@article {pmid41785450,
year = {2026},
author = {Sun, QQ and Bao, MY and Gao, R and Wang, SK and Zhang, Y and Wang, LB and Zhang, Y and Li, X},
title = {Advances in Understanding Lipid Metabolism in Oligodendrocyte Development and Neurodegenerative Diseases.},
journal = {Clinical science (London, England : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1042/CS20258150},
pmid = {41785450},
issn = {1470-8736},
support = {82471421,82271199,82571568//National Natural Science Foundation of China/ ; 23JHQ057//Scientific Research Program Funded by Education Department of Shaanxi Provincial Government/ ; GK202501001, GK202505004//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Lipids are indispensable architectural and functional components of central nervous system (CNS) myelin, with cholesterol, sphingolipids, and phospholipids collectively constituting 70-80% of myelin membrane composition. Oligodendrocytes (OLs), the sole myelin-producing cells in the CNS, exhibit exquisite metabolic specialization to sustain lifelong myelination and remyelination. Mounting evidence implicates lipid metabolic dysregulation-spanning cholesterol efflux defects, sphingolipid imbalance, and peroxisomal dysfunction-as a convergent mechanism underlying OL differentiation failure and progressive demyelination in neurodegenerative diseases. This review explores the role of lipid metabolic rewiring in governing oligodendrocyte precursor cells (OPCs) fate determination, highlighting three crucial axes: the interplay between mitochondria and peroxisomes in lipid biosynthesis, the potential toxicity of accumulated myelin debris in the microenvironment, and the regulation of OPC differentiation through lactylation modification on lipid metabolism and the interaction between glycolipid metabolisms. We further synthesize emerging therapeutic strategies targeting these pathways, including immunometabolism modulators, precision lipid interventions; diet-microbiome synergies: ketogenic diets combined with butyrate-producing probiotics to amplify endogenous remyelination. By integrating lipidomics datasets and recent clinical trial evidence, we propose a shift from broad metabolic suppression to spatially resolved modulation of lipid flux. This synthesis not only clarifies the dual roles of lipids in OL development and degeneration but also highlights druggable targets for personalized treatment of neurodegenerative diseases.},
}

@article {pmid41785249,
year = {2026},
author = {Pucci, N and Kaan, AM and Ujčič-Voortman, J and Verhoeff, AP and Zaura, E and Mende, DR},
title = {Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1013185},
doi = {10.1371/journal.pcbi.1013185},
pmid = {41785249},
issn = {1553-7358},
abstract = {Early-life oral microbiome development is a complex community assembly process that influences long-term health outcomes. Nevertheless, microbial functions and interactions driving these ecological processes remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated species and predict their metabolic interactions within a network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes). Metabolic modeling identified potential exchange of key amino acids, particularly ornithine and lysine, between these species, suggesting metabolic cross-feeding interactions that may explain their co-abundance across infant oral microbiomes. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.},
}

@article {pmid41785052,
year = {2026},
author = {Roy, P and Roy, D and Bhattacharjee, S and Ghosh, A and Saha, S},
title = {MDPD reveals specific microbial signatures in human pulmonary diseases.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
doi = {10.1093/bib/bbag017},
pmid = {41785052},
issn = {1477-4054},
abstract = {Pulmonary diseases are becoming a serious threat worldwide, and enormous data from different human microbiomes have been generated to understand these complex diseases. Here, we introduce Microbiome Database of Pulmonary Diseases (MDPD), an open-access, comprehensive systemic catalog of pulmonary diseases by manually curating global studies from 2012 to 2024 (13 years). We have compiled 59 362 runs from 430 BioProjects, encompassing data from 10 body sites related to 19 pulmonary diseases and healthy groups covering 278 distinct sub-groups. MDPD enables users to analyze each BioProject and customize analysis with multiple BioProjects to identify taxonomic profiles and disease group/sub-group specific microbial signatures. The re-analyzed intermediate Biological Observation Matrix files are provided for each BioProject for the accessibility of users for further applications, such as machine learning-based classification. Identified microbes (bacteria, fungi, viruses) in MDPD are annotated with several attributes, providing further insights into their disease-causing potential and specificity to certain diseases and body sites. MDPD is freely available at: https://bicresources.jcbose.ac.in/ssaha4/mdpd/.},
}

@article {pmid41784969,
year = {2026},
author = {Chen, Y and Xing, Z and Sheng, J and Liu, X and Ding, W and Chen, X},
title = {Trends in the Application of Multiomics Based on Machine Learning in the Development of Probiotics.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c15387},
pmid = {41784969},
issn = {1520-5118},
abstract = {With the rapid development of computational methods and high-throughput multiomics technologies, machine learning (ML) has emerged as an important analytical approach in probiotic research. This review summarizes recent ML-assisted applications across genomics, transcriptomics, metabolomics, microbiome profiling, and culturomics, and organizes current studies around four functional objectives: probiotic selection, functional prediction, metabolic activity prediction, and probiotic effectiveness optimization. We discuss how ML facilitates the integration of heterogeneous omics data to enable more systematic and quantitative probiotic development and highlight representative analytical tools and workflows. At the same time, key limitations remain, including cross-platform data heterogeneity, imbalanced functional labels, and limited robustness in capturing complex microbial and environmental interactions. Consequently, experimental validation remains essential for ensuring biological relevance. Future progress will rely on standardized multiomics integration and iterative computational-experimental frameworks to support rational probiotic optimization.},
}

@article {pmid41784899,
year = {2026},
author = {Colaco, VS and Boleij, A},
title = {The gut microbiome as a biomarker and modifiable risk factor in Lynch Syndrome.},
journal = {Familial cancer},
volume = {25},
number = {1},
pages = {},
pmid = {41784899},
issn = {1573-7292},
support = {WO24-54//Dutch Digestive Diseases Foundation (MDL-Fonds)/ ; WO24-54//Dutch Digestive Diseases Foundation (MDL-Fonds)/ ; KUN2015-7739//KWF Kankerbestrijding/ ; },
}

@article {pmid41784851,
year = {2026},
author = {Yoshioka, H and Mary-Huard, T and Aubert, J and Toda, Y and Ohmori, Y and Yamasaki, Y and Tsujimoto, H and Takahashi, H and Nakazono, M and Takanashi, H and Fujiwara, T and Tsuda, M and Kaga, A and Inaba, J and Fuji, Y and Hirai, MY and Nose, Y and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Narukawa, M and Ichihashi, Y and Iwata, H},
title = {Integration of proxy intermediate omics traits into a nonlinear two-step model for accurate phenotypic prediction.},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {139},
number = {3},
pages = {},
pmid = {41784851},
issn = {1432-2242},
support = {JP23KJ0506//Japan Society for the Promotion of Science/ ; JP22K21352//Japan Society for the Promotion of Science/ ; JPMJCR16O2//Japan Science and Technology Corporation/ ; JPMJAN23D1//Japan Science and Technology Corporation/ ; },
abstract = {Intermediate omics traits, which mediate the effects of genetic variation on phenotypic traits, are increasingly recognized as valuable components of genetic evaluation. In particular, rhizosphere microbiota play a crucial role in plant health and productivity; however, their complex interactions with host genetics remain challenging to model. Although two-step modeling frameworks have been proposed to integrate intermediate omics traits into phenotype prediction, existing approaches do not incorporate nonlinear relationships between different omics layers. To address this, we have proposed a two-step phenotype prediction framework that integrates genomic, rhizosphere microbiome, and metabolome (meta-metabolome) data, while explicitly capturing omics-omics nonlinearities. The first step is to predict meta-metabolome traits from genetic and microbial features, thus effectively isolating them from the environmental noise. In this process, intermediate "proxy" omics traits are generated as general biological information to provide robust models. The second step utilizes this "proxy" to enhance the accuracy of the phenotype prediction. We compared a linear mixed model (Best Linear Unbiased Prediction, BLUP) and a nonlinear model (Random Forest, RF) at each step, as demonstrated through simulations and empirical analysis of a multi-omics soybean dataset in which nonlinear modeling captures intricate omics interactions. Notably, our approach enables phenotype prediction without requiring the original meta-metabolome data used in model training, thereby reducing reliance on costly omics measurements. This framework integrates intermediate omics traits into genomic prediction to improve prediction accuracy and provide solutions for deeper insights into plant-microbiome interactions.},
}

@article {pmid41784506,
year = {2026},
author = {Ivanov, VA and Hartman, WH and Soheilypour, M},
title = {Decoding the Microbiome-Disease Axis with Interpretable Graph Neural Networks.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag063},
pmid = {41784506},
issn = {1365-2672},
abstract = {AIMS: The human gut microbiome is a complex ecosystem whose disruption is implicated in a wide spectrum of diseases, yet translating microbiome research into actionable therapeutics is hindered by a critical trade-off: existing models either prioritize predictive accuracy at the expense of interpretability or sacrifice performance for mechanistic insight, limiting their ability to pinpoint specific disease-driving microbial interactions and taxa.

METHODS AND RESULTS: To address this, we introduce Graph neural network for Interpretable Microbiome (GIM), a graph neural network framework that integrates minimally processed taxonomic metadata as sparse node embeddings within an unweighted complete graph, enabling direct modeling of high-order microbial interactions through message passing. GIM achieves state-of-the-art classification performance on microbiome-disease prediction tasks (e.g. healthy vs. allergic states) while generating finegrained, experimentally validated attributions at the level of taxonomic ranks, driver microbes, and putative microbe-to-microbe interactions.

CONCLUSIONS: By bridging the gap between predictive accuracy and biological interpretability, GIM overcomes a key limitation in current approaches, offering a unified framework to both predict dysbiosis-associated disease states and identify actionable microbial targets for therapeutic intervention. This dual capability represents a critical advance toward precision microbiome engineering and scalable hypothesis generation in translational microbiome research.},
}

@article {pmid41784373,
year = {2026},
author = {Aizpurua, O and Martin-Bideguren, G and Gaun, N and Alberdi, A},
title = {Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0369125},
doi = {10.1128/spectrum.03691-25},
pmid = {41784373},
issn = {2165-0497},
abstract = {Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyze the taxonomic and functional differences in the gut microbiota of 45 wild and captive European hares (Lepus europaeus), as well as to assess the impact of fresh grass supplementation to a pellet-based diet aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While grass supplementation induced some minor changes in the gut microbiota, it did not lead to statistically significant shifts toward a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggests that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions.IMPORTANCEThis study sheds light on the role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the collection of 860 near-complete genomes of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Grass supplementation to a pellet-based diet yielded limited success in restoring a microbiota similar to that of wild counterparts, highlighting the need for more tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasize that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.},
}

@article {pmid41784222,
year = {2026},
author = {Barr, SA and Davis, LJ and Vidar, W and Williamson, RT and Strangman, WK},
title = {Assessing Digestive Transformations of Withania somnifera Extracts via LC-MS/MS Profiling with a Focus on Bioactive Compounds Withaferin A, Withanolide A, Withanoside IV, and Untargeted Metabolomics.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09897},
pmid = {41784222},
issn = {1520-5118},
abstract = {Botanical extracts are widely employed as health care agents but lack the rigorous vetting required for FDA-approved pharmaceuticals. Research on phytochemical bioavailability and transformation has mainly focused on liver metabolism and plasma binding, while gastrointestinal and microbiome metabolism studies remain limited. This study combined digestive in vitro assays with mass spectrometry-based metabolomics and molecular networking to analyze metabolites in Withania somnifera leaf and root extracts, along with three known bioactive reference standards: withaferin A, withanolide A, and withanoside IV. Both withaferin A and withanoside IV underwent significant in vitro transformation, while withanolide A remained stable across conditions. Molecular networking revealed that withanolides in the root extract were largely stable, whereas many in the leaf extract were more labile under the assay conditions. Detailed network analysis also enabled the identification of specific metabolite transformations. These findings support the refinement of in vitro models to better predict in vivo behavior in complex botanical mixtures.},
}

@article {pmid41784027,
year = {2026},
author = {Mekonnen, YT and Indio, V and Lucchi, A and Manfreda, G and Serraino, A and De Cesare, A},
title = {Detection of Chlamydia ibidis in the neck skin microbiome of broiler carcasses at the end of slaughter.},
journal = {Italian journal of food safety},
volume = {},
number = {},
pages = {},
doi = {10.4081/ijfs.2026.14726},
pmid = {41784027},
issn = {2239-7132},
abstract = {Chlamydia is the etiological agent of chlamydiosis in wild and domestic birds, mammals, and humans. In this study, Chlamydia reads were detected in the microbiome of the neck skin of 76 broiler carcasses collected in the same slaughterhouse at the end of the chilling tunnel. The carcasses originated from four different flocks of female Ross 308, reared in two broiler houses located in Northern Italy. One flock from each poultry house was sampled in 2019 and one flock in 2023. The carcass neck skin microbiome was investigated by shotgun metagenomic sequencing. Chlamydia reads displayed a mean relative abundance of 7.38%, with significant differences between carcasses obtained from the two poultry houses, sampled at both sampling times. Chlamydia ibidis was the prevalent species among time points and poultry houses. The zoonotic potential of C. ibidis and foodborne transmission have never been demonstrated. However, it is known that the genus Chlamydia has "spore"-like extracellular forms able to survive for months outside the host. Therefore, the presence of C. ibidis reads on broiler carcasses at the end of the chilling tunnel deserves further investigation. The results of this study highlight the feasibility of microbiome investigations to detect unexpected biological hazards in foods.},
}

@article {pmid41783932,
year = {2026},
author = {Gomez, R and Sun, W and Shyy, M and Ou, J and Sihota, A and Liu, B and Mesarwi, O and Malhotra, A},
title = {Mechanisms Linking Sleep-Disordered Breathing and Cardiometabolic Disease Risk.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {},
number = {},
pages = {},
doi = {10.1161/ATVBAHA.125.322874},
pmid = {41783932},
issn = {1524-4636},
abstract = {Sleep-disordered breathing (SDB) is a group of disorders defined by intermittent closure or narrowing of the upper airway, caused either by mechanical obstruction or dysregulation of the respiratory centers in the brainstem. The effects of SDB on cardiovascular and metabolic health and disease have been an area of growing interest. Many studies have shown mechanistic links between physiological changes seen in SDB and important cardiometabolic outcomes. In particular, SDB induces alterations in autonomic function, swings in intrathoracic pressure, systemic inflammation, sleep fragmentation, and oxidative stress, with diverse effectors including alterations in cellular gene expression, for example, through microRNA and hypoxia-inducible factor 1, changes in the gut microbiome, and many others. Ultimately, these mechanistic pathways have implications on vascular and myocardial dysfunction, hypertension, insulin sensitivity, lipid metabolism, and weight gain. Several treatment modalities exist for SDB, and are chosen based on the specific disease process and patient preference/tolerance. These therapies result in an improvement in symptoms related to SDB severity and varying levels of cardiometabolic disease risk mitigation. In this review, we will present some important mechanisms of SDB that increase the risk for cardiometabolic disease, and we will discuss therapies and their intended targets.},
}

@article {pmid41783924,
year = {2026},
author = {Luo, S and Lou, F and Yang, P and Zhang, Y and Yan, L and Dong, Y and Yang, B and Wang, H and Liu, Y and Pu, J and Cannon, RD and Xie, P and Ji, P and Jin, X},
title = {Dysregulation of Oral Microbial Eicosapentaenoic Acid Induced by Chronic Restraint Stress Exacerbates Periodontitis via M1 Macrophage Polarization.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e21346},
doi = {10.1002/advs.202521346},
pmid = {41783924},
issn = {2198-3844},
support = {82370968//National Natural Science Foundation of China/ ; 2026MSXM055//Chongqing medical scientific research project (Joint project of the Chongqing Health Commission and the Science and Technology Bureau)/ ; CSTB2022NSCQ-MSX1148//Natural Science Foundation of Chongqing/ ; 2025JYJ099//Project of Luzhou Science and Technology Bureau/ ; },
abstract = {The intricate interplay between chronic psychological stress and periodontitis, mediated by oral microbiota and macrophage polarization, remains largely enigmatic. Here, we demonstrate that chronic restraint stress (CRS) exacerbates periodontitis by inducing oral microbial dysbiosis and a consequential shift in host metabolism. Clinical observations reveal a significant correlation between depressive symptoms and the severity of periodontitis, which is underpinned by a distinct oral microbiome. Crucially, fecal microbiota transplantation from CRS-exposed mice into germ-free mice was sufficient to transmit the heightened periodontitis phenotype, establishing a causal role for the stress-altered microbiota. Metabolomic profiling identified a depletion of eicosapentaenoic acid (EPA) in stressed, ligature-induced periodontitis mice. Mechanistically, supplementation with EPA ameliorates periodontitis by suppressing the NF-κB signaling pathway, thereby inhibiting the pro-inflammatory M1 polarization of macrophages. Our findings unveil a novel gut-oral axis mediated by microbiota and metabolites under stress, and position the omega-3 fatty acid EPA as a promising therapeutic agent for mitigating stress-aggravated inflammatory disorders.},
}

@article {pmid41783896,
year = {2026},
author = {Zhang, Q and Wang, W and Yu, H and Wang, F and Chen, X and Liang, Z and Lu, Y},
title = {Research progress on immune tolerance mechanisms in liver metastatic tumors and the "Liver-metastasis-oriented shared-mechanism therapeutic strategy" approach.},
journal = {Medical review (2021)},
volume = {6},
number = {1},
pages = {57-74},
pmid = {41783896},
issn = {2749-9642},
abstract = {Liver metastases pose a serious challenge in the field of systemic cancer treatment, as this organ has a particular microenvironment that favours malignant cells disseminating to settle there. We outline major steps of liver immune tolerance in metastasis including pre-metastatic niche formation, immune evasion during circulation, establishment of an intrahepatic immune desert and metabolism, myeloid cell networks and gut microbiome-mediated coordinated tolerance. We then combine new combination and integrative therapies that are intended to break this tolerance; these include immunochemotherapy regimens, synergistic antiangiogenics and immunotherapies, dual immune checkpoint blockade and myeloid-cell reprogramming, combined locoregional and systemic therapies and new microenvironmental targeting. Each strategy is assessed with regard to its potential disruption of hepatic immune quiescence, improved clinical translation and durable antitumour activity. We suggest a proposed solution termed Liver-metastasis-oriented shared-mechanism therapeutic strategy, which may target multiple metastatic bottlenecks due to similarities. This framework provides a basis for personalizing combination therapies and designing future clinical trials for treating liver metastases, with organ-specific considerations and will be the subject of a commentary.},
}

@article {pmid41783828,
year = {2026},
author = {Jurkovich, V and Fischer, L and Nagy, K and Ladányi, M and Hann, S and Dernovics, M},
title = {Targeting selenometabolites in the saliva of dairy cows: size-exclusion chromatography - inductively coupled plasma mass spectrometry-based characterization.},
journal = {Veterinary and animal science},
volume = {32},
number = {},
pages = {100600},
pmid = {41783828},
issn = {2451-943X},
abstract = {Selenium supply is an important input for milking cows, and the monitoring of selenium uptake has been carried out through total selenium determination in the blood serum samples or the concentration of selenoprotein P. While the optimum concentrations of these two parameters have already been established, the specific selenium requirement of cows' microbiomes has not been addressed. The oral cavity of cows contains basically the first, front-end microbiome of the animal. However, no information is available on its selenium-dependent/ independent strains, its distribution, and ratio. In any case, saliva would be the only readily accessible source of selenium for the microbiome of the oral cavity. Therefore, our study focused on the total selenium and selenium speciation analyses of saliva of Holstein cows, together with the determination of total selenium in whole blood and serum samples. A two-step feeding experiment was conducted with supplementing the selenite-containing daily ration with the hydroxy-analogue of selenomethionine (R,S-2-hydroxy-4-methylselenobutanoic acid, HMSeBA) at the highest authorized rate in the EU. Size-exclusion chromatography - inductively coupled plasma mass spectrometry was used for the speciation of saliva samples that revealed the presence of low molecular weight (LMW) selenometabolites in the 1.78-15.3 µg Se kg[-1] range. The supplementation of HMSeBA did not significantly increase the blood selenium concentrations, and no correlation was found between the LMW selenium concentration and blood selenium concentrations. While the identification of LMW selenometabolites with electrospray ionization high-resolution mass spectrometry could not be achieved, a dedicated sample preparation protocol has been suggested for future experiments.},
}

@article {pmid41783496,
year = {2026},
author = {Qin, X and Song, S and Xiang, G and Luo, S and Wen, X},
title = {Microplastics: a potential threat to gut microbiota and antioxidant capacity of broiler chickens.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1708036},
pmid = {41783496},
issn = {1664-302X},
abstract = {The detrimental effects of microplastics on environmental and biological health have been extensively documented, encompassing various aspects such as growth inhibition, metabolic disorders, and organ damage. However, current research predominantly focuses on model organisms, with limited studies investigating their effects on broiler chickens. Therefore, this study aims to examine the impact of microplastics exposure on the gut microbiota and antioxidant function in broiler chickens. The results indicated that microplastics significantly affect serum biochemical and antioxidant parameters, evidenced by marked increases in AST, ALT, and MDA levels, alongside decreases in SOD and GSH-Px levels. Microbiome analysis revealed a significant decrease in the alpha diversity of the gut microbiota, accompanied by significant alterations in microbial structure. Additionally, metastats analysis demonstrated a significant increase in the relative abundances of one phylum and 12 genera during microplastics exposure, contrasted with a significant decrease in the relative abundances of three phyla and 108 genera. Importantly, microplastics exposure also led to changes in gut microbial function, affecting energy metabolism, coenzyme transport and metabolism, and amino acid metabolism, etc. In summary, our study demonstrates that microplastics can adversely affect the health of broiler chickens by reducing their antioxidant capacity, and causing gut microbial dysbiosis. In light of the increasing pollution from microplastics, this study provides crucial information for assessing the risks posed by microplastics to livestock production. Furthermore, future research should prioritize monitoring the migration of microplastics within the food chain and examining their long-term effects on biological behavior and ecological functions.},
}

@article {pmid41783495,
year = {2026},
author = {Xu, L and Wan, Q and Yang, Q and Shen, W and Dai, Y and Sun, H and Huang, L and Wang, M and Jiang, W and Hao, C},
title = {Microbial and metabolomic profiling of the upper respiratory tract in children with asthma.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1672589},
pmid = {41783495},
issn = {1664-302X},
abstract = {BACKGROUND: This study aimed to investigate characteristic changes in the upper respiratory tract (URT) microbiome and metabolome in children with asthma and explore their associations with lung function.

METHODS: Children with asthma aged 6 years and above admitted to the Children's Hospital of Soochow University from December 2022 to December 2023 comprised the study group. Age-matched healthy children undergoing physical examinations in the Department of Child Health were recruited as controls. Throat swabs were collected for microbiome detection using 16S rDNA sequencing and metabolomics analysis using liquid chromatography-mass spectrometry (LC-MS).

RESULTS: (1) Significant differences in alpha and beta diversity were observed among the control group (H), chronic persistent asthma group (CA), and acute exacerbation group (AA). In both CA and AA groups, FVC% predicted (FVC%/Pred) and FEV1% predicted (FEV1%/Pred) were negatively correlated with URT microbiota abundance. Actinobacillus abundance was positively correlated with FEV1%/Pred, FEV1/FVC, FEF25%/Pred, FEF50%/Pred, and FEF75%/Pred. (2) Metabolite differences between CA and AA groups were analyzed, and the top 5 differential metabolites were evaluated for their accuracy as asthma assessment biomarkers. L-carnitine showed an AUC > 0.9, with a sensitivity of 85.7% and specificity of 85%. Other differential metabolites, including monoisobutyl phthalate, 4-hexyl-2,5-dimethyloxazole, and dibutyl phthalate, correlated with several lung function indices. The most relevant differential metabolic pathways included arginine biosynthesis, alanine-aspartate-glutamate metabolism, central carbon metabolism in cancer, and D-amino acid metabolism.

CONCLUSION: The URT microbiota in asthmatic children exhibits alterations in composition, structure, and diversity, with lower diversity in acute asthma compared to chronic persistent asthma. At the genus level, some microbiota (Actinobacillus, Fusobacterium) were correlated with FEV1%/Pred, FEV1/FVC, FEF25%/Pred, FEF50%/Pred, FEF75%/Pred. The differential metabolite L-carnitine may be a potential biomarker for asthma assessment.},
}

@article {pmid41783404,
year = {2026},
author = {Liu, D and Ma, Y and Ma, Q and Huang, H and Li, T and Wang, J and Zhang, J and Cheng, X and Ge, X and Chen, Y and Zhang, Y},
title = {Clinical pathogen profiles and lung microbiome features in lung infection patients and concurrent cancer: insights from metagenomics next-generation sequencing.},
journal = {Open life sciences},
volume = {21},
number = {1},
pages = {20251220},
pmid = {41783404},
issn = {2391-5412},
abstract = {Pulmonary infections in immunocompromised cancer patients present significant diagnostic and therapeutic challenges. From Dec 2021 to Aug 2023, 85 patients with pulmonary infection were enrolled and categorized into a cancer group (CP, n = 20) and a non-cancer control group (NCP, n = 18). Pathogen detection was performed using both mNGS and culture and lung microbiome analysis was conducted. mNGS demonstrated a significantly higher pathogen detection rate than culture (P < 0.0001). The CP group exhibited older age (P < 0.001), elevated neutrophil counts (NE) and higher procalcitonin (PCT) levels compared to the NCP group. Furthermore, fungal pathogens were significantly more prevalent in the CP group (P = 0.046). Both cancer status and advanced age were independent influencing factors for the detection of pulmonary fungi. Pulmonary microbiome analysis revealed no significant differences in α-diversity or β-diversity between groups. These findings indicate that mNGS offers superior sensitivity over culture. Cancer-related pulmonary infections present a distinct pathogen profile characterized by a higher prevalence of fungal pathogens. This underscores the need for enhanced clinical vigilance, especially among elderly cancer patients.},
}

@article {pmid41783048,
year = {2026},
author = {Wu, F and Zhu, B and Feng, S and Li, H and Zhou, J and Ning, Y and Huang, Y and Wu, K},
title = {The Brain-Gut Health Initiative (BIGHI): A Prospective Cohort on Psychiatric Disorders in China.},
journal = {Research (Washington, D.C.)},
volume = {9},
number = {},
pages = {1142},
pmid = {41783048},
issn = {2639-5274},
abstract = {Major psychiatric disorders are characterized by substantial clinical heterogeneity and high comorbidity, yet their underlying biological mechanisms are not fully uncovered. The microbiota-gut-brain axis (MGBA) offers a cross-system perspective for elucidating the pathophysiology of major psychiatric disorders. The Brain-Gut Health Initiative (BIGHI) was established as the first prospective longitudinal cohort in China dedicated to investigating major psychiatric disorders guided by the framework of MGBA, enabling large-scale, transdiagnostic, and longitudinal analyses of brain-gut interactions. To date, the BIGHI has enrolled over 1,200 participants with schizophrenia, major depressive disorder, bipolar disorder, and healthy controls, with multidimensional data collected including clinical symptomatology, neurocognitive performance, electroencephalography, magnetic resonance imaging, peripheral blood biomarkers, and gut microbiome profiles. The studies within the BIGHI reveal (a) brain-gut physiological alterations in psychiatric disorders; (b) systematic relationships among brain function, peripheral physiological markers, and gut microbiome; and (c) brain-gut network patterns with marked interindividual heterogeneity. In future studies, we will expand the BIGHI into a collaborative network and promote data harmonization and interdisciplinary collaboration to advance computational psychiatry as well as its clinical translation.},
}

@article {pmid41782929,
year = {2026},
author = {Gates, M and Schumacher, SM and Doyle, WJ and Sofaly, N and Roullet, JB and Ochoa-Repáraz, J},
title = {Farnesol, the farnesol pathway, and the immune-gut-brain axis.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1718322},
pmid = {41782929},
issn = {1663-9812},
abstract = {Experimental models and clinical evidence suggest that the gut and the central nervous system (CNS) interact in a multifactorial, bidirectional manner. A third player, the immune system, has recently been identified in these interactions, with research linking the gut microbiome to inflammatory conditions, including those affecting the CNS. The molecular signals involved in communication between the gut, brain, and immune system have been extensively studied. However, no unique signaling pathway has been identified for each component of the immune-gut-brain (IGB) axis to date. In this review, we argue that isoprenoids, and specifically farnesol, are key signaling molecules that link the gut and its microbiota, the immune system, and the CNS. The pharmacological properties of farnesol, an intermediate in the broadly conserved mevalonate pathway, are diverse and encompass quorum sensing and microbial biofilm inhibition, neuroinflammatory protection, and modulation of intracellular calcium (Ca[2+]) signaling pathways. Many of these signaling pathways are implicated in neuron-to-neuron communication and in the responses of immunocompetent cells to immunogenic stimuli. We will first address the biological relevance of the immune-gut-brain axis and the gut microbiome in regulating health and disease. Next, we will review the molecular and cellular mechanisms by which farnesol regulates both the gut microbiota and the host's innate and adaptive immune systems. Finally, we will provide a perspective on the immunoregulatory mechanisms underlying farnesol's protective properties in models of neuroinflammatory diseases. In summary, we propose a review of the most salient studies that establish farnesol as a significant modulator of the immune-gut-brain axis.},
}

@article {pmid41782866,
year = {2026},
author = {Shen, S and Li, J and Zheng, S and Cui, X and Gou, X},
title = {Synergistic carcinogenesis of the nasopharyngeal microbiome and Epstein-Barr virus: mechanisms of metabolic reprogramming and immune evasion.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1771414},
pmid = {41782866},
issn = {1664-3224},
abstract = {Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection, but EBV alone is insufficient for tumorigenesis. Recent evidence suggests that the nasopharyngeal microbiome plays a critical, yet underexplored, role in NPC development. This review investigates the synergistic interaction between EBV and the nasopharyngeal microbiome, focusing on microbial dysbiosis and its role in NPC pathogenesis. We highlight significant microbial dysbiosis in NPC patients, characterized by an overgrowth of opportunistic pathogens such as Fusobacterium nucleatum and Porphyromonas gingivalis. These pathogens interact with EBV-infected epithelial cells, amplifying oncogenic signaling through the NF-κB and PI3K/AKT pathways. Crucially, we explore the "SCFA paradox," where microbial short-chain fatty acids (SCFAs), typically beneficial, act as HDAC inhibitors that paradoxically trigger EBV lytic reactivation in B-cells. Additionally, the microbiome facilitates immune evasion through interactions between F. nucleatum Fap2 and the TIGIT receptor, in synergy with EBV's LMP1 protein. These findings underscore the importance of the microbiome in NPC pathogenesis and highlight the potential for integrating microbial signatures into diagnostic tools. We conclude by discussing precision therapies, such as bacteriophage treatment, and emphasize the role of next-generation models-specifically Air-Liquid Interface organoids-as functional 'patient avatars.' These systems are essential for advancing personalized medicine, as they enable the functional validation of individualized microbial interventions that sequencing alone cannot predict.},
}

@article {pmid41782637,
year = {2026},
author = {Ligezka, A and Lynch, BA and Saliba, M and Corral-Frias, MP and Johnson, S and Chen, J and Allen, SV and Frank, JM and Vande Voort, JL and Croarkin, PE and Romanowicz, M},
title = {Microbiome and Vocalization Biomarkers of Infant Distress, Maternal Depression and Parenting Styles.},
journal = {Chronic stress (Thousand Oaks, Calif.)},
volume = {10},
number = {},
pages = {24705470261425120},
pmid = {41782637},
issn = {2470-5470},
abstract = {INTRODUCTION: Psychiatric disorders have their genesis in early life. Standard screening approaches during well child visits for pathological infant distress, maternal depression, and dysfunctional parenting behaviors are likely inadequate. Microbiome measures and infant vocalizations have promise as scalable psychiatric biomarkers for infants. The purpose of this study was to examine associations among infant gut colonization based on microbiome measurements with maternal distress and maternal depressive symptoms in a sample of infants.

METHODS: This study sought to examine infant microbiome correlates of infant distress, parent-infant interactions, maternal distress, and maternal depressive symptoms. We collected (N = 31) microbiome samples, infant vocalizations during vaccination, and behavioral measures during a 4 month well child visit (WCV) and did a battery of clinical assessments to assess for maternal depression, parent-child interactions, family characteristics and family stress. Whole-genome SHOTGUN sequencing was utilized to identify three types of associations: alpha-diversity using Shannon and Inverse-Simpson indexes, beta-diversity using Bray-Curtis and Jaccard distances, and differential abundance using LinDA. Spectral measures of infant cries were also modeled to assess potential relationships with clinical assessments and the microbiome.

RESULTS: There were 19 phyla, 417 genera, and 1246 species identified with taxonomic classification. Maternal distress as measured by PHQ-9 scores obtained when infants were 2 months old were associated with 4 bacterial species (Actinomyces johnsonii, Bilophila wadsworthia, Clostridium dakarense and Ruminococcus flavefaciens; FDR < 0.1) and beta-diversity (p = 0.006-BC; p = 0.005-Jaccard). Infant cries with greater high frequency band power (p < 0.03) and a greater high-to-mid frequency ratio-metrics (p < 0.05) were associated with altered α-diversity of the microbiome. No correlations were present between maternal PHQ-9 at 4 months, PSI-IV and microbiome diversity.

CONCLUSION: The present findings suggest that an infant stress (assessed by quality of crying) is associated with lower microbiome diversity. Decreased diversity reflects an unhealthy microbiome. Parental depressive symptoms may also influence infant microbiome. Future interventional studies focused on the quality of the infant-caregiver relationship should examine related changes in intestinal microbiota.},
}

@article {pmid41782495,
year = {2026},
author = {Loublier, C and Taminiau, B and Seidel, L and Moula, N and Tano, C and Cesarini, C and Costa, M and Lecoq, L and Daube, G and Amory, H},
title = {Survey on Faecal Microbiota Transplantation and Probiotic Use in Equine Practice in France and Belgium.},
journal = {Veterinary medicine and science},
volume = {12},
number = {2},
pages = {e70854},
pmid = {41782495},
issn = {2053-1095},
support = {40005849//Fonds De La Recherche Scientifique - FNRS/ ; },
mesh = {Belgium ; *Probiotics/therapeutic use ; Horses ; France ; Animals ; *Fecal Microbiota Transplantation/veterinary/statistics & numerical data ; Cross-Sectional Studies ; *Horse Diseases/therapy ; *Veterinarians/statistics & numerical data/psychology ; Female ; Male ; Surveys and Questionnaires ; Humans ; },
abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) and probiotics are used in equine practice. Understanding veterinarians' perceptions and practices is crucial for effective implementation.

OBJECTIVE: (1) Evaluate the prevalence, usage patterns and perceived effectiveness of probiotics and FMT among equine veterinarians in France and Belgium. (2) Assess their knowledge, practices and influencing factors across demographics and settings. (3) Explore links between FMT protocols and treatment satisfaction.

STUDY DESIGN: Cross-sectional survey.

METHODS: An online survey collected demographic data and responses on the use of probiotics and FMT. Analyses included descriptive statistics, chi-square tests and logistic regression models.

RESULTS: Ninety-six equine veterinarians participated, practicing in Belgium (52.1%), France (39.6%) or both (8.3%). Probiotic use was reported by 82.1%, more frequent in field than clinical practice (odds ratio [OR] = 3.61, 95% CI [1.09, 12.02], p = 0.036) and in France than Belgium (OR = 5.08, 95% CI [1.44, 17.94], p = 0.012). Probiotics were used for chronic diarrhoea (88.0%), acute diarrhoea (67.6%) and inflammatory bowel diseases (45.9%). Most veterinarians (83.3%) defined probiotics well, but 16.7% misidentified non-probiotic products. FMT was used by 76.0%, mainly occasionally and therapeutically, more in clinical than field practice (OR = 4.79, 95% CI [1.03, 22.27], p = 0.046). In theory, 58.3% prioritized infection-free donors, but only 22.5% tested donors before FMT, mostly using coprology (93.8%). Those who tested donors reported higher perceived efficacy (p = 0.0029).

MAIN LIMITATIONS: Potential selection bias, as participation was voluntary. Generalizability might be limited by focus on France and Belgium. Sample size, while informative, should be expanded.

CONCLUSION: Probiotics and FMT were commonly used therapeutically by equine veterinarians in France and Belgium. Although probiotic use was widespread, some misunderstandings remained. FMT protocols varied, with donor faeces often untested. Treatment satisfaction was generally positive but estimated success rates varied. Standardized FMT protocols are needed to improve outcomes and consistency.},
}

Belgium
*Probiotics/therapeutic use
Horses
France
Animals
*Fecal Microbiota Transplantation/veterinary/statistics & numerical data
Cross-Sectional Studies
*Horse Diseases/therapy
*Veterinarians/statistics & numerical data/psychology
Female
Male
Surveys and Questionnaires
Humans

@article {pmid41782409,
year = {2026},
author = {Yang, J and Xiao, Y and Cui, J and Song, R and Ma, W and Liu, J and Miao, C and Sun, X and Kong, X and Zhang, ZS and Zhou, L and Yao, Z and Wang, Q},
title = {A 4-guanidinobutanoic acid-SLC36A1 axis drives a microbiota‒host feedback loop to regulate intestinal homeostasis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2639216},
doi = {10.1080/19490976.2026.2639216},
pmid = {41782409},
issn = {1949-0984},
abstract = {The role of gut microbiota‒derived metabolites in regulating the intestinal mucosal barrier remains poorly defined. Here, we identified 4-guanidinobutanoic acid (4-GBA), produced by Bacteroides stercorirosoris, as a critical regulator of intestinal homeostasis. Using untargeted metabolomics, organoid co-cultures, mouse models, and single-cell RNA sequencing, we demonstrated that 4-GBA enhances intestinal stem cells (ISCs) function and goblet cell differentiation. This promotes Akkermansia muciniphila enrichment through mucus-dependent niche expansion, establishing a microbiota‒host feedback loop. Mechanistically, 4-GBA upregulates the proton-coupled amino acid transporter SLC36A1 and activates the Hedgehog signaling pathway to drive epithelial reprogramming. Clinically, SLC36A1 expression inversely correlates with ulcerative colitis (UC) severity in human samples. Furthermore, the SLC36A1 agonist sarcosine enhances barrier homeostasis and attenuates colitis in mice, highlighting the diagnostic and therapeutic potential of this axis in UC. Our findings reveal a novel microbiome-host axis through which a microbial metabolite modulates epithelial function and microbial ecology, offering a potential therapeutic strategy targeting microbiota-epithelial crosstalk for UC management.},
}

@article {pmid41782343,
year = {2026},
author = {Xu, Y and Xiao, J and Zhuang, Y and Gao, D and Jiang, W and Hou, G and Zhao, X and Li, S and Chen, T and Li, S and Zhang, S and Huang, Y and Liu, S and Yoon, I and Shi, W and Li, M and Wang, W and Li, S and Cao, Z},
title = {Performance, blood parameters, ruminal fermentation and microbial community of dairy cows supplemented with Saccharomyces cerevisiae fermentation product from dry-off to early lactation.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag056},
pmid = {41782343},
issn = {1525-3163},
abstract = {Dairy cows experience oxidative stress, inflammation, and immune dysfunction during the transition from dry-off to early lactation. Postbiotics such as Saccharomyces cerevisiae fermentation product (SCFP), consisting of nonliving microorganisms with or without their components, have beneficial effects on the production efficiency and immune function of dairy cows. The objective of this study was to evaluate the effects of SCFP on milk production, milk composition, ruminal fermentation, blood metabolites, oxidative status, inflammatory responses, and the ruminal microbial community in Holstein dairy cows supplemented from the day of dry-off through early lactation. Two hundred cows were blocked on the basis of parity, BCS, milk yield and the time of dry-off, and were randomly allocated to specific treatment groups within each block. The treatments included the control group (CON, n = 100) receiving basal diets with no SCFP supplementation and the SCFP group (n = 100) receiving basal diets supplemented with 19 g/d of SCFP from d -60 to 60 relative to parturition. Milk yield-monitored for all 100 cows per treatment-was tracked until d 140 postpartum. In parallel, ruminal fluid, feces, milk, and blood samples were collected from a subset of cows (n = 20/treatment) during the treatment period for further analyses. Data were analyzed via the MIXED procedure in SAS (SAS Institute Inc.). The results revealed that the average milk yield of dairy cows in the SCFP group was greater than that in the CON group (43.93 vs. 42.08 kg/d, P = 0.04, n = 100) during the treatment period and remained greater (41.92 vs. 39.98 kg/d, P = 0.04, n = 100) throughout the 140 days postpartum recording period. Cows fed SCFP had significantly lower serum β-hydroxybutyrate and nonesterified fatty acid concentrations than did those in the CON group. Compared with the CON group, the SCFP group presented greater levels of superoxide dismutase and lower malonaldehyde concentrations. The SCFP group also presented a greater total antioxidant capacity prepartum and higher glutathione peroxidase levels postpartum. Additionally, the SCFP group had lower concentrations of proinflammatory factors, such as IL-1β, serum amyloid A, and haptoglobin, throughout the treatment period, indicating a stronger anti-inflammatory capability. Overall, SCFP supplementation improved the ruminal environment, reduced oxidative stress and the inflammatory status, and ultimately increased milk production.},
}

@article {pmid41782218,
year = {2026},
author = {Li, L and Chen, M and Zhai, F and Li, Q},
title = {Foliar Silicon Nanoparticles Induce Coordinated Defense against Cadmium in Rice via Jasmonate-Mediated Metabolic Reprogramming.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14175},
pmid = {41782218},
issn = {1520-5118},
abstract = {Foliar application of silicon nanoparticles (SiNPs) is a promising strategy for mitigating cadmium (Cd) contamination in rice; however, the systemic mechanisms remain poorly understood. Here, we reveal that foliar SiNPs activate a coordinated defense orchestrated by jasmonate (JA) signaling. 100 mg/L SiNPs reduced grain Cd by 66.58% and increased yield by 38.14%. Driven by this systemic regulation, the defense manifests in two dimensions: (1) internally, SiNP-activated JA signaling promoted Cd sequestration in leaf hemicellulose 2 fraction by 8.94% and regulated key transporter genes (upregulation of OsHMA3; downregulation of OsNramp1, OsZIP1, and OsZIP7); and (2) externally, this shoot-to-root signaling induced rhizosphere metabolic reprogramming (accumulation of secondary metabolites, lipids, and fatty acids) and recruited functional microbes (Desulfovibrio, Gallionellaceae, and Bacillus), resulting in a 17.02% reduction in bioavailable Cd via enriched oxygen-containing functional groups in soil. This work elucidates a novel biogeochemical framework for developing nanotechnology-based strategies for safe rice production in Cd-contaminated fields.},
}

@article {pmid41782168,
year = {2026},
author = {Park, DE and Mohammadi, A and Nelson, SG and Salazar, JE and Bagherichimeh, S and Aziz, M and Onos, A and Villani, J and Fazel, A and Tevlin, E and Huibner, S and Tharao, W and Kaul, R and Liu, CM},
title = {Post-coital dynamics of the penile and cervico-vaginal genital microbiome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02364-2},
pmid = {41782168},
issn = {2049-2618},
support = {PJT-156123 and TMI-138656/CAPMC/CIHR/Canada ; R01A123002-01A1/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The vaginal and penile coronal sulcus microbiome influence reproductive health outcomes and susceptibility to multiple sexually transmitted infections including HIV. There is evidence that genital bacteria are shared between heterosexual partners during sex, but the dynamics of this microbiota exchange remain poorly understood.

RESULTS: Using microbiome characterization from established heterosexual couples, we found that condomless penile-vaginal sex dramatically altered the coronal sulcus microbiome, with transient dominance by Lactobacillus spp. Conversely, condom-protected penile-vaginal sex did not result in significant shifts in overall composition (p = 0.63). Significant changes were observed in the female partner's genital microbiome, including increased Corynebacterium spp. and increased abundance of Bacteria Associated with Seroconversion, Inflammation, and Cells (BASICs) (Prevotella bivia, Peptostreptococcus anaerobius, Dialister micraerophilus, Prevotella disiens, Dialister propionicifaciens, Dialister succinatiphilus) in individuals with a colonized male partner. By 72 h post-coitus L. iners cell-normalized abundance remained elevated in the penile microbiome, but other taxa returned to baseline levels. Causal mediation analysis indicated a pH-mediated increase in vaginal Gardnerella at 72 h.

CONCLUSIONS: Condom-protected penile-vaginal sex was associated with minimal genital microbiome changes, whereas condomless penile-vaginal sex among established couples led to extensive exchange of genital microbiota. Most disruptions to the microbiome resolved within 2-3 days, although changes in vaginal pH were associated with longer-lasting increases in Gardnerella abundance. Video Abstract.},
}

@article {pmid41782027,
year = {2026},
author = {Han, B and Li, X and Li, J and Liu, Y and Li, S and Tian, J and Lv, Z and Liu, D and Li, M and Ji, S and Lu, J and Zhang, Z},
title = {Spatial and cellular composition of lung fibrosis induced by multi-walled carbon nanotubes.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04135-5},
pmid = {41782027},
issn = {1477-3155},
support = {JJ2024ZL0127//Key Projects of the Joint Fund of Heilongjiang Provincial Natural Science Foundation/ ; 31972754//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The pulmonary immune system orchestrates lung homeostasis and protects against environmental insults through coordinated actions of immune and structural cells. Traditional Chinese medicine recognized the functional interaction between the lungs and the large intestine more than 2000 years ago, but direct evidence for this relationship in modern biomedical research remains limited. Although inhaled nanomaterials can induce lung fibrosis, the underlying immune mechanisms and their impact on large intestine remain poorly understood. Here, we integrated spatial transcriptomics, mRNA-seq, metabolomics, microbiome profiling, and validation in vitro to investigate how multi-walled carbon nanotubes (MWCNTs) exposure affects pulmonary immune responses and gut homeostasis in mice.

RESULTS: MWCNTs were administered to mice via oropharyngeal aspiration. We integrated spatial transcriptomics, bulk RNA sequencing, serum metabolomics, 16S rRNA microbiome profiling, and macrophage experiments in vitro. This multi-omics approach mapped pulmonary cellular alterations, identified key cell-cell signaling pathways, and examined downstream metabolic and intestinal changes provoked by MWCNTs. The results suggested that inhaled MWCNTs induced distinct spatial reorganization of pulmonary cellular architecture, characterized by macrophage- and fibroblast-enriched clusters associated with localized immune activation. Furthermore, cell-cell communication analysis identified Slamf7-Slamf7 interactions as key drivers of macrophage superactivation evidenced by excessive pro-inflammatory cytokine release. Notably, knockdown of Slamf7 in alveolar macrophages in vitro effectively attenuated the superactivation. The macrophage superactivation altered serum metabolic profiles, particularly in pathways related to energy metabolism and inflammation. Finally, lung injury extended to the distal intestine, where rectal epithelial barrier integrity was compromised, resulting in microbial and metabolic imbalance.

CONCLUSION: These findings highlight the hazardous potential of inhaled MWCNTs based on macrophage superactivation induced by Slamf7 in the lung, providing mechanistic evidence for the lung-gut link described in traditional Chinese medicine. Together, our results identify molecular targets to mitigate nanomaterial immunotoxicity and inform the design and using of safer, surface-engineered MWCNTs.},
}

@article {pmid41782023,
year = {2026},
author = {Liu, J and Cao, J and Jia, L and Gan, Z and Zhao, X and Yang, A and Lai, S and Chen, F and Yang, YT and Zhao, XM},
title = {Impacts of host genetics on gut microbiome composition in Alzheimer's disease.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02342-8},
pmid = {41782023},
issn = {2049-2618},
support = {24JS2810100//Shanghai Science and Technology Commission Program/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; 24KXZNA11//Shanghai Municipal Education Commission/ ; T2225015//National Natural Science Foundation of China/ ; ZDYF2024SHFZ058//Key Science and Technology Project of Hainan Province/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; 2023YFF1204800//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: Host-microbiome interactions play essential roles in the development of Alzheimer's disease (AD), yet the host genetic impacts on gut microbial alterations in AD remain poorly understood.

RESULTS: Here, we simultaneously profiled host genotype and gut microbiome in 252 Chinese individuals with varying degrees of cognitive disability. Using the latent Dirichlet allocation topic model, we identified the Anaerostipes-enriched enterosignature (ES-Ana) at the microbial subgroup level as significantly negatively associated with cognitive disability, which could be recapitulated in external cohorts. With the whole-genome sequencing data, we performed microbiome genome-wide association studies for the ES-Ana relative abundance. We prioritized 41 lead genetic variants and confirmed that the high ES-Ana relative abundance showed a negative correlation with the polygenic risk score of AD, indicating its protective effect against AD. Furthermore, we identified 174 ES-Ana-associated genes, which are enriched in AD-related biological functions and phenotypes, and exhibite pervasive underexpression in glial cells during brain aging.

CONCLUSIONS: In summary, our study reveals the complex genetic effects on the gut microbiota in AD, and provides novel evidence for the roles of the gut-brain axis in AD. Video Abstract.},
}

@article {pmid41782011,
year = {2026},
author = {Wang, X and Tian, S and Zhang, Y and Yang, L and Hu, D and Wang, Z and Yang, X and Li, S and Wei, J and Zhou, W and Wang, S and Deng, L and Li, F and Hou, S and Li, P and Ru, J},
title = {Bacteria and phage consortia modulate cecal SCFA production and host metabolism to enhance feed efficiency in ducks.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02368-y},
pmid = {41782011},
issn = {2049-2618},
support = {CARS-42-2//China Agriculture Research System of MOF and MARA/ ; 32341055//National Natural Science Foundation of China/ ; 273124240//Deutsche Forschungsgemeinschaft/ ; 226-2025-00030//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The gut microbiota influences poultry health, nutrition, feed efficiency (FE), and overall productivity. However, the relationship between gut microbes, including bacteria and phages, and FE in ducks remains underexplored. To address this, we integrated cecal 16S amplicon, metagenome, microbiota-derived short-chain fatty acids (SCFAs) profiling, liver transcriptome, and serum metabolome data to illustrate the contribution of the gut microbiome (bacteria and viruses) to duck FE.

RESULTS: We reconstructed viral genomes and prokaryotic metagenome-assembled genomes (MAGs) and annotated their genes using comprehensive databases. Prokaryotic hosts of viruses were also predicted to understand virus-host dynamics within the gut ecosystem. Our results revealed that high-FE ducks have higher concentration of propionate and butyrate in cecum compared with low-FE ducks. The metagenome sequencing revealed distinct cecal microbiota profiles between two groups, with increased relative abundance of representative SCFA producers, especially Paraprevotella sp905215575 and Bacteroides sp944322345, and enhanced SCFA-biosynthesis pathways in high-FE ducks. Virome genome assembly identified two phages encoding auxiliary metabolic genes (AMGs) involved in pyruvate metabolism, enhancing nutrient availability for host bacteria to produce SCFAs (e.g., temperate phage-encoded pyruvate phosphate dikinase) or exploiting host central metabolic pathways for viral replication (e.g., lytic phage-encoded formate C-acetyltransferase). Furthermore, these representative SCFA-producing bacteria and phage consortia were associated with serum metabolites (including L-histidine and 4-hydroxydecanedioylcarnitine) linked to duck FE.

CONCLUSION: Collectively, these findings provide novel insights into the gut microbial factors regulating FE in ducks, offering potential strategies to optimize poultry nutrition and productivity. Video Abstract.},
}

@article {pmid41781966,
year = {2026},
author = {Srivastava, AK and Mishra, P and Kumari, S and Uddin, N and Chen, S and Zhao, Y and Xie, X},
title = {Post translational modifications as biomarkers of soil microbe responses to nano-pesticides.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04231-6},
pmid = {41781966},
issn = {1477-3155},
support = {32272514//National Natural Science Foundation of China/ ; },
abstract = {Nano-pesticides represent a significant technology advancement in modern agricultural, offering improved target specificity and reduced chemical load. However, their potential to induce subtle, sub-lethal disturbance in soil microbial function remains poorly resolved and is not adequately capture by conventional indicators such as microbial diversity, abundance, or bulk enzymatic activity. The central novelty of this review lies in proposing post-translational modifications (PTMs) as functional, early-warning biomarkers for nano-pesticide induced microbial stress, providing a molecular resolution that bridges exposure and ecological outcome. This review critically examines the current evidence on nano-pesticides-microbiome interaction and PTM-centric framework to interpret microbial responses at the protein regulation level. We highlight phosphorylation, acetylation, and ubiquitination regulate microbial stress responses, modulating detoxification enzymes, efflux pumps, and cellular signalling pathways under nanoparticle-induced stress. Unlike prior reviews that emphasize toxicity endpoints or gene-level responses, this work integrates metaproteomic evidence demonstrating PTM enrichment within stress-responsive functional protein groups across real environmental datasets, underscoring their relevance as conserved biomarkers of adaptive and maladaptive responses. By integrating metagenomics with metaproteomic and metabolomics, this review illustrates how PTM profiling enables mechanistic insight into microbial adaptation, functional impairment, and resilience under nano-pesticide pressure. Furthermore, we introduce a systems-level perspective that combines PTM data with computational modelling and AI-assisted bioinformatics to predict microbiome shifts and ecological risk, an approach not previously synthesized within the context of nano-pesticide assessment. Collectively, this review bridges nanomaterial design, microbial molecular regulation, and environmental risk evaluation, and proposes PTM-based assessment as a new paradigm for developing microbiome-safe, eco-compatible nano-pesticides and advancing molecular environmental monitoring strategies.},
}

@article {pmid41781883,
year = {2026},
author = {Xie, Y and Wang, R and Liu, X and Du, Q and Mo, S and Liu, Q and Yang, G and Fan, Z and Li, J},
title = {Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04902-2},
pmid = {41781883},
issn = {1471-2180},
support = {32171607//National Natural Science Foundation of China/ ; },
}

@article {pmid41781872,
year = {2026},
author = {Tian, N and Liu, M and Zhao, Y and Lian, Y and Jin, M and Yang, F},
title = {Gut microbiota dysbiosis and metabolic reprogramming in pediatric migraine: a multi-omics analysis revealing diagnostic biomarkers.},
journal = {The journal of headache and pain},
volume = {},
number = {},
pages = {},
doi = {10.1186/s10194-026-02315-0},
pmid = {41781872},
issn = {1129-2377},
support = {2022 Budget Approval No. 180 of Hebei Provincial Department of Finance//Provincial Medical Outstanding Talents Project funded by the Provincial Government in 2022/ ; Grant No. 20260868//Hebei Provincial Medical Science Research Project funded by the Health Commission of Hebei Province/ ; 2026 Hebei Provincial Introduction of Foreign Intelligence Project//Hebei Provincial Department of Science and Technology/ ; },
}

@article {pmid41781852,
year = {2026},
author = {Eldridge, N and Spörri, L and Kreuzer, M and Haldimann, G and Zinkernagel, MS and Zysset-Burri, DC},
title = {Uncovering the relationship between the human ocular surface microbiome and gut microbiome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04878-z},
pmid = {41781852},
issn = {1471-2180},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
}

@article {pmid41781851,
year = {2026},
author = {Mougeot, JC and Beckman, MF and Henry, AA and Lalla, RV and Brennan, MT and Mougeot, FB},
title = {Oral dryness related symptoms in radiation-treated head and neck cancer patients: a pilot study of oral microbiome composition and function.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04885-0},
pmid = {41781851},
issn = {1471-2180},
}

@article {pmid41781692,
year = {2026},
author = {Kim, H and Oh, S and Hong, JS and Kang, MS and Lee, HJ and Park, KU},
title = {Exploratory randomized trial of Weissella cibaria CMU and oral microbiome changes in peri implant mucositis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42961-7},
pmid = {41781692},
issn = {2045-2322},
support = {02-2022-0019//Seoul National University Bundang Hospital/ ; NRF-2023R1A2C2002783//National Research Foundation of Korea/ ; },
}

@article {pmid41781556,
year = {2026},
author = {Le Bras, A},
title = {Breath as a marker of gut microbiome health.},
journal = {Lab animal},
volume = {55},
number = {3},
pages = {71},
doi = {10.1038/s41684-026-01705-w},
pmid = {41781556},
issn = {1548-4475},
}

@article {pmid41781471,
year = {2026},
author = {Degraeve, AL and Cutignano, A and Piscitelli, F and Villano, R and De Simone, G and Verde, R and Thibaut, MM and Bindels, LB and Di Marzo, V},
title = {Changes in levels of endocannabinoidome mediators in mice with cancer cachexia: links with steatosis and gut microbial dysbiosis.},
journal = {BJC reports},
volume = {4},
number = {1},
pages = {},
pmid = {41781471},
issn = {2731-9377},
support = {F.R.S.-FNRS, MIS F.4512.20, 40009849//FNRS and the Walloon Region in the context of the funding of the strategic axis FRFS-WELBIO/ ; },
abstract = {BACKGROUND: Cachexia is a debilitating syndrome associated with involuntary weight loss, often occurring in cancer patients. In both humans and animal models, alterations in endocannabinoid (eCB) signaling occur in association with both metabolic disorders and several types of tumors. The wider signaling system, including the two eCBs, anandamide (AEA) and 2-arachidonoyl-glycerol (2-AG), their congeners and other long chain fatty acid amides, as well as their metabolic enzymes and receptors, is known as endocannabinoidome (eCBome). The eCBome is involved, among others, in the control of energy balance and cancer and interacts with the gut microbiome.

METHODS: Using mass spectrometry-based targeted lipidomics, we measured the hepatic and intestinal concentrations of eCBome mediators in mice injected with colon carcinoma 26 (C26) cells, a model of cancer cachexia characterized, among others, by weight loss, hepatic dyslipidemia, and gut microbiome dysbiosis.

RESULTS: We report that, 10 days after C26 cell injection, concomitant with >10% weight loss, eCBome lipids levels, namely 2-AG, AEA, and some of its N-acyl-ethanolamine congeners, as well as N-oleoyl-glycine, N-acyl-serotonins, and N-acyl-taurines (NATs), are altered in intestinal sections and the liver of C26 mice (e.g., hepatic 2-AG -30%, jejunal 2-AG + 30%, jejunal AEA -55%, hepatic N-oleoyl-ethanolamine (OEA) + 223%, hepatic NATs +144%, +141%, +216%). Gut dysbiosis was evident in these mice (PERMANOVA at the family level: R² = 69%, p < 0.001), with altered levels in 3 phyla (mainly the Proteobacteria, +1484%), 12 families, and 12 genera (all with adjusted p < 0.05). Additionally, 2-AG, AEA, OEA, N-arachidonoyl-serotonin, and NAT levels in the liver positively correlated with hepatic total lipids, triglycerides, and cholesterol, whereas N-docosahexaenoyl-ethanolamine and N-docosahexaenoyl-serotonin showed negative correlations. Jejunal AEA negatively, and hepatic OEA and NATs positively, correlated with weight loss. Intestinal eCBome mediators correlated with several cecal microbial taxa, including genera known to include strains beneficial in metabolic disorders, such as Bacteroides, Parabacteroides, Dysosmobacter, and Prevotella.

CONCLUSIONS: These observations pinpoint eCBome mediators as new multi-functional players in the hepatic complications and gut dysbiosis accompanying cancer cachexia.},
}

@article {pmid41781451,
year = {2026},
author = {Martins, B and Martins, J and Castelo-Branco, M and Gonçalves, J},
title = {Sex-dependent dysregulation of the gut-brain NPYergic system in a mouse model of autism spectrum disorder.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42601-0},
pmid = {41781451},
issn = {2045-2322},
support = {UI/BD/150837/2021//Fundação para a Ciência e a Tecnologia/ ; FCT/UIDP&B/04950/2025//Fundação para a Ciência e a Tecnologia/ ; 2022.01066.PTDC//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {The microbiome-gut-brain axis has been increasingly recognized for its role in the pathophysiology of autism spectrum disorder (ASD), yet the underlying molecular mechanisms remain poorly understood. Neuropeptide Y (NPY), a key modulator of gut-brain communication, may play a pivotal role in this axis. This study investigated the sex-specific molecular profile of the NPY system in gut-brain communication via a genetic mouse model of ASD, the Nf1[+/-] mice. Quantitative real-time PCR was performed to assess the expression of NPY and its receptor transcripts in the amygdala, hippocampus, prefrontal cortex and intestinal tissue of juvenile male and female Nf1[+/-] mice. Additionally, gut microbiota analysis focused on Lactobacillus species in stool samples. Special emphasis was placed on sex differences, an area underexplored in ASD research. Sex-specific differences in NPY and its receptor expression were observed in both the brain and intestinal tissues of Nf1[+/-] mice. In mutant females, estrous cycle fluctuations were partly associated with changes in the NPY system. Notably, distinct correlations between the brain and intestinal NPY systems were identified in both sexes of wild-type (WT) and Nf1[+/-] mice. Microbiota analysis revealed sex-dependent alterations in Lactobacillus abundance, which correlated with the intestinal NPY system. Importantly, the Y2 receptor exhibited sex-specific expression patterns in both the gut and brain of Nf1[+/-] mice. This study provides novel evidence that the NPY system may play a critical role in gut-brain communication in ASD, with sex-dependent alterations in both the brain and gut. The intestinal Y2 receptor has emerged as a potential molecular biomarker for ASD, underscoring the importance of incorporating sex as a biological variable in future ASD research.},
}

@article {pmid41781334,
year = {2026},
author = {Duan, Y and Huang, M and Ye, L and Ma, L and Wu, Y and Du, Y and Liu, J and Song, F and Tian, L and Cai, W and Li, H and Zhou, X and Luo, S},
title = {Dynamic A-to-I RNA editing in response to gut microbiome in honey bees.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280291.124},
pmid = {41781334},
issn = {1549-5469},
abstract = {ADAR-mediated adenosine-to-inosine (A-to-I) mRNA editing contributes to the proteomic diversity and behavioral complexity of animals. While recent studies indicate that the gut microbiome influences various aspects of animal behavior, the potential involvement of RNA editing in gut-brain interactions remains unexplored. Comparative transcriptomic analyses were performed between heads of germ-free (GF) versus conventional (CV) honey bees. A total of 1,528 A-to-I editing sites are identified in honey bee heads, among which nonsynonymous editing sites are overrepresented compared to random expectation. Overall editing levels are significantly downregulated in GF compared with CV, but Adar gene is not differentially expressed. However, Adar p.482 Ile>Met auto-recoding site, which is speculated to modulate Adar activity, is identified as a high-confidence differential editing site (DES) with decreased editing level in GF. Quantification of gut microbiota across 12 CV individuals reveals a significant positive correlation between p.482 Ile>Met editing level and Lactobacillus and Bombilactobacillus abundance. Colonization of a single bacterium Lactobacillus or Bombilactobacillus instead of Gilliamella in GF bees successfully restores the Adar p.482 Ile>Met and the global editing level. Our work demonstrates the complex and dynamic transcriptomic diversity exerted by A-to-I RNA editing, and discovers the axis of gut-Lactobacillus/Bombilactobacillus-brain-Adar-global RNA editing, providing an exciting scenario that gut microbiomes could impact RNA editing which might further facilitate phenotypic plasticity of social insects.},
}

@article {pmid41781219,
year = {2026},
author = {T Pallenberg, S and Zamarrón de Lucas, E and Párniczky, A and Lopes de Bragança, R},
title = {Cystic fibrosis year in review 2025.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.02.010},
pmid = {41781219},
issn = {1873-5010},
abstract = {Cystic fibrosis (CF) is being reshaped by CFTR modulators (CFTRm), yet infection, inflammation, and multisystem comorbidities persist. This review of the 2025 CF literature summarizes how CF is evolving into a chronic, heterogeneous condition in the modulator era. First, we discuss the consolidation of elexacaftor/tezacaftor/ivacaftor (ETI) and next-generation modulators, highlighting durable gains in lung function and survival alongside persistent gaps in eligibility, access, and long-term safety, particularly for individuals with advanced structural lung damage or class I variants. Second, emerging mutation-agnostic therapy strategies are outlined, including ENaC blockade, neutrophil-directed anti-inflammatories like brensocatib, and gene and nucleic acid-based therapeutic approaches . Third, we examine airway infection and inflammation: while ETI reduces pathogen detection and systemic inflammatory markers, chronic Pseudomonas aeruginosa and heterogeneous neutrophilic endotypes frequently persist, and mucosal immune defects remain incompletely corrected. In this context, bacteriophage therapy has emerged as a candidate for multidrug-resistant infections, while microbiome-focused interventions show limited clinical impact despite clear shifts in microbial communities. Finally, as survival improves, pregnancy, age-related malignancy, and cardiovascular disease are becoming increasingly relevant, necessitating new models of multidisciplinary, lifespan care. Collectively, these developments mark a shift towards equitable, lifelong, system-level management of health in an aging and increasingly diverse CF population.},
}

@article {pmid41781021,
year = {2026},
author = {Hume-Nixon, M and Clark, S and Ratu, T and Nguyen, C and Neal, EFG and Bright, K and Strobel, AG and Watts, E and Hart, J and Fong, JJ and Rafai, E and Sakumeni, K and Steer, A and Vereti, I and Russell, F},
title = {The efficacy of a single dose of oral azithromycin in labour to prevent infections in infants and birthing parents in Fiji: secondary outcomes from a randomised controlled trial.},
journal = {BMJ global health},
volume = {11},
number = {3},
pages = {},
doi = {10.1136/bmjgh-2025-019851},
pmid = {41781021},
issn = {2059-7908},
mesh = {Humans ; *Azithromycin/administration & dosage/therapeutic use ; Female ; Pregnancy ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Fiji/epidemiology ; Adult ; Administration, Oral ; Infant ; Infant, Newborn ; Labor, Obstetric ; *Soft Tissue Infections/prevention & control/epidemiology ; Male ; Young Adult ; },
abstract = {INTRODUCTION: Our Bulabula MaPei trial of azithromycin administered during labour in Fiji found no evidence of a reduction in the primary endpoint of infant skin and soft tissue infections (SSTIs) at 3 months of age. Here, we determine the efficacy of this intervention on several secondary outcomes.

METHODS: This randomised controlled trial included healthy pregnant adults presenting to hospital in labour. Prior to delivery, participants were randomly assigned a single dose of 2 g of oral azithromycin or placebo that were identical in appearance to mask treatment allocation, in a 1:1 ratio stratified by ethnicity. Cumulative incidence of infections and antibiotic prescription was compared using an intention-to-treat analysis of complete cases. Adverse events described as proportions by group at specified time points.

RESULTS: From June 2019 to January 2022, we enrolled 2110 pregnant people and their infants (n=2122; azithromycin n=1059; placebo n=1063). At 3 months, the cumulative incidence of infant infections was 13.6% in the azithromycin group compared with 17.3% in the placebo group (risk ratio (RR) 0.79; 95% CI 0.63 to 0.99; p=0.038). Infections among birthing parents, including SSTIs, were reduced with the greatest effect 1 week postdelivery (infections: RR 0.31; 95% CI 0.13 to 0.71; p=0.006, SSTIs: RR 0.25; 95% CI 0.08 to 0.75; p=0.013) but with a diminishing effect up to 6 months postdelivery. There was no effect on the prescription of antibiotics at any time point.

CONCLUSIONS: Intrapartum azithromycin prevents a variety of infections for birthing parents and infants up to 12 months post partum in Fiji. However, further research is required to identify target populations and better characterise potential impacts on antimicrobial resistance and the infant microbiome and resistome.

TRIAL REGISTRATION NUMBER: NCT03925480.},
}

Humans
*Azithromycin/administration & dosage/therapeutic use
Female
Pregnancy
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Fiji/epidemiology
Adult
Administration, Oral
Infant
Infant, Newborn
Labor, Obstetric
*Soft Tissue Infections/prevention & control/epidemiology
Male
Young Adult

@article {pmid41780872,
year = {2026},
author = {Vencek Enriquez, M and Waite-Cusic, J},
title = {Evaluation of bioprotective starter culture and aging temperature on gas formation by Paucilactobacillus wasatchensis in Gouda cheese using computed tomography imaging.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27847},
pmid = {41780872},
issn = {1525-3198},
abstract = {Late gas defects caused by nonstarter lactic acid bacteria (NSLAB) present significant economic and quality challenges in semi-hard aged cheeses. Finding practical mitigation strategies to defend against gas-producing NSLAB is important to reduce the economic impact of this defect. Paucilactobacillus wasatchensis is one species of NSLAB associated with late gas defects in Cheddar; however, little is known about its behavior in other semi-hard cheeses. This study investigated the behavior of Pa. wasatchensis in Gouda cheese and explored aging temperature and the use of bioprotective (nisin-producing) cultures to mitigate gas production. Gouda cheese was produced either using conventional or nisin-producing bioprotective starter culture with and without inoculation with Pa. wasatchensis SK0033 into the cheese milk (4 log cfu/mL). All treatment combinations of starter culture and inoculation status were replicated on 2 unique production days. Wheels (n = 4) from each production were randomized for aging at 4°C, 10°C, or 15°C for up to 40 wk. Computed tomography scanning was used as a novel, nondestructive method to observe gas formation and imaging analysis was used to quantify of gas volume within cheese wheels (n = 3/cheese make) throughout aging. Microbiome analysis was performed on selected cheese wheels at the end of aging. The fourth wheel for each treatment was used for intermittent sampling for destructive testing (i.e., pH, water activity, moisture, salt). The highest volume of gas was produced by Pa. wasatchensis in cheese made with the conventional starter at aged at 15°C. Gas volume in these wheels ranged from as low as 0.02% (0.5 wk) to as high as 2.54% (39 wk), which increased over the aging period. Considerable variability in gas volume between wheels from the same cheese make was observed which aligns with industry reports of defect variability at commercial scale. Reduced aging temperature (4°C) delayed but did not prevent gas production caused by Pa. wasatchensis during aging; growth of Pa. wasatchensis at all aging temperatures was confirmed by microbiome analysis. The replacement of the conventional starter with a nisin-producing bioprotective starter effectively prevented growth and gas formation caused by Pa. wasatchensis at all aging temperatures. The presence of nisin in the cheese made with bioprotective starter was confirmed to be active against Pa. wasatchensis using the soft agar overlay method. These findings illustrated the ability of Pa. wasatchensis to cause late gas defects in Gouda and demonstrated the efficacy of a bioprotective starter culture to mitigate this defect.},
}

@article {pmid41780827,
year = {2026},
author = {Austin, RR and Fiszman, M and Guerra, E and Zhang, R and Kilicoglu, H},
title = {Advancing Whole-Person Health through Informatics: A Narrative Review of Knowledge Resources for Complementary and Integrative Health.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101461},
doi = {10.1016/j.tjnut.2026.101461},
pmid = {41780827},
issn = {1541-6100},
abstract = {OBJECTIVE: Complementary and integrative health (CIH) interventions, including nutritional strategies, are widely used to support whole-person health, yet evidence on their efficacy, safety, and mechanisms remains fragmented. This narrative review maps existing CIH knowledge resources, identifies critical gaps, and highlights challenges in interoperability and integration. We propose artificial intelligence-driven informatics strategies to standardize, connect, and leverage these resources, with the goal of advancing discovery, precision nutrition, and personalized approaches to health and well-being.

MATERIALS AND METHODS: We conducted a narrative review of publicly available knowledge resources on complementary health interventions, focusing on their effectiveness, safety, and biological mechanisms, including the microbiome. Interventions were categorized as nutritional, physical, or psychological. Resources were then classified as knowledge bases, datasets, databases, ontologies, knowledge graphs, platforms, or initiatives, with summaries of their scope, functionality, and contributions.

RESULTS: We identified 47 resources that can support complementary and integrative health informatics (15 knowledge bases, 13 databases, 7 datasets, 4 platforms, 3 initiatives, 3 ontologies, 2 knowledge graphs). Categories included nutritional interventions (32, with 13 on the microbiome), physical interventions (4), psychological interventions (3), and comprehensive or multi-modal resources (7). Most resources (39) were publicly available.

CONCLUSION: Advancing whole-person health requires greater standardization and integration of knowledge resources, which in turn enables more effective application of AI and informatics methods. When well-structured, interoperable resources are coupled with these computational methods, they can unify diverse knowledge domains, advance the science of complementary and integrative health, and accelerate discovery in personalized nutrition.},
}

@article {pmid41780804,
year = {2026},
author = {Rotzetter, J and Spörri, L and Herzog, EL and Kreuzer, M and Zinkernagel, MS and Zysset-Burri, DC},
title = {A preliminary investigation on the influence of sample storage on the low-abundant ocular surface microbiome.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107437},
doi = {10.1016/j.mimet.2026.107437},
pmid = {41780804},
issn = {1872-8359},
abstract = {In this study, the impact of sample freezing prior to DNA extraction was investigated on a small sample set (n = 6) to determine whether this affects the composition of the ocular surface microbiome - a low biomass environment. Frozen samples exhibited a reduced detection of Gram-negative bacteria compared to directly processed samples.},
}

@article {pmid41780644,
year = {2026},
author = {Basilicata, MG and Scisciola, L and Pesapane, A and Fontanella, RA and Balzano, N and Maddalena Palazzo, AM and Joshi, R and Zia, A and Tortorella, G and Ulfat, Z and Arshad, M and Aquino, G and Sommella, E and Malavolta, M and Giuliani, A and Campiglia, P and Barbieri, M and Paolisso, G},
title = {Volatilomics insights in older adults with diabetes: from metabolic mechanisms to precision geriatric medicine.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113194},
doi = {10.1016/j.diabres.2026.113194},
pmid = {41780644},
issn = {1872-8227},
abstract = {AIMS: This review aims to evaluate the hypothesis that Volatilomics-the comprehensive analysis of volatile organic compounds (VOCs) from breath, skin, urine, and other biological matrices-can serve as a non-invasive tool to characterize metabolic alterations associated with aging and diabetes mellitus in older adults, supporting precision geriatric medicine.

METHODS: We conducted a narrative review of experimental and clinical studies investigating VOC signatures in aging individuals with diabetes. The analysis focused on associations between VOC profiles and key biological mechanisms, including oxidative stress, lipid peroxidation, mitochondrial dysfunction, inflammaging, and host-microbiome interactions. We also examined analytical technologies and methodologies, such as advanced mass spectrometry platforms, sensor-based devices, and artificial intelligence-driven pattern recognition approaches.

RESULTS: The reviewed evidence suggests that diabetes is associated with distinctive VOC patterns; however, direct evidence specifically derived from geriatric cohorts remains limited. These VOC patterns are associated with glycemic imbalance and age-related metabolic dysfunction and show potential utility for early detection, clinical phenotyping, and individualized monitoring, particularly in frail or multimorbid patients. Technological advances are facilitating translation toward portable and home-based applications.

CONCLUSIONS: Volatilomics represents a promising, non-invasive approach to improve diabetes management in aging populations. Despite its potential, challenges remain, including methodological heterogeneity, limited reproducibility, confounding effects of comorbidities and polypharmacy, and the lack of large longitudinal geriatric cohorts.},
}

@article {pmid41780449,
year = {2026},
author = {Wang, J and Zhang, Y and Ding, Y and Li, D and Zhang, Y},
title = {Hydrocarbon subsidy-stress and divergent reduced iron-manganese thresholds shape microbial resilience in anoxic aquifers.},
journal = {Water research},
volume = {296},
number = {},
pages = {125670},
doi = {10.1016/j.watres.2026.125670},
pmid = {41780449},
issn = {1879-2448},
abstract = {The co-occurrence of geogenic metal mobilization and anthropogenic hydrocarbon contamination represents a pervasive hydro-biogeochemical challenge, yet the non-linear mechanisms governing microbial resilience in these multi-stressor aquifers remain poorly constrained. Here, we decode these complex interactions by integrating high-resolution microbiome profiling with an interpretable machine learning framework (XGBoost-SHAP). We identify a "multi-threshold superposition" model for total petroleum hydrocarbons (TPHs) that delineates a tri-phasic ecological transition: a progression from carbon limitation to metabolic subsidization, culminating in a toxicity-driven regime shift beyond a mechanistically grounded tipping point (3.485 mg/L). Crucially, we unveil a "Fe(II)-Mn(II) Paradox" wherein geochemically similar metals exert divergent ecological controls. Deviating from the additive toxicity paradigm, elevated Fe(II) (>9.22 mg/L) serves as a redox-mediated buffer against hydrocarbon stress; in contrast, Mn(II) operates as a toxicological synergist, amplifying metabolic and structural impairments beyond predicted additive levels. Mechanistically, this resilience is underpinned by the rare taxa acting as a functional seed bank, which reconfigures network topology from competitive exclusion to cooperative syntrophy. These findings establish the stoichiometric Fe(II)/Mn(II) ratio (threshold: 1.935) as a master regulator of aquifer, providing a quantitative foundation for "precision zoned intervention" strategies-advocating for monitored natural attenuation in iron-buffered zones versus active engineering in manganese-aggravated hotspots.},
}

@article {pmid41780267,
year = {2026},
author = {Zhou, Y and González, CA and Manquian, J and Vergara, K and Gajardo, G and Guzmán, L and Espinoza-González, O and Carbonell, P and Riquelme, C and Ueki, S and Nagai, S and Fujiyoshi, S and Maruyama, F and Yarimizu, K and Uhanie Perera, I and Acuña, JJ and Zhang, Q and Jorquera, MA},
title = {Microbial communities in coastal seawater during Heterosigma akashiwo and Alexandrium catenella blooms in Chilean Patagonian fjords.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107949},
doi = {10.1016/j.marenvres.2026.107949},
pmid = {41780267},
issn = {1879-0291},
abstract = {Harmful algal blooms (HABs) are recurring events in Chilean coasts where free-living and associated microbiota (also known as HAB holobiont) may play a crucial role for occurrence, monitoring and prediction of HAB. Here, we investigated the associated microbial communities with Heterosigma akashiwo and Alexandrium catenella blooms in the Chilean Patagonia fjords by microscopic observations and rRNA metabarcoding sequencing. By microscopic observations, H. akashiwo and A. catenella cells were accompanied by abundant diatoms (Skeletonema) and athecate dinoflagellates, and diatoms (Thalassiosira and Leptocylindrus) and dinoflagellates (Heterocapsa), respectively. By 16S rRNA- and 18S rRNA-based metabarcoding sequencing, our results not only revealed significant differences in richness, diversity, and taxonomic structure of microbial communities between blooms but also between the studied seawater fractions (1 and 0.2 μm). In 18S rRNA-based communities, H. akashiwo bloom was generally dominated by eukaryotic Stramenopiles, Raphidophyceae_X and Heterosigma, while A. catenella bloom was dominated by eukaryotic Alveolata and protists Syndiniales (Dino-Group-I) at the phylum, order, and genus level, respectively. Proteobacteria (Rhodobacteriales), Bacteroidota (Flavobacteriales) and Cyanobacteria (Synechococcales) were dominant taxa in the structure of 16S rRNA-based communities in both blooms and both seawater fractions. Our study also suggested a high and differentiated interaction between 16S rRNA- and 18S rRNA-based microbial communities in both blooms, with the bacteria Blastopirellula and the dinoflagellate Dino-Group-I-Clade-1 as keystone taxa in A. catenella bloom.},
}

@article {pmid41779349,
year = {2026},
author = {González-González, A and Soria-Utrilla, V and Fontalba-Romero, MI and Núñez-Sánchez, MÁ and Adarve-Castro, A and Queipo-Ortuño, MI and Ramos-Molina, B and Martínez-Montoro, JI and Fernández-García, JC},
title = {The Role of Butyrate in People with Metabolic Dysfunction-Associated Steatotic Liver Disease and Related Metabolic Comorbidities: A Systematic Review.},
journal = {Current obesity reports},
volume = {15},
number = {1},
pages = {},
pmid = {41779349},
issn = {2162-4968},
abstract = {BACKGROUND: Metabolic dysfunction–associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease worldwide and is strongly linked to obesity, type 2 diabetes, and cardiovascular disease. Growing evidence highlights the role of the gut–liver axis, particularly microbial metabolites such as the short-chain fatty acid (SCFA) butyrate, in MASLD pathophysiology. However, clinical data on butyrate levels and the abundance of butyrate-producing bacteria in MASLD patients remain inconsistent.

OBJECTIVES: To systematically synthesize human evidence evaluating the associations between butyrate levels and butyrate-producing gut bacteria with MASLD presence and severity, as well as related metabolic comorbidities.

METHODS: A systematic search was conducted in PubMed and Embase from inception to April 7, 2025, following PRISMA 2020 guidelines (PROSPERO registration CRD420251162439). Eligible studies included observational human research assessing fecal or plasma SCFA concentrations and/or the abundance of butyrate-producing taxa in adults with MASLD and related metabolic disorders. Study quality was appraised using the Newcastle–Ottawa Scale, and results were narratively synthesized due to heterogeneity across methods and outcomes.

RESULTS: From 233 records, seven studies met inclusion criteria (2020–2025; n = 1,185). Most were cross-sectional or case–control designs of moderate to high quality (NOS 6–8/9). Individuals with MASLD generally exhibited lower fecal or serum butyrate concentrations and reduced abundance of Faecalibacterium prausnitzii, Eubacterium, and other butyrate-producing bacteria versus controls. These alterations were associated with hepatic steatosis, fibrosis, inflammation, and adverse metabolic profiles - higher BMI, insulin resistance, and dyslipidemia. Geographic and sex-related differences were also reported.

CONCLUSIONS: This systematic review suggests that reduced butyrate availability and alterations in butyrate-producing gut taxa are associated with MASLD presence and severity and with adverse metabolic traits. However, substantial methodological heterogeneity and the observational design of available studies preclude causal inference. Larger, well-phenotyped, multicentre studies using standardized SCFA quantification, dietary and medication ascertainment, and functional microbiome profiling are needed to validate these findings and clarify their diagnostic and therapeutic implications.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13679-026-00694-8.},
}

@article {pmid41779338,
year = {2026},
author = {Ringold, SM and Cermak, SA and Labus, JS and Mayer, EA and Aziz-Zadeh, L},
title = {Sensory Over-Responsivity in Autism: A Bidirectional Brain-Gut-Microbiome Model.},
journal = {Journal of autism and developmental disorders},
volume = {},
number = {},
pages = {},
pmid = {41779338},
issn = {1573-3432},
}

@article {pmid41779301,
year = {2026},
author = {Cheah, AS and Tan, JW and Jaafar, F and Yeo, WWY},
title = {Precision Microbiome Modulation: Exploring Lactobacillus spp. as A Targeted Strategy for Type 2 Diabetes Management.},
journal = {Current nutrition reports},
volume = {15},
number = {1},
pages = {},
pmid = {41779301},
issn = {2161-3311},
abstract = {PURPOSE OF REVIEW: The International Diabetes Federation projects a prevalence of 783.2 million cases of type 2 diabetes mellitus (T2DM) by 2045. The escalation in healthcare expenditure and adverse effects of current drugs necessitate a clinically effective and low-cost alternative therapeutic option with minimal health complications. Lactobacillus spp., a well-studied gut probiotic has shown promising antidiabetic effects against T2DM in several randomized controlled trials. However, the exact mechanisms of Lactobacillus spp. in regulating the glycaemic profile are not well elucidated, limiting the optimization of probiotic-based interventions. Therefore, this paper aims to explore the various antidiabetic mechanisms of Lactobacillus spp., with a focus on their integration into precision medicine approaches.

RECENT FINDINGS: Lactobacillus spp. supplementation alleviates insulin resistance in T2DM by modulating glucose metabolism and transport, exerting anti-inflammatory and anti-oxidative effects as well as restructuring gut microbiota. Lactobacillus spp. also enhance the functional properties of food by increasing the antioxidant capacity and improving glucose metabolism. Despite these promising effects, clinical translation is challenged by strain-specific survivability in the gastrointestinal tract and safety concerns. Thus, leveraging precision medicine via tailoring treatments based on individual microbiome profiles, genetic backgrounds and metabolic phenotype may unravel the full therapeutic potential of targeted Lactobacillus spp. for T2DM treatment. This approach can be reached by integrating multi-omics profiling and artificial intelligence technologies.

SUMMARY: Lactobacillus spp. may act as adjunctive support in the management T2DM rather than stand-alone therapies in T2DM management, as their efficacy is dependent on appropriate dietary interventions and metabolic context. Altogether, integrating Lactobacillus spp. into personalized treatment frameworks offers a promising avenue for developing more targeted, effective and safe interventions for T2DM.},
}

@article {pmid41779254,
year = {2026},
author = {Stefanelli, LF and Cattarin, L and Martino, FK and Del Prete, D and Pierantonio, B and Nalesso, F and Mazzitelli, M},
title = {Microbiome alterations and their potential impact on infection risk in chronic kidney disease and end-stage kidney disease: a narrative review.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {41779254},
issn = {1573-2584},
abstract = {Chronic kidney disease [CKD] is associated with profound alterations of both gut microbiota composition and functions, commonly referred to as gut dysbiosis. These changes are driven by several factors such as dietary restrictions, medications, and uremia, which further contribute to patients with CKD to their pro-inflammatory and immunocompromised state. Recent evidence suggests that dysbiosis may also increase susceptibility to infections, which remain a leading cause of morbidity and mortality in CKD patients. In this review, we aimed at examining the features of the altered gut microbiome in patients with CKD, its potential role in promoting infection risk, and current therapeutic strategies targeting the gut microbiota to mitigate CKD-related complications.},
}

@article {pmid41778788,
year = {2026},
author = {Lee, S and Kim, H-L and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Cho, J and Kim, H-N},
title = {Gut microbial community structure, metabolic signature, and resistome in dyslipidemia: implications for cardiovascular disease management.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0097125},
doi = {10.1128/spectrum.00971-25},
pmid = {41778788},
issn = {2165-0497},
abstract = {Dyslipidemia, characterized by abnormal blood lipid levels, constitutes a significant risk factor for cardiovascular disease. Emerging evidence indicates that the gut microbiota influences lipid metabolism, although findings across studies have been inconsistent. In this cross-sectional investigation, we analyzed the composition of gut microbiota, associated metabolic pathways, predicted gut metabolites, and the resistome in 1,384 participants (including 895 individuals with dyslipidemia and 489 controls) through shotgun metagenomic sequencing. Our findings demonstrated that Bacteroides caccae was enriched among dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism. Conversely, Coprococcus eutactus and Coprococcus catus, recognized producers of short-chain fatty acids (SCFAs) involved in lipid regulation, as well as Blautia obeum, known to be positively affected by SCFAs, were more prevalent in the control group. Additionally, we identified an enrichment of the gene family responsible for dTDP-beta-D-fucofuranose biosynthesis, associated with bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris serving as a major contributor. Dyslipidemia cases also exhibited depletion of glycogen and peptidoglycan biosynthesis pathways, which may compromise energy storage and immune function, alongside decreased levels of pseudouridine, a molecule involved in RNA metabolism. Furthermore, a marginal increase in abundance of antibiotic-resistance genes, tetQ, was observed in dyslipidemia cases, suggesting a potential link between the gut resistome and metabolic dysregulation. These results offer novel insights into the role of gut microbiota in the pathophysiology of dyslipidemia and underscore potential microbiome-targeted interventions for metabolic disease management.IMPORTANCEDyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. This study analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and antimicrobial resistance genes in 1,384 participants using shotgun metagenomic sequencing. Individuals with dyslipidemia exhibited an imbalance in gut bacteria, including an increase in Bacteroides caccae, a species associated with inflammation, and a decrease in short-chain fatty acid-producing bacteria such as Coprococcus eutactus and Blautia obeum, which support metabolic health. Furthermore, we identified significant changes in microbial metabolic pathways related to energy storage and immune function, as well as an increased abundance of tetracycline resistance genes (tetQ), suggesting a potential link between dyslipidemia and antimicrobial resistance. Our study provides a comprehensive overview of dyslipidemia-associated gut microbial alterations, highlighting potential mechanistic links and therapeutic targets.},
}

@article {pmid41778780,
year = {2026},
author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S},
title = {Beyond bacilli: integrating the microbiome into the TB research agenda.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638004},
pmid = {41778780},
issn = {1949-0984},
mesh = {Humans ; *Tuberculosis/microbiology/diagnosis/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; Antitubercular Agents/therapeutic use ; Metabolomics ; Lung/microbiology ; },
abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.},
}

Humans
*Tuberculosis/microbiology/diagnosis/therapy
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Animals
Antitubercular Agents/therapeutic use
Metabolomics
Lung/microbiology

@article {pmid41778628,
year = {2026},
author = {Wang, E and Yan, H and Kong, Z and Xu, X and Zhang, B},
title = {Gamma irradiation and heat exposure generate temperature-responsive microbiota shifts in predatory mite Phytoseiulus persimilis (Mesostigmata: Phytoseiidae).},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toag016},
pmid = {41778628},
issn = {1938-291X},
support = {6222052//Beijing Natural Science Foundation/ ; 32070402//National Natural Science Foundation of China/ ; BAIC01-2026//Beijing Innovation Consortium of Agriculture Research System/ ; },
abstract = {The growing urgency of climate change, particularly the rising frequency and severity of extreme heat events, has spotlighted the need for the thermal resilience of natural enemy in pest management. To understand the plasticity of predatory mite in response to thermal adaptation, 3 irradiated strains of Phytoseiulus persimilis Athias-Henriot were induced by Cobalt-60 gamma rays to evaluate the thermotolerance. We integrated both DNA- and RNA-based 16S rRNA gene sequencing to explore whether irradiation and heat stress could impact the microbiome of the predatory mites. Our findings revealed that irradiation enhanced the heat tolerance of predatory mites without compromising fecundity or predation efficiency. Unexpectedly, irradiation had minimal impacts on overall microbial diversity, whereas RNA-based 16S rRNA gene sequencing unveiled irradiation strain-specific enrichment of stress-responsive taxa (e.g., Bacillus sp.), while no such specific enrichment was observed at the DNA level. Furthermore, heat stress significantly restructured the microbiome of P. persimilis, particularly enriching Limnobacter thiooxidans. Methodologically, the DNA/RNA microbial profiles highlighted divergent functional partitioning: Gammaproteobacteria dominated at DNA level, while transcriptionally active Actinobacteria prevailed in RNA level. In conclusion, these results establish a "host-microbiota co-regulation" paradigm for resistance breeding, offering a sustainable pathway to reinforce biological control systems against global warming challenges.},
}

@article {pmid41778620,
year = {2026},
author = {Wang, Y and OuYang, J and Zhang, H and Shen, Y and Guo, Z and Lv, W},
title = {The Efficacy of Gut Microbiome-Modulating Therapies on Liver Cirrhosis: A Systematic Review and Network Meta-Analysis.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000001010},
pmid = {41778620},
issn = {2155-384X},
abstract = {OBJECTIVE: Gut microbiome-modulating therapies are potential strategies for managing liver cirrhosis (LC), yet head-to-head comparisons to determine the optimal intervention are lacking. This study aimed to evaluate and rank the therapeutic efficacy of these therapies on liver function and disease progression in patients with LC.

METHODS: We searched major databases (PubMed, Web of Science, Embase, Cochrane Library) for randomized controlled trials (RCTs) published from January 1, 2000, to December 30, 2024. Interventions included probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) versus placebo or standard care. Primary outcomes were hepatic function indicators; secondary outcomes included inflammatory markers. Data were analyzed using random-effects frequentist network meta-analyses. The study was registered on PROSPERO (CRD420251000506).

RESULTS: Seventeen studies comprising 1051 individuals were included. Synbiotics demonstrated the most significant efficacy among all interventions, showing superior reduction in blood ammonia levels compared to placebo (Mean Difference (MD): -5.57), probiotics, and prebiotics. Prebiotics showed significant differences in lowering endotoxin levels compared to placebo (MD: -3.29) and probiotics. Furthermore, relative to placebo, prebiotics significantly reduced tumor necrosis factor-alpha (MD: -2.30) and interleukin-6 levels (MD: -4.60).

CONCLUSIONS: This network meta-analysis advances current knowledge by establishing an evidence-based hierarchy of efficacy. Synbiotics are most effective for reducing blood ammonia, whereas prebiotics demonstrate superior efficacy in lowering endotoxin and inflammatory markers. These results support a personalized therapeutic approach: prioritizing synbiotics for patients with hyperammonemia, and prebiotics for those characterized by systemic inflammation. Future high-quality RCTs are needed to standardize specific strain combinations.},
}

@article {pmid41778161,
year = {2026},
author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z},
title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1755982},
pmid = {41778161},
issn = {1664-2392},
mesh = {Animals ; *Lacticaseibacillus rhamnosus/physiology ; *Probiotics/pharmacology ; Mice ; *Lipid Metabolism/drug effects ; Male ; *Gastrointestinal Microbiome ; *Lipopolysaccharides/biosynthesis/metabolism ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Metabolic Diseases/metabolism ; },
abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.

METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.

RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial β-oxidation of long-chain saturated fatty acids, α-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).

DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.},
}

Animals
*Lacticaseibacillus rhamnosus/physiology
*Probiotics/pharmacology
Mice
*Lipid Metabolism/drug effects
Male
*Gastrointestinal Microbiome
*Lipopolysaccharides/biosynthesis/metabolism
Mice, Inbred C57BL
Diet, High-Fat/adverse effects
*Non-alcoholic Fatty Liver Disease/metabolism
*Metabolic Diseases/metabolism

@article {pmid41778020,
year = {2026},
author = {Zou, Q and Zhang, W and Xie, H and Ying, S and Zeng, X and Yao, Y and Zeng, D and Wang, J and Zhang, C and Meng, F},
title = {Inflammatory bowel disease through the lens of microbe-host interactions: immunomodulation, metabolic effects, and genetic susceptibility in microbiota dysbiosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1745929},
pmid = {41778020},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/microbiology/immunology ; *Inflammatory Bowel Diseases/microbiology/immunology/genetics/therapy ; *Gastrointestinal Microbiome/immunology ; *Genetic Predisposition to Disease ; *Immunomodulation ; *Host Microbial Interactions/immunology ; Animals ; *Host-Pathogen Interactions ; Probiotics/therapeutic use ; Prebiotics ; },
abstract = {Inflammatory bowel disease (IBD), including ulcerative colitis, Crohn's disease, and inflammatory bowel disease-unclassified, is a complex intestinal disease influenced by microbial factors, genetic and environmental. IBD has become a global disease with an increasing prevalence, endangering human health worldwide. Through its interactions with host immunity, bacterial metabolites, and genetic components, the intestinal microbiome plays a crucial role in initiating and advancing IBD. Treatment for IBD includes not only corticosteroids, aminosalicylates, antibiotics, TNF-α, α4β7 integrins, IL-12/23 antibodies, and small molecule antibodies, but also complementary and alternative medical therapies such as probiotics and prebiotics. This review primarily explores the relationship between dysbiosis of the microbiota and IBD, including the immune system, metabolites, and genetics related to microorganisms, to provide a deeper and more systematic understanding of the mechanisms linking microbial imbalance to IBD.},
}

Humans
*Dysbiosis/microbiology/immunology
*Inflammatory Bowel Diseases/microbiology/immunology/genetics/therapy
*Gastrointestinal Microbiome/immunology
*Genetic Predisposition to Disease
*Immunomodulation
*Host Microbial Interactions/immunology
Animals
*Host-Pathogen Interactions
Probiotics/therapeutic use
Prebiotics

@article {pmid41777897,
year = {2026},
author = {Tang, X and Man, C and Liu, Z and Gong, D and Fan, Y},
title = {Research on microbial communities in tumor microenvironments: cutting-edge dynamics and future trends from a bibliometric perspective.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1745842},
pmid = {41777897},
issn = {1664-3224},
mesh = {*Tumor Microenvironment/immunology ; Humans ; *Neoplasms/microbiology/therapy/immunology ; Bibliometrics ; *Microbiota ; Animals ; Immunotherapy ; },
abstract = {BACKGROUND: In recent years, researchers have identified numerous potential biomarkers and therapeutic targets applicable to cancer immunotherapy, among which the role of tumor-internal microorganisms in the tumor microenvironment has been explored. However, this field is still in its early stages of development, facing limitations such as the unclear mechanisms of interaction between tumor-internal microorganisms and host immunity, as well as significant variations in microbial profiles among different tumor types and patients.

OBJECTIVE: This study aims to explore the research hotspots and development trends of tumor-internal microorganisms through bibliometric methods and to construct a systematic knowledge map.

METHODS: This study retrieved publications related to tumor-internal microorganisms from the Web of Science Core Collection (WOSCC) prior to December 22, 2025. Subsequently, the selected literature was analyzed using VOSviewer (v.1.6.20), CiteSpace (v.6.4.1R), and SCImago Graphica. In addition, we integrated PubMed data to assess status and trends in preclinical and clinical studies of intratumoral microbiota interventions for anti-tumor therapy efficacy.

RESULTS: From the Web of Science database, we retrieved 1,278 relevant articles. Since 2012, the number of papers published on the intratumoral microbiota has shown an overall upward trend. China and the United States are the two major countries in this field. Keyword analysis shows that "tumor microbiome," "gut microbiome," "cancer," and "Fusobacterium nucleatum" are frequent terms. 11 keyword groups have been identified, among which "tumor immunotherapy" and "immune microenvironment" form two important groups. A total of 69 preclinical and clinical studies has intervened in intratumoral microbiota and affected anti-tumor treatment outcomes. Among them, 25 studies involving Fusobacterium nucleatum account for a large proportion. However, most of these studies are still at the basic or preclinical stage, and clinical translation evidence is limited.},
}

*Tumor Microenvironment/immunology
Humans
*Neoplasms/microbiology/therapy/immunology
Bibliometrics
*Microbiota
Animals
Immunotherapy

@article {pmid41777702,
year = {2026},
author = {Zhang, YW and Li, RY and Wu, Y and Wang, P and Zhou, QR and Su, JC},
title = {Gut microbiota and bone aging: Focusing on the gut-X axis modes.},
journal = {Journal of orthopaedic translation},
volume = {57},
number = {},
pages = {101064},
pmid = {41777702},
issn = {2214-031X},
abstract = {UNLABELLED: As studies have continuously advanced, cross-linking interplay between various organs in aging individuals have continuously emerged as research hotspots. The role of gut microbiota in bone aging-related diseases, including osteoporosis, osteoarthritis, and intervertebral disc degeneration, has been extensively probed. This review first summarized the inseparable association between gut microbiota and osteoporosis, osteoarthritis, and intervertebral disc degeneration, which then explored potential mechanisms of gut-X axis through neuromodulation (microbiota-gut-brain-bone axis), immunomodulation (Th17 and Treg balance), endocrine regulation (gut-derived hormones and 5-HT), metabolite-mediated regulation (SCFAs), bacterial extracellular vesicles, and changes in microbial niche and gut microbiome-associated biomarkers. Moreover, potential intervention strategies including diet, probiotics, fecal microbiota transplantation, and physical activity were summarized to enhance clinical translation applicability. This review creatively exhibited integrated concept of "gut-X axis" to explore common, patterned mechanisms underlying "gut-bone axis", "gut-joint axis", and "gut-disc axis". Furthermore, it delves into potential mechanisms by which this shared pattern regulates bone aging-related diseases and prospectively outlines therapeutic strategies for bone aging based on this axis.

This review presents crucial role and regulatory significance of gut-X axis modes in common bone-aging related diseases. By anchoring the gut-X axis as intervention targets, the thinking of gut microbiota and its related metabolites in basic studies and clinical prevention and treatment of bone aging-related diseases might be expanded, and its clinical application transformation and development could be innovated.},
}

@article {pmid41777631,
year = {2026},
author = {Lin, F and Xu, Y and Lin, S and Zhao, Z and Zhao, J and Cheng, C and Luo, B},
title = {Unraveling volatile and microbial dynamics of Pukeng tea with different storage times using metabolomics, chemometrics, and microbiome analysis.},
journal = {Food chemistry: X},
volume = {34},
number = {},
pages = {103692},
pmid = {41777631},
issn = {2590-1575},
abstract = {Pukeng tea (PKT), a traditional Chinese dark tea, has been consumed for centuries, yet its volatile and microbial dynamics remain unclear. This study integrated metabolomics, chemometrics, and microbiome analysis to explore PKTs with 3-20 years of storage. HS-SPME-GC-MS identified 189 volatiles, mainly alcohols, aldehydes, and ketones. PCA and PLS-DA revealed distinct metabolite patterns, with 46 differential volatiles, such as 1-butanol and 1-penten-3-ol, characterized as potential discriminants among PKT samples. Microbiota analysis showed 11 dominant bacterial genera, shifting from Firmicutes in early storage to Actinobacteriota in later stages, while Aspergillus dominated fungal communities. Correlation analysis revealed significant associations between dominant microbes such as Staphylococcus and Saccharopolyspora and aroma-active volatiles, suggesting microbial contributions to PKT's evolving flavor. This study provides the first integrated characterization of volatile and microbial diversity in PKT, offering insights into quality control, product authentication, and functional microbe discovery for the sustainable development of traditional dark teas.},
}

@article {pmid41777547,
year = {2026},
author = {Maisto, L and Telegrafo, C and Rubino, F and Santamaria, M and Traka, MH and Tullo, A and Bouwman, J and Sbisà, E and Balech, B},
title = {Multifaceted human gut microbiome data associated with health and nutrition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1722500},
pmid = {41777547},
issn = {1664-302X},
abstract = {The microbiome, also considered the hidden organ, is a fundamental ecosystem directly associated with the disease and health status of the human body. With the availability of high-throughput DNA sequencing technologies, a growing number of studies from clinical and experimental (observation and intervention) samples are constantly revealing new findings on the relationship between human organs and their microbiomes. In such a context, diet and nutrition are among the key factors influencing microbiome composition, richness, and functional behavior. In this review, we illustrate how microbiome-related data and associated metadata are in recent times scattered across primary and specialized databases with different levels of curation, annotation, and standardization, limiting, to some extent, the possibility of deep data discovery, reuse, alignment, and harmonization. Therefore, we describe the way Findable, Accessible, Interoperable, and Reusable (FAIR) data principles would enhance the onset of novel scientific hypotheses and potential microbiome-targeted therapies by improving the standardization policies in data sources. Accordingly, using advanced semantic classification and data mining technologies based on suitable and comprehensive ontologies, annotations of studies present in source databases or in scientific literature would further improve the data and metadata enrichment, integration and alignment relevant to microbiome data associated with health, disease and nutrition.},
}

@article {pmid41777539,
year = {2026},
author = {Wang, M and Li, X and Liu, X and Ye, Y and Zhou, P and Liu, Y and Zhu, L and Wei, W and Li, Z and Li, Z and Wu, R and Peng, Y and Liu, Z and Lu, X and Zhao, J and Kan, B},
title = {Restaurant occupational exposure affects the profiles of oral and gut pathobiomes and resistomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771459},
pmid = {41777539},
issn = {1664-302X},
abstract = {INTRODUCTION: Restaurant occupational exposure refers to contact with food-processing environments, raw materials, and customers, which may influence the composition of the human microbiome. Differences and associations between human oral and gut pathobiome and their resistomes under restaurant occupational exposure remain unclear. We conducted a comprehensive metagenomic analysis of paired oral and fecal samples from Front-of-House (FOH) workers and Back-of-House (BOH) workers to elucidate the effects of occupational exposure in the restaurant environment on oral and gut pathobiome, antimicrobial resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs).

METHODS: We collected the oral and fecal samples from 35 FOH and 37 BOH workers across 24 Chinese restaurants in Zhengzhou, Henan, China. The diversity and relative abundances of microbial species, ARGs, VFs, and MGEs were compared. Clonal strains from paired oral and fecal samples were analyzed. The serovars of Salmonella were determined using the ucgMLST. Finally, we used the O2PLS method to explore relationships among ARG subtypes, bacterial communities (species-level), MGEs (subtype-level), and plasmids.

RESULTS: The gut microbiome acts as the primary reservoir, exhibiting greater alpha diversity and a higher burden of pathogens/resistomes (including high-risk Rank_I genes). In contrast, the oral microbiome was more sensitive to occupational differences. Significant beta diversity variations in microbiomes, antimicrobial resistance genes (ARGs), and virulence factors were observed exclusively in oral samples. Notably, Salmonella Typhimurium was significantly more prevalent in the oral cavity of BOH workers (R [2] = 0.032, p = 0.047), indicating their potential role as intermediaries in foodborne pathogen transmission. Strain-level analysis confirmed that clonal strains of the opportunistic pathogen and probiotics were shared between the oral cavity and the gut. O2PLS analysis identified plasmids as the main correlates of ARGs.

DISCUSSION: While the gut serves as the primary reservoir for pathogens/resistomes, restaurant occupational exposure distinctly shapes oral microbial/resistome profiles, underscoring the critical need for reinforced hygiene management, particularly for BOH workers, to mitigate pathogen and resistance transmission.},
}

@article {pmid41777533,
year = {2026},
author = {Wang, S and Ding, Y and Cai, C and Ou, M and Niu, C},
title = {16S ribosomal ribonucleic acid sequencing reveals bile microbiome features in gallstone disease and their links to blood lipid subtypes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741489},
pmid = {41777533},
issn = {1664-302X},
abstract = {BACKGROUND: Gallstone disease (GSD) represents a major global health burden with complex pathophysiology involving bile microbiome dysbiosis and metabolic dysfunction. Although previous studies have examined bile microbial communities, the relationship between bile microbiome composition and specific lipid phenotypes remains incompletely understood.

METHODS: We conducted a cross-sectional study of 28 adults undergoing cholecystectomy for radiologically and pathologically confirmed gallstones. Bile samples were collected intraoperatively and subjected to 16S ribosomal ribonucleic acid V3-V4 region sequencing. Patients were stratified by lipid subtypes based on contemporary dyslipidaemia guidelines. Microbial diversity, community structure and differential abundance analyses were performed alongside machine learning classification.

RESULTS: The bile microbiome exhibited distinct compositional patterns between the hypertriglyceridaemia (HTG) and non-HTG (NTG) groups, with key phyla (Proteobacteria, Firmicutes) showing group-specific abundance trends and alpha diversity indices reflecting reduced evenness in HTG. Beta diversity analyses demonstrated mild-to-moderate separation between groups, and the linear discriminant analysis effect size technique identified discriminatory taxa with potential functional relevance. Random forest classification achieved moderate accuracy in predicting lipid subtypes based on microbial features.

CONCLUSIONS: This study revealed associations between bile microbiome composition and systemic lipid metabolism in GSD, suggesting potential mechanistic links through bile acid metabolism and farnesoid X receptor-fibroblast growth factor 19 signaling pathways.},
}

@article {pmid41777408,
year = {2026},
author = {Qin, SD and Zhang, YW and Wang, JZ},
title = {Evaluating the association between oral microbiota and cardiovascular diseases: evidence from Mendelian randomization analysis.},
journal = {Journal of geriatric cardiology : JGC},
volume = {23},
number = {1},
pages = {36-44},
pmid = {41777408},
issn = {1671-5411},
abstract = {BACKGROUND: Recent studies have suggested a potential role of the oral microbiome in the development of cardiovascular diseases. This study aims to investigate the association between oral microbiota and cardiovascular disease risk, including atrial fibrillation, myocardial infarction, chronic heart failure, and hypertension.

METHODS: We analyzed GWAS data from East Asian populations' oral microbiome, involving 2,017 tongue and 1,915 saliva samples from 2,984 individuals with whole-genome sequencing. Additionally, we sourced cardiovascular disease GWAS data from NBDC, including atrial fibrillation (8,180 cases, 28,621 controls), myocardial infarction (14,992 cases, 146,214 controls), chronic heart failure (10,540 cases, 168,186 controls), and systolic blood pressure (145,505 individuals).

RESULTS: Several oral microbiota taxa were found to be significantly associated with cardiovascular disease outcomes. Specific microbiota, such as Centipeda, Corynebacterium, and Pseudomonas E, were negatively correlated with heart failure. In contrast, taxa like Neisseria D and Actinomyces were associated with an increased risk of atrial fibrillation and myocardial infarction. Additionally, certain oral microbiota showed correlations with changes in blood pressure, highlighting their potential role in hypertension.

CONCLUSION: Our findings suggest that the oral microbiota may influence the development and progression of cardiovascular diseases, providing new insights into the potential impact of oral health on cardiovascular risk.},
}

@article {pmid41715099,
year = {2026},
author = {Fan, W and Tan, T and Yang, C and Cao, Y and Jin, C and Liu, X and Shang, K and Wang, J and Xu, J and Li, Y},
title = {Indole-acetaldehyde from Rothia mucilaginosa activates the PXR/NRF2 axis to enhance alveolar macrophage phagocytosis and protect against ARDS.},
journal = {Respiratory research},
volume = {27},
number = {1},
pages = {},
pmid = {41715099},
issn = {1465-993X},
support = {82102252//National Natural Science Foundation of China/ ; 82272245//National Natural Science Foundation of China/ ; 202440093, 2024ZZ1022//Shanghai Municipal Health Commission/ ; },
abstract = {BACKGROUND: Despite advances in therapeutic strategies, acute respiratory distress syndrome (ARDS) mortality remains high. Growing evidence links respiratory microbiome composition to ARDS outcomes. This investigation sought to elucidate how colonizing bacteria and their metabolites influence ARDS pathogenesis.

METHODS: Bronchoalveolar lavage fluid (BALF) from patients with pulmonary infections was analyzed by metagenomic next-generation sequencing (mNGS) to identify characteristic bacteria. Bacterial culture supernatants were analyzed by untargeted metabolomics (LC-MS) to identify metabolites. A murine ARDS model was established through intratracheal LPS instillation. Single-cell sequencing datasets from the GEO database were analyzed to reveal differential cell populations and functional alterations in murine ARDS. Potential molecular mechanisms were explored through molecular docking, RNA-seq analysis, Western boltting, and targeted gene knockdown in murine and cellular model.

RESULTS: R. mucilaginosa demonstrated enrichment in patients without ARDS (nARDS). The bacterial culture supernatant conferred substantial protection in murine models, whereas viable bacteria showed minimal efficacy. LC-MS analysis identified indole-3-acetaldehyde (IAAld) as the predominant metabolite in the supernatant. Single-cell sequencing suggested that resident alveolar macrophages (RAMs) were pivotal cells in murine ARDS model. IAAld enhanced RAMs phagocytosis, facilitating neutrophil and LPS clearance. Mechanistic studies revealed that IAAld likely activated PXR signaling, promoted NRF2 nuclear translocation, and upregulated the phagocytosis-related gene CD36. Targeted PXR knockdown eliminated these protective effects.

CONCLUSION: The respiratory commensal R. mucilaginosa synthesizes IAAld, which—independent of bacterial colonization per se—ameliorates ARDS through PXR/NRF2/CD36 axis activation, thereby enhancing macrophage phagocytic function. These findings suggest that therapeutic targeting of microbial metabolites represents a novel ARDS treatment paradigm.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12931-026-03551-3.},
}

@article {pmid41634480,
year = {2026},
author = {Ren, L and Wang, Z and Yang, Z and Tian, R and Du, J and Dang, Z and Li, J and Guo, X and Xia, Y and Cui, W and Wang, Y},
title = {Microbial succession and machine learning for postmortem interval estimation in bromadiolone-poisoned cadavers.},
journal = {AMB Express},
volume = {16},
number = {1},
pages = {},
pmid = {41634480},
issn = {2191-0855},
support = {tsqn202507262//Special Foundation of Taishan Scholars Program/ ; 2023JJ40797//Natural Science Foundation of Hunan Province/ ; KF202303//Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science/ ; cx2025078//Student's Platform for Innovation and Entrepreneurship Training Program/ ; },
abstract = {UNLABELLED: Accurate estimation of the postmortem interval (PMI) remains a major challenge in forensic investigations. Although microbial succession has emerged as a promising biological clock, the impact of xenobiotic exposure on internal microbial communities during decomposition remain poorly understood. Here, we established a bromadiolone-poisoned rat model and systematically sampled gut and anus swabs at 6 h intervals over 96 h postmortem period. Bromadiolone exposure produced dose-dependent effects on decomposition, with high-doses delaying the progression, potentially by altering tissue integrity or microbial activity. 16 S rRNA sequencing revealed that Firmicutes and Proteobacteria were the dominant phyla during decomposition, followed by Bacteroidota, Desulfobacterota, and Actinobacteriota. Notably, microbial community dynamics were driven more strongly by anatomical location than by toxicant exposure, highlighting the critical role of sampling site. Furthermore, five machine-learning algorithms were evaluated for PMI prediction. GB regression outperformed RF, RR, SV, and LR, achieving an R[2] of 0.954 and an RMSE of 5.6 h. Feature analysis identified Proteus mirabilis and Morganella morganii as dominant positive biomarkers, while gut-associated taxa (e.g., Lactobacillus and Ligilactobacillus) declined over time. Together, these results demonstrate that bromadiolone exposure induces site-specific perturbations in microbial community, the underlying successional dynamics remain sufficiently robust to support accurate PMI estimation. The GB model provides both predictive accuracy and biological interpretability, highlighting the importance of incorporating anatomical location and toxicological stress into microbiome-based PMI estimation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13568-026-02023-7.},
}

@article {pmid41777393,
year = {2026},
author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D},
title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1685007},
pmid = {41777393},
issn = {1664-462X},
abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.},
}

@article {pmid41777263,
year = {2026},
author = {Wang, X and He, J and Ding, G and Tang, Y and Wang, Q},
title = {Artificial Intelligence-Enabled Multi-Omics for Predicting Immune Checkpoint Inhibitor Response and Resistance.},
journal = {Journal of multidisciplinary healthcare},
volume = {19},
number = {},
pages = {572089},
pmid = {41777263},
issn = {1178-2390},
abstract = {Immune checkpoint inhibitors (ICIs) have reshaped oncology, yet overall response rates remain modest and resistance is common, driven by tumor heterogeneity and evolving tumor-immune crosstalk. Established biomarkers (PD-L1, tumor mutational burden, microsatellite instability) provide incomplete prediction. Multi-omics profiling across genomic, transcriptomic, proteomic, epigenomic, metabolomic and microbiomic layers offers a systems-level view of malignant and immune states, uncovering determinants of ICI efficacy such as lineage plasticity, stromal remodeling, immunometabolic reprogramming and microbiome-associated immune modulation. Artificial intelligence (AI) is uniquely positioned to fuse these heterogeneous data, learn non-linear cross-layer signatures, and enable interpretable predictions using approaches such as SHAP and Grad-CAM. Representative models link routine histology or imaging to molecular phenotypes, stratify patients beyond single biomarkers, and may nominate rational combinations that target oncogenic pathways, lactate-driven immune suppression, or the gut microbiome. In this narrative review, we synthesize recent AI-multi-omics advances for response modeling, immune-relevant tumor subtyping, and clinical translation, including radiomics/pathomics integration and liquid-biopsy-based monitoring, as well as emerging applications in toxicity risk prediction. We also discuss barriers to implementation-platform heterogeneity, limited prospective validation, bias, interpretability and cost-and outline future directions, including single-cell and spatial multi-omics integration, federated learning and generative modeling to improve robustness and equity of precision immunotherapy.},
}

@article {pmid41777157,
year = {2026},
author = {Popova, PV and Loboda, AA and Liaudanski, A and Sitkin, SI and Anopova, AD and Vasukova, EA and O Isakov, A and Tkachuk, AS and Nemikina, IS and Akhmatova, M and Eriskovskaya, AI and Vasilieva, EY and Galyautdinov, IV and Babenko, A and Zgairy, S and Rubin, E and Even, C and Turjeman, S and Pervunina, TM and Kostareva, AA and Vatian, AS and Mohan, V and Grineva, EN and Koren, O and Shlyakhto, EV},
title = {Maternal Gut Microbiome as a Predictor of Insulin Therapy Requirement in Gestational Diabetes.},
journal = {Journal of diabetes science and technology},
volume = {},
number = {},
pages = {19322968261426025},
doi = {10.1177/19322968261426025},
pmid = {41777157},
issn = {1932-2968},
abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) often requires pharmacological intervention beyond lifestyle modification to achieve optimal glycemic control. This study aimed to develop machine learning models that integrate clinical and gut microbiome data to predict the need for insulin therapy (IT) in women with GDM.

METHODS: We characterized 205 pregnant women with GDM from the Genetic and Epigenetic Mechanisms of Developing Gestational Diabetes Mellitus and its Effects on the Fetus study, collecting clinical parameters, lifestyle questionnaires, self-monitored blood glucose records, and gut microbiome profiles based on 16S rRNA gene sequencing. Gradient-boosting models were trained to predict IT, basal insulin (BI), and prandial insulin (PI) requirements. Model discrimination was assessed using repeated stratified five-fold cross-validated area under the curve-receiver operating characteristic (AUC-ROC) (nested cross-validation). Feature importance and interpretability were evaluated with SHapley Additive exPlanations and permutation analyses. Differential microbial abundance was analyzed by ANCOM-BC2 (analysis of composition of microbiomes with bias correction, version 2), and metabolic pathways were predicted via PICRUSt2.

RESULTS: Women requiring insulin were older and had higher pre-pregnancy body mass index (BMI), fasting plasma glucose, 1-hour oral glucose tolerance test glucose, and glycated hemoglobin than diet-treated women (P < .05 for all). Adding microbiome data improved AUC-ROC for IT prediction from 0.63 (95% CI = 0.43, 0.83) to 0.70 (0.50, 0.89), BI from 0.77 (0.59, 0.95) to 0.82 (0.65, 0.99), and for PI from 0.69 (0.50, 0.88) to 0.70 (0.51, 0.89). Key influential features included glycemic markers, BMI, and microbial taxa, such as Phascolarctobacterium faecium, Alistipes ihumii, Cloacibacillus evryensis, Ruthenibacterium lactatiformans, and Methanosphaera stadtmanae, and the predicted microbial metabolic pathway PWY-5823.

CONCLUSION: Our findings demonstrate that integrating gut microbiome characteristics with clinical data improves the prediction of insulin treatment needs in GDM, particularly for BI initiation.},
}

@article {pmid41777065,
year = {2025},
author = {Zhang, Y and Zhang, T and Wang, H},
title = {[Research Progress on the Regulatory Mechanism of Respiratory Microbiota in the Comorbidity of Chronic Obstructive Pulmonary Disease and Lung Cancer].},
journal = {Zhongguo fei ai za zhi = Chinese journal of lung cancer},
volume = {28},
number = {12},
pages = {939-947},
doi = {10.3779/j.issn.1009-3419.2025.106.33},
pmid = {41777065},
issn = {1999-6187},
abstract = {Both chronic obstructive pulmonary disease (COPD) and lung carcinoma (LC) are major public health challenges in China. With the continuous advancement of microbial detection methods, the role of the respiratory microbiome in the pathogenesis and progression of respiratory diseases has become increasingly prominent. This article systematically reviews the dynamic characteristics of the respiratory microbiome during the progression of COPD and LC, then explores its crucial bridging role in COPD-LC comorbidity through mechanisms such as persistently driving chronic inflammation, mediating genomic damage, and participating in immune regulation. The aim is to deepen the understanding of the respiratory microbiome, and to provide new perspectives for optimizing existing treatment strategies, exploring microbial biomarkers for early cancer screening, and improving the clinical management of chronic respiratory diseases. .},
}

@article {pmid41777057,
year = {2026},
author = {Singh, A and Bhardwaj, A and Midha, V and Sood, A},
title = {Deciphering the diet-inflammatory bowel disease relationship: knowledge gaps and future perspectives.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2025.00278},
pmid = {41777057},
issn = {1598-9100},
abstract = {Diet is increasingly recognized not as a passive exposure but as a dynamic determinant of inflammatory bowel disease (IBD) pathogenesis, progression, and treatment response. This review article redefines diet as a multidimensional modifier acting through complex interactions with genetics, microbiota, intestinal barrier function, and environmental exposures. Beyond nutrient composition, we highlight how age, sex, habitual diet, cooking methods, contaminants, and lifestyle collectively shape disease trajectories. We also identify key research priorities: incorporation of long-term, mechanistically anchored trials; development of digital, biomarker-informed dietary assessment tools; and integration of polygenic, microbial, and metabolic data to inform individualized therapy. Emerging evidence also calls for culturally tailored and patient-centered frameworks that ensure real-world adherence and equity in dietary interventions. Reframing diet as a biological, behavioral, and environmental nexus shifts it from the periphery to the forefront of IBD care, transforming it from a confounder in research to a therapeutic frontier in clinical practice.},
}

@article {pmid41776947,
year = {2026},
author = {Mitchell, A and Hayes, C and Hudson, CJ and Connell, SD and Harvey, BP and Agostini, S and Jolly, J and Ravasi, T and Booth, DJ and Nagelkerken, I},
title = {Marine Heatwaves, Ocean Warming and Acidification Reshape Reef Fish Gut Microbiomes.},
journal = {Molecular ecology},
volume = {35},
number = {5},
pages = {e70275},
doi = {10.1111/mec.70275},
pmid = {41776947},
issn = {1365-294X},
support = {DP230101932//Australian Research Council/ ; JPJSCCA20210006//Japan Society for the Promotion of Science/ ; 23K26924//Japan Society for the Promotion of Science/ ; },
abstract = {Extreme climatic events and gradual climate change are increasingly anticipated to interact and reshape ecological communities. However, the combined effects of ocean warming, acidification and marine heatwaves on host-associated microbial communities and their potential role in host adaptation remain poorly understood. Here, we assessed shifts in gut microbiome communities and their associations with physiological performance in one tropical (Abudefduf vaigiensis) and one subtropical (Microcanthus strigatus) reef fish species, across three temperate reefs representing natural analogues of climate change: a present-day baseline ('cool reef'), a chronically warmed reef ('warm reef') and a reef experiencing combined warming and extreme acidification ('extreme reef'). We also examined gut microbiome changes in A. vaigiensis before and during a severe marine heatwave. A. vaigiensis had lower gut microbiome evenness and diversity at the warm (43% and 44% decrease, respectively) and extreme (38% and 31% decrease) reefs compared to the cool reef, and its gut microbiome community shifted at the extreme reef with a 122% increase in abundance of opportunistic bacteria Vibrio. A. vaigiensis also had lower gut microbiome richness at the warm (42% decrease) and extreme (52% decrease) reefs during the heatwave compared to pre-heatwave individuals. In contrast, M. strigatus showed higher microbiome evenness (99% increase) and diversity (98% increase) at the warm reef compared to the cool reef; however, these gains were lost at the extreme reef, with microbiome diversity and evenness returning to cool reef levels. Microbiome changes in both species were generally not associated with their physiological performance (protein content, oxidative stress, antioxidant capacity or body condition). Our findings suggest that marine heatwaves, ocean warming and acidification can reshape reef fish gut microbiomes, driving simplification in Abudefduf vaigiensis but distinct restructuring in Microcanthus strigatus. We conclude that climate-driven microbiome reshuffling may alter host-microbiome relationships and functions in fishes in a future ocean.},
}

@article {pmid41776819,
year = {2026},
author = {Holstein, T and Verschaffelt, P and Van Den Bossche, T and Van de Vyver, S and Martens, L and Mesuere, B and Muth, T},
title = {The Peptonizer2000: Bringing Confidence to Metaproteomics.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.5c00567},
pmid = {41776819},
issn = {1535-3907},
abstract = {Metaproteomics, the large-scale study of proteins from microbial communities, faces challenges in identifying species due to similarities in protein sequences across different organisms. Current methods often rely on simple counting of matches between proteins and taxa, which can lead to low accuracy. We introduce the Peptonizer2000, a new tool that uses advanced modeling to provide more precise taxonomic identifications along with confidence scores. It combines peptide scores from any proteomic search engine with peptide-to-taxon links from the Unipept database. By applying statistical models, the Peptonizer2000 improves taxonomic resolution and delivers more reliable results. We validate its performance using publicly available data sets, demonstrating its ability to produce high-confidence identifications. Our results suggest that the Peptonizer2000 improves the specificity and confidence of taxonomic assignments in metaproteomics, providing a valuable resource for the study of complex microbial communities.},
}

@article {pmid41776759,
year = {2025},
author = {Fernhout, L and Lambrechts, H and van Zyl, JHC},
title = {Ovine balanoposthitis: observations on the microbiome and immunoglobulin response.},
journal = {Journal of the South African Veterinary Association},
volume = {96},
number = {2},
pages = {73},
doi = {10.36303/JSAVA.679},
pmid = {41776759},
issn = {2224-9435},
abstract = {The incidence of ulcerative balanoposthitis (UB) in rams contributes to significant economic losses in the national sheep population. Understanding the immune response in the reproductive tract can aid in developing preventive measures. This study aimed to characterise the immunoglobulin profiles and microbial diversity in the reproductive tract of rams affected by UB, providing insight into the immune responses to this disease. Serum and glans tissue samples from healthy and UB-affected rams were analysed using an ELISA approach to quantify IgG, IgA, and IgM levels. The microbial diversity in nasal, penile swabs, and smegma samples was assessed using an ARISA approach. Significant differences (p ≤ 0.001) were observed between the systemic and localised immune responses. UB-affected rams exhibited higher IgG and IgM levels but lower IgA levels in both serum and glans tissue compared to healthy rams. The study confirmed UB-induced shifts in the microbiome, with significant differences in microbial diversity indices in nasal, penile, and smegma samples. Specifically, there were changes in the nasal fungi Shannon (p = 0.047) and Simpson (p = 0.038) indices, the penile Shannon (p = 0.015) and Simpson (p = 0.006) bacterial indices, and the smegma bacterial species number index (p = 0.042). Correlations between microbial populations and immunoglobulin profiles indicated an interactive immune response in different health statuses. This study highlights the need to understand the immune system of the lower reproductive tract and its interaction with commensal organisms to develop therapeutic immunomodulators for preventing UB in sheep.},
}

@article {pmid41776699,
year = {2026},
author = {Song, Y and Wen, S and Guan, LL},
title = {Unraveling the dynamic changes in the intestinal microbiome: impacts on pre-weaning calf health and productivity.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41776699},
issn = {1674-9782},
abstract = {The early life gut microbial colonization in pre-weaning calves plays a pivotal role in shaping their health, growth, and productivity. This review delves into the dynamic changes of intestinal microbiota during early life, emphasizing key factors such as colostrum management, feeding strategies, roughage supplementation, and microbial interventions including probiotics, prebiotics, and fecal microbiota transplantation (FMT), and non-nutritional stressors that can shape the early life microbial colonization. We highlight the microbiota's critical functions in nutrient metabolism, immune development, gut barrier integrity, and gut-brain axis regulation. Additionally, the consequences of microbial dysbiosis on calf health and its long-term effects on production performance in beef and dairy cattle are discussed. While current research has provided valuable insights, understanding causal mechanisms remains a challenge. This review aims to guide practical strategies for targeted microbial management, offering a pathway to optimize early-life interventions for improved calf health and productivity.},
}

@article {pmid41776621,
year = {2026},
author = {Yadav, B and Banerjee, G and Srivastava, A and Madan, AK and Kumar, R and Banerjee, P},
title = {Host-microbiome interplay supports heat stress resilience in zebu calves.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00539-8},
pmid = {41776621},
issn = {2524-4671},
}

@article {pmid41776571,
year = {2026},
author = {Ni, Z and Wang, G and Li, Q and Wu, X and Song, Z and Yu, H and Yu, P and Chen, Y and Li, L and Chen, H and Hou, H and Hu, Q},
title = {Sex-specific metabolic and microbial remodeling in a rotenone-induced rat model of Parkinson's disease following nicotine administration.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-026-00865-1},
pmid = {41776571},
issn = {2042-6410},
support = {2023100CC0190//the Science and Technology Project of Beijing Life Science Academy/ ; 2024100CC0090//the Science and Technology Project of Beijing Life Science Academy/ ; 2024100CC0100//the Science and Technology Project of Beijing Life Science Academy/ ; },
abstract = {BACKGROUND: Parkinson's disease (PD) is a neurodegenerative disorder with established sex differences in incidence and progression. Epidemiological evidence suggests nicotine may confer protection against PD, but its mechanisms, particularly regarding sex-specific effects, remain unclear. This study investigated the neuroprotective mechanisms of nicotine in a rotenone-induced PD rat model, with a specific focus on evaluating sex-dependent modulation across behavioral, pathological, and gut-related outcomes.

METHODS: Male and female Sprague-Dawley rats were administered rotenone (2 mg/kg/day, s.c.) for four weeks to induce PD. Nicotine (0.5 mg/kg/day, s.c.) was administered 30 min after rotenone. Motor function was assessed using rotarod and CatWalk XT gait analysis. Neuropathology in the substantia nigra was evaluated via immunofluorescence for α-synuclein and tyrosine hydroxylase (TH). Gut pathology was analyzed through colon histopathology (H&E staining) and ELISA for IL-6 and α-synuclein. Gut microbiota composition was assessed by 16 S rDNA sequencing, and serum metabolomics was performed using UPLC-MS/MS. Data were analyzed by two-way ANOVA with Tukey's post-hoc test.

RESULTS: Nicotine significantly attenuated rotenone-induced motor impairments: males showed a superior response in balance-related parameters, while females exhibited enhanced efficacy in dynamic gait metrics. Pathologically, nicotine reduced nigral α-synuclein accumulation and TH depletion in both sexes, with males showing greater α-synuclein accumulation following rotenone exposure. Crucially, nicotine exclusively ameliorated colon histopathology, reduced plasma α-synuclein, and suppressed colon IL-6 in females, while attenuating intestinal α-synuclein accumulation in both sexes. Microbiota analysis revealed sex-divergent taxonomic shifts with nicotine treatment. Metabolomics showed significantly more extensive metabolic reprogramming in females, particularly affecting indole derivatives. Pearson correlations revealed significant sex-specific associations between altered serum indole derivatives and gut microbiota genera.

CONCLUSIONS: Nicotine exerts neuroprotection in PD through sex-dependent modulation of multiple pathological pathways, primarily involving the gut-microbiota-metabolite axis. Females benefit from enhanced gastrointestinal protection and metabolic reprogramming, while males show preferential motor balance restoration. These findings underscore the critical importance of sex-stratified therapeutic strategies for PD.},
}

@article {pmid41776310,
year = {2026},
author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA},
title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {41776310},
issn = {2662-8465},
support = {#00034120//Pew Charitable Trusts/ ; T32 AG052374/AG/NIA NIH HHS/United States ; No. 58-1950-7-707//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
abstract = {The decline in ovarian function with age affects fertility and is associated with increased risk of age-related diseases, including osteoporosis and dementia. Notably, earlier menopause is linked to shorter lifespan, yet the molecular mechanisms underlying ovarian aging remain poorly understood. Recent evidence suggests the gut microbiota may influence ovarian health. Here we show that ovarian aging is associated with distinct gut microbial profiles in female mice and that the gut microbiome can directly influence ovarian health. Using fecal microbiota transplantation from young or estropausal female mice, we demonstrate that heterochronic microbiota transfer remodels the ovarian transcriptome, reduces inflammation-related gene expression and induces transcriptional features consistent with ovarian rejuvenation. These molecular changes are accompanied by enhanced ovarian health and increased fertility. Integrating metagenomics-based causal mediation analyses with serum untargeted metabolomics, we identify candidate microbial species and metabolites that may contribute to the observed effects. Our findings reveal a direct link between the gut microbiota and ovarian health.},
}

@article {pmid41776177,
year = {2026},
author = {Liu, J and Li, J and Li, Y and Gao, Z and Wang, L and Song, Q and Ye, Y and Liang, J},
title = {Mechanism of Morchella polysaccharide in anti-fatigue: the role of the gut microbiota-metabolite axis in mice.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00763-1},
pmid = {41776177},
issn = {2396-8370},
support = {2023-ZJ-904T//Science and Technology Plan Project of Qinghai Province/ ; },
abstract = {This study aims to investigate the anti-fatigue effects of crude Morchella polysaccharide (MP) extracted from the Qinghai-Tibet Plateau region in mice, and to preliminarily explore its potential mechanisms based on the gut microbiota-metabolite axis. Chemical analysis indicates that MP exhibits typical characteristics of crude polysaccharides: it consists of multiple monosaccharides (primarily glucose at 72.33%, along with mannose, galactose, etc) and possesses a broad molecular weight distribution (dispersion index (Mw/Mn) of 30.97). To investigate its material basis, we further isolated and purified the primary water-soluble neutral fraction MP1-1. Structural characterization confirmed MP1-1 as a homogeneous glucan composed solely of glucose units, with a backbone linked via →4)-α-D-Glcp-(1 → 4)-type bonds. A negative control group (NC), a positive control group (PC, Rhodiola glycoside,100 mg/kg), and low-, medium-, and high-dose MP groups (50, 100, 200 mg/kg) were established, with continuous gavage for four weeks. Following the final gavage, a weight-bearing swimming test was conducted to record the time to exhaustion and establish a fatigue model. Subsequently, fatigue-related biochemical indicators, gut microbiota composition, and metabolite changes were assessed. The results indicate that MP intervention is significantly associated with an anti-fatigue phenotype. This may occur through regulating the gut microbiota by enriching beneficial bacteria (such as Lactobacillus and Bifidobacterium) and suppressing harmful bacteria (such as Desulfovibrio and Helicobacter), thereby reshaping the intestinal microbiome. These alterations were associated with changes in the host's metabolic profile, particularly the upregulation of energy metabolism pathways (e.g., β-alanine metabolism, pentose phosphate pathway, glycerolipid metabolism) and the disruption of inflammation- and oxidative stress-related metabolic pathways. Ultimately, the MP intervention group exhibited increased glycogen reserves, enhanced antioxidant capacity (elevated SOD and GSH-Px; reduced MDA), and reduced systemic inflammation (decreased IL-6 and TNF-α; increased IL-10). Collectively, these effects delayed fatigue onset, promoted recovery, and significantly prolonged swimming duration. In summary, this study suggests that the polysaccharide extract from Morchella elata, native to the Qinghai-Tibet Plateau, may exert anti-fatigue effects by regulating the "gut microbiota-metabolite-host physiological phenotype" network, providing preliminary experimental evidence for its application in the functional food sector.},
}

@article {pmid41776098,
year = {2026},
author = {Xiang, X and Zhu, J and Jiang, J and Ding, P and Zhu, Y and Cheng, K and Ming, Y},
title = {Unique gut microbiota and metabolomic profiling as biomarker of post-transplant recovery in acute-on-chronic liver failure after liver transplantation.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {41776098},
issn = {1432-0614},
support = {81771722 and 82570782//National Natural Science Foundation of China/ ; },
abstract = {Acute-on-chronic liver failure (ACLF) is a severe condition arising from chronic liver disease, characterized by acute decompensation, organ failure, and high short-term mortality. Poor outcomes have also been observed in patients with ACLF after liver transplantation (LT). Emerging evidence, including a study from our center, suggests that gut microbiota plays an important role in ACLF. Patients who underwent LT at our center between October 2022 and June 2024 were included. Fecal samples were collected within 1 month post-LT for 16S rRNA and untargeted metabolomic sequencing. In this study, 144 samples from 69 patients with ACLF, cirrhosis, or hepatocellular carcinoma (HCC) were analyzed. Distinct microbiota and metabolic profiles were observed among the groups. ACLF patients exhibited significantly altered beta diversity, with notable depletion of g__Anaerostipes. Metabolomic analysis revealed substantial differences, including enrichment of tangeritin and depletion of candesartan in the ACLF group. Network analysis identified g__Anaerostipes as a key node linking differential taxa and metabolites. A random forest model based on these features effectively distinguished patient groups, with the highest classification accuracy observed in HCC. Multi-omic signatures were also associated with early allograft dysfunction (EAD), particularly g__Lachnoclostridium. Several microbial and metabolic features, including g__Lachnoclostridium, showed significant correlations with clinical indicators. The gut microbiome after LT is closely associated with ACLF. This study offers valuable insights for further investigation into the pathogenesis and post-LT prognosis. KEY POINTS: • ACLF patients have a unique gut microbiota and metabolic profile after LT • g__Anaerostipes is the prominent biomarker of ACLF's multi-omics signature • g__Lachnoclostridium is a promising indicator of recovery after LT.},
}

@article {pmid41776009,
year = {2026},
author = {Kumar, Y and Xu, B},
title = {A critical review on the roles of natural products in shaping oral microbiota and preventing chronic diseases.},
journal = {Natural products and bioprospecting},
volume = {16},
number = {1},
pages = {},
pmid = {41776009},
issn = {2192-2195},
support = {UICR0400015-24B//Beijing Normal-Hong Kong Baptist University/ ; UICR0400016-24B//Beijing Normal-Hong Kong Baptist University/ ; },
abstract = {The oral microbiome plays a central role in maintaining both oral and systemic health, and disruptions in its balance can contribute to a wide range of diseases. This review brings together current evidence on how natural products modulate oral microbial communities, promote microbial equilibrium, and help prevent conditions such as dental caries, periodontitis, and chronic systemic disorders linked to oral dysbiosis. Recent studies highlight that phytochemicals particularly polyphenols, terpenoids, saponins, and alkaloids exert antimicrobial, anti-inflammatory, and antioxidant effects that influence bacterial adhesion, biofilm development, gene expression, and acid production. These compounds not only inhibit key oral pathogens but also support beneficial species, helping to sustain a stable and resilient microbiome. Evidence was gathered from PubMed, Scopus, ScienceDirect, and Google Scholar using relevant keywords and focusing on literature from 2015 to 2025. Insights into microbial diversity, environmental influences, host genetics, and advanced sequencing tools further strengthen understanding of oral microbial dynamics. While natural products show strong potential, challenges related to safety, bioavailability, regulatory clarity, and clinical translation remain to explore. This review outlines current progress and future directions needed to transform natural compounds into effective, evidence-based strategies for improving oral and systemic health through microbiome modulation.},
}

@article {pmid41776008,
year = {2026},
author = {Ticinesi, A and Maggi, S and Nouvenne, A and Zuliani, G and Franceschi, C},
title = {The gut microbiome and ageing trajectories: mechanisms and clinical implications.},
journal = {Nature reviews. Endocrinology},
volume = {},
number = {},
pages = {},
pmid = {41776008},
issn = {1759-5037},
abstract = {This Review discusses the current state of knowledge on the contribution of the gut microbiome as a potential key actor in defining how we age. The gut microbiome is a complex ecosystem that establishes lifelong dynamic interactions with the host at multiple levels (several gut-organ axes), differently influencing ageing patterns and age-related disease onset and progression across populations. Accordingly, the definition of a 'normative' gut microbiome remains elusive, depending largely on the interaction with the external environment. In this complex scenario, the causal role of the gut microbiome in defining the ageing trajectory and its precise contribution to various organ-specific age-related diseases is still uncertain in clinical terms and could be context specific. Multiparametric and uniqueness indexes within a given population have shown a certain capacity for predicting disability and mortality. However, the gut microbiome is shaped over time by exposure to different intrinsic and environmental factors, resulting in a high degree of inter-individual variability, a key phenomenon that should be considered to develop novel personalized strategies to counteract age-related disease and frailty.},
}

@article {pmid41775773,
year = {2026},
author = {Chowdhury, SF and Sarkar, MMH and Al Sium, SM and Naser, SR and Hossain, MS and Habib, MA and Akter, S and Banu, TA and Goswami, B and Jahan, I and Chakrovarty, T and Molla, MMA and Nafisa, T and Yeasmin, M and Ghosh, AK and Khan, MS},
title = {Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40563-x},
pmid = {41775773},
issn = {2045-2322},
support = {GOB 224125200//Ministry of Science and Technology, Government of the People's Republic of Bangladesh/ ; },
}

@article {pmid41775715,
year = {2026},
author = {Zhu, B and Wang, J and Zhang, X and Zhang, B and Li, Z and Hao, L},
title = {A bacteria community sequencing data set from pothos (Epipremnum aureum).},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06677-7},
pmid = {41775715},
issn = {2052-4463},
abstract = {Pothos, with the scientific name of Epipremnum aureum, is a popular ornamental plant widely utilized for indoor greening, which is adaptable to both soil-based and hydroponic cultivation. Plant-associated microorganisms significantly influence plant health and productivity by facilitating nutrient acquisition and enhancing stress tolerance. Pothos, which is tolerant to low-nutrient conditions, is thus a suitable model plant to study plant-microorganisms interaction. However, knowledge about the microbiome of pothos is lacking, especially under hydroponic cultivation conditions. In this study, we recorded the dynamic changes of the bacterial communities associated with pothos during a transition from soil-based to hydroponic growth conditions in a 86-day cultivation. Bacterial communities from root tissues, hydroponic solutions, leaves, and soils were characterized through 16S rRNA gene amplicon sequencing, generating 98 community composition profiles. Significant shifts in microbial diversity and composition were observed during the transition, highlighting specific bacterial taxa associated with hydroponic adaptation. Across sample types, Proteobacteria dominated, with Actinobacteriota as the second most abundant group, while Bacteroidota and Firmicutes were present at lower relative abundances. This is the first high resolution and comprehensive data set of the pothos microbiome, offering a foundational resource for studying plant-microbe interactions in aquatic systems.},
}

@article {pmid41775278,
year = {2026},
author = {Kim, YS and Woo, SY and Ha, E and Ahn, SH and Kim, E and Kim, SI and Lim, WJ and Kim, SY},
title = {Role of Gut Microbiota in Psychiatric Disorders: From Mechanistic Insights to Therapeutic Strategies.},
journal = {Journal of Korean medical science},
volume = {41},
number = {8},
pages = {e78},
pmid = {41775278},
issn = {1598-6357},
support = {/NRF/National Research Foundation of Korea/Korea ; },
abstract = {Mental health disorders are a global health challenge, and the underlying biological mechanisms remain unclear. Recent evidence has linked gut microbiota to psychiatric symptoms through complex bidirectional interactions along the gut-brain axis, which involve neural, endocrine, and immune pathways. This narrative review aims to synthesize current findings on how gut microbiota contributes to the pathophysiology of major psychiatric disorders, and explore microbiota-based therapeutic interventions, and discusses emerging strategies for personalized treatment. Relevant literature up to July 2025 was reviewed using targeted keywords in major databases, including PubMed and Google Scholar. Rather than applying formal systematic review criteria, we focused on selecting influential and high-impact studies, and the findings were synthesized thematically to provide a comprehensive overview. Consistent findings across psychiatric conditions include a decreased abundance of short-chain fatty acid-producing bacteria and an increased presence of pro-inflammatory taxa. These shifts correlate with heightened systemic inflammation, disrupted neurotransmitter synthesis, and dysregulation of the hypothalamic-pituitary-adrenal axis. Thus, the gut microbiota is increasingly recognized as playing a potential role in the pathophysiology of psychiatric disorders through multifaceted mechanisms involving the gut-brain axis. Probiotics, prebiotics, and dietary modifications show promise in modulating gut microbiota and alleviating psychiatric symptoms, although clinical outcomes remain heterogeneous. Emerging precision medicine strategies indicate promising potential for personalized microbiota-based treatments. Although microbiota-targeted therapies offer promising adjunctive strategies, large-scale, mechanistically informed clinical trials remain warranted. Future research should leverage artificial intelligence and multi-omics tools to develop personalized interventions tailored to individual microbiome profiles.},
}

@article {pmid41775266,
year = {2026},
author = {Han, Z and Sun, Z and Zhao, Q and Du, L and Zhen, D and Liu, X and Jiang, S and Liu, YY and Zhang, J},
title = {Competition and compromise between exogenous probiotics and native microbiota.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101516},
doi = {10.1016/j.cels.2025.101516},
pmid = {41775266},
issn = {2405-4720},
abstract = {Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium animalis subsp. lactis V9 (BV9), to mechanistically investigate its competitive strategies. We perform metagenomic and whole-genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.},
}

@article {pmid41775198,
year = {2026},
author = {Xiao, J and Wang, Y and Chen, H and Bu, F and Xu, W and Qiu, S and Kang, Y and Wang, D and Wu, H and Hu, Z and Zhang, J and Guo, Z},
title = {Overlooked fate and associated pathogens of antimicrobial resistance in the Yellow River Delta, China.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141645},
doi = {10.1016/j.jhazmat.2026.141645},
pmid = {41775198},
issn = {1873-3336},
abstract = {The spread of antibiotic resistance genes (ARGs) within terrestrial inputs and marine dispersal in estuarine deltas has posed significant environmental challenges, exacerbated by diverse microbial habitats, estuarine eutrophication, and other anthropogenic impacts. However, the precise mechanisms governing persistence and associated risks of ARGs in this region remain poorly understood. In this study, the distribution, mobility, removal and hosts of ARGs in wetlands and rivers of the Yellow River Delta (YRD) region were systematically investigated through metagenomic approaches. A total of 23 antibiotics were detected in water (0.07-4.67 ng/L) and 14 antibiotics in sediment (0.0042-0.4768 ng/g). Following wetland treatment, despite a 67.5% reduction in antibiotic concentrations, the relative abundance of antibiotic resistance genes decreased by only 7.60%, indicating substantial persistence of genetic resistance. Moreover, Proteobacteria were identified as primary hosts for ARGs. ARGs carried by resistant pathogens, especially ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), also showed a significant reduction in the abundance and diversity throughout the wetland. Notably, total nitrogen in water (Water-TN) greatest shaped the composition of the resistome and microbiome, while the presence of antibiotics exerted stronger selective pressure on ARGs in wetland than in river. Collectively, this study highlights the associated risks of ARGs in YRD, offering insights for controlling antimicrobial resistance in deltas.},
}

@article {pmid41634593,
year = {2026},
author = {Narem, RSR and Mathakala, V and Sallabathula, ST and Peddiboyina, VL and Palempalli, UMD},
title = {Probiotics as emerging adjuncts in metabolic associated fatty liver disease therapy-a systemic review.},
journal = {BMC gastroenterology},
volume = {26},
number = {1},
pages = {},
pmid = {41634593},
issn = {1471-230X},
abstract = {Metabolic associated fatty liver disease (MAFLD), a leading cause of chronic liver disorders globally, is closely linked with the dysbiosis of the gut. These microbial imbalances contribute to pathogenesis of MAFLD through intestinal barrier dysfunction, systemic inflammation, and hepatic fat accumulation. This review aims to provide an in-depth analysis of the complex interaction between the gut microbiome and MAFLD, through literature search of articles published in open access journals of two electronic data bases PubMed, Medline from January 2015 to May 2025. Among 602 publications identified initially, 54 studies were considered based on inclusion and exclusion criteria as per the PRISMA guidelines. The results assimilate the findings from both preclinical models and human clinical trials, highlighting the influence of probiotic strains on key metabolic pathways. Lactobacillus and Bifidobacterium species were shown to regulate lipid metabolism, normalize liver enzyme activity, reduce insulin resistance, and attenuate hepatic inflammation. These effects are mediated through multiple mechanisms, including enhancement of gut barrier integrity, modulation of bile acid metabolismsuppression of endotoxemia and modulation of gut–liver axis. By summarizing emerging insights, this review offers an updated perspective on the role of probiotic interventions as a promising adjunct strategy in the prevention and management of MAFLD.},
}

@article {pmid41775960,
year = {2024},
author = {Liu, Y and Du, Z and Lu, Y and Ma, Y and Yang, Y and Osmanaj, F and Zhang, Y and Guo, X and Qin, Y and Yang, X and Hua, K},
title = {Gut microbiota metabolism disturbance is associated with postoperative atrial fibrillation after coronary artery bypass grafting.},
journal = {NPJ cardiovascular health},
volume = {1},
number = {1},
pages = {},
pmid = {41775960},
issn = {2948-2836},
support = {82100295//National Natural Science Foundation of China/ ; CI2021A04110//China Academy of Chinese Medical Sciences/ ; 7222049//Beijing Natural Science Foundation of China/ ; },
abstract = {Postoperative atrial fibrillation (POAF) is a common complication after coronary artery bypass grafting (CABG) surgery. Gut microbiota and its metabolites have been implicated in the development of AF. However, whether the gut-host metabolic interaction contributes to POAF is still unknown. This study aimed to investigate the POAF-associated gut microbiota metabolism biomarkers and related risk model. The POAF (N = 30) patients and non-POAF (N = 60) patients from the discovery cohort exhibited significantly different microbiome and metabolome profiles. The differentiated features were mainly implicated in the bile acids (BAs) and short-chain fatty acids metabolism, inflammation, and oxidative stress. Random forest analysis identified the combination of five secondary BAs showed a powerful performance on predicting POAF in the discovery cohort, highlighting significant values of area under the curve (AUC = 0.954) and correct classification rate (CCR, 93.3%). In addition, the five secondary BAs-based risk model also exhibited good performance in differentiating the POAF (N = 114) and non-POAF individuals (N = 253) in an independent validation cohort (AUC = 0.872; CCR = 90.4%). This work revealed perturbed microbial and metabolic traits in POAF, providing potential avenues for the prediction and prevention of POAF after CABG.},
}

@article {pmid41774605,
year = {2026},
author = {Wang, T and Lu, S and Sun, L and Cheng, Y},
title = {Skin Barrier Compromise: A Central Early Event in Ultraviolet Radiation-Induced Skin Pathogenesis.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-11},
doi = {10.1159/000551027},
pmid = {41774605},
issn = {1421-9832},
abstract = {Ultraviolet radiation (UVR) is a major environmental stressor to the epidermal barrier, extending beyond erythema or photoaging. Emerging evidence reframes barrier impairment as an early and central event, integrating DNA and oxidative injury with inflammatory, immune, and microbial disturbances in a self-reinforcing cycle of fragility. This perspective challenges the traditional view of UVR damage as isolated mechanisms and highlights the need for barrier-focused research. Sunscreens remain essential, and recent formulations now extend beyond optical filtering by incorporating biologically active components such as antioxidants and photolyase that enhance photostability and support DNA lesion clearance. Emerging research also suggests that microbiome-preserving compositions may help maintain commensal balance during UVR exposure. Together, these developments point to a shift toward multifunctional photoprotection, although evidence is still accumulating. This review synthesizes recent advances alongside remaining gaps in the field. By integrating mechanistic evidence on UVR-induced barrier injury, it identifies directions that can support the design of more biologically grounded photoprotective strategies and delineates priority topics for future research.},
}

@article {pmid41774204,
year = {2026},
author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M},
title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774204},
issn = {1432-0991},
abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.},
}

@article {pmid41774188,
year = {2026},
author = {Yadav, A and Melkani, GC},
title = {Microbes, mood, and metabolism/obesity: Pharmacological insights into the gut-obesity-depression triad.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-025-06022-y},
pmid = {41774188},
issn = {1420-9071},
support = {AG065992//National Institute of Aging/ ; },
}

@article {pmid41773937,
year = {2026},
author = {Wang, A and Dao, LQ and Ramos-Gomez, F and Wang, Y},
title = {Maternal influences on oral microbiome development and implications for early childhood health: a systematic review.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0058525},
doi = {10.1128/iai.00585-25},
pmid = {41773937},
issn = {1098-5522},
abstract = {A deeper understanding of how maternal-infant interactions shape the establishment and diversification of the oral microbiome could have significant clinical applications; however, relatively few studies emphasize early maternal-infant microbial connections. This systematic review provides a longitudinal analysis of oral microbiome development from birth to five years, focusing on the relationship between maternal and infant microbiomes. We conducted a systematic search (June 2025) using keywords "mother," "children," "oral microbiome," and "longitudinal" across PubMed, Cochrane Library, and Embase. Twelve studies fulfilled the inclusion criteria: longitudinal design, healthy mother-child dyads, saliva sample collection, and relevant age range. We excluded review articles, non-English publications, and studies with overlapping data. Results were synthesized by developmental stage and topic. Overall, current literature agrees that the mother is an important source of exposure for initial colonization of the newborn's oral microbiome. Several studies indicated that the oral microbiome at birth is diverse and unspecialized, composed mostly of maternally derived strains. Rapid selection occurs over the first few weeks, as the relative abundances of typical oral bacterial species increase. Throughout the first year, increases in diversity strengthen the resemblance between infant and maternal microbiomes. The microbiome appears to stabilize around 3-5 years. In conclusion, maternal-infant connections play a significant role in influencing oral microbiome development during the first 5 years of life. This review highlights the need for future studies to incorporate larger, longitudinal designs with metadata and advanced tools to clarify the roles of delivery mode, tooth eruption, and parental lifestyle habits in shaping early oral microbiome development.},
}

@article {pmid41773902,
year = {2026},
author = {Vidal, VM and Montes-Cobos, E and Canto, FB and Bozza, MT},
title = {The different meanings of tolerating the gut microbiome.},
journal = {mBio},
volume = {},
number = {},
pages = {e0173624},
doi = {10.1128/mbio.01736-24},
pmid = {41773902},
issn = {2150-7511},
abstract = {Multicellular life arose in a world dominated by microorganisms, a reality that has imposed a constant and pervasive selective pressure on all subsequent complex organisms. The immune system has been historically defined by its role in pathogen clearance through resistance mechanisms. However, a complementary and equally critical strategy is to enable the peaceful and inevitable coexistence with microorganisms, allowing each host species to shelter a unique associated microbiome. The term tolerance holds multiple meanings in immunology, yet all underlie a balanced and cooperative host-microorganism relationship. Each represents a different aspect of how the immune system limits tissue damage while maintaining functionality in the presence of microbial or inflammatory stimuli. Using the intestinal mucosa as a paradigm, we explore how epithelial barrier integrity, toxin neutralization, tissue repair, and stress response underpin disease tolerance; how microbial exposure calibrates innate immunity via epigenetic and metabolic reprogramming (LPS tolerance); and how the gut microenvironment fosters the generation of tolerogenic antigen-presenting cells and microbe-specific regulatory T cells to enforce immunological tolerance. We further explore how the microbiota itself is a potent inducer of these tolerogenic pathways and highlight IL-10 as a major hub, connecting different tolerogenic circuits. Finally, we examine the hygiene hypothesis, arguing that lifestyle changes during the Anthropocene disrupt these finely tuned tolerance mechanisms, thereby contributing to the rising incidence of immune-mediated diseases. We posit that these tolerance programs are fundamental prerequisites for engendering host-microbiota symbiosis, a relationship forged over millennia of co-evolution and endangered in the contemporary world.},
}

@article {pmid41773862,
year = {2026},
author = {Makori, TO and Gicheru, ET and Mburu, MW and Sada, MS and Nyawa, O and Mutunga, M and Lewa, C and Cheruiyot, R and Kiguli, S and Olupot-Olupot, P and Muhindo, R and Mogaka, C and Williams, TN and Agoti, CN and Maitland, K and Sande, CJ},
title = {Nasopharyngeal Microbiome Composition and its Clinical Correlates in Children Hospitalized with Severe Pneumonia in East Africa.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag093},
pmid = {41773862},
issn = {1537-6613},
support = {P46493//Imperial College London/ ; //Medical Research Council Department for International Development/ ; MR/L004364/1/WT_/Wellcome Trust/United Kingdom ; 102231/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: Pneumonia remains the leading cause of infectious mortality in children under 5, with the highest burden in sub-Saharan Africa. Dysbiosis in nasopharyngeal (NP) microbiota may influence pneumonia susceptibility and progression, but little is known about its composition or clinical relevance in low- and middle-income countries. We characterized the NP microbiota of children hospitalized with severe pneumonia in East Africa and investigated associations with clinical outcomes.

METHODS: We performed 16S rRNA partial gene sequencing of NP swabs collected at hospital admission from 876 children enrolled in the COAST trial across 5 sites in Kenya and Uganda. Clinical, demographic, and virological data were prospectively collected. Microbial profiles were analyzed using hierarchical clustering, nonmetric multidimensional scaling, and multivariable regression to assess associations with respiratory viral infections, sepsis, cyanosis, bacteremia, coma, HIV status, malnutrition, sickle cell disease, malaria, and mortality.

RESULTS: The NP microbiome was structured in 6 distinct clusters, each dominated by different genera, including Staphylococcus, Streptococcus, Haemophilus, Dolosigranulum, Corynebacterium, and Moraxella. Multivariable models adjusting for study site and age showed a positive association between Corynebacterium and early mortality. Temporal analysis showed elevated Corynebacterium abundance in children who died within 48 hours of admission, then declined over longer 56 survival intervals, approaching levels observed in survivors. However, time-continuous models did not support this persistent association, suggesting a subgroup effect.

CONCLUSIONS: We provide one of the largest high-resolution surveys of the pediatric upper airway microbiome in Africa, identifying microbial patterns associated with viral infection, HIV status, early death, and bacteremia.},
}

@article {pmid41773858,
year = {2026},
author = {Vijayakumar Padmavathy, B and Shanmugavel, AK and Shanmugam, S and Narayanan, M},
title = {Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0222025},
doi = {10.1128/spectrum.02220-25},
pmid = {41773858},
issn = {2165-0497},
abstract = {UNLABELLED: Tuberculosis (TB) and COVID-19 are both respiratory diseases, and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole-genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa, including Capnocytophaga gingivalis. Functional profiling with PICRUSt2 revealed elevated pathways, including the pulmonary surfactant lipid metabolism pathway (with a fold change of 7.46) in the TBCOVID group. Further clustering of these pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster had a respiratory pathogen, Stenotrophomonas maltophilia-knowing such information on key respiratory pathogens in a patient can help personalize the patient's antibiotic regimen. Overall, our study reveals the effect of COVID-19 on the airway microbiome of TB patients and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment.

IMPORTANCE: The community of microbes in an individual's airway tract can play a complex role in respiratory diseases like tuberculosis (TB) and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway-tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not in TB-only patients. This species and other differentially abundant species we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded data sets to understand the role of concomitant pathogens and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.},
}

@article {pmid41773303,
year = {2026},
author = {Ma, H and Hu, K and Wang, Y},
title = {Dynamic changes of cervical microbiome during pregnancy for preterm birth risk prediction: A prospective cohort study.},
journal = {African journal of reproductive health},
volume = {30},
number = {4},
pages = {50-63},
doi = {10.29063/ajrh2026/v30i4.5},
pmid = {41773303},
issn = {1118-4841},
abstract = {This prospective cohort study investigated the dynamic changes in the cervical microbiome during pregnancy and developed a predictive model for preterm birth risk. Ninety-three singleton pregnant women were enrolled, including 41 with preterm birth and 52 with term delivery. Cervical secretions were collected at four gestational stages and analyzed using 16S rRNA sequencing, alongside ELISA testing for inflammatory markers. The preterm group exhibited significantly lower microbial diversity and a progressively increasing ratio of Lactobacillus iners to Lactobacillus crispatus throughout pregnancy. Early pregnancy IL-6 levels were also significantly elevated in this group. Logistic regression identified the L. iners/L. crispatus ratio, IL-6, history of preterm birth, and short cervical length as independent risk factors. The integrated prediction model demonstrated high accuracy (AUC 0.847), with even stronger performance in predicting births before 34 weeks (AUC 0.892). These findings suggest that microbiome patterns and inflammatory markers can effectively predict preterm birth risk, supporting early clinical intervention.},
}

@article {pmid41773092,
year = {2026},
author = {Lamanna, OK and Hu, R and Khemmani, M and Wolfe, AJ and Groah, SL and Forster, CS},
title = {Differential Effects of Uropathogenic and Non-Uropathogenic E. coli on the Mouse Urobiome and Urine NGAL Levels.},
journal = {Research and reports in urology},
volume = {18},
number = {},
pages = {580953},
pmid = {41773092},
issn = {2253-2447},
abstract = {OBJECTIVE: To determine whether urine neutrophil gelatinase-associated lipocalin (uNGAL) or urobiome alterations can differentiate urinary tract infections (UTI) from asymptomatic bacteriuria (ASB).

METHODS: Female 8-week-old C57BL/6 mice were instilled with either Escherichia coli CFT073 (UTI model, n=12), E. coli 83972 (ASB model, n=12), or saline (control, n=3). uNGAL was measured daily for 3 days post-instillation. Urobiome composition was assessed pre- and post-instillation using 16S rRNA sequencing. At day 3, kidneys were harvested for culture. Comparisons were made across groups for uNGAL levels and urobiome diversity.

RESULTS: Baseline β diversity did not differ between groups. Post-instillation, β diversity significantly differed across groups (p=0.01), driven by increased relative abundance of E. coli in UTI mice compared to ASB mice. Median uNGAL levels increased significantly in both UTI and ASB groups relative to controls, but no significant difference was observed between UTI and ASB groups.

CONCLUSION: Introduction of a uropathogenic E. coli strain reduced urobiome diversity, while a non-uropathogenic strain did not, suggesting strain-specific effects on microbial ecology. Bladder instillation itself also altered the urobiome. Elevated uNGAL levels were observed in both UTI and ASB models, indicating that while uNGAL reflects bacterial exposure, it does not distinguish between uropathogenic and non-uropathogenic E. coli. These findings highlight urobiome analysis as a potential tool for differentiating UTI from ASB, whereas uNGAL alone is insufficient.},
}

@article {pmid41772961,
year = {2026},
author = {Li, M and Zong, H and Yang, X and Liu, Q and Wang, J and Wang, M and Wu, D and Zheng, S and Wang, H and Long, Q},
title = {A flavonoid-rich medicinal herb extract ameliorates high-fat diet-induced obesity and insulin resistance in mice.},
journal = {Acta biochimica et biophysica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.3724/abbs.2026007},
pmid = {41772961},
issn = {1745-7270},
abstract = {Obesity has emerged as a critical global health challenge, contributing to severe metabolic and neoplastic complications. However, most existing anti-obesity drugs exhibit significant adverse effects, necessitating the development of safer therapeutic alternatives. In this study, we evaluate the efficacy and safety of a flavonoid-rich medicinal herb extract (MHE) in a high-fat diet (HFD)-induced murine obesity model. Daily oral administration of MHE does not alter food intake or induce hepatic injury but significantly attenuates HFD-induced weight gain (P < 0.05) and adiposity accumulation. Furthermore, MHE treatment improves systemic insulin sensitivity and glycemic control. Notably, MHE enhances whole-body energy expenditure, as evidenced by elevated oxygen consumption (VO 2), carbon dioxide production (VCO 2), and heat generation (P < 0.01). Mechanistically, MHE selectively promotes the proliferation of beneficial gut microbiota, including Lactobacillus, Akkermansia, and Bifidobacterium species, resulting in increased production of the short-chain fatty acid propionate (PA). Elevated circulating PA levels subsequently stimulate the browning/beiging of inguinal white adipose tissue (iWAT) and upregulate thermogenic pathways. Collectively, our findings demonstrate that MHE exerts anti-obesity effects through gut microbiota modulation and adipose tissue remodeling, offering a promising natural alternative for obesity management.},
}

@article {pmid41772824,
year = {2026},
author = {Ndhlovu, A and von der Heyden, S},
title = {Spatial Patterns and Overlap of Sedimentary and Rhizosphere Microbiomes of the Seagrass Zostera capensis.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70313},
pmid = {41772824},
issn = {1758-2229},
support = {//African Research Universities Alliance/ ; //National Research Foundation/ ; },
abstract = {Seagrasses are important nature-based solutions for climate change mitigation and adaptation due to their carbon stocks and ecosystem service co-benefits. Characterising microbial communities in seagrass sediments and rhizospheres is essential for understanding their roles in biogeochemical cycling, seagrass health, and potential contributions to ecosystem functioning. However, the extent to which seagrass microbiomes are shared at different spatial scales is not well understood. We utilised 16S rRNA metabarcoding to characterise prokaryotic communities in the sediments of the seagrass Zostera capensis at three estuaries spanning the environmental gradient of South Africa. In addition, we characterised the rhizosphere microbiome (rhizobiome) to better understand rhizosphere and sediment community dynamics. Overall, after accounting for community in adjacent seawater, we found that Z. capensis sediment and rhizosphere microbiomes largely overlap, sharing 34 genera but also harbour core genera. The sediment microbiome and rhizobiome showed significant spatial variability, suggesting that both local-scale and broader estuary-specific factors shape site-level microbial signatures. Further, predictive functional analysis showed that the rhizobiome was enriched for nutrient cycling pathways potentially beneficial to Z. capensis. Our findings support the exploration of sediment and rhizosphere microbial communities for monitoring ecosystem health and assessing impacts from threats such as pollution and climate change.},
}