechanisms of the therapeutic benefits of SWT to MASLD via regulating the gut-liver axis. Methods: The components of SWT were analyzed by liquid chromatograph mass spectrometer (LC-MS). After establishing an MCD-induced MASLD mice model, we invested the protective mechanism of SWT through 16S rRNA sequencing combined with molecular biological experiments. After eliminating the intestinal microbiota through an antibiotic cocktail experiment, we identified the key microbiota by which SWT improves MASLD. Results: SWT markedly reduced MASLD injury by alleviating intestinal inflammation and restoring the intestinal mucosal barrier, which could be reversed following alcohol exposure. Additionally, SWT altered the intestinal flora of MASLD mice, significantly raising the relative abundance of Parabacteroides goldsteinii-like taxa, while alcohol caused the destruction of P. goldsteinii-like-taxa-centered probiotic habitats and a proliferation of pathogenic bacteria, especially Bacteroides intestinalis-like taxa. After the elimination of intestinal flora, the anti-MASLD effect of SWT was lost. Moreover, the supplement of P. goldsteinii could significantly ameliorate liver damage caused by an MCD diet, functioning similarly to SWT. However, the liver-protective effect of SWT was suppressed following the administration of B. intestinalis. Conclusions: SWT ameliorates MCD diet-induced MASLD via modulating intestinal microbiota homeostasis and restoring intestinal mucosal barriers. Given that P. goldsteinii is effective for treating MASLD, it provides insights into new therapeutic strategies.},
}
@article {pmid41901456,
year = {2026},
author = {Tian, S and Zhang, N and Lin, G and Cheng, X and Wang, F and Chang, P and Ahammed, GJ and Shi, Q and Nie, WF and Zhang, Y},
title = {Epigenetic Regulation of Root-Associated Microbiota: Mechanisms and Horticultural Applications.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
pmid = {41901456},
issn = {2223-7747},
abstract = {The dynamic interaction between plants and their root-associated microbiota represents a sophisticated and profound biological communication that regulates plant development and the formation of adaptation to the surrounding environment. These interactions function as critical regulators of multiple physiological processes, finally influencing soil fertility and agricultural productivity. Plants have evolved epigenetic networks that regulate beneficial plant-microbe interactions through regulating immune responses, gene regulation, and metabolite production to enhance stress tolerance and soil adaptation. These regulations collectively govern microbial colonization patterns while establishing reciprocal feedback loops through root exudate-microbe interactions. This review systematically updates contemporary advances in understanding how epigenetic modifications shape rhizosphere microbiome composition and function, and discusses their potential applications in enhancing the yield and quality of horticultural crops, as well as in mitigating continuous cropping obstacles.},
}
@article {pmid41901493,
year = {2026},
author = {Curci, LM and Carrozzo, S and Pecatelli, G and Semeraro, T and Tafuro, C and Lenucci, MS and De Caroli, M},
title = {Environmental and Cultivation Effects on Growth and Phytochemical Profiles of Chicory (Cichorium intybus L.) in Soil, Hydroponics, and Aquaponics.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
pmid = {41901493},
issn = {2223-7747},
abstract = {The increasing demand for sustainable food production has intensified interest in controlled-environment agriculture and soilless cultivation systems. This study evaluated the performance of local chicory (Cichorium intybus L., cultivar "Otrantina") grown for 45 days in soil, hydroponics, and decoupled aquaponics under two different environments: a fully controlled growth chamber and a naturally variable greenhouse. Morphological, anatomical, biochemical, and physiological traits were analyzed to assess the combined influence of growth environment and cultivation system on plant development and nutritional quality. Across all parameters, the growth environment emerged as the main driver of plant performance. Greenhouse-grown plants exhibited greater leaf expansion, enhanced mesophyll and vascular development, and higher fresh and dry biomass than those cultivated in the growth chamber. Within each environment, hydroponics consistently supported vigorous growth, whereas aquaponics produced smaller leaves and pronounced root elongation, likely reflecting nutrient and pH instability in the decoupled system. Biochemical analyses revealed system-specific adaptive responses. Soilless cultivation promoted higher lipid accumulation and, under growth chamber conditions, increased protein content. Aquaponically grown plants, particularly in the greenhouse, accumulated elevated levels of soluble sugars and phenolic antioxidants, consistent with stress-related metabolic activation. In contrast, soil-grown plants displayed the highest flavonoid concentrations, suggesting a prominent role of rhizosphere-microbiome interactions in modulating secondary metabolism. Overall, these results indicate that, under the tested conditions, environmental control exerts a stronger influence than cultivation systems on chicory growth and metabolism. Hydroponics proved to be the most efficient system for biomass production, whereas aquaponics requires improved nutrient management to ensure stable growth and quality. The distinct metabolic profiles associated with each cultivation system highlight opportunities to tailor chicory nutraceutical traits within sustainable controlled-environment agriculture.},
}
@article {pmid41901497,
year = {2026},
author = {Liang, A and Wang, F and Liu, T and Liao, Y and Mu, Z},
title = {Habitat Filtering Shapes Root Endophytic Microbiome Assembly and Its Association with Fruit Quality in Lycium ruthenicum from the Tarim Basin.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
pmid = {41901497},
issn = {2223-7747},
support = {no. 32160390//the National Natural Science Foundation of China/ ; no. 524307001//the Tianchi Talents-Innovative Leaders of Xinjiang/ ; no. TDZKBS202206//the President's Fund of Tarim University/ ; },
abstract = {Lycium ruthenicum is a typical desert halophyte with strong stress resistance and high medicinal value in the Tarim Basin. Root endophytic microbes play critical roles in host adaptation, nutrient cycling, and secondary metabolite accumulation. To clarify the diversity patterns of root endophytic bacteria and fungi and their relationships with environmental factors and fruit quality, high-throughput sequencing was used to analyze microbial community characteristics of Lycium ruthenicum collected from different habitats in the Tarim Basin. The results showed that rarefaction curves of alpha diversity indices (Chao1, Shannon, Pielou_e) tended to be saturated, indicating sufficient sequencing depth. Principal coordinate analysis (PCoA) revealed significant habitat-driven differentiation in both bacterial and fungal community structures. Community composition analysis showed that the relative abundance of dominant taxa at the phylum and genus levels differed significantly among sampling sites. Co-occurrence network analysis indicated that bacterial and fungal networks exhibited high modularity and were dominated by positive synergistic interactions, with Pseudomonas, Bacillus, Sphingomonas, Alternaria, and Fusarium as key hub genera. Moreover, root endophytic communities were significantly correlated with climatic variables, soil physicochemical properties, and fruit quality traits, including anthocyanin (AC), proanthocyanidin (PA), total flavonoids (TF), and total polyphenols (TP). Several keystone microbial genera were closely associated with the accumulation of functional metabolites in fruits. This study reveals the biogeographic distribution and co-occurrence characteristics of root endophytes in Lycium ruthenicum and provides a theoretical basis for understanding microbe-host-environment interactions and the quality improvement of desert medicinal plants.},
}
@article {pmid41901529,
year = {2026},
author = {Bečić, T and Jukić, I and Prižmić, P&#x160; and Matulić, I and Đogaš, H and Radić, M and Radić, J and Vuković, J and Fabijanić, D},
title = {Heart-Gut Axis in Cardiometabolic Disease: Microbiome-Mediated Pathways Linking Metabolic Syndrome to Cardiovascular Risk.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {3},
pages = {},
pmid = {41901529},
issn = {1648-9144},
mesh = {Humans ; *Metabolic Syndrome/complications/physiopathology/microbiology ; *Gastrointestinal Microbiome/physiology ; *Cardiovascular Diseases/physiopathology/etiology/microbiology ; Dysbiosis/complications ; Cardiometabolic Risk Factors ; },
abstract = {Background and Objectives: Cardiometabolic disease, a term encompassing metabolic syndrome (MS) and cardiovascular disease (CVD), represents a major and growing global health burden driven by interconnected metabolic and cardiovascular dysfunction. Emerging evidence suggests that the gut microbiota plays a central role in modulating metabolic, inflammatory, and cardiovascular (CV) pathways, giving rise to the concept of the heart-gut axis. However, human evidence integrating microbiome-mediated mechanisms across the cardiometabolic spectrum remains incompletely synthesized. This focused systematic review aimed to synthesize the current human evidence on microbiome-mediated mechanisms linking metabolic syndrome (MS) and related metabolic phenotypes with cardiovascular risk (CVR) and subclinical cardiovascular (CV) outcomes within the conceptual framework of the heart-gut axis. Materials and Methods: A systematic literature search was conducted in PubMed, Scopus, Web of Science, and the Cochrane Library in accordance with PRISMA 2020 guidelines. Human observational and interventional studies evaluating gut microbiota composition, function, or microbiota-derived metabolites in relation to cardiometabolic, and CV outcomes were included. Risk of bias was assessed using the Cochrane RoB 2 and ROBINS-I tools, and findings were synthesized narratively. Results: Ten human studies published between 2016 and 2025 met the inclusion criteria. Across these studies, gut dysbiosis was consistently associated with adverse cardiometabolic risk profiles and subclinical CV outcomes, including insulin resistance, systemic inflammation, subclinical atherosclerosis, and CV prognosis in high-risk populations. Microbiota-derived metabolites, particularly trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFAs), as well as emerging metabolites such as phenylacetylglutamine (PAGln) and imidazole propionate (ImP), were identified as key mediators linking metabolic syndrome and related metabolic disturbances with CVR and subclinical cardiovascular disease (CVD). Markers of intestinal barrier dysfunction and endotoxemia further supported the role of chronic low-grade inflammation within the heart-gut axis. Conclusions: Current human evidence supports the heart-gut axis as a biologically plausible and clinically relevant contributor to cardiometabolic disease. Gut microbiota-derived metabolites, intestinal barrier dysfunction, and systemic inflammation represent interconnected pathways linking MS with CVR. Advancing our understanding of these mechanisms may inform the development of microbiome-targeted strategies to complement established approaches for cardiometabolic and CV prevention.},
}
@article {pmid41901547,
year = {2026},
author = {Theofilis, P and Iliakis, P and Karanikola, AE and Botis, M and Mavromoustakou, K and Xydis, P and Ktenopoulos, N and Karakasis, P and Leontsinis, I and Chrysohoou, C and Tsioufis, K},
title = {Pleiotropic Effects of Cardiac Resynchronization Therapy on Cardiometabolic Modulation in Heart Failure.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {3},
pages = {},
pmid = {41901547},
issn = {1648-9144},
mesh = {Humans ; *Heart Failure/therapy/physiopathology/metabolism ; *Cardiac Resynchronization Therapy/methods/standards ; Energy Metabolism/physiology ; },
abstract = {Cardiac resynchronization therapy (CRT) is a cornerstone intervention for patients with heart failure (HF) and electrical dyssynchrony, improving quality of life, functional capacity, and survival. Beyond mechanical synchrony, mounting evidence suggests CRT exerts systemic and myocardial cardiometabolic benefits. CRT acutely enhances mechanical efficiency and shifts substrate utilization toward greater oxidation of fatty acids and ketones, effects that correlate with long-term reverse remodeling on cardiac magnetic resonance imaging. Earlier metabolomic profiling demonstrated that CRT normalizes circulating energy metabolites, improving Krebs cycle intermediates and substrate balance between glucose and lipids, while baseline metabolite patterns may differentiate responders from non-responders. These metabolic adaptations accompany favorable changes in diastolic performance, right ventricular function, and ventriculo-arterial coupling. In parallel, improved splanchnic perfusion and reduced congestion may ameliorate gut dysbiosis and endotoxemia, mitigating systemic inflammation. Collectively, these findings position CRT as a therapy capable of both mechanical and metabolic restoration in advanced HF. In this review, we discuss the emerging data on how CRT reconditions myocardial energy metabolism, influences ventricular-arterial interactions, and modulates peripheral and gut-derived metabolic pathways.},
}
@article {pmid41901695,
year = {2026},
author = {Philips, CA and Oommen, TT and Theruvath, AH and Sreemohan, A and Baby, A and Alex, AA and Thomas, S and John, SM and Ahamed, R and Tharakan, A and Augustine, P},
title = {Novel Insights on Clinical Outcomes Using Integrated Shotgun Metagenomic Profiling of the Gut Microbiome, Resistome, and Host Immune-Inflammatory Response in Hospitalized Patients with Decompensated Cirrhosis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41901695},
issn = {2076-0817},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Liver Cirrhosis/microbiology/immunology/mortality ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; Aged ; Hospitalization ; Adult ; India ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Background and Aims: Sepsis drives mortality in cirrhosis, yet the gut antimicrobial resistance (AMR) landscape remains unmapped in high-burden settings like India. This study aimed to integrate shotgun metagenomics with deep immunophenotyping to define the gut-immune-resistome axis and correlate specific microbial and genetic signatures with clinical outcomes in decompensated cirrhosis. Methods: We analysed 78 hospitalized patients with cirrhosis using stool shotgun metagenomics, multiplex cytokine arrays, and flow cytometry. The microbiome and resistome (AMR genes) were mapped and correlated with disease severity, immune function (monocyte HLA-DR, neutrophil CD64), and clinical endpoints including mortality. Results: Disease severity was characterized by a "Gram-negative bloom" (Klebsiella) alongside pathogenic Enterococcus expansion and novel markers: Clostridium sp. C5-48 (severe decompensation) and Sutterella (ascites). A specific, dense resistome predicted adverse outcomes; the quinolone-resistance gene QnrB4 correlated with mortality and immune paralysis, while the carbapenemase OXA-833 gene was linked to gastrointestinal bleeding. Notably, the commensal Ligilactobacillus salivarius was associated with systemic inflammatory cytokines. Conclusions: This study reveals a "pathogenic ecosystem" in Indian decompensated cirrhosis where the resistome is intrinsically linked to host immune failure. The identification of specific prognostic markers (QnrB4, OXA-833) and inflammatory associations with L. salivarius challenges generic probiotic use and underscores the urgent need for precision, resistome-targeted therapies.},
}
@article {pmid41901728,
year = {2026},
author = {Mougiou, D and Gioula, G and Skoura, L and Minti, F and Karampatakis, T and Malandris, D and Pelekoudas, K and Kachrimanidou, M},
title = {Characterization of the Gut Microbiome of Patients with Clostridioides difficile Infection and Healthy Individuals in Greece.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41901728},
issn = {2076-0817},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Clostridium Infections/microbiology ; Middle Aged ; Greece ; Aged ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Clostridioides difficile/genetics ; Adult ; Feces/microbiology ; Aged, 80 and over ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND/OBJECTIVES: The gut microbiome plays an important role in the colonization of an individual by Clostridioides difficile and in the development of Clostridioides difficile infection (CDI). The main purpose of this study was to compare the gut microbiomes of patients with CDI and healthy individuals.<br><br>METHODS: We prospectively included 48 individuals: 32 patients with CDI and 16 healthy individuals. Microbiomes were analyzed by sequencing the hypervariable regions of the 16S rRNA gene using an Ion GeneStudio&#x2122; S5 System. Further statistical analysis of microbiome data was performed with the open-source programming language R version 3.5.2.<br><br>RESULTS: Among the CDI patients, Firmicutes and Proteobacteria were the most abundant phyla, while Enterobacteriaceae and Enterococcaceae were the most abundant families. Genus-level analysis showed that Enterococcus was the dominant genus in CDI patients; in contrast, in healthy individuals, Faecalibacterium was the most abundant. The MaAsLin2 tool revealed that members of the family Enterococcaceae and the genus Enterococcus were more abundant in patients with CDI than in healthy individuals. Alpha and beta diversity did not reveal differences between the two study groups.<br><br>CONCLUSIONS: We observed differences in microbiome patterns between healthy individuals and CDI patients that were consistent with the literature. Further studies are needed.},
}
@article {pmid41901740,
year = {2026},
author = {Pazmiño-Gomez, B and Rodas-Pazmiño, K and Pazmiño-Pérez, R and Tapia-Guijarro, T and Balcazar-Quimi, W and Valle-Asan, S and Salazar-Vera, S and Villalva-Vera, M and Ochoa-Fajardo, D and Rodas-Neira, E},
title = {Native Bacillus-Based Probiotic Consortia Suppress Vibrio parahaemolyticus and Restructure Hatchery Water Microbiomes in Shrimp Larval Systems.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41901740},
issn = {2076-0817},
mesh = {*Probiotics/pharmacology/administration &amp; dosage ; Animals ; *Vibrio parahaemolyticus/drug effects ; *Bacillus/physiology ; *Penaeidae/microbiology/growth &amp; development ; *Microbiota ; Larva/microbiology ; Aquaculture/methods ; Water Microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Shrimp aquaculture is constrained by opportunistic bacterial pathogens, particularly Vibrio parahaemolyticus, whose proliferation in hatchery systems is shaped by microbial community structure. We evaluated the antagonistic activity and microbiome effects of two native Bacillus-based probiotic consortia (CN5, RS3) applied alone or combined (MIX) in shrimp larval culture water over 30 days, relative to a no-probiotic control. Treatments were assessed using standardized in vitro inhibition assays, 16S rRNA gene (V3-V4) amplicon sequencing, functional inference, and integrative multivariate and structural modeling. All probiotic treatments showed consistently high antagonistic activity against V. parahaemolyticus, whereas the control showed no inhibition. Amplicon profiling indicated treatment-associated microbiome restructuring, with increased Bacillus dominance and reduced relative abundance of Vibrio spp. under probiotic conditions. Multivariate analyses separated probiotic and control groups, and PLS-SEM identified Bacillus dominance as a central driver of antagonistic activity mediated by inferred bioactive functional potential, while water-quality variables had limited direct effects. Probiotics were administered directly to the culture water once daily after routine water exchange to 1 × 10[6] CFU mL[-1] (CN5 or RS3); MIX was applied 1:1 (v/v) at the same total dose.},
}
@article {pmid41901742,
year = {2026},
author = {Kavvada, A and Gioula, G and Protopapas, A and Protopapas, AA and Christoforidi, M and Minti, F and Savopoulos, C and Chatzidimitriou, M},
title = {Characterization of the Gastric Antrum Microbiome in Helicobacter pylori-Negative Individuals: Insights from a Greek Population Using 16S rRNA Next-Generation Sequencing.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41901742},
issn = {2076-0817},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; Greece ; Female ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Helicobacter pylori ; *Pyloric Antrum/microbiology ; *Gastrointestinal Microbiome/genetics ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Helicobacter Infections/microbiology ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: Once considered a sterile organ, the human stomach is now known to harbor a diverse microbial community that may influence both gastric homeostasis and disease. While extensive research has been conducted worldwide, regional variation in the gastric microbiome remains insufficiently characterized. This study aimed to describe the gastric antrum microbiome of Helicobacter pylori-negative Greek adults using 16S rRNA next-generation sequencing (NGS).<br><br>METHODS: Samples of gastric biopsies were obtained from patients undergoing gastroscopy at a tertiary hospital in Greece. H. pylori infection was excluded through a combination of bacterial culture and patient medical history. The final study group consisted of 9 subjects. Following DNA extraction, the 16S rRNA gene was sequenced on the Ion Torrent&#x2122; platform. Bioinformatic processing and statistical analyses were performed using the phyloseq, vegan, and ggplot2 R packages. Microbial composition, relative abundance, and alpha diversity (Shannon and Inverse Simpson indices) were evaluated at the genus level.<br><br>RESULTS: The gastric microbiome comprised 19 phyla, 150 families, 213 genera, and 391 species. The predominant phyla were Proteobacteria (36.92%), Firmicutes (34.21%), and Bacteroidetes (12.97%). The most prevalent families were Streptococcaceae, Helicobacteraceae, Prevotellaceae, and Pasteurellaceae. At the genus level, Streptococcus (21.71%), Helicobacter (18.39%), and Prevotella (9.99%) accounted for nearly half of the total relative abundance. Alpha diversity indices indicated moderate richness and evenness across samples.<br><br>CONCLUSIONS: The gastric antrum microbiome of H. pylori-negative Greek individuals exhibits substantial taxonomic diversity dominated by Proteobacteria and Firmicutes. The microbial community structure aligns closely with profiles reported in other global populations. These findings provide a reference baseline for future comparative analyses involving H. pylori-positive individuals to better understand microbiome shifts associated with colonization and gastric disease.},
}
@article {pmid41902183,
year = {2026},
author = {Cardoso, MA and Vieira, CSD and Moreira, ICF and Saraiva, FMS and Brito, IAA and Gandara, ACP and Menna-Barreto, RFS and Oliveira, PL and Paes, MC and Pane, A},
title = {Rhodnius prolixus Viruses Interfere with Proliferation and Metacyclogenesis of the Chagas Disease Agent Trypanosoma cruzi.},
journal = {Viruses},
volume = {18},
number = {3},
pages = {},
pmid = {41902183},
issn = {1999-4915},
support = {428100/2018-0//National Council for Scientific and Technological Development (CNPq)/ ; E-26/210.339/2024//the Research Support Foundation of the State of Rio de Janeiro/ ; },
mesh = {*Trypanosoma cruzi/virology/growth &amp; development ; Animals ; *Rhodnius/virology/parasitology ; *Chagas Disease/parasitology/transmission ; Insect Vectors/virology/parasitology ; },
abstract = {The protozoan Trypanosoma cruzi is the etiological agent of Chagas disease, a neglected tropical disease that mostly affects the population of Latin American countries, with an estimated 7 million infected people and more than 10,000 deaths per year worldwide. T. cruzi is typically transmitted by hematophagous triatomine insects, with Rhodnius prolixus being a major insect vector in South America. While the microbiome of triatomine insects has been investigated to a certain extent, the ternary interaction between triatomes insects, T. cruzi, and viruses remains virtually unexplored. In this study, we show by transmission electron microscopy and by RT-PCR that Rhodnius prolixus viruses (RpVs) can infect the intestine of R. prolixus, which places them in close contact with the gut microbiota. These observations suggest that T. cruzi can be infected by the insect viruses while transiting through the gut. Here, we show that the RpVs are capable of infecting the epimastigote forms of T. cruzi in vitro and maintain the viral load stabilized for 3 to 7 days after infection. We also show that, at least in the case of the iFlavirus RpV1, viral genomes are detectable in the T. cruzi cytoplasm. Interestingly, R. prolixus ovarian extracts enriched with RpVs decrease epimastigote proliferation and their capacity for differentiation into the ineffective metacyclic trypomastigotes in vitro. Our results start to shed light on the interaction between RpVs and T. cruzi, suggesting possible routes of infection and unveiling a role for viral infections in the development of this important pathogen.},
}
@article {pmid41902219,
year = {2026},
author = {Wang, X and Zhang, J and Chen, J and Huang, Q and Duan, X and Zhu, W},
title = {The Role of Viral Infection and Microbial Dysbiosis in Glaucoma: From Pathogenesis to Therapeutic Strategies.},
journal = {Viruses},
volume = {18},
number = {3},
pages = {},
pmid = {41902219},
issn = {1999-4915},
support = {Grant No. 82471079//the National Natural Science Foundation of China/ ; Grant No. 82501363//the Young Scientists Fund of the National Natural Science Foundation of China/ ; Grant No. 22507154//the Young Scientists Fund of the National Natural Science Foundation of China/ ; Grant No. kq2502222//the Changsha Municipal Natural Science Foundation of China/ ; Grant No. 2025M772429//the Science Foundation for Post Doctorate Research of the Ministry of Science and Technology of China/ ; Grant No. AMF2406D01//the Science and Technology Foundation of Aier Eye Hospital Group of China/ ; },
mesh = {*Dysbiosis/microbiology/complications/therapy ; Humans ; *Glaucoma/microbiology/therapy/virology/etiology ; Animals ; *Virus Diseases/complications ; Gastrointestinal Microbiome ; },
abstract = {Glaucoma is a leading cause of irreversible blindness, yet vision loss often progresses despite effective intraocular pressure (IOP) control, suggesting the involvement of non-hydrodynamic mechanisms. This review explores the potential synergistic interaction between viral persistence and microbial dysbiosis in pathogenesis. While acknowledging that current evidence regarding the microbiome is largely associative and derived from small cohorts or animal models, we analyze how these environmental insults may disrupt autophagic flux and induce immune dysregulation to drive chronic neuroinflammation. Furthermore, we explore theoretical therapeutic strategies targeting this distinct pathological nexus, ranging from metabolic restoration of the