@article {pmid42946394,
year = {2026},
author = {Zhuang, R and Wu, Z and Zheng, R and Chen, Y and Tan, X and Deng, X and Zhang, C and Zeng, J and Wang, Y and He, H and Liu, Y and Zhou, Q and Yao, K},
title = {Intratumoral Klebsiella pneumoniae drives metabolic-immune remodeling and immunotherapy resistance in bladder cancer.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {10},
pages = {},
pmid = {42946394},
issn = {2051-1426},
abstract = {Background: Immune checkpoint blockade has expanded the therapeutic landscape of bladder cancer, yet durable clinical benefit remains limited, and the tissue-level ecological determinants of therapeutic resistance are incompletely understood. Intratumoral microbiota are increasingly recognized as spatially organized components of cancer ecosystems, but whether microbial dysbiosis within bladder cancer tissues functionally shapes antitumor immunity remains unclear. Methods: We integrated contamination-controlled 2bRAD-M microbiome profiling with fluorescence in situ hybridization, single-cell transcriptomics, metabolomics, clinical annotation, organoids, and mouse models to characterize intratumoral microbial states and investigate their roles in immune remodeling and immunotherapy response. Results: Bladder tumors harbored compositionally heterogeneous intratumoral microbial states. Enrichment of Klebsiella pneumoniae (K. pneumoniae) was associated with aggressive disease and reduced immunotherapy benefit, with receiver operating characteristic AUCs of 0.77 and 0.72 in the discovery and validation cohorts, respectively. Mechanistically, K. pneumoniae-associated valylphenylalanine (Val-Phe engaged an SLC15A1-linked epithelial response, activated NF-κB/p65 signaling, and induced an immunoregulatory cytokine program that promoted M2-like macrophage polarization, impaired CD8+ T-cell effector function, remodeled the tumor immune microenvironment, and limited anti-PD-1 efficacy. SLC15A1-guided virtual screening identified MK-0557 as a candidate modulator that restrained tumor growth and improved anti-PD-1 response in preclinical models. Conclusions: These findings identify intratumoral microbial dysbiosis as a functional regulator of metabolic-immune remodeling in bladder cancer and define the K. pneumoniae-associated valylphenylalanine–SLC15A1–NF-κB/p65 axis as a potential therapeutic target for overcoming resistance to immune checkpoint blockade.},
}

@article {pmid42965357,
year = {2026},
author = {Yimamuyushan, S and Muheremu, A and Yi, J and Aimaier, A and Yuan, L and Aili, A},
title = {Bibliometric Analysis of Global Research Trends on Probiotic-Based Interventions for Postmenopausal Osteoporosis.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {236},
pages = {},
doi = {10.3791/73901},
pmid = {42965357},
issn = {1940-087X},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Female ; *Bibliometrics ; *Osteoporosis, Postmenopausal/therapy/drug therapy ; },
abstract = {Postmenopausal osteoporosis (PMOP) is a major skeletal disorder associated with increased fracture risk and substantial morbidity. Growing evidence links the gut microbiota with bone homeostasis, supporting investigation of probiotic-based interventions through immunomodulation, maintenance of intestinal barrier function, and production of short-chain fatty acids. Existing bibliometric studies have examined broader relationships between the gut microbiota, bone metabolism, and osteoporosis; the present analysis focuses specifically on probiotic-based interventions relevant to PMOP. Records indexed in the Web of Science Core Collection were retrieved from the earliest eligible publication in 2005 to a fixed search cut-off of 17 September 2026. Relevance was determined from titles, abstracts, and author keywords, followed by independent screening. A total of 274 records were analyzed using VOSviewer and CiteSpace to characterize publication trends, geographic and institutional contributions, author productivity, journal distribution, document co-citation, and keyword co-occurrence. Publication output remained sparse through 2019 and increased after 2020, reaching 44 publications in 2025, the latest complete year. China contributed the most publications, while the United States had the highest international co-authorship link strength. Michigan State University and Sichuan University each contributed 21 publications, and Claes Ohlsson had the highest number of publications. Co-citation and keyword analyses indicated a shift from prebiotic, calcium-absorption, and fermented-dairy research toward gut-microbiome mechanisms, immunomodulatory pathways, short-chain fatty acid signaling, and randomized clinical trials. These findings provide a reproducible descriptive map of an emerging and heterogeneous research area and identify directions for further clinical investigation.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Female
*Bibliometrics
*Osteoporosis, Postmenopausal/therapy/drug therapy

@article {pmid42965368,
year = {2026},
author = {Hudson, LA and Russo, J and Wright, AT},
title = {Stool Processing for Functional Characterization by Activity-Based Protein Profiling of Bacterial Enzymes in Complex Human Gut Microbiome Systems.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {236},
pages = {},
doi = {10.3791/73546},
pmid = {42965368},
issn = {1940-087X},
mesh = {Humans ; *Feces/microbiology ; *Bacterial Proteins/metabolism/analysis ; Tandem Mass Spectrometry/methods ; *Proteomics/methods ; Liquid Chromatography-Mass Spectrometry/methods ; *Bacteria/enzymology ; *Gastrointestinal Microbiome ; Chromatography, Liquid/methods ; *Microbiota ; },
abstract = {The human gut microbiome is a complex ecosystem composed of trillions of microorganisms whose metabolic activities influence human health, disease progression, and therapeutic outcomes. While sequencing-based approaches provide valuable information regarding microbial composition and genetic potential, they do not directly measure enzyme activity within microbial communities. Activity-based protein profiling (ABPP) enables the selective labeling, enrichment, and identification of active enzymes, providing a functional readout of microbiome activity. Successful application of ABPP to human stool samples requires robust sample processing methods that efficiently isolate bacterial cells while minimizing interference from dietary material, host-derived components, and other contaminants present within the fecal matrix. The goal of this protocol is to provide a reproducible workflow for processing human stool samples for functional characterization of active bacterial enzymes using ABPP and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics. This method describes stool homogenization, bacterial cell isolation, lysate preparation, probe labeling, enrichment of labeled proteins, and downstream LC-MS/MS measurement. The protocol is designed to generate high-quality bacterial protein extracts suitable for profiling active enzyme populations within complex gut microbiome samples.},
}

Humans
*Feces/microbiology
*Bacterial Proteins/metabolism/analysis
Tandem Mass Spectrometry/methods
*Proteomics/methods
Liquid Chromatography-Mass Spectrometry/methods
*Bacteria/enzymology
*Gastrointestinal Microbiome
Chromatography, Liquid/methods
*Microbiota

@article {pmid42965706,
year = {2026},
author = {Haferkamp, S and Schilling, B and Baumgart, L and Gesierich, A and Glutsch, V and Drexler, K and Wein, L and Morak, M and Erdmann, M and Berking, C and Piccinno, G and Derosa, L and Zitvogel, L and Wang, Y and Heinzerling, L},
title = {Microbiome-derived TOPOSCORE is associated with response to immune checkpoint inhibitor re-induction after chemotherapy in primary resistant metastatic melanoma.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {75},
number = {11},
pages = {},
pmid = {42965706},
issn = {1432-0851},
support = {70113416//German Cancer Aid / Stiftung Deutsche Krebshilfe/ ; },
mesh = {Humans ; *Melanoma/drug therapy/microbiology/pathology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Male ; *Drug Resistance, Neoplasm ; Female ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; Prospective Studies ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; },
abstract = {BACKGROUND: Primary resistance to immune checkpoint inhibitors (ICIs) remains a major challenge in metastatic melanoma. The prospective multicenter PROMIT trial showed that intermittent chemotherapy could restore sensitivity to ICI re-induction in a subset of patients. We investigated whether gut microbiome ecosystem states characterized by TOPOSCORE were associated with tumor response in this setting.

METHODS: In the phase II PROMIT trial (NCT04225390), 24 patients with longitudinal stool samples were included in this exploratory microbiome analysis. ICI-resistant patients received two cycles of dacarbazine followed by ICI re-induction. Stool samples underwent shotgun metagenomic sequencing. Microbiome ecosystem states were classified into SIG1- or SIG2-associated ecosystem states using the TOPOSCORE framework, which is based on species-interacting groups (SIGs) defined by ecological co-abundance patterns.

RESULTS: Baseline TOPOSCORE distributions and s-scores were not associated with clinical outcome. In the nine patients with complete BL-CTX-ICI sampling, six retained the same TOPOSCORE category throughout treatment and three changed category. Of the two patients with PR, one remained SIG2 throughout, whereas the other changed from SIG2+ to SIG1+ after chemotherapy and returned to SIG2+ during ICI re-induction. Analyses using all available samples at each phase likewise did not show significant differences in s-score among PR, SD, and PD groups.

CONCLUSIONS: Baseline TOPOSCORE classification was insufficient to predict treatment outcome in this cohort. Longitudinal TOPOSCORE patterns were heterogeneous, and the small number of complete longitudinal profiles precludes conclusions that chemotherapy induced a favorable microbiome transition. These exploratory findings support further evaluation of microbiome ecosystem dynamics in larger prospective cohorts.},
}

Humans
*Melanoma/drug therapy/microbiology/pathology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Male
*Drug Resistance, Neoplasm
Female
*Gastrointestinal Microbiome/drug effects
Middle Aged
Prospective Studies
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use
Aged

@article {pmid42965863,
year = {2026},
author = {Lomeli-Ortega, CO and Balcázar, JL},
title = {Arbitrium crosstalk enables shared signaling among phages.},
journal = {Cell reports},
volume = {45},
number = {11},
pages = {118254},
doi = {10.1016/j.celrep.2026.118254},
pmid = {42965863},
issn = {2211-1247},
abstract = {The arbitrium system has transformed our understanding of phage biology by demonstrating that temperate phages communicate through extracellular peptides to coordinate lysis-lysogeny decisions. Initially considered a highly specific signaling pathway restricted to individual phage lineages, arbitrium communication has now been shown to extend beyond lineage boundaries in some phage systems. Recent studies have shown that non-cognate arbitrium peptides can interact with heterologous receptors, providing evidence of inter-phage crosstalk. Here, we synthesize current knowledge of the molecular basis of arbitrium signaling, the structural determinants of peptide-receptor specificity, and the potential ecological and evolutionary consequences of inter-phage communication. We suggest that arbitrium crosstalk may shape phage ecology by mediating competitive and potentially cooperative interactions within shared signaling environments. We also discuss its potential uses in engineered phage systems, synthetic biology, and microbiome engineering. Collectively, the available evidence broadens the concept of viral communication beyond lineage-specific signaling, while the ecological significance and practical applications of arbitrium crosstalk remain to be established.},
}

@article {pmid42965892,
year = {2026},
author = {Chen, H and Xia, Y and Wang, Y and Chen, H and Sang, T},
title = {Lactobacillales-Enriched Oral Microbiome Profile as a Potential Link in the Tooth Loss-Cognition Association: A Cross-Sectional Analysis of NHANES 2011-2012.},
journal = {Special care in dentistry : official publication of the American Association of Hospital Dentists, the Academy of Dentistry for the Handicapped, and the American Society for Geriatric Dentistry},
volume = {46},
number = {6},
pages = {},
doi = {10.1111/scd.70273},
pmid = {42965892},
issn = {1754-4505},
mesh = {Humans ; *Tooth Loss/microbiology ; *Microbiota ; Cross-Sectional Studies ; Female ; Male ; Nutrition Surveys ; Aged ; *Mouth/microbiology ; United States ; },
abstract = {AIM: This study aimed to examine oral microbial features in the association between tooth loss and cognitive status in older adults from the US population and evaluate the role of oral microbiota in tooth loss and cognition.

METHODS AND RESULTS: Eligible 568 participants from the National Health and Nutrition Examination Survey (Nhanes) 2011-2012 were recruited. Oral rinse sampleses were collected, and the 16S ribosomal RNA gene was sequenced. α-diversity and β-diversity was analyzed to depict microbiome profile. Mediation models were used to investigate the role of a-diversity in the association between tooth loss and cognitive function. The co-occurring group exhibited significantly reduced α-diversity and distinct β-diversity compared to CI (cognitive impairment) only group and the control group (p < 0.001). Differential taxa analysis identified group‑specific microbial signatures, particularly enriched Lactobacillales in the co-occurring group. Mediation analysis further revealed that observed amplicon sequence variants (ASVs) and phylogenetic diversity significantly affected the association between tooth loss and cognitive decline, whereas evenness indices did not.

CONCLUSION: This pioneering study investigated the oral microbiota composition in relation to varying levels of tooth loss and cognitive status. It revealed the complex role of mucosal colonization in both dental and cognitive health, thereby underscoring the need to integrate the oral microbiome into cognitive research.},
}

Humans
*Tooth Loss/microbiology
*Microbiota
Cross-Sectional Studies
Female
Male
Nutrition Surveys
Aged
*Mouth/microbiology
United States

@article {pmid42965910,
year = {2026},
author = {Kumar, V and Nandish, BT and Rao, S and K M, M},
title = {Chitosan-Based Hydrogels for Periodontal Therapy: From Drug-Polymer Chemistry to Smart Multifunctional and Regenerative Systems.},
journal = {Chemistry & biodiversity},
volume = {23},
number = {11},
pages = {},
pmid = {42965910},
issn = {1612-1880},
mesh = {*Hydrogels/chemistry ; Humans ; *Chitosan/chemistry ; *Periodontitis/drug therapy ; Animals ; *Polymers/chemistry ; Biocompatible Materials/chemistry ; Anti-Bacterial Agents/chemistry/pharmacology/therapeutic use ; },
abstract = {Periodontitis is a chronic, multifactorial inflammatory disease driven by microbial dysbiosis, oxidative stress, and dysregulated host immune responses, resulting in progressive destruction of periodontal tissues and, ultimately, tooth loss. Traditional treatments, including scaling and root planing and systemic antibiotics, have limitations due to incomplete bacterial elimination, poor site specificity, short drug retention, systemic side effects, and limited regenerative support. Recently, chitosan (CS)-based hydrogels have emerged as promising biomaterials for localized periodontal treatment owing to their biocompatibility, biodegradability, mucoadhesive nature, and ease of chemical modification. This review critically discusses recent developments in CS-based hydrogel systems functionalized with antibiotics, phytochemicals, anti-inflammatory agents, nanoparticles, regenerative molecules, and stimuli-responsive materials for the management of periodontitis. It primarily focuses on periodontal pathophysiology, therapeutic strategies, and drug-polymer interactions that affect its performance. Furthermore, it highlights emerging smart hydrogel systems that respond to pH, reactive oxygen species, temperature, and enzymatic activity within the periodontal microenvironment for controlled, targeted drug delivery. Future perspectives involve the development of multi-stimuli-responsive, microbiome-preserving, self-healing, and personalized hydrogel platforms capable of sequential drug delivery and periodontal regeneration. On the whole, this review bridges the gap between materials chemistry and clinical applicability, providing insights into design of next-generation CS-based hydrogels for targeted periodontal therapy.},
}

*Hydrogels/chemistry
Humans
*Chitosan/chemistry
*Periodontitis/drug therapy
Animals
*Polymers/chemistry
Biocompatible Materials/chemistry
Anti-Bacterial Agents/chemistry/pharmacology/therapeutic use

@article {pmid42966018,
year = {2026},
author = {de Mello, VVC and Funnicelli, MIG and Barbier, E and Micolta, LFB and Machado, RZ and Barros-Battesti, DM and Pinheiro, DG and André, MR},
title = {Bacterial diversity associated with Streblidae flies parasitizing cave-dwelling bats from northeastern Brazil.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {130},
number = {},
pages = {102544},
doi = {10.1016/j.cimid.2026.102544},
pmid = {42966018},
issn = {1878-1667},
abstract = {Bats (Chiroptera) are highly diverse mammals that play key ecological roles and harbor a wide range of microorganisms, yet the microbiome of their ectoparasitic flies remains poorly understood. This study characterized and compared the bacterial microbiomes associated with two bat-ectoparasite systems, Pteronotus gymnonotus-Trichobius johnsonae and Desmodus rotundus-Trichobius parasiticus, from cave-dwelling bat populations in northeastern Brazil using 16S rRNA gene sequencing. Sixty-eight bat fly samples were successfully sequenced, and 67 were retained for downstream ecological analyses after quality filtering. Bacterial communities were dominated by members of the classes Gammaproteobacteria and Alphaproteobacteria, with Arsenophonus, Bartonella, and unresolved endosymbiont-associated taxa among the most abundant bacterial groups. Alpha-diversity patterns varied according to the metric considered: observed ASV richness was influenced by bat fly species, sex, and their interaction, Shannon diversity differed according to streblid fly species and sex, and Faith's phylogenetic diversity differed between bat fly sexes. Notably, male T. johnsonae exhibited greater observed ASV richness than females, whereas no significant sex difference was detected in T. parasiticus. Beta-diversity analyses consistently revealed differences in bacterial community composition between the two bat-ectoparasite systems, while the influence of sex was system-dependent, with significant differentiation between T. johnsonae males and females but not between sexes of T. parasiticus in phylogenetically informed analyses. Differential abundance analysis further identified Romboutsia, Bartonella, Bacteroides, and an unclassified Pseudomonadota genus as discriminatory taxa among groups. Overall, these findings reveal distinct bacterial diversity and composition patterns between the two bat-ectoparasite systems and indicate that sex-associated microbiome variation is not uniform across bat fly species.},
}

@article {pmid42966027,
year = {2026},
author = {Kim, B and Joe, HI and Yang, AI and Lee, JY and Kim, HS and Bae, JW and Shin, NR},
title = {Senimuribacter muris sp. nov., a butyrate-producing bacterium isolated from mouse feces, and reclassification of members of the family Eubacteriaceae into the family Anaerovoracaceae.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126782},
doi = {10.1016/j.syapm.2026.126782},
pmid = {42966027},
issn = {1618-0984},
abstract = {Two strictly anaerobic, Gram-stain-positive, non-motile, and rod-shaped bacterial strains, designated rT4E-8[T] and mB4P-1, were isolated from the feces of specific-pathogen-free Mus musculus (C57BL/6J). Both strains were catalase- and oxidase-negative and produced butyrate as a major fermentation product, with optimal growth at 37 °C and pH 7. The two strains shared 100% pairwise 16S rRNA gene sequence similarity and showed high similarity to Senimuribacter intestinalis DSM 106208[T] (95.1-95.3%). Genome sizes of strains rT4E-8[T] and mB4P-1 were 2.9 Mbp and 2.8 Mbp, with genomic DNA G+C contents of 44.9% and 45.1%, respectively. Orthologous average nucleotide identity and digital DNA-DNA hybridization values between strain rT4E-8[T] and S. intestinalis were 75.9% and 25.4%, respectively, supporting their classification as a novel species. Based on the phenotypic, chemotaxonomic, and genomic evidence, strains rT4E-8[T] and mB4P-1 represent a novel species, for which the name Senimuribacter muris sp. nov. is proposed. The type strain is rT4E-8[T] (=KCTC 25664[T] =JCM 36407[T]). Phylogenomic analyses supported the reassignment of Senimuribacter and several related taxa from the family Eubacteriaceae to the family Anaerovoracaceae. In addition, Eubacterium sulci and Eubacterium infirmum are reclassified into Pareubacterium gen. nov., with Pareubacterium sulci comb. nov. and Pareubacterium infirmum comb. nov. Amplicon sequence variant analysis of mouse fecal microbiome datasets revealed that sequences corresponding to strain rT4E-8[T] exhibited a significant positive correlation with host age and were detected exclusively in C57BL/6J mice from a specific vendor. Large-scale metagenomic screening further supported the association of the novel strains with mouse gut environments.},
}

@article {pmid42966084,
year = {2026},
author = {Li, J and Cai, B and Ge, J},
title = {Quorum sensing-mediated rhizosphere engineering: Synthetic microbial consortia as a next-generation strategy to induce soybean resistance against Heterodera glycines.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128800},
doi = {10.1016/j.micres.2026.128800},
pmid = {42966084},
issn = {1618-0623},
abstract = {Soybean cyst nematode (Heterodera glycines, SCN) severely threatens global soybean yields. Traditional genetic resistance relying on Rhg1 and Rhg4 loci is increasingly compromised by virulent SCN populations. This review synthesizes current knowledge on the molecular interplay among soybean (Glycine max), SCN, and rhizosphere microbiome with a specific focus on quorum sensing (QS) as a central regulatory mechanism enabling novel biotechnological interventions. Emphasis is placed on how soil molecular microbiology approaches can facilitate the transfer of disease-suppressive microbiomes from resistant to susceptible soybean genotypes through strategic inoculation. QS molecules, including N-acyl homoserine lactones (AHLs) and autoinducer-2 (AI-2), prime plant immune responses, while root exudates mediate bidirectional plant-microbe feedback loops. It is proposed that rationally designed synthetic microbial consortia (SynComs), microbiome-smart breeding, and optimized inoculation technologies offer complementary strategies to conventional genetic resistance for sustainable SCN management.},
}

@article {pmid42966106,
year = {2026},
author = {Chen, Y and Chu, J and Guo, Y and Farhan, MHR and Lu, X and Wei, H and Xie, C and Wang, X and Huang, L and Cheng, G},
title = {Dynamic changes of chicken gut microbiota and resistome during enrofloxacin treatment against multidrug-resistant Salmonella based on metagenomics.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143929},
doi = {10.1016/j.jhazmat.2026.143929},
pmid = {42966106},
issn = {1873-3336},
abstract = {Antibiotics are widely used to treat and prevent bacterial infections in human and animals. However, the impact of antibiotic dose on bacterial burden and diachronic changes and transfer of antibiotic resistance genes (ARGs) in gut bacterial infections remains unclear. Here, we used enrofloxacin (ENR) at sub-inhibitory (1 mg/kg b.w.), prophylactic (3.03 mg/kg b.w.), and therapeutic (10 mg/kg b.w.) doses to treat infections with Salmonella harboring plasmid pJX-4, with infected but untreated groups as controls. We found that subtherapeutic ENR may pose potential risks to the gut ecosystem. Specifically, sub-inhibitory ENR led to persistently high Salmonella and its carried resistance gene qnrS1 levels; under this dose condition, preliminary evidence suggested that intestinal Escherichia coli was a potential host for in vivo transfer of plasmid pJX-4. The prophylactic dose group showed significantly higher relative abundances of human bacterial pathogens and ARGs, especially during treatment. Furthermore, this group was enriched in genes related to oxidative stress, cellular signaling, and secretion systems, and these functional genes were primarily associated with ARGs. Overall, different ENR doses shaped distinct evolutionary trajectories of the gut microbiome and resistome. This study provides a theoretical basis for the rational use of antibiotics in treating bacterial infections.},
}

@article {pmid42966154,
year = {2026},
author = {Cui, Y and Chen, J and Huang, L and Yao, J and Zhang, Y and Wang, Y and Yang, J and Tian, L},
title = {Metabolic conversion of dioscin-diosgenin and their interactions with gut microbiota: recent advances.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158873},
doi = {10.1016/j.phymed.2026.158873},
pmid = {42966154},
issn = {1618-095X},
abstract = {BACKGROUND: HMF plants are rich sources of steroidal saponins, and dioscin and diosgenin are the widely distributed and bioactive compounds. Despite their poor oral bioavailability, these saponins undergo extensive microbial transformation, yielding bioavailable metabolites with enhanced lipophilicity and pharmacological potential. Recent studies indicate that the interaction between diosgenin and the gut microbiota plays a crucial role in regulating metabolic, immune, and neuroendocrine functions. Understanding this bidirectional relationship may provide a foundation for developing novel microbiota-targeted nutritional and therapeutic strategies.

PURPOSE: The purpose of this review was to summarize current research progress on the biotransformation, biological functions, and health implications of diosgenin and its precursors. We elucidate how microbial metabolism modulates diosgenin activity and how diosgenin reshapes gut microbial composition and function to maintain intestinal homeostasis.

METHODS: A comprehensive literature search was conducted using four major electronic databases, including PubMed, Web of Science, Embase, and CNKI, were searched from inception to January 2026. Key words used in the literature search were "diosgenin", "dioscin", "steroidal saponins", "gut microbiota", "homology of medicine and food", "β-glucosidase", "microbial transformation", "mucosal immunity", "metabolic and inflammatory disorders" and "gut brain axis". Keywords are linked with AND/OR. Chemical structure data and biotransformation pathways were confirmed through peer-reviewed sources and authoritative databases such as NIH and PubChem.

RESULTS: Evidence indicates that intestinal microbial β-glucosidases catalyze the deglycosylation of dioscin into lipophilic aglycone diosgenin, thereby enhancing its membrane permeability and bioactivity. Diosgenin selectively enriches beneficial microbial populations and promotes the production of key microbial metabolites, including SCFAs and tryptophan-derived indoles. These microbial metabolites play pivotal roles in intestinal epithelial integrity and mucosal immune homeostasis. They modulate the Treg balance by activating key host signaling pathways. The primary receptors involved include GPRs, AHR, and PPARs. Preclinical studies strongly support the therapeutic potential of the microbiota-diosgenin axis in alleviating T2D, NAFLD, IBD, neuroinflammation, and age-related pathologies.

CONCLUSION: This review highlights the gut microbiota as an important modulator of diosgenin bioavailability and biological activity, based largely on preclinical evidence. Differences in microbial composition and metabolic capacity may contribute to interindividual variability in host responses to diosgenin. In this context, we propose the concept of diosgenin metabotypes as a conceptual framework to describe microbiota-dependent differences in diosgenin metabolism, which may inform future microbiome-guided nutritional and therapeutic strategies.},
}

@article {pmid42966262,
year = {2026},
author = {Mi, X and Wang, Z and Ran, M and Shi, B and Wang, H},
title = {Coupled physicochemical and microbial recovery of aged premise plumbing following water-supply interruption.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127227},
doi = {10.1016/j.watres.2026.127227},
pmid = {42966262},
issn = {1879-2448},
abstract = {Water-supply interruptions can cause pronounced deterioration of premise-plumbing water quality, yet the coordinated responses of bacterial communities, antibiotic resistance, bacteriophages, and microbial functional potential during water-supply resumption remain poorly resolved. Here, a full-scale 24-h water-supply interruption in an approximately 25-year-old cast-iron premise-plumbing system was investigated by integrating physicochemical measurements, quantitative PCR, metagenomics, virus-host prediction, and functional analyses. At 1 min after water supply resumption, residual chlorine was undetectable, whereas turbidity and total iron ranged from 149.9 to 155.3 NTU and 13.4 to 13.8 mg/L, respectively. By 40 min, residual chlorine reached 0.52 to 0.56 mg/L, while turbidity and total iron declined to levels of 0.56 to 0.61 NTU and 0.028 to 0.041 mg/L, respectively. Concurrently, Legionella pneumophila decreased from 4.12 to 0.83 log10 (gene copies/mL), and mexA from 5.55 to 1.77 log10 (gene copies/mL). Metagenomic analyses revealed pronounced succession of bacterial communities, putative human pathogen-associated taxa, and the resistome. Caudoviricetes dominated the viral community and showed coordinated temporal changes with predicted bacterial hosts. Biofilm-associated functional genes, extracellular polymeric substances (EPS), and putative phage-encoded auxiliary metabolic genes were more abundant in the initially discharged water and generally decreased following water supply resumption. The elevated EPS may have reflected both microbial production and detachment of pre-existing biofilm-associated material. Collectively, the results identify the initially discharged water as a distinct post-stagnation physicochemical and microbiological state. Water-supply resumption represents a rapid ecological transition in which restoration of disinfectant residual and displacement of stagnant/pipe-associated material jointly restructure the microbiome, resistome, and virome.},
}

@article {pmid42966288,
year = {2026},
author = {Wang, H and Shen, S and Liu, M and Cheng, S and Cordeiro, CM and Sindhøj, E and Liang, J and Zeng, Y and Zhang, K and Zhi, S},
title = {Impact of half-amount fertilization patterns on antibiotic resistance gene dynamics in a soil-root-crop system on a long-term manure-amended farm.},
journal = {Ecotoxicology and environmental safety},
volume = {326},
number = {},
pages = {120995},
doi = {10.1016/j.ecoenv.2026.120995},
pmid = {42966288},
issn = {1090-2414},
abstract = {Optimizing manure recycling and mitigating antibiotic resistance gene (ARG) dissemination are critical for sustainable agriculture. This field study evaluated nutrient-matched half-dose fertilization regimes (T1: organic-chemical mix; T2: organic alone; T3: chemical alone) against conventional full-dose fertilization (TF) and a no-current-season-fertilizer control (CK) along the soil-root-crop continuum. Topsoil under T2 maintained a total nitrogen concentration (1.29 g·kg[-1]), showed a comparatively narrow nitrate concentration range (4.59-7.39 mg·kg[-1]), and decreased antibiotic residues by approximately 45% (20.41 μg·kg[-1]) relative to TF. Hierarchical partitioning showed that soil pH (27.20%) and available nitrogen-related variables had the largest relative explanatory contributions to bulk-soil ARG variation. The rhizosphere-root compartment showed strong microbiome filtering, with the highest relative explanatory contributions from Chloroflexi (96.60%) and WD2101_soil_group (98.10%), whereas bacterial profiles in washed edible tissue samples were most strongly associated with Pantoea and Sphingomonas (combined contribution 23.40%) among the measured genera. Under TF, higher nutrient and contaminant loading was associated with greater enrichment of key resistance genes (fexA, ISCR1, strA, tetQ) in roots and washed edible tissues (BCFRoot > 1.0, TFTotal > 1.0). Under equal macronutrient inputs, T1 and T2 reduced total bulk-soil ARG abundances by 60%-90% compared with TF (p < 0.05), with no significant difference between them. T1 reduced the proportion of manure applied through partial synthetic substitution, whereas T2 retained organic substrate inputs at the reduced rate. Both regimes showed low root and tissue enrichment indices (BCFRoot ≤ 0.03, TFTotal ≤ 0.04), indicating markedly lower relative enrichment than TF. These findings support reduced-input fertilization as a promising strategy for mitigating resistome pressure; regulatory compliance and food-safety implications require separate evaluation.},
}

@article {pmid42966311,
year = {2026},
author = {Huang, J and Zhang, N and Xu, J and Guan, L and Zhang, W and Zhou, Y and Lin, X and Hu, C},
title = {Eco-friendly mulching with Camellia oleifera Abel. shell waste: Weed suppression and soil nutrient improvement.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131260},
doi = {10.1016/j.jenvman.2026.131260},
pmid = {42966311},
issn = {1095-8630},
abstract = {This study offers a simple, feasible approach for utilizing Camellia oleifera Abel. shell (COS) waste as mulch for weed control in plantations. The mechanism of weed management under COS mulching and its effects on plantation soil properties were comprehensively investigated via phytotoxicity bioassays, field experiments, soil characterization, and microbiome sequencing. Phytotoxicity bioassays showed that COS aqueous extract resulted in oxidative damage and inhibited physiological activities during seed germination. Field experiments revealed that with up to 77.72% weed reduction, higher dosages of crushed COS augmented the shading and the weed suppression rate. Soil-dissolved organic matter content, soil-available phosphorus, and soil-available potassium contents were increased by 127.87%, 112.06%, and 201.04%, respectively, after mulching. COS mulching significantly enriched lignocellulolytic bacterial taxa (Proteobacteria, Bacteroidota, Actinobacteriota) and phosphate-solubilizing microorganisms. A comprehensive interactive model linking COS coverage, weed growth, soil nutrients, and soil microorganisms was constructed, revealing the synergistic interaction mechanisms among these components. This work provides scientific guidance for returning COS to plantation land as a mulch to achieve eco-friendly treatment and improve the ecological environment of the plantation.},
}

@article {pmid42966336,
year = {2026},
author = {Stephens, S and Da Silva, T and Zhu, F and Arnold, DL and Banwell, B and Bar-Or, A and Bernstein, CN and Bonner, C and Graham, M and Knox, N and O'Mahony, J and Marrie, RA and Mirza, AI and Van Domselaar, G and Waubant, E and Zhao, Y and Tremlett, H and Yeh, EA and , },
title = {Gut microbiome and physical activity in paediatric-onset multiple sclerosis.},
journal = {Multiple sclerosis and related disorders},
volume = {116},
number = {},
pages = {108023},
doi = {10.1016/j.msard.2026.108023},
pmid = {42966336},
issn = {2211-0356},
abstract = {OBJECTIVES: To examine associations between physical activity (PA) and gut microbiome diversity and composition in youth with pediatric onset multiple sclerosis (POMS) versus monophasic demyelinating syndromes (mono-ADS) and unaffected controls (UC), and to compare active versus inactive POMS.

METHODS: Thirty-seven youth with POMS, 40 mono-ADS, and 36 UC from the Canadian Pediatric Demyelinating Disorders Study were included. Stool samples underwent 16S rRNA sequencing. PA was assessed using the Godin Leisure-Time Exercise Questionnaire and analyzed as continuous (total PA, moderate and vigorous PA, strenuous PA) and binary (active vs. inactive) variables. Alpha diversity (Shannon, Simpson, Chao1) and beta diversity (UniFrac, Bray-Curtis) were assessed using permutation-based linear regression and PERMANOVA, adjusting for age, sex, and BMI. LEfSe identified differentially abundant taxa, and Spearman correlations assessed associations with PA.

RESULTS: No differences in alpha diversity were observed. In POMS, total PA showed modest associations with UniFrac beta diversity (R²≈0.04-0.05, p≈0.08; FDR p=0.13), but not Bray-Curtis. Inactive POMS had lower Firmicutes and higher Bacteroidetes, with enrichment of Bifidobacterium, Escherichia-Shigella, and Lactobacillus, whereas active POMS showed higher Firmicutes (e.g., Roseburia, Lachnospiraceae); Bifidobacterium was ∼4-fold higher in inactive POMS. These patterns were not observed in controls or mono-ADS. Firmicutes positively correlated with PA intensity, while Actinobacteria, Bacteroidetes, and Bifidobacterium were inversely correlated INTERPRETATION: PA-microbiome associations appear unique in POMS demonstrated by specific compositional patterns. These findings should be confirmed in larger cohorts with objective measures of physical activity and more comprehensive assessment of potential confounding factors.},
}

@article {pmid42966564,
year = {2026},
author = {Li, Z and Shi, B and Luo, N and Zhao, C and Weng, Q and Chen, J and Wang, M and Zhu, D},
title = {Metagenomic Features of Oral Microbiome in Tibetan Dental Caries Patients: An Exploratory Study.},
journal = {Journal of stomatology, oral and maxillofacial surgery},
volume = {},
number = {},
pages = {103062},
doi = {10.1016/j.jormas.2026.103062},
pmid = {42966564},
issn = {2468-7855},
abstract = {OBJECTIVE: This study aimed to preliminarily explore the composition and functional potential of oral bacteria in Tibetan patients with dental caries, and to explore potential associations between the observed functional features and the high-altitude living environment and dietary habits.

METHODS: Saliva samples were collected from nine Tibetan individuals with dental caries. Sequencing was performed on an Illumina high-throughput sequencing platform. The obtained genomes were annotated and analyzed using the non-redundant protein (nr) database, Clusters of Orthologous Genes (COG) database, Kyoto Encyclopedia of Genes and Genomes (KEGG), Carbohydrate-Active Enzymes (CAZy) database, Comprehensive Antibiotic Resistance Database (CARD), and Virulence Factor Database (VFDB).

RESULTS: Across the nine samples, seven dominant phyla and ten dominant genera were identified. At the phylum level, Bacillota (44.06%) and Actinomycetota (26.2%) were predominant. At the genus level, Streptococcus (25.96%) predominated. Functional annotation showed that genes and pathways linked to cell wall/membrane biogenesis (32,623 genes) and carbohydrate metabolism (39,616 genes) accounted for a notable proportion of the total, thereby forming an efficient metabolic cascade encompassing carbohydrate uptake, metabolism, and acid production. Furthermore, multidrug resistance-related annotations represented the largest CARD category (53.05%), whereas immune modulation-related annotations predominated in VFDB annotation (52.48%).

CONCLUSIONS: This study provides a preliminary description of the community composition and functional annotation features of the oral microbiome in Tibetan patients with dental caries, showing prominent annotations related to carbohydrate metabolism and biofilm-associated functions, as well as resistance- and virulence-related annotations. These exploratory findings may serve as an initial reference for future studies on dental caries in Tibetan communities using larger cohorts and experimental validation.},
}

@article {pmid42966637,
year = {2026},
author = {Price-Christenson, G and Yannarell, A},
title = {Influence of Competitor Niche on the Ability of Enterobacter cloacae to Suppress the Germination Globisporangium ultimum Sporangia.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-03-26-0071-R},
pmid = {42966637},
issn = {0031-949X},
abstract = {Enterobacter cloacae is a bacterium that can prevent seedling damping-off by Globisporangium ultimum (formerly Pythium ultimum). This bacterium suppresses damping-off by metabolizing the fatty acid cue released by germinating seeds that initiates G. ultimum sporangia germination and infection. However, this suppression mechanism has been unreliable because it only occurs only when carbohydrates are scarce. We hypothesized that niche preemption by competitor bacteria in carbohydrate rich environments could enhance the pathogen suppression success by E. cloacae by narrowing its realized niche to consist mainly of fatty acids. We tested this hypothesis through pair-wise competition experiments between E. cloacae and bacteria with varying niche overlap profiles and measured the germination of G. ultimum sporangia. After these trials, we postulated that other chemical substrates may influence the behavior of G. ultimum and E. cloacae based on patterns witnessed; namely amygdalin, hydroxybenzoic acid, palatinose, D-gluconic acid, and L-glutamic acid. We then exposed G. ultimum and E. cloacae to these compounds to determine how they influenced the suppression behavior of E. cloacae and the germination of G. ultimum sporangia. We found that although niche preemption does not predict pathogen suppression patterns between E. cloacae and competitor bacteria, niche overlap was inversely correlated with sporangia germination for gram-negative bacteria; the opposite pattern predicted by niche overlap. We also found several taxa that significantly enhanced the pathogen suppression by E. cloacae. Finally, we found that amygdalin and 4-hydroxybenzoic acid inhibited the suppression performance E. cloacae and found that 4-hydroxybenzoic acid, palatinose, and L-glutamic acid inhibited sporangia germination.},
}

@article {pmid42966652,
year = {2026},
author = {John, AS and Bai, J and Calamaro, C and Brown, AM and Keiffer, R and Huang, H and Gillespie, S and Denning, PW and Sanders-Lewis, K and Fundora, MP},
title = {Social and Environmental Exposures and the Developing Gut of Newborns With Congenital Heart Disease.},
journal = {American journal of critical care : an official publication, American Association of Critical-Care Nurses},
volume = {35},
number = {6},
pages = {e7-e24},
doi = {10.4037/ajcc2026557},
pmid = {42966652},
issn = {1937-710X},
mesh = {Humans ; Infant, Newborn ; *Heart Defects, Congenital/microbiology ; Female ; Male ; Prospective Studies ; *Gastrointestinal Microbiome/physiology ; *Environmental Exposure/adverse effects ; *Dysbiosis ; Milk, Human ; Infant Formula ; Socioeconomic Factors ; },
abstract = {BACKGROUND: Dysbiotic gut microbiomes are linked to morbidity, mortality, and poor outcomes, so it is critical to understand their influencing factors.

OBJECTIVES: To investigate the impact of nosocomial and socioecological factors on the gut microbiome in newborns with congenital heart disease (CHD).

METHODS: This was a secondary analysis of a prospective cohort of newborns with CHD matched to healthy newborns by age, sex, and race and ethnicity. Data on feeding type and routes and disease-related factors were collected from electronic medical records. Stool samples were collected at 3 perioperative time points. Gut microbiome diversity and abundance were analyzed using QIIME 2.

RESULTS: Newborns with CHD (n = 41) showed higher alpha diversity (P = .007) and dissimilar beta diversity (P = .001) versus controls (n = 40). Beta diversity was dissimilar between those receiving human milk versus formula (P = .05), between those receiving fortified versus nonfortified human milk (P = .04), and between those receiving naso-orogastric tube feeds versus other routes (P = .02). Newborns with CHD fed only human milk had higher relative abundance of Haemophilus (P = .04), those with longer duration of aortic cross-clamping had lower relative abundance of Streptococcus (P = .10), and those of higher socioeconomic deprivation had higher relative abundance of Enterococcus (P = .03).

CONCLUSIONS: Feeding tubes, formula exposure, aortic cross-clamp, and socioeconomic status were associated with altered gut microbiome diversity. Further study is needed to determine the causal relationships leading to gut microbial dysbiosis in newborns in the cardiac intensive care unit.},
}

Humans
Infant, Newborn
*Heart Defects, Congenital/microbiology
Female
Male
Prospective Studies
*Gastrointestinal Microbiome/physiology
*Environmental Exposure/adverse effects
*Dysbiosis
Milk, Human
Infant Formula
Socioeconomic Factors

@article {pmid42966961,
year = {2026},
author = {Alwithanani, NA},
title = {Bidirectional Interplay Between Periodontitis and Alzheimer's Disease: Mechanisms, Clinical Management, and Preventive Strategies.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e117264},
pmid = {42966961},
issn = {2168-8184},
abstract = {Alzheimer's disease (AD) is a major neurodegenerative disorder, whereas periodontitis is a highly prevalent chronic inflammatory disease that may have important systemic consequences. Increasing evidence suggests a bidirectional relationship between periodontitis and AD, with periodontal inflammation potentially contributing to cognitive decline and neurodegeneration, while cognitive and motor impairment may simultaneously worsen oral hygiene and periodontal health. This narrative review synthesizes current evidence regarding the epidemiological association, potential biological mechanisms, clinical implications, and emerging preventive and therapeutic strategies linking the two conditions. Evidence indicates that periodontitis is associated with an increased risk of cognitive impairment and AD, although causality remains unproven. Proposed mechanisms include translocation of periodontal pathogens, particularly Porphyromonas gingivalis, systemic inflammation and neuroinflammation, blood-brain barrier disruption, oxidative stress, microbiome alterations, and effects on amyloid-β and tau pathology. In patients with AD, progressive cognitive impairment can compromise oral self-care and increase dependence on caregivers, contributing to periodontal deterioration. Early periodontal assessment, individualized treatment, caregiver-supported oral hygiene, regular maintenance, and interdisciplinary care may therefore be clinically beneficial. Emerging approaches targeting periodontal pathogens, gingipains, and the oral microbiome are promising but require stronger clinical validation. Overall, maintaining periodontal health represents a potentially modifiable component of comprehensive strategies for reducing the oral and systemic burden associated with AD.},
}

@article {pmid42967594,
year = {2026},
author = {Liang, L and Hu, F and Wang, X and Tang, C and Wang, C and Jiang, G and Zhao, C and Zhang, Y and Li, C},
title = {The microbiome and brain metastasis in non-small cell lung cancer: A graded appraisal and a framework for prevention-oriented research.},
journal = {Clinical and translational medicine},
volume = {16},
number = {11},
pages = {},
pmid = {42967594},
issn = {2001-1326},
support = {YXYX2407//the Sichuan Clinical Research Center for Medical Imaging Open Funding Project/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/complications/pathology ; *Brain Neoplasms/secondary/prevention & control ; *Lung Neoplasms/complications/pathology ; *Microbiota/physiology ; *Preventive Medicine/methods ; },
abstract = {BACKGROUND: Brain metastasis remains a major cause of mortality and treatment failure in non-small cell lung cancer (NSCLC). However, current models of cerebral dissemination rarely integrate microbiome-dependent systemic and intratumoral biology.This Review examines the potential microbiome-brain metastasis axis linking gut, lung, and intratumoral microbial communities to intracranial dissemination and therapeutic response.

METHODS: A reproducible literature search was conducted to evaluate proposed mechanisms underlying microbiome-associated brain metastasis. Evidence for each mechanistic claim was graded using a four-level evidence scheme (E1-E4), while microbial detection confidence was assessed using a four-tier hierarchy (D1-D4).

RESULTS: No component of the proposed axis reached E1 evidence, and all published microbial observations in NSCLC brain metastasis rests on nucleic-acid detection alone. Five mechanisms are examined: circulating microbial metabolites acting on endothelial permeability and glial reactivity; microbiome-imprinted immune-cell trafficking;intracellular bacteria within primary lung tumours; cross-kingdom MR1/MAIT and Dectin-CARD9 signalling; and candidate host genetic determinants. The available human data are small, single-centre and cross-sectional, reporting association with brain-metastasis status rather than prediction or causation; that bacteria accompany disseminating tumour cells into the brain remains a hypothesis awaiting paired sampling, spatial localization and experimental perturbation.We therefore reserve the term prevention for proposed trials, integrate microbial features with established molecular risk models, and specify the genetic-perturbation program and research-only decision pathway that would convert these claims into E1 evidence.

CONCLUSIONS: The microbiome-brain metastasis axis provides a hypothesis-generating framework for investigating microbial contributions to cerebral dissemination. Multi-centre validation, paired primary-brain metastasis profiling and gnotobiotic models are required before microbiome-directed strategies can be said to improve intracranial outcomes;until then this framework is hypothesis-generating, not practice-changing.

KEY POINTS: The proposed microbiome-brain metastasis axis links gut, lung and intratumoral microbial communities to intracranial dissemination in NSCLC. Current evidence remains insufficient to establish causality, with no proposed mechanism reaching the highest evidence level (E1). Five candidate mechanisms involve microbial metabolites, immune-cell trafficking, intratumoral bacteria, MR1/MAIT and Dectin-CARD9 signalling, and host genetic determinants. Multicentre validation, paired primary and brain metastasis profiling, spatial microbial localisation and experimental perturbation are needed to establish causality and assess clinical relevance. Microbiome-directed prevention and therapeutic strategies remain investigational and should not yet inform routine clinical practice.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/complications/pathology
*Brain Neoplasms/secondary/prevention & control
*Lung Neoplasms/complications/pathology
*Microbiota/physiology
*Preventive Medicine/methods

@article {pmid42967701,
year = {2026},
author = {Liu, Y and Niu, Y and Xu, N and Li, M and Dong, M and Zhou, Z and Ma, Y and Wang, C and Li, Y and Si, Z and Fang, H and Chai, H and Sun, Y and Chen, P},
title = {Unraveling multidimensional heterogeneity of the Astragalus microbiome: An integrative multi-omics and machine learning framework for biomarker discovery.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 4},
pages = {120864},
doi = {10.1016/j.foodres.2026.120864},
pmid = {42967701},
issn = {1873-7145},
mesh = {*Machine Learning ; Multiomics ; *Microbiota/genetics ; Rhizosphere ; Biomarkers/analysis ; Plant Roots/microbiology ; *Astragalus Plant/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; China ; },
abstract = {Astragalus (primarily represented by A. mongholicus and A. membranaceus) is a widely used functional food whose quality is closely associated with geographical origin, a concept known as geoherbalism. However, the relationship between its microbiota and bioactive constituents across different plant species, production regions, cultivation patterns, and chemotypes remains poorly understood. In this study, we characterized the endophytic microbial communities of Astragalus roots from 61 samples collected across six major cultivation regions in four Chinese provinces using high-throughput amplicon sequencing (targeting the 16S rRNA and ITS regions). We further integrated publicly available rhizosphere metagenomic (PRJNA1119562) and root transcriptomic (PRJNA1119057) datasets to explore microbial functional potential and host-microbe interactions. Machine learning models were developed to predict the levels of key bioactive ingredients (Astragaloside IV [AS-IV] and Calycosin-7-O-β-D-glucoside [CG]), and candidate biomarkers were validated by qPCR. The composition and diversity of endophytic microbiota varied significantly with plant species, geographical origin, cultivation pattern (cultivated, imitated-wild, and wild), and chemotype. Specific taxa, including Penicillium, Coprinopsis, and Pseudomonas, were enriched in high-quality samples, and species-specific microbial signatures were also observed. Rhizosphere metagenomic profiling revealed enhanced energy and amino acid metabolism in low-quality samples, suggesting potential competition for key substrates. Transcriptomic analysis identified differentially expressed genes involved in secondary metabolism, some of which correlated with specific rhizosphere microbes. Lactarius and Alistipes were identified as candidate microbial biomarkers through machine learning and further validated by qPCR assays targeting their corresponding ITS and 16S rRNA gene sequences, respectively, achieving accuracies of 85% and 95% in internal and external validation. However, the relatively limited validation cohorts may not fully represent the geographic and cultivation diversity of Astragalus, and larger-scale validation using samples covering broader geographic origins and cultivation conditions is required to further confirm the robustness and generalizability of these microbial biomarkers. Overall, this study provides a comprehensive characterization of the Astragalus microbiome, highlighting its strong associations with plant species, geoherbalism, cultivation practices, and bioactive accumulation. The validated biomarkers offer promising tools for quality assessment and support microbiome-based strategies for improving the functional quality of Astragalus as a food ingredient.},
}

*Machine Learning
Multiomics
*Microbiota/genetics
Rhizosphere
Biomarkers/analysis
Plant Roots/microbiology
*Astragalus Plant/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
Metagenomics
China

@article {pmid42967713,
year = {2026},
author = {Chen, S and Chen, R and Tong, S and Liu, W and Ni, L and Lv, X},
title = {Deciphering the microbial regulation of volatile flavor compounds and biogenic amines in Hongqu vinegar fermentation: An integrated metagenomic and metabolomic insight.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 4},
pages = {120889},
doi = {10.1016/j.foodres.2026.120889},
pmid = {42967713},
issn = {1873-7145},
mesh = {*Fermentation ; *Biogenic Amines/analysis/metabolism ; *Acetic Acid/metabolism/analysis ; *Volatile Organic Compounds/analysis/metabolism ; *Metagenomics/methods ; *Metabolomics/methods ; Taste ; *Food Microbiology ; *Flavoring Agents/analysis ; Gas Chromatography-Mass Spectrometry ; China ; Microbiota ; },
abstract = {Hongqu vinegar (HQV), one of China's four most prestigious traditional vinegars, is celebrated for its unique sensory attributes and potential health benefits, which are closely associated with the complex microbial communities within the fermentation starter, Hongqu. However, the microbial determinants driving the divergence in flavor quality and safety profiles among HQVs produced using distinct regional starters remain poorly defined. This study employed an integrated metabolomic and metagenomic approach to dissect the microbial regulation of volatile flavor compounds (VFCs) and biogenic amines (BAs) throughout the fermentation of HQVs produced with two geographically distinct starters: Gutian Hongqu and Wuyi Hongqu. Key microbial regulatory mechanisms driving flavor formation and BAs accumulation were elucidated through comprehensive functional gene annotation and metabolic pathway reconstruction. Our results reveal significant divergence in BA and VFC profiles between Gutian Hongqu vinegar (GT-HQV) and Wuyi Hongqu vinegar (WY-HQV). Notably, WY-HQV exhibited approximately 2.3-fold higher total BAs, particularly the hazardous amines histamine and tyramine, by the end of the acetic acid fermentation stage, underscoring critical safety considerations for starter selection. GC-MS-based metabolomic profiling revealed that GT-HQV was characterized by significantly higher levels of desirable VFCs (e.g., ethyl acetate, isoamyl lactate, α-terpineol, hexanoic acid, acetoin). Concurrently, GT-HQV showed a 7.5-fold higher lactic acid content, which contributed to its smoother and more balanced sensory profile. Metagenomic analysis linked these phenotypic disparities to distinct microbial community structures and functional potentials, with Weissella, Pediococcus, Klebsiella, Pantoea, Lentilactobacillus, Lactiplantibacillus, Monascus, and Aspergillus identified as key differentiating taxa differentiating GT-HQV and WY-HQV fermentation, suggesting their pivotal roles in shaping the distinct final product attributes. Functional gene annotation confirmed that the divergence in BA profiles and VFC formation is largely attributed to the distinct functional potentials, specifically the genes governing amino acid decarboxylation and fatty acid/ester metabolism. Lactic acid bacteria (LABs), particularly Lentilactobacillus species, were identified as key microbial taxa harboring the primary genetic potential for hazardous BA accumulation in WY-HQV. Collectively, this study elucidates the core functional microbiota and key metabolic genes influencing the biosynthesis of BAs and characteristic VFCs during HQV brewing, providing a scientific foundation for targeted enhancement of flavor quality and safety through starter culture optimization and microbiome engineering.},
}

*Fermentation
*Biogenic Amines/analysis/metabolism
*Acetic Acid/metabolism/analysis
*Volatile Organic Compounds/analysis/metabolism
*Metagenomics/methods
*Metabolomics/methods
Taste
*Food Microbiology
*Flavoring Agents/analysis
Gas Chromatography-Mass Spectrometry
China
Microbiota

@article {pmid42967716,
year = {2026},
author = {Koper, JEB and Ghyselinck, J and Van Meulebroek, L and Duysburgh, C and Chabrand, L and Machuron, F and Mourey, F and Marzorati, M and Bosco, N},
title = {Effects of Saccharomyces cerevisiae CNCM I-3856 and vitamin K2 on the gut microbiota of patients with osteoporosis and healthy controls using in vitro short-term colonic simulations.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 4},
pages = {120894},
doi = {10.1016/j.foodres.2026.120894},
pmid = {42967716},
issn = {1873-7145},
mesh = {Humans ; *Saccharomyces cerevisiae/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Osteoporosis/microbiology ; Female ; Middle Aged ; Feces/microbiology ; Male ; *Probiotics/pharmacology ; *Vitamin K 2/pharmacology ; *Colon/microbiology ; Aged ; Fermentation ; Adult ; },
abstract = {The gut microbiome may be involved in bone health through the gut-bone axis. Saccharomyces cerevisiae CNCM I-3856 benefits gut health in patients with irritable bowel syndrome, which is more prevalent in women and may be associated with higher osteoporosis prevalence. We evaluated the effects of S. cerevisiae CNCM I-3856 ± vitamin K2 (K2) on the gut microbiota of patients with osteoporosis and healthy controls. Short-term in vitro colonic fermentations were performed using feces from healthy and osteoporosis-diagnosed individuals (n = 12/cohort). Three conditions were tested: untreated, probiotic, probiotic+K2. Colonic supernatants (48 h) were evaluated for microbial metabolic and community profile. While there was a distinct separation of the microbial community composition between the donor cohorts, S. cerevisiae CNCM I-3856 ± K2 induced significantly higher acetate, propionate, butyrate, and lactate production versus untreated control for both cohorts (p = 0.003 to <0.001). S. cerevisiae CNCM I-3856 ± K2 supplementation generally reduced bacterial alpha-diversity and beta-diversity analysis revealed a distinct separation between the S. cerevisiae CNCM I-3856 ± K2 samples and the untreated samples for both cohorts. There were statistically significant changes in 11 taxa with S. cerevisiae CNCM I-3856 ± K2 supplementation (healthy, n = 4; osteoporosis, n = 6; both, n = 1). Metabolomic fingerprinting demonstrated significant differences in metabolic profile between the S. cerevisiae CNCM I-3856-supplemented samples and the untreated control. Overall, it could be concluded that a single administration of S. cerevisiae CNCM I-3856 enhanced microbial function through SCFA-mediated species and pathways in both a healthy population and osteoporosis patients, suggesting a potential for bone health through the gut-bone axis.},
}

Humans
*Saccharomyces cerevisiae/metabolism
*Gastrointestinal Microbiome/drug effects
*Osteoporosis/microbiology
Female
Middle Aged
Feces/microbiology
Male
*Probiotics/pharmacology
*Vitamin K 2/pharmacology
*Colon/microbiology
Aged
Fermentation
Adult

@article {pmid42967720,
year = {2026},
author = {Li, Y and Wu, C and Jin, L and Shi, J and Li, L and Han, H and Chen, Y and Zhang, M and Yu, Z and Gu, Q},
title = {Taste hidden in bone: spatial evidence of microorganisms and metabolites deciphers the aftertaste profile of ham.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 4},
pages = {120902},
doi = {10.1016/j.foodres.2026.120902},
pmid = {42967720},
issn = {1873-7145},
mesh = {Animals ; *Taste ; Fermentation ; Swine ; *Bone and Bones/chemistry ; Humans ; *Food Microbiology ; *Meat Products/microbiology/analysis ; Metabolomics ; Microbiota ; Food Handling/methods ; },
abstract = {The unique flavor of dry-cured ham has been described as "savor cached in the bone". Herein, ham was spatially stratified into skin, adipose, muscle, and bone layers to investigate the contribution of bone, with emphasis on substrate composition as a key determinant of the spatial distribution of taste compounds and microbiota. Sensory evaluation and non-volatile metabolomics revealed that eight metabolites significantly contributed to the characteristic aftertaste of the bone layer. Microbiome profiling and correlation analysis identified Mortierella sp. as a key microorganism strongly associated with these metabolites. Further in vitro fermentation experiments showed that Mortierella sp. significantly increased four of the eight core metabolites. Microstructural and textural analyses revealed that fermentation induced degradation of bone matrix, facilitating the internal migration of these metabolites. This study advancing the fundamental understanding of flavor formation in dry-cured ham, offering practical strategies to enhance product quality through process optimization.},
}

Animals
*Taste
Fermentation
Swine
*Bone and Bones/chemistry
Humans
*Food Microbiology
*Meat Products/microbiology/analysis
Metabolomics
Microbiota
Food Handling/methods

@article {pmid42967863,
year = {2026},
author = {Hu, M and Zhang, X and Shi, H and Gao, J and He, R and Zhang, Q and Dang, H},
title = {Aridity reshapes leaf and root trait dispersion through distinct microbial pathways.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71720},
pmid = {42967863},
issn = {1469-8137},
support = {2026AFB243//Natural Science Foundation of Hubei Province/ ; 32401662//National Natural Science Foundation of China/ ; 32571830//National Natural Science Foundation of China/ ; 32571862//National Natural Science Foundation of China/ ; 32660451//National Natural Science Foundation of China/ ; XJNUQB2023-14//Xinjiang Normal University Young Top Talent Project/ ; //Biological Resources Programme of Chinese Academy of Sciences/ ; 4374-PRC//Selection of Consulting Services for: Academy of Agricultural Sciences Subproject - Research on Agricultural Production Technology in the Three Gorges Region (4374-PRC)/ ; },
abstract = {Aridity is a primary driver of plant community assembly, yet most trait-based studies focus on mean traits rather than trait dispersion. Soil microbes may mediate plant responses to aridity, but whether leaf and root trait dispersion responds to aridity through shared or distinct microbial pathways remains unclear. Using 535 species-by-plot records (247 species) along an aridity gradient in north-west China, we quantified four leaf and four root traits, soil properties, microbial diversity and composition, and microbial carbon use efficiency. We tested whether aridity differentially regulates leaf vs root functional dispersion (FDis), and whether these responses are associated with different microbial predictors. Leaf traits shifted more consistently with aridity and were more tightly linked to environmental variation than root traits. Leaf FDis negatively correlated with CUE, whereas root FDis negatively correlated with fungal diversity and bacterial community composition. These associations weakened toward less arid sites. Structural equation modeling further showed that leaf FDis linked primarily to microbial functioning, whereas root FDis linked more strongly to microbial diversity and composition. Our results reveal that aridity reshapes trait dispersion through organ-specific plant-microbe pathways, highlighting that predicting dryland community responses to increasing drought must treat above- and belowground traits separately.},
}

@article {pmid42967955,
year = {2026},
author = {Zhang, H and Zhang, C and Yang, Y and Zhang, Y and Hu, B and He, T and Zhang, J and Song, X and Su, Y and Su, Y},
title = {Engineering functional microbial inoculants for cigar tobacco fermentation: metabolic mechanisms, synthetic consortia, and translational challenges.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42967955},
issn = {1573-0972},
support = {2023530000241002//Science and Technology Plan Project of the China National Tobacco Corporation, Yunnan Provincial Company/ ; yxyc2023007//General Project of the Science and Technology Program of Yuxi Company, Yunnan Provincial Tobacco Company/ ; },
mesh = {*Fermentation ; *Nicotiana/microbiology/metabolism ; Bacteria/metabolism/genetics ; *Microbial Consortia ; Biotransformation ; Metabolic Engineering ; Fungi/metabolism ; Microbiota ; },
abstract = {Cigar tobacco fermentation is a microbiome-dependent solid-state process in which deliberate microbial intervention can alter macromolecule degradation, aroma formation, undesirable chemical constituents, and mould risk. This critical review evaluates whether published interventions support a transition from empirical bioaugmentation to controllable microbial biotechnology. Literature identified through Web of Science and ScienceDirect, principally covering 2010-2026, is assessed by separating process proximity from measured function, causal mechanism, and scale of validation. Functional microbial inoculant is used instead of probiotic except when reporting source terminology. Controlled studies support hydrolytic bacterial inoculants, strain-specific yeast fermentation, nitrate-pathway intervention for tobacco-specific nitrosamine control, engineered carotenoid biotransformation, defined synthetic communities, and volatile-mediated suppression of postharvest cigar-leaf moulds. These findings do not establish universal superiority of mixed cultures, industrial repeatability, or application-specific biosafety. Many lactic-acid-bacterial antifungal and mycotoxin-control mechanisms remain supported mainly by non-tobacco matrices. The evidence framework therefore records representative sources, experimental context, mechanistic limitations, and missing validation separately. We propose measurable, application-dependent decision gates for strain identity, safety, matrix efficacy, metabolic stability, community compatibility, scale-up, and formulation. These gates are research and development proposals, not empirically validated industrial standards. Dominant bacterial guilds and complementary yeasts should be evaluated without conflating chemical-hazard reduction with the health risks of tobacco use.},
}

*Fermentation
*Nicotiana/microbiology/metabolism
Bacteria/metabolism/genetics
*Microbial Consortia
Biotransformation
Metabolic Engineering
Fungi/metabolism
Microbiota

@article {pmid42967965,
year = {2026},
author = {Chau, KD and Sless, TJL and Nguyen, PN and Rehan, SM},
title = {Bee Microbiomes Across Phylogeny and Functional Traits: Examining Host-Cleptoparasite Associations.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42967965},
issn = {1432-184X},
mesh = {Animals ; Bees/microbiology/physiology/classification/parasitology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; *Fungi/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Host-Parasite Interactions ; },
abstract = {Studies on microbiomes are essential for understanding the various roles microbes play in the health of bees, yet many wild bees including cleptoparasitic species and their microbiomes continue to be underexplored. To alleviate this gap, we analyzed bacterial and fungal microbiomes of cleptoparasitic species with 16 S rRNA and ITS1 metabarcoding and compared results to the microbiomes of their hosts and other wild bees across families and functional traits. We found that a parasitic lifestyle was associated with a significantly more diverse bacterial microbiome compared to other social or dietary traits, and that ground-nesting bees have a richer bacterial microbiome than stem-nesting bees. Fungal diversity was only found to be greater in solitary bees compared to eusocial species. Hosts and cleptoparasites had broadly similar bacterial and fungal microbiomes, with a few exceptions. N. articulata had a significantly more diverse bacterial microbiome compared to its hosts Agapostemon virescens and A. sericeus, and H. calliopsidis boasted greater bacterial diversity compared to its host Calliopsis andreniformis. Fungal communities were also different for N. illinoensis - Andrena crataegi and for N. articulata - A. virescens, whereas several host-cleptoparasite pairs harboured distinct bacterial communities. Individual cleptoparasites were also uniquely associated with several understudied bacterial microbes. Our study is the first to assess the microbiomes of six cleptoparasitic species and reveals important insight into the unique and shared microbes in wild bees and host-cleptoparasite pairs.},
}

Animals
Bees/microbiology/physiology/classification/parasitology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Phylogeny
*Fungi/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Host-Parasite Interactions

@article {pmid42968172,
year = {2026},
author = {Lee, HY and Kim, MJ and Naskar, M and Serrano-Arevalo, K and Cho, YJ and Shin, HB and Choi, HW and Kim, YH},
title = {Gardnerella piotii enhances uropathogenic Escherichia coli infection through a succinate-GPR91-uroplakin axis.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42968172},
issn = {2049-2618},
mesh = {*Uropathogenic Escherichia coli/pathogenicity/physiology ; *Urinary Tract Infections/microbiology/metabolism ; Animals ; *Succinic Acid/metabolism ; *Escherichia coli Infections/microbiology/metabolism ; Humans ; *Receptors, G-Protein-Coupled/metabolism/genetics ; Female ; Bacterial Adhesion ; Urinary Bladder/microbiology ; Mice ; Cystitis/microbiology ; Signal Transduction ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Epithelial Cells/microbiology ; },
abstract = {BACKGROUND: Uropathogenic Escherichia coli (UPEC) is the principal causative agent of urinary tract infections (UTIs); however, urine samples from patients with recurrent cystitis frequently harbor diverse coexisting bacterial taxa. How such polymicrobial urobiota can functionally modulate bladder susceptibility to UPEC infection remains unclear.

RESULTS: We integrated 16S rRNA-based microbiota profiling of a recurrent cystitis cohort with mechanistic in vitro and in vivo models to assess host-microbe interactions within the urinary tract. We identified Gardnerella piotii as a microbial modifier that enhances the infectivity of UPEC without inducing overt epithelial damage or inflammation. Exposure to G. piotii increased UPEC burden in the bladder and in bladder epithelial cells by promoting early bacterial adhesion. Mechanistically, G. piotii actively produced succinate, which acted as a host-active metabolite to selectively upregulate uroplakin expression through signaling via the succinate receptor GPR91. Genetic ablation of GPR91 abolished succinate- and G. piotii-induced uroplakin upregulation and UPEC adhesion, establishing that this epithelial signaling axis is necessary for infection sensitization. Importantly, the heightened UPEC susceptibility induced by G. piotii could be partially mitigated; introduction of the beneficial commensal Lactobacillus crispatus or exposure to lactate partially reduced UPEC burden in vivo, highlighting the functional plasticity of the bladder microenvironment.

CONCLUSIONS: These findings unravel a metabolite-driven mechanism by which members of the urinary microbiota modulate host epithelial programs to influence UPEC infection. By identifying a succinate-GPR91-uroplakin signaling axis that links polymicrobial community structure to epithelial susceptibility, our study reframes recurrent cystitis as a dynamic ecological process shaped by microbial existence and metabolic signaling rather than by an individual pathogen. Video Abstract.},
}

*Uropathogenic Escherichia coli/pathogenicity/physiology
*Urinary Tract Infections/microbiology/metabolism
Animals
*Succinic Acid/metabolism
*Escherichia coli Infections/microbiology/metabolism
Humans
*Receptors, G-Protein-Coupled/metabolism/genetics
Female
Bacterial Adhesion
Urinary Bladder/microbiology
Mice
Cystitis/microbiology
Signal Transduction
Microbiota
RNA, Ribosomal, 16S/genetics
Epithelial Cells/microbiology

@article {pmid42968220,
year = {2026},
author = {Zhang, Y and Qiu, L and Wu, J and Shi, Y and Niu, S and Zhao, C and Chen, T and Cui, C and Ma, Y and Zhang, X and Yao, X and Meng, Y and Zhao, L and Xing, Y and Wu, X and Chen, Z and Zheng, K and Cai, Y and Chen, J and Wu, J},
title = {A microbiota-metabolite-glial axis drives white matter repair via isorhamnetin-PSAP-GPR37 signaling after ischemic stroke.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748092},
doi = {10.1080/19490976.2026.2748092},
pmid = {42968220},
issn = {1949-0984},
mesh = {Animals ; Mice ; *White Matter/metabolism ; Signal Transduction ; *Gastrointestinal Microbiome ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Ischemic Stroke/metabolism/microbiology ; Humans ; Microglia/metabolism ; *Quercetin/analogs & derivatives/metabolism ; Mice, Inbred C57BL ; Male ; Disease Models, Animal ; Oligodendroglia/metabolism ; Akkermansia ; },
abstract = {Ischemic stroke (IS) induces persistent neuroinflammation and white matter injury that limit neurological recovery, yet effective repair-oriented therapies remain lacking. Although microbiota influences stroke outcomes, how microbial activity drives central nervous system repair is unclear. Here, we integrate clinical microbiome profiling, experimental stroke models, multi-omics analyses, and mechanistic validation to define a microbiota-metabolite-glial signaling axis that promotes post-stroke recovery. Akkermansia muciniphila (Akk) is associated with favorable outcomes in patients and improves recovery in mice without altering infarct size, supporting a repair-promoting rather than neuroprotective mechanism. Mechanistically, Akk increases circulating isorhamnetin (Iso), a key systemic mediator that suppresses lipid-laden, pro-inflammatory microglia and promotes oligodendrocyte maturation and white matter repair. Iso reprograms microglia to secrete PSAP, and conditioned medium-but not direct Iso-activates GPR37-ERK signaling in oligodendrocytes. In vitro knockdown of Psap or Gpr37 markedly attenuates these effects, demonstrating a microglia-dependent mechanism. In vivo adeno-associated virus (AAV)-mediated Gpr37 knockdown abolishes the beneficial effects of Akk and Iso on functional recovery and white matter repair, establishing the necessity of PSAP-GPR37 signaling. These findings identify a microbiota-driven metabolic pathway linking gut activity to white matter repair after IS.},
}

Animals
Mice
*White Matter/metabolism
Signal Transduction
*Gastrointestinal Microbiome
*Receptors, G-Protein-Coupled/metabolism/genetics
*Ischemic Stroke/metabolism/microbiology
Humans
Microglia/metabolism
*Quercetin/analogs & derivatives/metabolism
Mice, Inbred C57BL
Male
Disease Models, Animal
Oligodendroglia/metabolism
Akkermansia

@article {pmid42968401,
year = {2026},
author = {Arredondo-Hernandez, R and Orduña, P and Schcolnik-Cabrera, A and Castillo-Rojas, G and López-Filloy, M and Morales-Nava, P and Mejía Estrada, A and Barrios-Plata, BG and Ponce-de-León-Rosales, S and Gutierrez-Castrellon, P and Li, L and López-Vidal, Y},
title = {Integrated multi-omics analysis reveals distinct metabolic signatures and gut microbiome alterations across the pediatric obesity spectrum.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2755119},
doi = {10.1080/19490976.2026.2755119},
pmid = {42968401},
issn = {1949-0984},
mesh = {Humans ; Multiomics ; Male ; Child ; Female ; *Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Pediatric Obesity/microbiology/metabolism ; Metabolomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Metabolome ; Biomarkers ; Liver/enzymology ; Adolescent ; gamma-Glutamyltransferase/metabolism ; Overweight/microbiology/metabolism ; },
abstract = {Pediatric obesity drives extensive metabolic remodeling across gut and systemic compartments, yet integrated multi-omics characterization across the full obesity spectrum remains incomplete. We studied 57 Mexican children stratified by BMI into normal weight (NW, n = 15), overweight (Ow, n = 8), and obese (Ob, n = 34) groups using liver enzyme profiling, untargeted fecal and serum metabolomics, 16S rRNA gut microbiome sequencing, and antimicrobial resistance assessment. Demographic parameters were comparable across groups (p = 0.632), minimizing confounding. Gamma-glutamyl transferase (GGT) showed the strongest obesity association (25.5 ± 6.0 vs. 15.0 ± 3.0 U/L in NW; p < 0.001), outperforming ALT and AST as an early hepatic stress biomarker. Metabolomic profiling identified 1088 altered fecal and 1041 altered serum metabolites (Ob vs. NW), with enriched pathways spanning aromatic amino acid metabolism, one-carbon metabolism, glycolysis/TCA cycle, and nucleotide biosynthesis. Key perturbations included upregulation of kynurenine and 3-nitrotyrosine alongside downregulation of bile acids and purine metabolites. 16S rRNA sequencing revealed 78, 95, and 28 differentially abundant taxa in Ow vs. NW, Ob vs. Ow, and Ob vs. NW comparisons, with elevated beta-diversity dispersion in obesity. Co-abundance network analysis uncovered disrupted metabolite-metabolite and taxon‒taxon interactions, including loss of beneficial SCFA-producing consortia, bile acid dysregulation, and altered amino acid-microbiome coupling. Integration of microbiome and metabolome data revealed high-magnitude genus-metabolite correlations-including Lachnospiraceae with acetate (ρ = 0.92) and Tyzzerella with vulpecholate (ρ = 0.94)-mapping to mechanistic pathways linking SCFAs, bile acids, tryptophan-indole derivatives, and aromatic amino acids to obesity pathogenesis. These findings identify GGT as a sensitive pediatric metabolic biomarker and provide mechanistic insights and therapeutic targets for early intervention.},
}

Humans
Multiomics
Male
Child
Female
*Gastrointestinal Microbiome
Feces/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Pediatric Obesity/microbiology/metabolism
Metabolomics
*Bacteria/classification/genetics/isolation & purification/metabolism
*Metabolome
Biomarkers
Liver/enzymology
Adolescent
gamma-Glutamyltransferase/metabolism
Overweight/microbiology/metabolism

@article {pmid42968622,
year = {2026},
author = {Khatib, H and Zeiser, R},
title = {Updates in acute graft-versus-host disease: From novel pathogenic mechanisms to emerging therapeutic targets.},
journal = {British journal of haematology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bjh.70877},
pmid = {42968622},
issn = {1365-2141},
support = {SFB-1479//Deutsche Forschungsgemeinschaft/ ; RU5659 TARGET-MPN: ZE 872/6-1 (TP 7)//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Acute graft-versus-host disease (aGVHD) remains a major complication following allogeneic haematopoietic stem cell transplantation (allo-HSCT), representing a leading cause of non-relapse mortality (NRM) and significant morbidity despite decades of intensive research. Its pathogenesis involves human leucocyte antigen (HLA) mismatch between donor and recipient and is initiated by conditioning-induced tissue damage that triggers alloreactive donor T-cell activation. Beyond classical immunological mechanisms, the intestinal microbiome and microbiome-derived metabolites have emerged as fundamental modulators of disease initiation and progression. Significant advances have been made in staging and risk stratification, with novel scoring systems integrating clinical parameters and biological biomarkers to more accurately predict treatment response and overall outcome. In the treatment of aGVHD, the last decade has witnessed considerable progress, most notably the approval of ruxolitinib, which has fundamentally changed the management landscape of steroid-refractory aGVHD (SR-aGVHD). Intestinal aGVHD, which carries the highest mortality among disease manifestations, remains a particularly challenging entity. Notably, the enteroendocrine system has recently gained attention as a pathogenic contributor, with early-phase trials exploring the therapeutic potential of exogenous hormone administration. In this review, we discuss both well-established and emerging evidence on the pathogenesis, staging and risk stratification and treatment of aGVHD, with particular focus on novel therapeutic strategies.},
}

@article {pmid42968651,
year = {2026},
author = {Chojnacka, K and Grivennikov, SI},
title = {Breaking Barriers: Gut Pathobionts Promote Hepatocellular Carcinoma.},
journal = {Cancer discovery},
volume = {16},
number = {11},
pages = {2214-2216},
doi = {10.1158/2159-8290.CD-26-1747},
pmid = {42968651},
issn = {2159-8290},
mesh = {*Carcinoma, Hepatocellular/microbiology/pathology/metabolism ; Humans ; *Liver Neoplasms/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome ; Animals ; Bacteroides fragilis ; },
abstract = {Although studies of microbiota in hepatocellular carcinoma (HCC) and possible involvement of the gut-liver axis are of significant interest, the origin and functional role of the liver and intratumoral microbiota in HCC have remained unclear. Liu and colleagues show that gut pathobionts, in particular Bacteroides fragilis, translocate through the gut-liver axis, colonize and reshape the intrahepatic microbiome, and promote HCC through a distinct mechanism in which bacterial enolase binds hepatocyte vimentin, revealing potential therapeutic opportunities. See related article by Liu et al., p. 2392.},
}

*Carcinoma, Hepatocellular/microbiology/pathology/metabolism
Humans
*Liver Neoplasms/microbiology/pathology/metabolism
*Gastrointestinal Microbiome
Animals
Bacteroides fragilis

@article {pmid42968806,
year = {2026},
author = {Bani-Amer, M and Hundam, S and Ababneh, M and Al-Zghoul, MB and Alghizzawi, D and Abualghusein, I and Al-Ghawanmeh, AA},
title = {Preliminary association between infectious bronchitis virus viral load and the tracheal microbiome of broiler chickens.},
journal = {Virusdisease},
volume = {37},
number = {3},
pages = {372-381},
pmid = {42968806},
issn = {2347-3584},
abstract = {Infectious bronchitis virus (IBV) is a major respiratory pathogen in poultry, yet its impact on the tracheal microbiota under field conditions remains insufficiently understood. This study investigated the effects of IBV infection intensity on tracheal microbial diversity and composition in broiler chickens using 16 S rRNA gene sequencing. A total of 200 tracheal samples were collected from commercial farms and screened using RT-qPCR. Samples were stratified into high, low, and negative viral load groups based on cycle threshold (Ct) values, and a representative subset was selected for microbiome analysis. Alpha diversity analysis revealed a significant reduction in microbial richness (Observed species and Chao1 indices; q < 0.05) in the low-viral-load group compared with controls, while Shannon diversity remained unchanged, suggesting a selective loss of rare taxa. In contrast, no significant changes in alpha diversity were observed in the high viral load group. Beta-diversity analysis based on Bray-Curtis dissimilarity (PERMANOVA) revealed significant differences in microbial community composition among different viral load groups. Taxonomic analysis showed stability at the phylum level, with more pronounced shifts at the genus level. These findings indicate that IBV infection induces selective and load-dependent alterations in the tracheal microbiota. Notably, treating infection as a binary variable may obscure ecologically meaningful and biologically relevant microbial shifts. This preliminary field study provides evidence that IBV viral load is associated with differences in the respiratory microbiome of broiler chickens under field conditions.},
}

@article {pmid42969058,
year = {2026},
author = {Dhadse, S and Chole, A},
title = {Phytoremediation potential of native plants in fly ash-contaminated sites: a review on heavy metal uptake and soil restoration strategies.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/15226514.2026.2741672},
pmid = {42969058},
issn = {1549-7879},
abstract = {Fly ash generated from coal-fired thermal power plants represents one of the largest industrial solid wastes worldwide and poses significant environmental challenges due to its high alkalinity, poor nutrient status, and elevated concentrations of potentially toxic elements such as arsenic (As), cadmium (Cd), chromium (Cr), lead (Pb), nickel (Ni), and mercury (Hg). The uncontrolled disposal of fly ash threatens soil quality, groundwater resources, ecosystem stability, and human health, highlighting the urgent need for sustainable remediation strategies. Among the available technologies, phytoremediation using native plant species has emerged as an environmentally friendly and potentially lower-input because indigenous plants are naturally adapted to local climatic and edaphic conditions, enabling long-term establishment and ecological restoration with minimal external inputs. This review critically synthesizes current knowledge on the physicochemical characteristics of fly ash, heavy metal speciation and bioavailability, and the physiological, biochemical, molecular, and rhizosphere-mediated mechanisms governing heavy metal uptake, translocation, detoxification, and sequestration in native plant species. Unlike previous reviews that primarily provide descriptive accounts of phytoremediation, this review integrates plant functional traits, rhizosphere interactions, soil microbial dynamics, and ecosystem restoration processes into a comprehensive framework for selecting suitable native species for fly ash rehabilitation. The review further discusses recent advances in microbiome-assisted phytoremediation, biochar-assisted remediation, omics technologies, artificial intelligence-assisted species selection, remote sensing, and ecological risk assessment as emerging tools for improving remediation efficiency and long-term restoration monitoring. Existing knowledge gaps, including limited long-term field validation, biomass disposal challenges, insufficient economic assessment, and the need for standardized evaluation criteria, are critically examined. Finally, the review proposes future research priorities and emphasizes the integration of phytoremediation with sustainable land management and environmental policy to support resilient ecosystem restoration and the long-term rehabilitation of fly ash-contaminated landscapes.},
}

@article {pmid42969299,
year = {2026},
author = {Neubert, KJ and Walch, S and Schloter, M and Brüggemann, N},
title = {Microplastics affect belowground performance of winter wheat and microbial networks in the rhizosphere.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6em00205f},
pmid = {42969299},
issn = {2050-7895},
abstract = {Microplastics (MPs) are increasingly recognized as environmental pollutants affecting soil ecosystems and plant development, but their specific impacts on plant-soil-microbiome interactions remain unclear. This study investigated the effects of different MP types, including particulate polypropylene (PP), low-density polyethylene (LDPE), polystyrene (PS), and fibrous polyester (PES), individually on early-stage winter wheat root growth, nutrient concentrations, soil conditions and the rhizosphere microbiome using rhizotrons. Our findings revealed that PP and PES MPs significantly reduced root length. We observed increased soil ammonium concentrations with the addition of all MPs, likely due to reduced nitrifying bacterial activity, while PS MP enhanced soil nitrate concentration, potentially reflecting impaired root absorption. Because polymer size and morphology covaried, the results are interpreted as MP-type-specific. No significant effects of MPs on plant potassium (K) and phosphorus (P) uptake were observed. Despite changes in soil nutrient levels, we found no significant alterations in leaf growth, nutrient uptake, or chlorophyll content, indicating that root systems, though affected by MPs, remained sufficiently functional to support shoot development. Microbial co-occurrence analysis revealed two distinct microbial clusters in the rhizosphere, confirming modular microbial structure. Among all treatments, LDPE exposure induced the most pronounced increase in network complexity, as reflected by higher edge density, clustering coefficient, and natural connectivity compared to the control. Many amplicon sequence variants (ASVs), e.g., members of Vicinamibacteraceae, Pseudolabrys and Nitrospira japonica, showed an increased degree and eigenvector centrality in the LDPE treatment, suggesting enhanced co-occurrence and higher influence within the microbial community structure. In contrast, the PES and PP treatments resulted in lower average node degree and reduced clustering. The PS treatment only had a small effect on the microbial co-occurrence networks. Overall, our data indicate that MP-induced stress can alter microbial network topology, reduce community integration, and drive shifts in ecologically important taxa in the rhizosphere, which are linked to changes in the availability of nutrients for plants. Our findings highlight the complex and variable influence of MPs on soil-plant interactions.},
}

@article {pmid42969360,
year = {2026},
author = {Wang, H and Jiang, A and He, Y and Ding, K and Xu, Y and Wang, Z and Wu, R and Zeng, Y and Zhao, Z-B and Zeng, L and Gong, S and Li, J and Li, L},
title = {Faecalibacterium prausnitzii-associated 18β-glycyrrhetinic acid protects against sepsis via ABCC1-mediated suppression of MAPK/NF-κB signaling.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0094026},
doi = {10.1128/msystems.00940-26},
pmid = {42969360},
issn = {2379-5077},
abstract = {Gut microbiota dysbiosis is increasingly recognized as a modifiable determinant of sepsis susceptibility and outcomes, yet protective commensals and microbiota-associated metabolites with actionable host mechanisms remain incompletely defined. Here, fecal 16S rRNA sequencing of septic and non-septic patients revealed a marked depletion of Faecalibacterium prausnitzii during sepsis. Oral administration of F. prausnitzii improved survival and alleviated multiorgan injury in mice subjected to cecal ligation and puncture. Untargeted metabolomics and liquid chromatography-tandem mass spectrometry identified 18β-glycyrrhetinic acid (18β-GA) as a major metabolite enriched in F. prausnitzii culture supernatants, and exogenous 18β-GA recapitulated key protective effects in vivo. In lipopolysaccharide-stimulated macrophages, 18β-GA reduced pro-inflammatory mediator expression and suppressed mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-κB) activation. Proteomics-guided prioritization and complementary pharmacological and genetic validation implicated ATP-binding cassette subfamily C member 1 (ABCC1) as a mediator involved in the protective effects of 18β-GA. Genetic silencing of ABCC1 attenuated the anti-inflammatory effects of 18β-GA, while pharmacological inhibition of ABCC1 by probenecid (PBN) and MK-571 partially reproduced the protective effects of 18β-GA. Collectively, these findings identify a F. prausnitzii-18β-GA-associated ABCC1 regulatory axis that contributes to the control of septic inflammation and highlight microbiota-derived metabolites as potential modulators of host inflammatory responses.IMPORTANCESepsis is a life-threatening syndrome with limited effective therapies beyond supportive care. Gut microbiota disruption is increasingly recognized as an important contributor to sepsis, but the protective microbes, effector metabolites, and host pathways involved are not well understood. Here, we show that F. prausnitzii is markedly depleted in sepsis and that supplementation with this commensal improves outcomes in experimental sepsis. We further identify 18β-glycyrrhetinic acid as a microbiota-associated metabolite with anti-inflammatory and organ-protective activity and implicate ABCC1 as a functionally relevant host target. Our findings provide mechanistic insight into how protective commensals can influence sepsis progression and support microbiome-informed, host-directed therapeutic strategies.},
}

@article {pmid42969400,
year = {2026},
author = {Kapur, S and Solone, XK and Mi, R and Sidhu, KS and Gershater, M and Cruz, J and Hamzavi, I and Adrianto, I and Zhou, L and Mi, QS},
title = {Obesity-associated transcriptomic remodelling in hidradenitis suppurativa and treatment response.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70829},
pmid = {42969400},
issn = {1468-3083},
support = {R21AR079089/NH/NIH HHS/United States ; R01AR078688/NH/NIH HHS/United States ; R01AR083553/NH/NIH HHS/United States ; T71016//Henry Ford Health/ ; T71017//Henry Ford Health/ ; },
abstract = {Obesity is characterized by chronic low-grade inflammation and metabolic dysfunction. It is a major risk factor for hidradenitis suppurativa (HS), where it is associated with increased disease severity and metabolic comorbidity. Obesity promotes a pro-inflammatory, immunometabolic state marked by adipokine imbalance and alters the local skin environment through mechanical stress, occlusion and microbiome disruption. Mechanistic transcriptomic analyses further suggest that obesity induces tissue-specific changes in HS skin, including metabolic signalling in lesions and early barrier dysfunction in perilesional skin. In practice, obesity is associated with more severe and treatment-refractory disease but remains a modifiable risk factor. Weight loss, bariatric surgery and metabolism-directed therapies show potential to reduce disease burden, although controlled studies are limited. Overall, obesity acts as both a systemic and local modifier of HS, supporting its classification as an immunometabolic disorder.},
}

@article {pmid42969403,
year = {2026},
author = {Satheesh Babu, AK and Petersen, C and Robeson, MS and Iglesias-Carres, L and Paz, HA and Ratliff, JG and Zhong, Y and Bell, R and Shankar, K and Wankhade, UD and Neilson, AP and Anandh Babu, PV},
title = {Blueberry phytochemicals modulate the gut-vascular axis through microbiome-metabolome interaction.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
pmid = {42969403},
issn = {2042-650X},
abstract = {Dietary phytochemicals are metabolized by gut microbes into bioactive metabolites that mediate their physiological effects. This study investigated whether microbiome-metabolome interactions contribute to the vascular benefits of blueberry phytochemicals via the gut-vascular axis. Both conventionally raised and germ-free mice received freeze-dried blueberries via oral gavage, and plasma metabolites were analyzed at multiple time points. In other cohorts, mice were fed a standard or high-fat diet (HFD) with or without freeze-dried blueberry powder (∼1.5 human servings) and treated with or without antibiotics (Abx; to deplete gut microbes) for 12 weeks. Metabolic parameters, vascular endpoints, plasma metabolites, and the gut microbiome were assessed. Blueberry intake increased plasma blueberry-derived metabolites in conventionally raised but not germ-free mice, indicating that gut microbes are essential for metabolizing phytochemicals. This was also confirmed in Abx-treated mice. Blueberries reduced HFD-induced vascular inflammation. However, microbial depletion reduced plasma blueberry metabolites and abolished the benefits of blueberries in reducing vascular inflammation. HFD-enriched genera such as Faecalimonas were positively associated, whereas blueberry-derived metabolites (hippuric acid and 3-hydroxy hippuric acid) were negatively associated with vascular inflammation. Furthermore, Turicibacter and Clostridia UGC-014 (incertae sedis), which are enriched by dietary blueberries, were positively associated with hippuric acid. These findings provide insight into the importance of the interaction between the microbiome and metabolome in regulating the benefits of dietary phytochemicals on vascular inflammation via the gut-vascular axis.},
}

@article {pmid42969974,
year = {2026},
author = {Sen, A and Srinivasan, SK and Mohanraj, PS and Nagaram, S and Kumar, R and Velu, A and Yadav, P},
title = {Emerging biochemical targets in chronic pain: bridging molecular mechanisms and public health policy in the Indian context.},
journal = {Pain management},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/17581869.2026.2754354},
pmid = {42969974},
issn = {1758-1877},
abstract = {INTRODUCTION: India confronts a chronic-pain paradox widespread under-treatment of pain coexisting with intense restriction of opioid prescribing. India's prevailing opioid-constrained pain-management model, constrained by narcotic legislation, institutional caution, and cultural stigma, is biochemically and clinically inadequate for the maladaptive pathophysiology of chronic pain.

AREAS COVERED: This narrative review synthesizes emerging evidence on non-opioid biochemical targets relevant to chronic pain management in the Indian context, including glial modulators, cytokine inhibitors, NMDA and NK-1 receptor antagonists, selective sodium-channel blockers, TRPV1 antagonists, histone deacetylase inhibitors, and microbiome-based interventions. We discuss the molecular pathophysiology of chronic pain neuroinflammation, central sensitization, and glial activation and integrate preclinical and emerging clinical data. The literature was identified through PubMed, Scopus, and Google Scholar searches up to April 2026, focusing on chronic pain mechanism-based therapeutics relevant to the Indian clinical context.

EXPERT OPINION: Translating mechanism-based pain therapeutics into Indian practice requires concurrent reform across medical education, pediatric pain prevention, and national drug policy. Embedding biochemical literacy in training, expanding equitable access to non-opioid agents, supporting indigenous translational research, and integrating validated Ayurvedic phytochemicals into mechanism-informed care offer a culturally grounded path forward.},
}

@article {pmid42970211,
year = {2026},
author = {Park, YJ and Huang, M and Lee, YS and Kim, HS and Kang, HY and Kim, CH},
title = {Non-thermal argon plasma therapy alleviates atopic dermatitis by reducing keratinocyte oxidative stress.},
journal = {Molecular biomedicine},
volume = {7},
number = {1},
pages = {},
pmid = {42970211},
issn = {2662-8651},
support = {HR21C1003//Korea Health Industry Development Institute/ ; RS-2024-00407544//Korea Health Industry Development Institute/ ; RS-2024-00406579//Korea Health Industry Development Institute/ ; 2021003350001//Ministry of Environment/ ; 2023R1A2C3002835//Ministry of Science, ICT and Future Planning/ ; },
mesh = {*Oxidative Stress/drug effects ; Animals ; *Dermatitis, Atopic/therapy/pathology/metabolism/microbiology/drug therapy ; *Argon/pharmacology/therapeutic use ; *Plasma Gases/pharmacology/therapeutic use ; Humans ; *Keratinocytes/metabolism/drug effects ; Mice ; Disease Models, Animal ; Cytokines/metabolism ; Male ; Female ; Skin Microbiome ; Quality of Life ; },
abstract = {Atopic dermatitis (AD) is a prevalent inflammatory skin disorder associated with a considerable disease burden. Despite the advent of biologics a substantial unmet need remains for effective treatment. We aimed to evaluate the effects of non-thermal argon plasma (NAP) in patients with mild-to-moderate AD. The Eczema Area Severity Index (EASI), Numeric Rating Scale (NRS), and Dermatology Life Quality Index (DLQI) were evaluated following AD treatment. 16 S rRNA sequencing was used to assess alterations in the skin microbiome. A mouse model of house dust mite (HDM)-induced AD was used to evaluate the effects of NAP on AD-like lesions, immune cell recruitment, and cytokine expression. Oxidative stress parameters and related molecular markers were analyzed after NAP treatment. NAP treatment led to a significant reduction in EASI, NRS, and DLQI scores compared with the sham group, reflecting an alleviation of AD symptoms and an enhancement in the quality of life. Microbiome analysis revealed significant alterations in the microbial diversity after NAP treatment. NAP ameliorated HDM-induced AD in mice, showing a decrease in epidermal thickness, immune cell recruitment, and the expression of key cytokines, particularly interleukin (IL)- 33, in keratinocytes. Furthermore, NAP treatment downregulated oxidative stress markers, corroborating the reduced IL-33 expression and underscoring the role of oxidative stress in AD pathology. Our study suggests the therapeutic potential of nonthermal plasma in the management of mild-to-moderate AD. Further extensive clinical trials are warranted to validate these findings and understand their long-term effects and implications.Trial registration: CRIS, KCT0008949, retrospectively registered on October 10, 2023, at https://cris.nih.go.kr/cris/search/detailSearch.do?seq=25713 .},
}

*Oxidative Stress/drug effects
Animals
*Dermatitis, Atopic/therapy/pathology/metabolism/microbiology/drug therapy
*Argon/pharmacology/therapeutic use
*Plasma Gases/pharmacology/therapeutic use
Humans
*Keratinocytes/metabolism/drug effects
Mice
Disease Models, Animal
Cytokines/metabolism
Male
Female
Skin Microbiome
Quality of Life

@article {pmid42970238,
year = {2026},
author = {Radfar, P and Gritsiuta, AI and Marinelli, M and Yazditabar, J and Nishi, SP and Willis, M and Petrov, RV},
title = {Pretreatment antibiotic exposure and mortality following immune checkpoint inhibitor therapy in non-small cell lung cancer: an infection-stratified propensity-matched analysis.},
journal = {Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {42970238},
issn = {1699-3055},
abstract = {PURPOSE: Pretreatment antibiotic exposure has been associated with inferior outcomes during immune checkpoint inhibitor (ICI) therapy, but whether this reflects an ICI specific effect or underlying clinical vulnerability remains uncertain.

METHODS: Adults with non-small cell lung cancer (NSCLC) treated with ICIs from 2015 through 2024 were identified in the TriNetX Research Network. Recent antibiotic exposure was defined as systemic antibiotic use during days 30 to 1 before ICI initiation. Propensity score matching balanced clinical and treatment-related covariates. Primary outcomes were all cause mortality at 90 and 365 days. Sensitivity analyses included landmarking, remote exposure, infection stratification, and a non-ICI comparator.

RESULTS: Among 68,723 patients, 19,080 had recent antibiotic exposure; 17,955 per group remained after matching. Mortality was higher with antibiotic exposure at 90 days (17.7% vs 13.7%; HR 1.34, 95% CI 1.27 to 1.41; P<0.001) and 365 days (43.0% vs 37.2%; HR 1.23, 95% CI 1.19 to 1.27; P<0.001). Associations attenuated after exclusion of early deaths. The association was similar between ICI and non-ICI cohorts at 90 days but modestly stronger with ICI at 365 days. Remote exposure did not reproduce the adverse association.

CONCLUSIONS: Recent antibiotic exposure was associated with increased mortality during ICI therapy, but the non-ICI comparison and landmark analyses suggest that much of the short-term excess mortality reflects clinical vulnerability rather than an ICI specific effect. The modestly stronger 1-year association with ICI therapy is hypothesis generating.},
}

@article {pmid42970338,
year = {2026},
author = {Lakade, AJ},
title = {Artificial Intelligence in Dietary Management and Nutritional Interventions: A Narrative Review of Current Evidence, Applications, and Translational Challenges.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/27697061.2026.2755960},
pmid = {42970338},
issn = {2769-707X},
abstract = {This narrative review examines the applications of artificial intelligence (AI) in nutrition and dietetics, focusing on AI-assisted dietary assessment, precision nutrition, generative AI for dietary counselling, and the ethical, regulatory, and implementation challenges affecting clinical translation. A critical narrative synthesis of evidence on AI applications in nutrition and dietetics was undertaken, covering convolutional neural network (CNN)-based food image recognition and portion estimation, machine learning (ML) models for predicting postprandial glycaemic response (PPGR), and large language model (LLM)-based chatbots for dietary counselling, meal planning, and behaviour change. Evidence on clinical outcomes, model performance, validation, and implementation barriers was considered. AI-assisted dietary assessment may improve accessibility and achieve performance comparable to human assessment for portion and energy estimation under controlled conditions; however, limited external validation and under-representation of diverse foods constrain generalisability. ML models integrating anthropometric, clinical, dietary, and gut microbiome data can improve individual PPGR prediction, with a limited number of randomised trials reporting beneficial glycaemic or metabolic outcomes from ML-guided personalised diets. LLM-based chatbots can provide broadly satisfactory dietary guidance and support conversational engagement, but inaccuracies, micronutrient omissions, and lower empathic quality than human dietitians remain concerns. Evidence from rigorous randomised controlled trials with clinically meaningful, long-term outcomes is limited. Additional barriers include algorithmic bias, data privacy and security risks, limited explainability, and evolving regulatory frameworks. AI has considerable potential to support dietary assessment, personalised nutrition, and nutrition counselling, but current evidence does not justify replacing registered dietitians and nutrition professionals. Standardised validation, rigorous clinical trials, improved model transparency, and equity-focused governance are essential to enable safe, effective, and responsible integration of AI into routine nutrition practice.},
}

@article {pmid42964690,
year = {2026},
author = {Lei, S and Chen, T and Xie, X and Zhang, X and Song, T and Khan, I and Li, Z},
title = {Alterations in oral microbiome and salivary metabolome profiles associated with myocardial infarction: a case-control study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2735104},
pmid = {42964690},
issn = {2000-2297},
abstract = {BACKGROUND: Few studies have comprehensively profiled both the salivary microbiome and metabolome in myocardial infarction (MI). This case-control study therefore characterized microbial and metabolic alterations in MI patients and identified potential diagnostic signatures.

METHODS: Seventy participants (35 MI patients and 35 matched healthy controls) were enrolled. Salivary microbiota were profiled via 16S rRNA (V3-V4) sequencing, and metabolites were analyzed using untargeted LC-MS. Microbial diversity, taxonomic composition, and predicted functional pathways were assessed. Diagnostic performance was evaluated by ROC analysis, and microbiota-metabolite correlations.

RESULTS: Significant differences in oral microbial diversity were observed between MI patients and controls. MI patients exhibited significantly higher alpha diversity and a distinct community structure, with beta diversity separating between groups. Enriched taxa included Bacteroidota, Veillonella, and Prevotella_7, while Streptococcus and Porphyromonas were depleted in MI patients. A four-metabolite panel comprising elevated L-2-aminoadipic acid and reduced thromboxane B2, 4-oxo-2-nonenal, and arginyl-glutamate distinguished MI from controls with high diagnostic accuracy (AUC = 0.92-0.94). Pathway analysis implicated ferroptosis and arginine/proline metabolism as candidate mechanisms. Correlation analysis revealed a significant positive association between Streptococcus and L-2-aminoadipic acid.

CONCLUSION: MI is associated with distinct oral microbial and salivary metabolomic signatures. A four-metabolite panel shows promise as a potential non-invasive biomarker signature, though external validation is required. Given the cross-sectional design, causality cannot be established.},
}

@article {pmid42964708,
year = {2026},
author = {Xu, B and Hu, D and Lu, H and Chen, Y and Guo, X and Liu, K and He, W},
title = {Osteoimmuno-microbial feedback loops in medication-related osteonecrosis of the jaw: from dysbiosis to persistent structural osteonecrosis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2751863},
pmid = {42964708},
issn = {2000-2297},
abstract = {BACKGROUND: Medication-related osteonecrosis of the jaw is a severe adverse event associated with antiresorptive, antiangiogenic and other targeted therapies. Although suppressed bone remodeling and impaired vascularity are central to its pathogenesis, these mechanisms alone do not fully explain the strong clinical associations among local trauma, infection, chronic inflammation and persistent bone exposure.

OBJECTIVE: To synthesize evidence on microbial dysbiosis, host immune dysregulation, and bone metabolic imbalance in MRONJ, and to propose an integrated osteoimmuno-microbial feedback framework.

DESIGN: This narrative review examined English-language clinical and experimental studies, reviews, and guidelines identified through PubMed, Web of Science, and Scopus, supplemented by reference-list screening. The final search was performed on May 31, 2026.

RESULTS: The reviewed evidence suggests that reduced bone turnover, impaired mucosal repair, and altered immune defense create a vulnerable local niche that permits microbial persistence and multispecies biofilm formation. Dysbiotic biofilms may sustain macrophage-associated inflammatory signaling, disturb bone homeostasis, and contribute to pyroptosis- and necroptosis-related tissue injury. These processes may form a self-perpetuating cycle of microbial colonization, inflammation, bone exposure, and impaired repair. However, microbial dysbiosis has not been established as a universal initiating event.

CONCLUSIONS: The proposed framework may help explain progression from potentially reversible local imbalance to persistent structural osteonecrosis. It highlights potential phase-adapted strategies targeting microbial ecology, inflammatory amplification, bone repair, and tissue vitality beyond conventional infection control and debridement.},
}

@article {pmid42964722,
year = {2026},
author = {He, L and Wang, J and Bai, T and Hou, X and Ran, D and Yang, J},
title = {Does the mouth seed the small bowel? Mechanisms and hypothesis-generating framework via the oral-gut axis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2735085},
pmid = {42964722},
issn = {2000-2297},
abstract = {BACKGROUND: As the starting segment of the digestive tract, the oral cavity harbors a complex microbial community that closely interacts with the distal gut microbiota. Recent evidence suggests that oral hygiene status and oral dysbiosis may correlate with gut microbial homeostasis and play a potential role in the initiation or exacerbation of small intestinal bacterial overgrowth (SIBO).

OBJECTIVE: This review aims to integrate existing evidence, outline a hypothesis-generating framework, identify critical knowledge gaps, and provide new perspectives for future interdisciplinary mechanistic research and clinical translation in SIBO and related gastrointestinal disorders.

DESIGN: This narrative review synthesizes and evaluates preliminary clinical correlations, metagenomic surveys, and animal models that support the oral microbiota as a potentially modifiable factor associated with SIBO, and discusses the proposed underlying molecular pathways.

RESULTS: Existing evidence supports the oral microbiota as a potentially modifiable factor associated with SIBO. However, direct high-level evidence testing oral hygiene interventions against definitive SIBO outcomes is currently lacking.

CONCLUSIONS: The oral-gut axis may play a critical role in SIBO pathogenesis. Future research requires high-quality clinical trials to validate the impact of oral hygiene interventions on SIBO outcomes, bridging the current critical knowledge gaps.},
}

@article {pmid42964734,
year = {2026},
author = {Campisciano, G and Aldegheri, L and Zanotta, N and Catamo, E and Robino, A and Mione, F and Cadenaro, M and Navarra, C and Tornese, G and Comar, M},
title = {Oral mycobiome composition and fungi-bacteria associations in children and young adults with type 1 diabetes.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2750003},
pmid = {42964734},
issn = {2000-2297},
abstract = {BACKGROUND: Oral mycobiome in children and young adults with type 1 diabetes (T1D) remains poorly characterized.

OBJECTIVE: We investigated oral fungal community structure and its associations with bacterial communities and immune mediators in individuals with established T1D compared with healthy controls (HC).

DESIGN: Oral fungal and bacterial communities were characterized in 68 participants with T1D and 69 HC by ITS and 16S rRNA gene sequencing, alongside multiplex assessment of soluble immune factors. Sequencing data were processed with QIIME 2, immune factors with BioPlex Manager and statistical analyzes with R v.4.3.3.

RESULTS: Fungal alpha and beta diversity did not differ significantly between groups. However, several taxa were differentially abundant or prevalent in T1D, including Fusarium, Hanseniaspora, Meyerozyma, Cyberlindnera jadinii, Candida albicans, C. dubliniensis and Malassezia globosa. No significant differences emerged by HbA1c category (<7% vs. ≥7%) within T1D. Notably, Cystobasidium/C. slooffiae and Trichoderma, detected exclusively in T1D, showed stronger positive associations with MCP-1/MCAF and IP-10, respectively, than in HC, while several fungal genera were inversely associated with distinct bacterial taxa.

CONCLUSIONS: These findings indicate that T1D is associated with selective, taxon-specific oral mycobiome alterations rather than generalized dysbiosis. The observed fungal-immune and fungal--bacterial links suggest biological relevance, warranting longitudinal and functional investigation.},
}

@article {pmid42964741,
year = {2026},
author = {Krishnavajhala, A and Gingras, MC and Santiago-Rodriguez, TM and Chen, Y and Bandaranaike, D and Bhamidipati, S and Qin, X and Kottapalli, K and Momin, Z and Santhanam, A and Walker, K and Wang, Q and Griffin, SM and Masternak, MM and Ross, MC and Muzny, D and Wu, J and Urquieta, E and Gibbs, RA and Doddapaneni, H},
title = {Microbial dynamics across commercial spaceflights of varying duration.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117988},
pmid = {42964741},
issn = {2589-0042},
abstract = {Spaceflight introduces environmental stressors that can alter human microbiomes and immune responses. We analyzed 259 and 17 biospecimens for microbiome and single-cell studies from n = 6 astronauts across two commercial International Space Station (ISS) missions: Axiom 2 (10-day mission) and Axiom 3 (21-day mission). Samples included saliva, stool, urine, and body swabs from 10 anatomical sites, profiled via 16S ribosomal RNA (rRNA) gene amplicon sequencing. Gut and oral microbiomes remained stable, while skin-associated communities exhibited transient diversity shifts post-flight. Taxonomic analysis revealed individual and site-specific patterns, as well as from the spaceflight/ISS environment. Cytokine profiling from single-cell data indicated immune activation, with IL-32 and IL-16 transcripts elevated in Axiom 2 and Axiom 3. Microbiome and interleukin correlation analyses found 14 significant associations in Axiom 2 data. These findings provide an integrated view of microbiome individuality. Our study represents a descriptive comparison of two missions, informing strategies for crew health on future long-duration missions.},
}

@article {pmid42964834,
year = {2026},
author = {Al-Beltagi, M and Saeed, NK and Elbeltagi, YM},
title = {Psychobiotics in pediatric autism spectrum disorder: A systematic review of efficacy, mechanisms, and clinical translation.},
journal = {World journal of clinical pediatrics},
volume = {15},
number = {4},
pages = {121115},
pmid = {42964834},
issn = {2219-2808},
abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a complex neurodevelopmental condition frequently associated with gastrointestinal (GI) disturbances and alterations in gut microbiota composition. Increasing evidence suggests that the microbiota-gut-brain axis may play a role in the pathophysiology of ASD, raising interest in microbiome-targeted therapies, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT). However, the clinical effectiveness and mechanisms of these interventions remain incompletely understood due to heterogeneous study designs and variable outcomes across trials.

AIM: To systematically evaluate the clinical efficacy and mechanistic implications of psychobiotic interventions, including probiotics, prebiotics, synbiotics, and FMT, in children with ASD.

METHODS: We conducted this systematic review in accordance with PRISMA 2020 guidelines. We also followed the methodological recommendations of the Cochrane Handbook. We searched different electronic databases, including PubMed/MEDLINE, EMBASE, Web of Science, PsycINFO, CENTRAL, and CINAHL, from inception till February 2026. We included eligible randomized controlled trials, controlled clinical trials, cohort studies, and pre-post intervention studies evaluating psychobiotic therapies in children and adolescents (≤ 18 years) with ASD. The main outcomes were: (1) Changes in severity as assessed by a broad-spectrum measure of ASD symptomatology at the 3-month follow-up; and (2) Variation of core symptoms, based on validated behavioral scales, including the Autism Diagnostic Observation Schedule, the Childhood Autism Rating Scale (CARS), and the Social Responsiveness Scale (SRS). We measured the severity of GI symptoms, microbiome composition, biologicals, and safety as secondary outcomes. Risk of bias was determined with Risk of Bias tool version 2 and Risk of Bias in Non-randomized Studies of Interventions tools. Meta-analysis using random-effects models was conducted where appropriate.

RESULTS: We reviewed 35 clinical studies that examined microbiome-targeted therapies in children with ASD. Overall, probiotics were associated with obvious improvements in GI symptoms and smaller, but noticeable, improvements in behavioral outcomes, although the benefits varied depending on the probiotic strains used, treatment duration, and whether children had GI problems at baseline. When data from selected probiotic studies were pooled, a moderate-to-large overall benefit was observed for GI symptom severity. Prebiotic supplementation mainly benefited gut function and microbial metabolic activity, with little and inconsistent impact on core autism symptoms. Synbiotic approaches-which combine probiotics with fermentable substrates-produced broader effects on the gut microbiome and were linked to modest improvements in both GI and behavioral symptoms. We observed that FMT showed the strongest overall effects among all microbiome-based interventions. Using quantitative analyses, we observed marked improvements in GI symptoms (GI SRS pooled SMD -2.71), along with a significant decrease in key behavioral measures, including social responsiveness (SRS pooled SMD -4.06), aberrant behavior (Aberrant Behavior Checklist -3.00), and overall autism severity (CARS -1.60). However, the strength of this evidence is tempered by the fact that many FMT studies were open-label or non-randomized, which limits confidence in the robustness of these findings. Across all microbiome-targeted therapies, benefits were most consistently observed for GI outcomes, whereas improvements in core ASD symptoms were more variable and less predictable.

CONCLUSION: Microbiome-targeted therapies are a promising adjunctive strategy in managing children with ASD, especially for associated GI disorders. Probiotics and prebiotics provided the most reliable benefits for GI symptoms, while synbiotics may offer broader microbiome modulation, and FMT has the greatest observed improvements in both GI and behavioral outcomes. However, considerable heterogeneity across studies and limited high-quality randomized trials highlight the need for large, well-designed clinical trials with standardized intervention protocols to clarify clinical efficacy and guide future therapeutic recommendations.},
}

@article {pmid42965106,
year = {2026},
author = {ElAdawy, SM and Talkhan, H and Orayj, K and Balata, GF and Saeed, M and Abdelkader, AA and Azzam, HN and Abdelrazek, NA and Mahmoud, IA and ElHaddad, M and Momen, SM and Hamada, M and Hamada, M and Elyousefy, AO and Hashem, KA and Alshikhari, MA and Deeb, GM and Elgohary, SM and Albakri, MM and Mohamed, A and Arshad, T and El-Sayed, NS and Etman, RS and Nawar, MM and Sobhy, EE},
title = {Lifestyle-associated gut microbiota signatures in colorectal cancer patients: a pilot case-control study.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21829},
pmid = {42965106},
issn = {2167-8359},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; Case-Control Studies ; Pilot Projects ; Female ; *Life Style ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Diet ; Egypt ; Aged ; Adult ; },
abstract = {BACKGROUND AND OBJECTIVES: Colorectal cancer (CRC) is the third most common cancer in men and the second in women, accounting for 9.4% of cancer-related deaths worldwide in 2020. Increasing evidence highlights the role of gut microbiota in CRC pathogenesis, prognosis, and therapeutic response. Data from Middle Eastern and North African populations remains scarce. This study aimed to analyze gut microbiota profiles in Egyptian patients with CRC and to explore their associations with dietary and lifestyle factors.

MATERIAL AND METHODS: A pilot case-control study was conducted, involving patients with CRC and healthy controls. Gut microbiota composition was assessed using 16S rRNA gene sequencing, with analysis of microbial diversity and differential taxonomic abundance at the family and genus levels. Dietary patterns, physical activity, and demographic variables were evaluated for their associations with microbial profiles.

RESULTS: CRC patients exhibited greater microbial heterogeneity, with higher Bray-Curtis distances compared to controls. Several taxa, such as Coprococcus_2, Ruminococcus, Blautia, and Dorea, were abundant in controls and adjacent normal tissues, whereas Lachnospiraceae UCG-010 was increased in CRC samples. Spicy food intake was linked to enrichment of Prevotellaceae and Christensenellaceae R-7, while processed meat consumption was associated with reduced abundance of Fusicatenibacter. Regular physical activity was associated with increased Akkermansia abundance among CRC patients. Additionally, sex-specific microbial patterns were observed, with Collinsella, Eggerthella, and Prevotella_9 more abundant in males.

CONCLUSIONS: This pilot study identifies clinically relevant, exploratory associations between lifestyle factors and CRC-related microbial signatures in an understudied population. All findings should be considered hypothesis-generating, given the small sample size and cross-sectional design. These results highlight the potential role of modifiable behaviors in microbiome-informed risk stratification. Larger, multi-center studies incorporating multi-omics approaches are warranted to confirm and extend these preliminary observations.},
}

Humans
*Colorectal Neoplasms/microbiology
Male
Case-Control Studies
Pilot Projects
Female
*Life Style
Middle Aged
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Diet
Egypt
Aged
Adult

@article {pmid42960201,
year = {2026},
author = {Luo, L and Zhao, J and Zhuge, J and Fang, H and Yuan, L and Wang, J and Hua, Z and Cui, Y},
title = {BALF-mNGS-Derived Microbial Detection Profiles and Their Associations with Clinical Severity in Immunocompromised Patients with Community-Acquired Pneumonia.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {657668},
pmid = {42960201},
issn = {1178-6973},
abstract = {BACKGROUND: Immunocompromised patients with community-acquired pneumonia (CAP) have heterogeneous pulmonary microbial profiles and frequently experience a severe clinical course. Whether bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS)-derived microbial features are associated with clinical severity in this population remains unclear.

OBJECTIVE: To characterize pulmonary microbial features in immunocompromised patients with CAP and evaluate their association with ICU admission and length of hospital stay (LOHS).

METHODS: This multicenter retrospective study included 1072 patients with CAP who underwent BALF-mNGS at five hospitals (August 2021-June 2025), including 362 immunocompromised and 710 immunocompetent patients. Microbial diversity, composition, and differentially enriched taxa were compared by immune status. Among immunocompromised patients, taxon-outcome associations were assessed using adjusted logistic and negative binomial regression, with sensitivity analyses additionally adjusting for antibiotic and antifungal exposure before BALF.

RESULTS: Immunocompromised patients had higher alpha diversity (P<0.001), with limited overall community separation. Five taxa were enriched: Burkholderia multivorans, Klebsiella pneumoniae, Candida glabrata, Candida tropicalis, and Streptococcus pseudopneumoniae. In primary analyses, B. multivorans abundance was associated with ICU admission (adjusted odds ratio [aOR] 1.400, 95% CI 1.088-1.801; false discovery rate [FDR]-adjusted P=0.045) and longer LOHS (adjusted incidence rate ratio [aIRR] 1.108, 95% CI 1.036-1.186; FDR-adjusted P=0.014). C. glabrata was associated with longer LOHS (aIRR 1.101, 95% CI 1.023-1.185; FDR-adjusted P=0.026). K. pneumoniae showed a nominal ICU association that did not survive FDR correction (FDR-adjusted P=0.084). After additional adjustment for antibiotic and antifungal exposure, the associations of B. multivorans and C. glabrata with longer LOHS remained significant (both FDR-adjusted P=0.044), whereas the association between B. multivorans and ICU admission did not (FDR-adjusted P=0.168).

CONCLUSION: BALF-mNGS-derived microbial features showed limited overall community differences but distinct taxon-specific associations with clinical severity. These exploratory findings require further validation before their prognostic or clinical utility can be established.},
}

@article {pmid42960262,
year = {2026},
author = {Li, Y and Zhang, H and Hu, L and Wang, H},
title = {Multi-Niche Microbiome Alterations in Endometrial Cancer: Drivers, Biomarkers and Translational Targets.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {643435},
pmid = {42960262},
issn = {1179-1411},
abstract = {Endometrial cancer (EC) is the commonest gynecological malignancy in high-income countries and one of the few solid tumors whose incidence and mortality are rising despite advances in oncological care. Conventional hormonal, metabolic and genetic risk factors fail to fully explain EC tumorigenesis, and the multi-niche human microbiome has emerged as a novel, modifiable regulatory axis governing EC onset, progression and immunotherapy responsiveness. However, existing reviews have largely examined individual anatomical sites in isolation, and a cross-compartment synthesis that integrates the gut, cervicovaginal, uterine cavity, and intratumoral niches-together with their mechanistic and therapeutic implications-remains lacking. This narrative review screened English articles from PubMed, Web of Science, Scopus and Google Scholar using keywords covering EC, microbiome, reproductive tract microbiome alterations, the estrobolome and immune checkpoint inhibitors (ICIs), prioritizing prospective cohorts, clinical trials and multi-omics mechanistic studies. We synthesize evidence across four interconnected niches and integrate them into a unified mechanistic framework. Reproducible compartmental signatures characterize EC: cervicovaginal samples show severe Lactobacillus depletion and enrichment of pathogenic anaerobes including Porphyromonas, Prevotella and Atopobium; malignant endometrial tissues display elevated α-diversity dominated by Anaerococcus, Peptoniphilus and Gardnerella, together with poorly explored fungal community shifts; the intratumoral niche harbors distinct taxa that directly modulate tumor proliferation, immune evasion and therapeutic responsiveness; and gut microbiome alterations deplete short-chain fatty acid-producing Firmicutes while expanding β-glucuronidase-rich Enterobacteriaceae, driving estrogen reactivation via the estrobolome and systemic pro-tumor inflammation. The PRIMMO trial further validates gut microbial clusters as predictive biomarkers of pembrolizumab efficacy in recurrent EC. By positioning the intratumoral microbiome as a distinct niche and linking multi-niche alterations to hormonal, inflammatory, immunological and genotoxic pathways, this review provides a new cross-compartment perspective that reframes the microbiome as both a mechanistic contributor and a translational target in EC. Standardized analytical workflows and large-scale prospective cohorts are urgently needed to translate these discoveries into routine clinical practice.},
}

@article {pmid42960341,
year = {2026},
author = {Prokopenko, YA and Faizullina, EA and Serova, OV and Protsenko, SV and Mokrushina, YA and Gong, N and Zheng, H and Kuzmin, YB and Tsarapaev, PV and Malabuiok, DM and Vereveyko, YR and Smirnov, IV and Kushlinskii, NE and Zhang, H and Gabibov, AG and Terekhov, SS},
title = {Optimization of Antibiotic and Antimycotic Compositions for the Eradication of Microorganisms from Cell Cultures.},
journal = {Acta naturae},
volume = {18},
number = {3},
pages = {94-101},
pmid = {42960341},
issn = {2075-8251},
abstract = {Cell cultures underlie the vast majority of in vitro research. Despite strict sterility requirements and the availability of high-tech equipment to prevent contamination, laboratory practice remains associated with a significant risk of contamination of mammalian cell cultures with bacterial and fungal agents. According to the American Type Culture Collection (ATCC), 15-35% of cell lines are contaminated with mycoplasma, posing a high risk of cross-contamination and leading to significant distortions of the experimental data obtained using such cultures. Furthermore, microbial contamination is a major risk factor when working with cell cultures isolated from patient surgical biospecimens. Despite the availability of ready-made solutions for eradicating microorganisms and preventing cell culture contamination, the problem of antibiotic resistance is particularly relevant for such contamination, and commercially available agents are often ineffective. In this study, combinations of antimicrobial agents were selected to address two of the most common practical challenges in cell culture: (i) complete elimination of mycoplasma infection and (ii) preventing contamination of primary cell cultures with bacteria and fungi that are components of the patient microbiome. A combination of tylosin, tetracycline, ciprofloxacin, erythromycin, and chloramphenicol was shown to completely eradicate mycoplasma from infected cell cultures. A combination of levofloxacin, polymyxin B, vancomycin, meropenem, and the antifungals micafungin and voriconazole completely eliminated the risk of microbial contamination during primary culture isolation, including from complex specimens such as surgical resections from colorectal cancer patients. The selected compositions successfully combine low cytotoxicity with a broad spectrum of antimicrobial activity, allowing for their effective use in laboratory practice. Nonetheless, the principle of minimizing the use of antimicrobial agents should be strictly adhered to in order to control the spread of antibiotic resistance.},
}

@article {pmid42960423,
year = {2026},
author = {Rajan, R and Nandakumar, D and Kapoor, N},
title = {Recent advances in polyendocrine metabolic ovarian syndrome and obesity: a comprehensive review.},
journal = {Current opinion in endocrinology, diabetes, and obesity},
volume = {33},
number = {6},
pages = {257-268},
pmid = {42960423},
issn = {1752-2978},
mesh = {Humans ; Female ; *Obesity/metabolism/complications/physiopathology ; Multiomics ; *Metabolic Syndrome/metabolism/complications/therapy/diagnosis ; *Polycystic Ovary Syndrome/metabolism ; Biomarkers/metabolism ; Precision Medicine/trends ; Insulin Resistance ; },
abstract = {PURPOSE OF REVIEW: This review evaluates recent advances in polyendocrine metabolic ovarian syndrome (PMOS), emphasizing its complex association with obesity and the ongoing transition toward precision medicine. The synthesis of current evidence addresses pathophysiology, emerging biomarkers, and multiomics approaches, highlighting their potential to enhance diagnosis, risk stratification, and individualized management.

RECENT FINDINGS: PMOS is a multifactorial disorder involving insulin resistance, hyperandrogenism, genetic predisposition, gut dysbiosis, and environmental factors. Obesity intensifies metabolic and reproductive dysfunction through mechanisms including chronic inflammation, adipose tissue dysfunction, and altered gut-ovary signalling. Traditional phenotype-based classifications do not adequately capture this biological heterogeneity. Multiomics approaches that integrate genomics, transcriptomics, proteomics, metabolomics, and microbiome data have identified distinct molecular subtypes, including insulin-resistant, steroidogenic, inflammatory, and neuroendocrine clusters. Novel biomarkers, including anti-Müllerian hormone, free androgen index, and specific metabolomic and lipidomic signatures, have the potential to improve diagnostic accuracy and phenotyping.

SUMMARY: The integration of multiomics represents a pivotal advancement toward patient-centred care in PMOS by enabling early risk prediction and mechanism-based therapies. While current evidence remains largely exploratory, these developments support a shift from uniform treatment strategies to precision endocrinology, with the potential to substantially improve long-term metabolic and reproductive outcomes.},
}

Humans
Female
*Obesity/metabolism/complications/physiopathology
Multiomics
*Metabolic Syndrome/metabolism/complications/therapy/diagnosis
*Polycystic Ovary Syndrome/metabolism
Biomarkers/metabolism
Precision Medicine/trends
Insulin Resistance

@article {pmid42960740,
year = {2026},
author = {Larysz, K and Ludynia, M and Trzebny, A and Klencz, W and Malcherczyk, N and Sierka, E},
title = {Plant Identity Shapes Core Microbiomes on Green Roofs.},
journal = {Environmental microbiology reports},
volume = {18},
number = {6},
pages = {},
pmid = {42960740},
issn = {1758-2229},
support = {2020/39/B/ST10/00862//National Science Centre, Poland/ ; 119118//Student Research Grants of the European City of Science Katowice/ ; FESL.10.25-IZ.01.0369/23-003//jUŚt transition-Potencjał Uniwersytetu Śląskiego podstawą Sprawiedliwej Transformacji regionu/ ; //Director's Reserve of the Institute of Biology, Biotechnology and Environmental Protection of the University of Silesia in Katowice/ ; },
mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Plants/microbiology/classification ; *Lotus/microbiology ; Ecosystem ; Soil Microbiology ; },
abstract = {Extensive green roof substrates support plant-microbe interactions that may contribute to ecosystem functioning. Yet the role of plant identity in shaping substrate-associated microbiomes remains insufficiently resolved beyond Sedum-dominated systems. We examined bacterial and fungal communities associated with three plant species representing contrasting functional groups in sterilized and non-sterilized green roof substrates, integrating taxonomic differentiation with plant functional traits and predicted metabolic pathways. Plant identity was associated with distinct microbial community patterns in sterilized and non-sterilized substrates, and these associations varied with the substrate's initial microbial state. LEfSe identified 13 discriminant fungal genera in ITS data and 65 bacterial genera in V4 data; strong discriminant taxa included Mortierella, Schizothecium, and Serendipita in fungal communities, and Sphingomonas, Brevundimonas, and Tumebacillus in bacterial communities. Lotus corniculatus showed particularly distinct plant-associated microbial patterns, while differences in predicted metabolic pathways provided a complementary functional perspective on taxonomic differentiation. Integrating plant functional traits with bacterial and fungal community analyses provided an ecological framework for interpreting plant-associated microbiome differentiation in extensive green roof substrates. Integrating plant functional traits with microbial community analyses provides an ecological framework for interpreting plant-associated microbiome differentiation in extensive green roof substrates.},
}

*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Plants/microbiology/classification
*Lotus/microbiology
Ecosystem
Soil Microbiology

@article {pmid42961031,
year = {2026},
author = {Sánchez, ICC and Margis-Pinheiro, M and Dias-Oliveira, M and Ponte, LR and Ricachenevsky, FK and Margis, R},
title = {The impact of OsASR5 on rice microbiome: Implications for nutrient cycling and stress response.},
journal = {Genetics and molecular biology},
volume = {49Suppl 3},
number = {Suppl 3},
pages = {e20250064},
pmid = {42961031},
issn = {1415-4757},
abstract = {Plant-microorganism interactions contribute to plant health by enhancing nutrient acquisition. The transcription factor OsASR5 regulates detoxification gene expression under aluminum stress in rice and is implicated as a positive regulator of responses to iron and phosphorus deficiency. Given its role in nutrient regulation, we investigated whether OsASR5 influences the assembly of the rice microbiome. In this study, we characterized the bacteria communities associated with the leaves and roots of OsASR5-RNAi rice plants compared to wild-type Oryza sativa cv. Nipponbare. Notably, OsASR5-RNAi plants showed altered bacterial beta diversity compared with wild type. The bacterial composition of OsASR5-RNAi plants differed in both organs, with decreased Desulfobacteriota and increased in Acidobacteria abundance in leaves. At the genus level, Methylobacterium, a known plant growth promoter, was less prevalent in leaves, while Magnetospirillum, associated with iron cycling, was less abundant in roots. Conversely, several bacteria were more abundant in OsASR5-RNAi plants, including Aneurinibacillus, Anaeromyxobacter, and Methylobacter, which are associated with nitrogen cycling and phosphorus solubilization. Additionally, Geobacter and Geothrix, both known for their role in metal reduction, particularly iron, were more abundant in OsASR5-RNAi plants. These suggest that OsASR5 affects plant-microbe interactions, potentially influencing nutrient cycling and plant stress responses through microbiome modulation.},
}

@article {pmid42961039,
year = {2026},
author = {Hooper, PM and Vincent, WF and Girard, C and Feil, EJ and Bass, D and Jungblut, AD},
title = {Diversity and connectivity of microbial eukaryotes in High Arctic terrestrial and aquatic ecosystems.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag096},
pmid = {42961039},
issn = {1574-6941},
abstract = {High Arctic ecosystems are being rapidly altered by climate change. Increased permafrost thaw and rainfall are making terrestrial landscapes more hydrologically active, increasing the input of organic and inorganic material into freshwater systems and freshening coastal marine ecosystems. Understanding the ecological implications of this environmental change requires an improved taxonomic and ecological resolution for less-studied microbial eukaryote communities. Microbial communities were investigated from freshwater, terrestrial, and coastal marine ecosystems on Ward Hunt Island, Ward Hunt Ice Shelf and Ellesmere Island along the coastal margin of the Last Ice Area, Canadian High Arctic. For the first time, Arctic microbial eukaryotic diversity was assessed using full-length 18S rRNA gene metabarcoding sequencing. Terrestrial microbial eukaryotic richness correlated with soil moisture, extending biogeographical patterns observed in lower latitudes. A greater connectivity between terrestrial and freshwater, than to coastal communities was identified, with a predicted input of terrestrial microbial eukaryotes into the Ward Hunt Lake microplankton. As Arctic catchments become more hydrologically active, increased transport of microbial eukaryotes may strengthen connectivity and homogenisation between terrestrial and freshwater ecosystems, while greater freshwater inputs may alter microbial diversity in adjacent coastal waters.},
}

@article {pmid42961044,
year = {2026},
author = {Chandran, S and Gibson, KE},
title = {Ligilactobacillus salivarius inhibits GII.4[P16] human norovirus replication in zebrafish larvae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0127826},
doi = {10.1128/aem.01278-26},
pmid = {42961044},
issn = {1098-5336},
abstract = {Human gut bacteria can modulate human norovirus (HuNoV) infection, underscoring the need to characterize virus-bacterium interactions. This study evaluated the effect of Ligilactobacillus salivarius on HuNoV GII.4[P16] replication using a zebrafish larva model. A GII.4[P16]-positive stool specimen was resuspended in phosphate-buffered saline (PBS), centrifuged, and the supernatant stored at -80°C. L. salivarius was grown overnight in de Man, Rogosa, and Sharpe broth, from which bacterial cells and cell-free supernatant (CFS) were collected. The overnight broth (OB), cells, and CFS were each mixed with virus suspension at a 1:1 ratio, and 3 nL were microinjected into 3-day post-fertilization larvae; controls received PBS with virus. Daily until 4 days post-infection (dpi), 2 samples of 10 pooled larvae were collected, and RNA was extracted and quantified by droplet digital PCR. Two-way analysis of variance showed that treatment and time significantly influenced viral RNA levels (P < 0.001), with a marginal interaction (P = 0.051) indicating consistent inhibitory trends across the study period. CFS-injected larvae showed replication comparable to controls (P > 0.05), peaking at 5.31 log RNA copies/larva at 1 dpi, whereas cell-containing treatments (cells and OB) significantly reduced replication (P < 0.01) throughout the 4-day period. An in vitro binding assay showed that 67% of the virus inoculum physically bound to L. salivarius. In a further comparison, both live and heat-killed bacteria reduced replication initially; live L. salivarius significantly inhibited replication at 3 dpi (P < 0.05). These findings support the hypothesis that L. salivarius physically binds to HuNoV GII.4[P16] and inhibits viral replication, highlighting its potential as a probiotic intervention for HuNoV infection.IMPORTANCENorovirus remains the leading cause of acute gastroenteritis worldwide, responsible for nearly 700 million cases and substantial economic burden annually, yet no vaccine or antiviral therapy currently exists. This study's findings are significant because they identify a specific probiotic strain, Ligilactobacillus salivarius, capable of directly binding to and inhibiting replication of a clinically relevant norovirus genotype (GII.4[P16]), which is responsible for many recent outbreaks globally. By demonstrating that live bacterial cells-not just secreted metabolites-drive this antiviral effect, the study points toward a mechanistic, cell-mediated mode of action that could inform targeted probiotic formulations. The use of a zebrafish larva model also offers a valuable, scalable in vivo system for studying norovirus-microbiome interactions, addressing a major bottleneck in norovirus research caused by the lack of robust cell culture systems. Together, these findings advance understanding of bacterium-virus interactions and support further development of probiotic-based strategies for preventing or reducing norovirus infection severity.},
}

@article {pmid42961062,
year = {2026},
author = {Lehr, K and Stegemann-Koniszewski, S and Scharlach, M and Thon, C and Lücke, E and Link, A and Schreiber, J},
title = {Changes in respiratory and gut microbiota in asthma and depression associate with disease markers.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0233426},
doi = {10.1128/spectrum.02334-26},
pmid = {42961062},
issn = {2165-0497},
abstract = {Asthma is heterogeneous and frequently accompanied by depression, affecting disease mechanisms and management. Both asthma and depression have been associated with inflammation and microbiota alterations, but their combined impact on microbial compositions remains unclear. Our exploratory study analyzed lung and gut microbiota in patients with asthma and depression to identify associations between microbiota composition and disease markers. This cross-sectional study included 20 healthy controls, 20 patients with asthma, and 20 patients with asthma and comorbid depression. Participants underwent clinical characterization and assessment of asthma control, depression, anxiety, and perceived stress. Induced sputum and fecal samples were collected for microbiota analysis, and inflammatory cytokines were measured in serum and sputum. Microbial profiling was performed using 16S rRNA gene sequencing. Lung function and FeNO levels were comparable between all groups. Asthma control scores were lower, and psychological scores were significantly higher in patients with asthma and comorbid depression compared with asthma alone and controls. Despite similar alpha and beta diversity across groups, sputum and fecal microbiota, particularly of healthy controls and comorbid patients, significantly differed in genus-level taxonomic composition. Correlation analyses demonstrated associations between clinical and psychological parameters and microbial profiles, including a consistent negative correlation between psychological scores and Neisseria abundance in both sputum and fecal samples. Asthma with comorbid depression is associated with distinct alterations in respiratory and gut microbiota, including reduced Neisseria perflava abundance correlating with psychological symptom severity.IMPORTANCEAsthma and depression frequently coexist, yet the potential contribution of microbial alterations to this comorbidity remains poorly understood. Because both respiratory and gut microbiota have been implicated in immune regulation and disease pathophysiology, characterizing microbiota patterns associated with asthma and depression may provide new insights into the biological links between these conditions. In this exploratory study, we investigated respiratory and gut microbiota in individuals with asthma, with and without comorbid depression, and healthy controls. Genus-level community composition differed between groups, particularly between controls and patients with asthma and depression. Notably, reduced abundance of Neisseria perflava in sputum and fecal samples was consistently associated with greater psychological symptom severity. These findings suggest that asthma accompanied by depression is associated with distinct alterations in microbial communities at multiple body sites. Further studies are warranted to determine whether such microbiota-psychological associations contribute to disease mechanisms or may serve as biomarkers of asthma-depression comorbidity.},
}

@article {pmid42961241,
year = {2026},
author = {Wang, Z and Huang, L and Liu, X and Cheng, X and Liang, Y and Chen, J and Ma, R and Song, W and Li, X},
title = {Pathobiont-directed mucosal immunotherapy targets Ruminococcus gnavus and remodels host-microbiota interactions in colitis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2754605},
doi = {10.1080/19490976.2026.2754605},
pmid = {42961241},
issn = {1949-0984},
mesh = {Animals ; *Ruminococcus/immunology ; *Immunotherapy/methods ; Mice ; *Colitis/therapy/microbiology/immunology ; *Host Microbial Interactions/immunology ; Immunity, Mucosal ; Intestinal Mucosa/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Humans ; Disease Models, Animal ; *Colitis, Ulcerative/therapy/microbiology/immunology ; Mice, Inbred C57BL ; Immunoglobulin A, Secretory/immunology ; Eubacteriales ; },
abstract = {Disease-associated pathobionts are recurrently enriched in inflammatory bowel disease (IBD), yet their causal contribution and selective therapeutic control remain incompletely defined. Here, through clinical microbiome profiling and causal animal studies, we identified Ruminococcus gnavus (Rg) as a key ulcerative colitis (UC)-associated pathobiont whose abundance positively correlates with intestinal oxidative stress and inflammatory levels. To selectively constrain Rg, we engineered CP-EV@Ca, an oral microbiota-directed mucosal immunotherapy that combines pathogen-specific immune targeting with redox modulation. CP-EV@Ca enhanced mucosal antigen presentation, promoted T follicular helper cell-germinal-center B-cell responses and induced robust Rg-specific secretory IgA (sIgA). CP-EV@Ca-induced mucosal immune responses, including enhanced Rg-specific sIgA production, were associated with increased immune coating and reduced Rg expansion. In both acute and chronic colitis models, CP-EV@Ca outperformed 5-aminosalicylic acid (5-ASA), suppressing inflammation and restoring microbial, epithelial and immune homeostasis. These findings demonstrate that pathobiont-specific mucosal immunity can be harnessed to selectively constrain disease-associated bacteria and restore intestinal homeostasis.},
}

Animals
*Ruminococcus/immunology
*Immunotherapy/methods
Mice
*Colitis/therapy/microbiology/immunology
*Host Microbial Interactions/immunology
Immunity, Mucosal
Intestinal Mucosa/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Humans
Disease Models, Animal
*Colitis, Ulcerative/therapy/microbiology/immunology
Mice, Inbred C57BL
Immunoglobulin A, Secretory/immunology
Eubacteriales

@article {pmid42961282,
year = {2026},
author = {Coelho, CPES and Munduri, JMS and Oliveira, JAVC and Moreira, MI and Cena, JA and Dame-Teixeira, N},
title = {From enemy to ally: an update for dental professionals on oral microbiome ecology and its systemic implications.},
journal = {Journal of applied oral science : revista FOB},
volume = {34},
number = {},
pages = {e20260384},
doi = {10.1590/1678-7765-2026-0384},
pmid = {42961282},
issn = {1678-7765},
mesh = {Humans ; *Microbiota/physiology ; *Dysbiosis/microbiology ; *Mouth/microbiology ; *Mouth Diseases/microbiology ; },
abstract = {The oral microbiome is a natural and essential component of the human body, maintaining a symbiotic relationship with the host and contributing to health. Rather than being caused simply by the presence of microorganisms, oral diseases are now understood as ecological dysbioses, in which disruption of the oral microbiome precedes and drives the development of clinical signs. This perspective challenges traditional clinical approaches, as strategies focused exclusively on detecting or eliminating specific microorganisms are unlikely to address the ecological nature of oral diseases and may, in some cases, be counterproductive. Furthermore, far beyond local effects, oral dysbiosis may have systemic repercussions. Through mechanisms such as chronic inflammation and interactions along the oral-gut axis, oral dysbiosis may influence systemic health and has been associated with cardiovascular, metabolic, neurodegenerative, and autoimmune diseases. This relationship is bidirectional: oral dysbiosis may contribute to systemic inflammatory and metabolic alterations, while systemic conditions can also modify the oral environment. As oral microbiome discoveries increasingly reach dental professionals, there is a growing need to critically translate this body of evidence into clinically meaningful concepts. This review aims to help bridge the gap between rapidly evolving oral microbiome research and everyday dental practice by providing dental professionals with an integrated ecological perspective of the oral microbiome. By synthesizing emerging concepts in microbiome homeostasis, dysbiosis, resilience, and oral-systemic interactions into clinically relevant principles, this review can support evidence-based decision-making in contemporary dentistry. The role of dental professionals in maintaining oral microbiome balance is part of a broader strategy to support both oral and systemic health. Recognizing oral diseases as ecological dysbiosis highlights the need for a shift in dental practice, in which preserving microbiome eubiosis and ecological stability becomes central to care. In dysbiosis, the microbiome becomes an enemy, so it is better kept on our side.},
}

Humans
*Microbiota/physiology
*Dysbiosis/microbiology
*Mouth/microbiology
*Mouth Diseases/microbiology

@article {pmid42961364,
year = {2026},
author = {Alghafri, M and Edwards, L and Moyes, D and Nibali, L},
title = {Antimicrobial Resistance in Periodontal Disease: Rethinking Adjunctive Therapy in the Metagenomics Era, the Pressing Need for Precision Treatment and Periodontal Resistome Mapping.},
journal = {Journal of cellular and molecular medicine},
volume = {30},
number = {21},
pages = {},
pmid = {42961364},
issn = {1582-4934},
mesh = {Humans ; *Metagenomics/methods ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Microbiota/drug effects ; *Periodontal Diseases/microbiology/drug therapy ; *Precision Medicine ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial ; },
abstract = {Systemic antibiotics are effective when used as adjunctive therapy in the treatment of periodontitis; however, their use must be balanced against antimicrobial resistance, which is a major threat to global public health. This review provides an expert synthesis of the literature and a field-level overview of antimicrobial resistance in periodontal therapy, highlighting current knowledge and emerging directions, while examining how adjunctive antibiotic protocols may contribute to resistance within the periodontal microbiome through emerging metagenomic insights. To provide this synthesis, the PubMed database was searched for English-language publications using combinations of the terms periodontitis, systemic antibiotics, antimicrobials, resistance, resistome, therapeutic adjuncts, resistance genes, susceptibility, antibacterial and drug resistance, and the findings are presented as a narrative review. The evidence indicates that a substantial proportion of patients with periodontitis harbour subgingival microbiota that are non-susceptible to at least one antibiotic used in periodontal therapy. Across the included studies, antimicrobial resistance was most frequently reported in Prevotella and Porphyromonas species, while some studies also identified virulence-associated factors in Staphylococcus aureus, a non-classical periodontal organism detected within the subgingival microbiota. Overall, current evidence indicates a high prevalence of antibiotic resistance genes in the subgingival microbiota of patients with periodontitis and highlights the ecological consequences of adjunctive antibiotic use. These findings reinforce the need to optimize antibiotic prescribing protocols within an antibiotic stewardship framework and support further metagenomic investigations to refine understanding of resistance patterns, gene-transfer mechanisms and microbiome disruption, with the aim of advancing precision-based periodontal care.},
}

Humans
*Metagenomics/methods
*Anti-Bacterial Agents/therapeutic use/pharmacology
Microbiota/drug effects
*Periodontal Diseases/microbiology/drug therapy
*Precision Medicine
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial

@article {pmid42961539,
year = {2026},
author = {Ahmad, N and Khan, NA and Shah, AA and Aziz, U and Khan, N and Zhang, L and Yuan, H and Song, Y},
title = {Phytogenic feed additives for climate-resilient camel production in arid and semi-arid regions: current evidence and research priorities.},
journal = {Tropical animal health and production},
volume = {58},
number = {8},
pages = {},
pmid = {42961539},
issn = {1573-7438},
support = {2022YFD1600101-02//Key Technologies Research and Development Program/ ; },
mesh = {Animals ; *Camelus/physiology ; *Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; *Animal Husbandry/methods ; Desert Climate ; *Food Additives ; Dietary Supplements/analysis ; Diet/veterinary ; },
abstract = {Camels play a vital role in supporting food security and livelihoods under the harsh feed, water, and environmental conditions of arid and semi-arid regions (ASARs), owing to their remarkable ability to tolerate heat stress and prolonged dehydration, travel long distances, and efficiently utilize low-quality forage resources available in these regions. Nevertheless, increasing climatic stress, coupled with fluctuating feed availability, infectious and parasitic diseases, and limited access to veterinary services, continues to constrain camel production in ASARs. Phytogenic feed additives are increasingly being explored as nutritional strategies to support foregut function, animal health, and product quality; however, the strength and directness of the available evidence for these effects in camels remain critically underexplored. This structured narrative review, grades available evidence from controlled camel studies, camel-specific mechanistic investigation, other foregut fermenters, and biologically more distant animal models. Its novel contribution is a camel-centered evidence hierarchy that separates demonstrated effects from comparative mechanisms and hypothesis-generating evidence while linking each candidate additive to specific research requirements. Potential applications include the modulation of foregut fermentation, oxidative and inflammatory status, microbial ecology, immune responses, parasite management, and milk and meat quality. However, direct camel evidence remains insufficient to establish effective doses, long-term safety, residues, sensory effects, or economic returns. Phytogenic feed additives therefore merit investigation as potential nutritional interventions, but current evidence does not support their routine use in camels. Future studies should use chemically characterized preparations, dose-response designs, clinically and economically meaningful outcomes, together with integrated assessments of foregut function, immune status, animal health, product quality, safety, and feasibility under dryland production conditions.},
}

Animals
*Camelus/physiology
*Animal Feed/analysis
Animal Nutritional Physiological Phenomena
*Animal Husbandry/methods
Desert Climate
*Food Additives
Dietary Supplements/analysis
Diet/veterinary

@article {pmid42961615,
year = {2026},
author = {Dolker, S and Ghosh, A and Singh, VK and Joshi, BD and Sharma, LK and Thakur, M},
title = {Exploring sex- and captivity-associated gut microbial diversity in Bengal Tigers (Panthera tigris tigris).},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42961615},
issn = {1573-4978},
mesh = {Animals ; *Tigers/microbiology/genetics ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Feces/microbiology ; Bacteria/genetics/classification ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Endangered Species ; },
abstract = {BACKGRO UND: The gut microbiome plays a critical role in host nutrition, immune regulation, metabolic stability, and overall physiological health in wildlife. However, gut microbiome data from large carnivores remain limited, particularly for endangered tiger populations. This study conducted a comparative analysis of fecal microbiomes from captive and wild Bengal tigers, integrated with publicly avai lable datasets from Amur, Malayan, and South China tigers, to understand how captivity and host factors influence microbial assembly. ME THOD S AND RESULTS: Across all tiger subspecies, Firmicutes and Proteobacteria dominated as core bacterial phyla, with Actinobacteriota, Bacteroidota, and Fusob acteriota forming a conserved microbial backbone. Wild Bengal tigers exhibited higher microbial richness and diversity than captive tigers . Beta diversity analyses demonstrated clear clustering by habitat (captive versus wild), but substantial overlap between male and female captive Bengal tigers, indicating that captivity-associated conditions exert influences on gut microbiome structure than sex. Comparative analyses among tiger subspecies revealed broad overlap in microbial community composition, suggesting limited phylogenetic influence. South China and Amur tigers displayed the lowest richness compared to Bengal and Malayan tigers. Furthermore, analysis identified an enrichment of protein fermentation-associated taxa in captive tigers, whereas wild tigers showed a greater abundance of environmentally associated taxa. CONCLUSIONS: The study provides evidences that captivity promotes reduction in gut microbial diversity in Bengal tigers, and highlights the potential utility of microbiome-informed captive management. Integrating gut microbiome monitoring into conservation breeding, zoo exchange and reintroduction programmes may improve adaptive fitness in endangered tiger populations.},
}

Animals
*Tigers/microbiology/genetics
Female
Male
*Gastrointestinal Microbiome/genetics
Phylogeny
Feces/microbiology
Bacteria/genetics/classification
Biodiversity
RNA, Ribosomal, 16S/genetics
Sex Factors
Endangered Species

@article {pmid42961986,
year = {2026},
author = {Tractenberg, RE and Groah, SL and Newcomb, E and Khemmani, M and Joyce, C and Wolfe, AJ and Riegner, CR},
title = {Variation in urobiome composition over time in asymptomatic individuals with spinal cord injury and disease using intermittent catheterization.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0356391},
pmid = {42961986},
issn = {1932-6203},
mesh = {Humans ; *Spinal Cord Injuries/complications/microbiology ; Female ; Male ; *Urinary Tract Infections/microbiology ; *Microbiota ; Adult ; Middle Aged ; *Intermittent Urethral Catheterization ; },
abstract = {Urinary tract infection (UTI) remains the most common infectious complication among individuals with neurogenic lower urinary tract dysfunction (NLUTD) due to spinal cord injury or disease (SCI/D). Despite widespread reliance on microbiological and symptom-based criteria for UTI diagnosis, significant ambiguity persists-especially in distinguishing clinically meaningful change from normal variability in urinary analysis results. This uncertainty contributes to overdiagnosis, inappropriate antibiotic use, and antimicrobial resistance. The present study sought to operationalize "normal variability" of the urinary microbiome (urobiome) among adults with NLUTD due to SCI/D. Using repeated samples collected from asymptomatic individuals over time, we analyzed inter- and intra-individual microbial composition to determine stability and fluctuation under baseline conditions. We observed wide intra- and inter-individual variability, substantial overlap between asymptomatic and pre-symptomatic states, and a consistent predominance of genera conventionally labeled as "uropathogens" including Escherichia/Shigella, Klebsiella, Enterococcus, Staphylococcus, and Streptococcus, even in the absence of symptoms. Bray-Curtis dissimilarities between paired samples ranged from 0 to 1, confirming substantial within-person compositional change over time. These findings suggest that assumptions drawn from cross-sectional studies-linking particular taxa or diversity values to health or disease-are not supported within individuals over time, at least in people with NLUTD due to SCI/D. Empirically characterizing normal within-person variability is a prerequisite both for interpreting urobiome results in this high-risk population and for improving the accuracy and stewardship of UTI diagnosis and treatment.},
}

Humans
*Spinal Cord Injuries/complications/microbiology
Female
Male
*Urinary Tract Infections/microbiology
*Microbiota
Adult
Middle Aged
*Intermittent Urethral Catheterization

@article {pmid42961994,
year = {2026},
author = {Cho, KC and Lee, WJ},
title = {How early microbial encounters shape adult behavior.},
journal = {PLoS biology},
volume = {24},
number = {10},
pages = {e3004101},
doi = {10.1371/journal.pbio.3004101},
pmid = {42961994},
issn = {1545-7885},
abstract = {Microbes are increasingly recognized as modulators of host behavior, but the underlying mechanisms are poorly understood. A new PLOS Biology study reveals a microbiome-to-gut-to-neuron pathway linking developmental microbial exposure to later food avoidance.},
}

@article {pmid42962075,
year = {2026},
author = {Alihosseini, C and Stein, M and Madiedo, ASA and Hesari, R and Kauffman, M and Zaiac, MN},
title = {Asymptomatic Tattoo-Associated Cutaneous Nontuberculous Mycobacterial Infection: Case Report.},
journal = {JMIR dermatology},
volume = {9},
number = {},
pages = {e108587},
pmid = {42962075},
issn = {2562-0959},
mesh = {Humans ; Male ; *Tattooing/adverse effects ; *Mycobacterium Infections, Nontuberculous/etiology/drug therapy/diagnosis/pathology ; Adult ; *Skin Diseases, Bacterial/etiology/drug therapy/pathology/diagnosis/microbiology ; *Mycobacterium abscessus/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Tattoo-associated nontuberculous mycobacterial infections can present in a variety of ways, including papular, pustular, nodular, and abscess-like morphologies. We report the case of an immunocompetent 28-year-old male who presented with diffusely distributed monomorphic papules with collarettes of scale confined to recently tattooed skin. Histopathologic evaluation demonstrated an atypical lichenoid vacuolar interface dermatitis, and tissue culture ultimately confirmed infection with Mycobacterium abscessus complex following prolonged incubation. This case highlights the diagnostic challenges posed by atypical clinical and histopathologic features of tattoo-associated nontuberculous mycobacterial infections, emphasizing the importance of early biopsy, mycobacterial culture, and prolonged combination antimicrobial therapy for optimal patient outcomes.},
}

Humans
Male
*Tattooing/adverse effects
*Mycobacterium Infections, Nontuberculous/etiology/drug therapy/diagnosis/pathology
Adult
*Skin Diseases, Bacterial/etiology/drug therapy/pathology/diagnosis/microbiology
*Mycobacterium abscessus/isolation & purification
Anti-Bacterial Agents/therapeutic use

@article {pmid42962337,
year = {2026},
author = {Dias-Alves, A and Marco, I and Jasso, MV and García-Ulloa, M and Asiimwe, C and Hobaiter, C and Akankwasa, JW and Babweteera, F and Kayaga, E and Malavé, A and Migura-Garcia, L and Aguilar, XF and Martínez-Urtaza, J and Cabezón, O},
title = {Microbiome-based survey of pathogenic bacteria at the chimpanzee-human-livestock interface, Uganda.},
journal = {Veterinary microbiology},
volume = {323},
number = {},
pages = {111251},
doi = {10.1016/j.vetmic.2026.111251},
pmid = {42962337},
issn = {1873-2542},
abstract = {Anthropogenic land-use change is intensifying contact among wildlife, humans, and livestock in tropical ecosystems, increasing opportunities for cross-species transmission of infectious agents. Chimpanzees (Pan troglodytes schweinfurthii), owing to their close phylogenetic relationship with humans, are particularly susceptible to pathogen spillover. We performed a microbiome-based screening of potentially pathogenic bacteria in faecal samples from a chimpanzee-human-livestock interface in western Uganda using full-length 16S rRNA gene sequencing. A total of 21 bacterial genera, categorized as potentially pathogenic, were detected across all three studied host groups, from which several taxa of potential zoonotic or health relevance, including Clostridium perfringens, Salmonella enterica, Shigella spp., and Streptococcus suis, were detected in chimpanzees, humans, and goats. Our findings indicate an overlap in bacterial taxa across the interface. The relative abundance of potentially pathogenic bacterial taxa was descriptively lower in chimpanzees than in humans and livestock, but carried both enteric and respiratory bacterial species previously associated with disease outbreaks in captive and wild populations. These findings support integrating bacterial monitoring into conservation-oriented One Health frameworks.},
}

@article {pmid42962471,
year = {2026},
author = {Zou, D and Fu, Y and Lv, Z and Liu, Z and Huang, Z and Yan, B and Liu, J and Kuang, Y and Li, M and Lin, L and He, M and Jing, T and Huang, S},
title = {Associations of environmental phenols exposure with gut microbiota in a general population from Shenzhen, China.},
journal = {Ecotoxicology and environmental safety},
volume = {326},
number = {},
pages = {120990},
doi = {10.1016/j.ecoenv.2026.120990},
pmid = {42962471},
issn = {1090-2414},
abstract = {The gut microbiota is considered an important target for the toxicity of environmental phenols, yet the epidemiological evidence elucidating their associations in adults remains limited. This study investigated associations between phenol exposure and gut microbiota in 241 adults from Shenzhen, China. We quantified 38 urinary phenols via ultrahigh performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) and profiled the gut microbiome via shotgun metagenomics. Linear regression, permutational multivariate analysis of variance (adonis), and Multivariable Association with Linear Models 2 (MaAsLin2) were used to assess links with α-diversity, β-diversity, microbial taxa, and functional pathways. We found that exposure to environmental phenols was significantly associated with altered gut microbiota diversity, composition and function. Bisphenol C was negatively associated with α-diversity, whereas benzylparaben and ethylparaben were positively associated with it. Exposure to methylparaben, triclosan, isopropylparaben and propylparaben was significantly associated with altered gut microbial community structure. Taxa analysis showed that methylparaben was negatively associated with the relative abundance of two beneficial species, Bacteroides salyersiae and Anaerostipes caccae. Additionally, functional profiling revealed that parabens inhibited amino-acid, carbohydrate and terpenoid metabolism, whereas triclosan up-regulated pathways for aromatic compound degradation and mixed-acid fermentation. Further prospective investigations are warranted to validate our findings.},
}

@article {pmid42962555,
year = {2026},
author = {Cordova, B and Milletich, PL and Jones, MP and McKinley, KL and Mearig, AJ and Triplett, EW and Ludvigsson, J},
title = {Gut microbial functional associations with subsequent irritable bowel syndrome in a prospective, paediatric case-control study.},
journal = {EBioMedicine},
volume = {133},
number = {},
pages = {106521},
doi = {10.1016/j.ebiom.2026.106521},
pmid = {42962555},
issn = {2352-3964},
abstract = {BACKGROUND: The infant gut microbiome undergoes rapid maturation that shapes lifelong gastrointestinal health. Although adults with irritable bowel syndrome (IBS) show characteristic microbial and metabolic alterations, it remains unclear whether these differences precede disease onset. Here, microbiome composition and function in infancy were prospectively associated with future IBS development.

METHODS: Stool samples collected from the All Babies in Southeast Sweden (ABIS) cohort at a mean age of 12.4 (±1.5) months, were analysed using a nested case-control design. Cases included future IBS and/or pelvic and abdominal pain, with the average time between age at stool collection and diagnosis being 11.8 (±5.2) years and a mean age at diagnosis of 12.8 (±5.2) years. Microbial composition was profiled with 16S rRNA gene sequencing (n = 396). Data were processed with DADA2, taxonomically assigned using SILVA database, and predicted functionally with PICRUSt2. Descriptive statistics were analysed using χ[2] or Fisher's exact test, global differences with PERMANOVA, differential abundance with ANCOM-BC2, and pathway enrichment with GSEA.

FINDINGS: Infants with future IBS risk demonstrated microbial divergence, marked by depletion of short-chain fatty acid producers and expansion of facultative and mucosa-disruptive taxa. Inferred functional profiles exhibited reduced fermentative capacity, greater respiratory potential, accelerated degradation of neuroactive aromatic amines, and case-enrichment of cytochrome bc1 complex respiratory unit.

INTERPRETATION: Gut microbiome dysbiosis in infants with IBS risk is present many years prior to diagnosis and includes early disruptions in fermentation, redox balance, and amine metabolism that potentially compromise epithelial resilience and promote visceral hypersensitivity. Early detection of microbiome dysbiosis suggests probiotic-based interventions.

FUNDING: Barndiabetesfonden; Swedish Council for Working Life and Social Research; Swedish Research Council; Östgöta Brandstodsbolag; Medical Research Council of Southeast Sweden; JDRF-Wallenberg Foundation; Linköping University; Horizon Europe INITIALISE grant.},
}

@article {pmid42962574,
year = {2026},
author = {Yu, X and Liu, S and Gutang, Q and Wang, Y and Yin, X and Li, Y and Wang, X},
title = {Unveiling the mechanism of microplastic-mediated antibiotic bioavailability, gut microbiota and antibiotic resistome in marine fish: Importance of microplastic aging and antibiotic-loading.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127177},
doi = {10.1016/j.watres.2026.127177},
pmid = {42962574},
issn = {1879-2448},
abstract = {Microplastics and antibiotics co-occur commonly in coastal aquatic ecosystems. Environmental aging of microplastics and interactions with antibiotics are inevitable, which alter the fate of antibiotics and associated ecotoxicological effects, yet the distinct impacts and underlying mechanisms remain largely unknown. Here, polyethylene (PE) microplastics, derived from a widely used polymer and frequently detected in aquatic environments, were selected to investigate the effects of aging and ciprofloxacin (CIP) loading on CIP bioaccumulation and toxicity in marine medaka (Oryzias melastigma). The intake of microplastics by fish visualized via a novel in situ hyperspectral imaging revealed aged PE (APE) easily accumulated in the fish gut. The presence of microplastics exacerbated CIP-induced gill and intestinal lesions. CIP-loaded pristine PE (PPE-CIP) increased CIP accumulation by 0.87-fold, 1.18-fold and 0.10-fold in the gastrointestinal tract, gill and muscle, respectively, and CIP-loaded aged PE (APE-CIP) further amplified this promoting effect. Conversely, PPE and APE without CIP-loading decreased CIP accumulation in the fish gut, but this clean effect varied with exposure duration, tissue distribution and microplastic aging status. The presence of microplastics altered the gut microbiota composition, and APE-CIP exacerbated the effects of microplastics on the gut microbiota by decreasing the stability of the microbiome network. The presence of PPE-CIP and APE-CIP amplified the abundance of Vibrio and CIP-associated antibiotic resistance genes (i.e., norM gene) in fish feces via enhancing CIP bioaccumulation, increasing the risk of ARGs spread through fish feces. These findings highlight the importance of considering aging and antibiotic-loading when evaluating the carrier effects and toxicity of microplastics.},
}

@article {pmid42962646,
year = {2026},
author = {Zakari, A and Chen, YH and Chen, PJ and Peng, SW and Lan, SC and Shih, YS and Hsiao, TC and Chung, KF and Chuang, KJ and Chang, JH and Chi, KH and Chuang, HC},
title = {Associations of particulate matter-associated microbial profiles with lung and intestinal microbiomes in healthy mice.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143978},
doi = {10.1016/j.jhazmat.2026.143978},
pmid = {42962646},
issn = {1873-3336},
abstract = {Ambient air pollution has detrimental effects on human health. We investigated exposure-related differences and microbial overlap among PM1, lung, and gut microbiomes in mice exposed to PM1, high-efficiency particulate air (HEPA)-filtered air, or clean air. PM1 was characterized for soluble ions, metals, carbonaceous fractions, and oxidative potential, while gaseous pollutants data were obtained from air-quality monitoring stations. PM1, lung, and gut microbiomes were analyzed using 16S rRNA sequencing, and short-chain fatty acids (SCFAs) were quantified by gas chromatography-mass spectrometry (GC-MS). Proteobacteria was the dominant phylum in PM1. PM1 contained diverse chemical constituents, including soluble ions, metals, and oxidative species. Lung microbial diversity remained largely unchanged, whereas the gut microbiome was significantly altered. Compared with control, the PM1 group showed reduced Actinobacteriota and Bacteroidota, while Campylobacterota and Patescibacteria decreased in both HEPA and PM1 groups. Verrucomicrobiota increased in the HEPA group, and Proteobacteria increased in the PM1 group compared with both HEPA and control groups. Correlation analyses identified associations between lung and gut microbiomes, environmental variables, PM1 characteristics, gaseous pollutants, and SCFAs. Eleven bacterial families and six genera overlapped among PM1, lung, and gut microbiomes in the PM1 group. Overall, ambient air pollution was associated with gut dysbiosis in mice.},
}

@article {pmid42962704,
year = {2026},
author = {May, L and Wolstenholme, J and Bajaj, J},
title = {Targeting the Microbiome to Treat Alcohol Use Disorder and Liver Disease.},
journal = {Seminars in liver disease},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2993-3789},
pmid = {42962704},
issn = {1098-8971},
abstract = {Alcohol use disorder and alcohol-associated liver disease represent a global health burden, yet treatment options remain limited. Emerging evidence has shown the intestinal microbiome to be a mediator of alcohol-associated organ injury, establishing gut dysbiosis, intestinal barrier dysfunction, and aberrant microbial metabolite production as drivers of disease. The gut-liver-brain axis provides a mechanistic framework in which microbial products and signals fuel hepatic inflammation, steatosis, fibrosis, and neuroinflammation that drive alcohol consumption. This review discusses current evidence on how chronic alcohol exposure shapes microbial communities, disrupts the gut epithelium, and alters innate immune and metabolic circuits in the liver and the brain. We examine how microbiome-targeted interventions, such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, non-absorbable antibiotics, and short-chain fatty acid supplementation, can act on mechanistic targets along this axis. Finally, we highlight knowledge gaps, including the roles of causal microbial taxa, sex differences in gut-immune-brain signaling, and windows of reversibility that must be further investigated and understood to translate microbial modulation into effective therapies. In conclusion, this review summarizes the current literature on targeting the microbiome and the gut-liver-brain axis as a treatment approach, with a focus on the mechanisms within this axis and the interventions that target them.},
}

@article {pmid42962970,
year = {2026},
author = {Islam Bhuiyan, MN},
title = {Food as Biological Information: A Testable Dietome Framework for Precision Nutrition and Whole-Food Meal Design.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101909},
doi = {10.1016/j.tjnut.2026.101909},
pmid = {42962970},
issn = {1541-6100},
abstract = {Nutrition science has established the importance of energy, essential nutrients, dietary patterns, and food matrices, yet researchers often study these dimensions separately from the biological systems that transform and interpret a meal. This Perspective proposed the Dietome as a testable, systems-level description of food-derived inputs and the Informational Nutrition Framework (INF), comprising encoding, transmission, decoding, execution, and biological memory. The framework integrates sensory perception and eating behaviour with digestion, microbial metabolism, host signalling, and context-dependent responses. Its novelty is not the claim that food contains a literal code, but the proposal to connect food composition and structure to measurable, falsifiable predictions about meal-level responses. Evidence from personalized postprandial prediction, foodome network analysis, microbial short-chain fatty acid (SCFA)-associated chromatin regulation, and computational diet modelling illustrates both opportunity and limitations. A worked meal example shows how to evaluate minimally processed foods and their combinations before considering engineered formulations. The Perspective also identifies sustainability, developmental nutrition, and food-allergy prevention as domains requiring cautious, evidence-specific application. Dietary microRNAs and long-term nutritional memory remain less established than conventional nutrient and microbial-metabolite pathways. The framework should therefore be judged by prospective validation, causal evidence, clinical utility, cultural acceptability, and environmental performance, not by terminology alone.},
}

@article {pmid42963088,
year = {2026},
author = {Durr, KM and Hum, C and Kain, T and Tran, A and English, S and McIntyre, L},
title = {Randomised controlled trials of faecal microbiota transplantation in adult inpatients: a scoping review study protocol.},
journal = {BMJ open},
volume = {16},
number = {10},
pages = {e122741},
doi = {10.1136/bmjopen-2026-122741},
pmid = {42963088},
issn = {2044-6055},
}

@article {pmid42963223,
year = {2026},
author = {Fu, W and Sun, C and Guo, Q and Lai, H},
title = {Cross-kingdom endosymbiosis rewires the rhizobiome for fungal pathogenicity.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.10.005},
pmid = {42963223},
issn = {1878-4380},
abstract = {Soil-borne fungal pathogens undermine crop health by disrupting the protective rhizosphere microbiome. Zhou et al. uncovered a cross-kingdom endosymbiotic mechanism that enables Fusarium oxysporum f. sp. lycopersici to subvert rhizosphere protection: intracellular bacterial endosymbionts drive fungal metabolic reprogramming to produce a selective toxin, thereby suppressing keystone beneficial rhizobacteria.},
}

@article {pmid42963493,
year = {2026},
author = {van Wesemael, AJ and de Kroon, RR and van Eijk, LMHE and Frerichs, NM and Vermeulen, MJ and van den Akker, CHP and Raets, MMA and Hulzebos, CV and de Boode, WP and van Kaam, AH and de Meij, TGJ and Niemarkt, HJ},
title = {Clinical effects of multi-strain probiotics in extremely preterm infants: a multicenter pre-post implementation study in the Netherlands.},
journal = {European journal of pediatrics},
volume = {185},
number = {11},
pages = {},
pmid = {42963493},
issn = {1432-1076},
mesh = {Humans ; *Probiotics/therapeutic use ; Infant, Newborn ; Netherlands/epidemiology ; *Enterocolitis, Necrotizing/prevention & control/epidemiology ; *Infant, Extremely Premature ; Male ; Female ; Intensive Care Units, Neonatal ; *Infant, Premature, Diseases/prevention & control/epidemiology ; Gestational Age ; Sepsis/prevention & control/epidemiology ; Incidence ; Treatment Outcome ; Streptococcus thermophilus ; },
abstract = {UNLABELLED: Probiotics may reduce the risk of necrotizing enterocolitis (NEC), late-onset sepsis (LOS), and mortality in preterm infants. However, their efficacy in extremely preterm infants (gestational age < 28 weeks) is still regularly questioned due to limited data and safety concerns. In Dutch Neonatal Intensive Care Units (NICUs), a three-strain probiotic product (ProPrems®; Bifidobacterium infantis Bb-02, Bifidobacterium lactis BB-12, and Streptococcus thermophilus TH-4) was implemented as standard of care from 2021 onwards. This study evaluates the clinical effects of these probiotics in extremely preterm infants. Pre- and postimplementation cohorts of extremely preterm infants from 6 Dutch NICUs (2018-2023) were compared. Clinical data from the first 29 days of life were collected. Incidence of NEC (modified Bell's stage ≥ IIA), LOS, and mortality were compared with logistic regression; growth velocity with linear regression; and time to full enteral feeds (tFEF) with survival analyses. In total, 481 extremely preterm infants (212 pre-, 269 post-implementation) were included. After implementation, the adjusted odds ratio was 0.49 (0.25-0.99; p = 0.049) for NEC; 0.87 (0.59-1.28; p = 0.49) for LOS; and 0.67 (0.35-1.27; p = 0.22) for all-cause mortality. Furthermore, tFEF decreased by 2 days (p < 0.001) and probiotic use was associated with an increase in growth velocity of 1.8 g/kg/day (p < 0.001). One infant (0.4%) developed probiotic-associated sepsis.

CONCLUSION:  This multicenter pre-postimplementation study showed that multi-strain probiotic administration was associated with lower NEC incidence, shorter tFEF, and greater growth velocity in extremely preterm infants during the first four weeks of life. Probiotic-associated sepsis was rare. These results support continued use of probiotics in this vulnerable population.

WHAT IS KNOWN: • Certain probiotic strains effectively reduce incidence of necrotizing enterocolitis (NEC) in preterm infants, but the efficacy and safety for extremely preterm infants (GA < 28 weeks) remain under debate.

WHAT IS NEW: • This study shows that a multi-strain probiotic supplement was associated with lower NEC incidence, shorter time to full enteral feeds, and greater early postnatal growth in a Dutch multicenter cohort of extremely preterm infants. • The incidence of probiotic-associated sepsis in extremely preterm infants was very low in our cohort with just 1 case (0.4%), consistent with the rare occurrence reported previously.},
}

Humans
*Probiotics/therapeutic use
Infant, Newborn
Netherlands/epidemiology
*Enterocolitis, Necrotizing/prevention & control/epidemiology
*Infant, Extremely Premature
Male
Female
Intensive Care Units, Neonatal
*Infant, Premature, Diseases/prevention & control/epidemiology
Gestational Age
Sepsis/prevention & control/epidemiology
Incidence
Treatment Outcome
Streptococcus thermophilus

@article {pmid42963768,
year = {2026},
author = {Khan, HW and Iqbal, MA and Reyer, H and Trakooljul, N and Hadlich, F and Oster, M and Kuhla, B and Keiler, J and Wimmers, K and Ponsuksili, S},
title = {Breed and housing system shape jejunal transcriptome and digesta microbiota in German Landrace and Saddleback pigs.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42963768},
issn = {2524-4671},
abstract = {BACKGROUND: Sustainable pig farming balances animal welfare, productivity, and social acceptance. Organic systems offer enriched environments for the pigs and represent a model for sustainable production, but require an understanding of how breed, intestinal microbiome, and housing interact. In this study, we compared a commercial breed (German Landrace, GL) and a traditional breed (German Saddleback, GS) reared in different housing systems (Conventional, CON; Organic, ECO). Jejunal mucosa transcriptomes (n = 56) and digesta microbiota (n = 100) were collected from growing pigs at 70 days of life; 54 samples overlapped between the two datasets and were used for all integrated host-microbiome analyses. Data from RNA-seq and 16 S-seq were evaluated through differential expression analysis, microbial community profiling, and DIABLO-based data integration.

RESULTS: Jejunal transcriptome variation was influenced primarily by breed. GL pigs exhibited a profile supporting anabolic pathways, including upregulated oxidative phosphorylation, whereas GS pigs showed a profile focused on lipid metabolism and a shift toward energy storage as an adaptation. In contrast, the housing system was the main driver of microbial composition, with ECO housing enriching fermentative taxa such as Lactobacillus and Campylobacter, presumably due to outdoor exposure, while CON housing enriched fewer Lactobacillus but more Clostridium. Breed-Housing combinations analysis revealed distinct adaptive strategies: the modern GL breed responded strongly to housing conditions at both the transcriptional and microbial levels, whereas the traditional GS breed, while also transcriptionally responsive, maintained a more stable microbial community phenotype across environments. Integrated host-microbiome analysis identified a core set of host genes (e.g., PCSK9 and SCD) that were strongly correlated with housing-specific microbes, defining a lipid-inflammation axis.

CONCLUSION: Breed and rearing environment jointly shape the porcine jejunal transcriptome and microbiota through distinct strategies. Together, these data provide molecular insight into how traditional and modern breeds differentially respond and potentially adapt to divergent husbandry systems, with implications for health and productivity.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid42963927,
year = {2026},
author = {Chang, H and Gu, C and Zou, D and Wang, X and Xu, R and Zheng, S and Ran, M and Wang, T and Zhao, Y and Wang, D},
title = {Host seasonal trophic strategies linked to dietary-microbiota coupling: A potential mechanism mediating the coexistence of sympatric small rodents.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70383},
pmid = {42963927},
issn = {1365-2656},
support = {//Double-First Class Initiative of the School Life Sciences Shandong University/ ; 31970417//National Natural Science Foundation of China/ ; 32330012//National Natural Science Foundation of China/ ; },
abstract = {The coexistence mechanisms of sympatric species have long attracted widespread research attention. However, it remains unclear whether sympatric species experiencing the same seasonal conditions exhibit convergent or host-specific gut microbiota responses. We compared the herbivorous Brandt's vole (Lasiopodomys brandtii) and the granivorous Mongolian gerbil (Meriones unguiculatus), two sympatric rodent species with divergent trophic strategies inhabiting the grasslands of Inner Mongolia, China. By integrating plant DNA metabarcoding, gut microbiota profiling and microbial functional output analyses across seasons, we investigated seasonal dietary-microbiome associations. Our results revealed that although seasonal dietary variation affects the composition of the host gut microbiota, the taxonomic and functional plasticity of gut microbiota is strongly influenced by host trophic strategies. Brandt's voles maintained a fermentation-oriented microbiota tightly coupled with seasonal shifts in Poaceae and Cyperaceae intake, exhibiting coordinated changes in microbial taxa, short-chain fatty acid production and cellulase activity. In contrast, Mongolian gerbils exhibited substantial seasonal dietary turnover between Chenopodiaceae and Caragana plants, while maintaining comparatively stable microbial functional outputs, suggesting metabolic buffering. Host trophic strategy, rather than shared environmental seasonality, is related to the strength and functional consequences of the coupling between diet and microbiome. Our results emphasize the gut microbiome as a potential key mechanism underlying trophic niche differentiation and ecological coexistence in wild mammalian communities.},
}

@article {pmid42964032,
year = {2026},
author = {Li, H and Hou, C and Pan, Y},
title = {Targeting the gut-tumor axis: probiotic therapy as an adjunct strategy in colorectal cancer treatment.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1873871},
pmid = {42964032},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/therapy/drug therapy ; *Probiotics/therapeutic use/pharmacology ; Multiomics ; Apoptosis/drug effects ; Cell Survival/drug effects ; Metabolomics ; Proteomics ; Gastrointestinal Microbiome/drug effects ; Cytokines/metabolism ; Cell Line, Tumor ; Systems Biology ; Signal Transduction/drug effects ; Caco-2 Cells ; Gene Expression Profiling ; Butyrates/pharmacology ; Indoleacetic Acids ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is a multifactorial disease driven by interactions among host genetics, immune dysregulation, environmental factors, and gut microbiota. The gut-tumor axis regulates CRC progression through inflammatory signaling, oxidative stress, epithelial barrier disruption, and immune imbalance. Probiotic-derived metabolites act as bioactive molecules capable of restoring host-microbiome homeostasis and modulating tumor-associated pathways.

OBJECTIVE: To evaluate probiotic metabolites as adjunct therapeutic agents in CRC using integrative multi-omics analysis and in vitro validation.

METHODS: A systems biology approach integrating network pharmacology, transcriptomics, proteomics, metabolomics, and microbiome profiling was applied. Twelve probiotic metabolites yielded 428 predicted targets, with 162 overlapping CRC-associated genes. CRC cell lines (HCT116, HT-29, Caco-2, SW480) were treated and analyzed for viability, apoptosis, gene/protein expression, cytokines, metabolites, and microbial composition.

RESULTS: Sodium butyrate (5 mM) reduced cell viability by 35.5-42.3% (p < 0.001) and increased apoptosis from 8.6% to 32.4%, reaching 41.2% when combined with indole-3-acetic acid (IAA, 100 μM), suggesting a synergistic pro-apoptotic effect. RNA-seq identified 1,248 DEGs, with upregulation of BAX and CASP3 (log2FC +1.8 to +2.3) and downregulation of IL6, TNF, and NFKB1 (-1.5 to -2.1). Proteomics revealed 412 differentially expressed proteins, including downregulation of AKT1 (-1.6-fold), MAPK1 (-1.4-fold), and EGFR (-1.3-fold), and upregulation of CASP3 (+1.7-fold) and BAX (+1.5-fold). Cytokines IL-6, TNF-α, and IL-1β decreased by 48.2%, 44.7%, and 39.5%, respectively, while IL-10 increased by 26.3%. Metabolomics showed a 2.8-fold increase in butyrate and ~35% reduction in oxidative stress. Microbiome diversity improved (Shannon index 2.8-3.6).

CONCLUSION: Probiotic-derived metabolites modulate NF-κB, PI3K-Akt, MAPK, and apoptosis pathways, supporting their potential role as adjunct therapeutic agents in CRC management.},
}

Humans
*Colorectal Neoplasms/therapy/drug therapy
*Probiotics/therapeutic use/pharmacology
Multiomics
Apoptosis/drug effects
Cell Survival/drug effects
Metabolomics
Proteomics
Gastrointestinal Microbiome/drug effects
Cytokines/metabolism
Cell Line, Tumor
Systems Biology
Signal Transduction/drug effects
Caco-2 Cells
Gene Expression Profiling
Butyrates/pharmacology
Indoleacetic Acids

@article {pmid42964048,
year = {2026},
author = {Rahman, MA and Islam, SMS and Alabdallah, NM and Latif, S and Hoque, M and Hasan, MM},
title = {New insights into root 2-naphtholic acid exudation, microbiome recruitment, and designing of drought-smart future crops.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1938013},
pmid = {42964048},
issn = {1664-462X},
}

@article {pmid42964076,
year = {2026},
author = {Pandey, S and Skidmore, J and Dhillon, J},
title = {A systematic review of the effects of diet on the gut microbiota in individuals at elevated risk for colorectal cancer.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1818522},
pmid = {42964076},
issn = {2296-861X},
abstract = {BACKGROUND: Colorectal cancer (CRC) poses a major public health concern, with emerging evidence highlighting the critical role of the gut microbiota in CRC progression. Considering that diet is a major modifiable factor influencing CRC risk, partly through its interaction with the gut microbiome, this systematic review evaluated the effects of dietary intervention RCTs, including supplements, functional foods, whole foods, and dietary patterns, on the gut microbiome in elevated-risk individuals.

METHODS: A search of PubMed, Scopus, and Web of Science, and manual sourcing of systematic reviews, meta-analyses, and reference lists of relevant papers identified 5,558 records.

RESULTS: Following screening, seven studies met inclusion criteria, focusing on microbial diversity and taxonomic composition. Findings demonstrate that effects on microbial diversity metrics were minimal and were observed only with a general healthy eating dietary pattern, navy bean powder interventions, and with one rice bran intervention. No consistent patterns emerged by intervention type (functional compounds, whole foods, or dietary pattern), intervention duration, or by diversity metric. In contrast, genus-level compositional shifts were more frequently reported, although directionality varied by dietary exposure. Enrichment of Faecalibacterium, Bifidobacterium, and Lactobacillus was reported in some rice bran and navy bean interventions, whereas reductions in Akkermansia, Ruminococcus, Bacteroides, Prevotella, and Porphyromonas were observed in others. Among the four trials assessing microbial-derived metabolites, some were associated with increased short-chain fatty acids and plant-derived metabolites while others reported reductions in secondary bile acids, p-cresol sulfate, and branched-chain bacterial fatty acids.

CONCLUSION: Overall, this review highlights the potential of dietary strategies to modulate the gut microbiome in populations at risk for CRC, while also addressing critical gaps in the current evidence and offering direction for the development of evidence-based dietary interventions that incorporate microbiome assessment. Limited RCTs and heterogeneity in outcomes limit generalizability. Future research should conduct rigorous RCTs across the lifespan, using microbiome and metabolite analyses such as shotgun metagenomics, meta-transcriptomics, or metabolomics and examining understudied dietary patterns to guide CRC prevention.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42024530038, identifier CRD42024530038.},
}

@article {pmid42964104,
year = {2026},
author = {Ramos-Nino, ME and Doshi, A and Ramdass, PVAK},
title = {The emerging oral microbe-host axis in endometriosis: a systematic review of Fusobacterium nucleatum.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1994934},
pmid = {42964104},
issn = {2235-2988},
mesh = {*Endometriosis/microbiology ; Humans ; Female ; *Fusobacterium nucleatum/pathogenicity/physiology ; Animals ; *Fusobacterium Infections/microbiology/complications ; *Mouth/microbiology ; Microbiota ; *Host Microbial Interactions ; },
abstract = {BACKGROUND: Fusobacterium nucleatum, an oral-associated bacterium implicated in several extraoral diseases, has recently been proposed as a potential contributor to endometriosis through microbial translocation, inflammation, and fibrosis. However, the consistency and clinical significance of this association remain uncertain. This systematic review evaluated the human and experimental evidence linking F. nucleatum with endometriosis and assessed the plausibility of a proposed oral microbe-host axis.

METHODS: PubMed/MEDLINE, Embase, Web of Science, and Google Scholar were searched from inception through August 31, 2026, following PRISMA 2020 guidelines. Human and animal studies reporting F. nucleatum or historically related F. nucleatum-complex taxa in relation to endometriosis were included. Risk of bias was assessed using a prespecified adapted ROBINS-I framework for human observational studies and SYRCLE for animal studies. Owing to substantial heterogeneity in anatomical compartments, detection methods, and outcomes, meta-analysis was not appropriate and findings were synthesized qualitatively.

RESULTS: Four human studies encompassing 384 participants at the study level were included, although analysis-specific denominators varied. Direct tissue evidence came from two studies and was conflicting: Muraoka et al. reported Fusobacterium positivity in 64.3% of endometrial samples from women with endometriosis versus 7.1% of controls in a 42-versus-42 tissue subset, whereas Graciano-España et al. found no significant case-control difference in F. nucleatum abundance among 55 cases and 37 controls. Indirect microbiome studies reported oral Fusobacterium enrichment in moderate/severe endometriosis and vaginal F. animalis depletion in chronic pelvic pain with endometriosis. All human studies were judged at serious overall risk of bias, and certainty of evidence was very low. Experimental evidence suggesting TGF-β-mediated lesion growth and fibrosis derived principally from one translational study and lacked independent replication.

CONCLUSIONS: Current evidence supports biological plausibility but not a consistent or causal association between F. nucleatum and endometriosis. Direct tissue evidence is limited to two conflicting studies, while non-tissue microbiome findings are indirect. Standardized contamination-controlled sampling, paired anatomical-site sampling, strain-level analyses, and longitudinal studies are required before microbial translocation, temporality, causality, or antimicrobial treatment can be established.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420261337885.},
}

*Endometriosis/microbiology
Humans
Female
*Fusobacterium nucleatum/pathogenicity/physiology
Animals
*Fusobacterium Infections/microbiology/complications
*Mouth/microbiology
Microbiota
*Host Microbial Interactions

@article {pmid42964215,
year = {2026},
author = {Ali, WH and Omar, A and Ali, AH and Hefny, HM and Nabil, G and Mahmoud, Y and Nasr, AEA and Abdelhamid, SM and Amin, HM and Omar, MM and El-Attar, LM and Mohamed, FS and Elgamal, R and Ibrahem, M and Abdelmotogaly, HSM},
title = {Targeted Quantitative Polymerase Chain Reaction Analysis of Gut Microbiota and Its Association With Feeding and Mealtime Behavior and Intestinal Permeability in Children With Autism Spectrum Disorder.},
journal = {Journal of clinical medicine research},
volume = {18},
number = {10},
pages = {759-769},
pmid = {42964215},
issn = {1918-3003},
abstract = {BACKGROUND: Gastrointestinal (GI) symptoms and feeding and mealtime problems are common in children with autism spectrum disorder (ASD). It is important to note that the gut microbiome is a hypothesized mechanism of action, but it is not yet known if specific bacterial profiles and markers of intestinal barrier function predict feeding problems in the target group of ASD.

METHODS: This is a cross-sectional case-control study that examined 70 children with ASD (aged 3-12 years) and 70 matched neurotypical children. Autism was evaluated using the Childhood Autism Rating Scale (CARS), and mealtime behaviors were evaluated using the Brief Autism Mealtime Behavior Inventory (BAMBI). Six important bacterial taxa were quantified using real-time polymerase chain reaction (PCR), and fecal zonulin and calprotectin were quantified by enzyme-linked immunosorbent assay (ELISA).

RESULTS: Children with ASD had significantly higher levels of fecal zonulin and calprotectin than controls (both at P < 0.001) and lower abundances of beneficial taxa (Prevotella, Bifidobacterium, Lactobacillus) and higher abundances of Clostridium difficile and Bacteroidetes (all P < 0.01). The overall BAMBI scores did not differ among the groups, but within the ASD group, feeding problem severity was highly correlated with lower Bifidobacterium (r = -0.68) and higher Clostridium difficile (r = 0.74) and was not significantly correlated with autism severity, zonulin, or calprotectin.

CONCLUSION: Children with ASD have increased levels of gut dysbiosis and barrier dysfunction compared to their non-autistic peers, but the severity of their feeding and mealtime problems tracked the degree of gut microbial imbalance rather than the severity of their ASD symptoms in general. This suggests that feeding behavior is a characteristic that has been under-recognized as a component of the ASD phenotype and is related to the microbiome; if confirmed in longitudinal studies, these microbial associations could represent a candidate target for future gut-directed intervention research.},
}

@article {pmid42964395,
year = {2026},
author = {Xue, L and Chen, Y and Zhong, Y and Wan, C},
title = {Microclimate characteristics, temporal dynamics of soil bacterial communities, and potential co-occurrence network differences between greenhouse and open-field cultivation environments.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1988234},
doi = {10.3389/fmicb.2026.1988234},
pmid = {42964395},
issn = {1664-302X},
abstract = {INTRODUCTION: Greenhouse cultivation modifies agricultural microclimates and may be associated with temporal changes in soil microbial communities. We investigated a representative vegetable greenhouse and an adjacent open-field site in the subtropical red-soil region of Jiangxi Province, China.

METHODS: Air temperature and relative humidity were monitored continuously for one year in both environments, while soil temperature and volumetric water content were monitored within the greenhouse. Monthly soil samples were analyzed using 16S rRNA gene amplicon sequencing.

RESULTS: The greenhouse exhibited pronounced daytime warming, nighttime heat retention, and generally higher relative humidity. Soil bacterial community composition differed significantly between greenhouse and open-field soils, while alpha-diversity differences varied among seasons. Month-resolved analyses revealed significant temporal dynamics. Air temperature and relative humidity jointly explained 15.59% of the variation in bacterial community structure. Potential co-occurrence networks also differed between the two environments in topology and in the proportions of positive and negative correlations.

DISCUSSION: The results document year-round differences in microclimate and soil bacterial community dynamics between greenhouse and open-field cultivation environments. The measured atmospheric microclimate variables showed statistically detectable but limited associations with bacterial community composition, providing a basis for soil microbiome monitoring and environmental management in subtropical protected agriculture.},
}

@article {pmid42964681,
year = {2026},
author = {Al-Beltagi, M},
title = {Clinical guidelines for the diagnosis and management of pediatric fecal incontinence: A comprehensive review and treatment algorithm.},
journal = {World journal of clinical pediatrics},
volume = {15},
number = {4},
pages = {120203},
doi = {10.5409/wjcp.120203},
pmid = {42964681},
issn = {2219-2808},
abstract = {Pediatric fecal incontinence (FI) is a multifactorial condition with functional, neurodevelopmental, and organic etiologies. Despite its prevalence, FI remains underdiagnosed, stigmatized, and associated with significant psychosocial and family burden. This review synthesizes current evidence on the diagnosis, pathophysiology, and management of pediatric FI and proposes practical, algorithm-based guidance for frontline clinicians and subspecialists. A structured literature search of PubMed, Scopus, and Cochrane databases was conducted, focusing on pediatric FI, functional and organic subtypes, neurodevelopmental comorbidities, and multidisciplinary interventions. Emphasis was placed on evidence-based management strategies, emerging therapeutic innovations, and psychosocial considerations. Functional retentive FI often responds to structured disimpaction, maintenance laxatives, and behavioral interventions, whereas non-retentive forms require tailored psychological and behavioral therapies. Organic etiologies often require long-term, multidisciplinary care, surgical intervention, or neuromodulation. Special populations-including children with autism spectrum disorder, attention-deficit/hyperactivity disorder, developmental delay, and postoperative anorectal conditions-require individualized, developmentally adapted programs. Psychosocial impacts on children and families are significant and require coordinated counseling. Emerging research highlights the gut-brain axis, microbiome modulation, digital behavioral applications, and precision bowel management as future directions. Limitations include heterogeneous study designs, lack of long-term pediatric randomized controlled trials, and variable outcome measures. Pediatric FI is a complex condition requiring early recognition, subtype-specific management, and multidisciplinary care. Algorithm-based, individualized strategies that integrate physiological, behavioral, and psychosocial components optimize long-term continence, psychosocial well-being, and quality of life. Future research should focus on standardized outcomes, neuromodulatory interventions, and precision, technology-enhanced therapies.},
}

@article {pmid42804785,
year = {2026},
author = {Kailasam, S and Panigrahi, R},
title = {Phylogeny and ecosystem jointly shape metabolite sensing by structured noncoding RNAs.},
journal = {Genome},
volume = {69},
number = {},
pages = {1-17},
doi = {10.1139/gen-2026-0048},
pmid = {42804785},
issn = {1480-3321},
mesh = {*Riboswitch ; Animals ; *Ecosystem ; *Phylogeny ; *RNA, Untranslated/genetics/metabolism ; *Microbiota/genetics ; Humans ; Bacteria/genetics/classification/metabolism ; },
abstract = {Noncoding RNAs (ncRNAs) regulate gene expression through diverse structural and sequence-based mechanisms, often acting without protein intermediates. Riboswitches are cis-regulatory ncRNAs that directly sense small molecule metabolites to control gene expression. Many riboswitches operate through kinetic control, meaning the rate at which a ligand binds to the aptamer domain determines whether gene expression is turned ON or OFF. Here, we present a comparative survey of riboswitch repertoires across eight microbiomes: human gut, oral, skin, vaginal, mouse gut, pig gut, sheep rumen, and marine environment, spanning 13 946 prokaryotic genomes. Using covariance models, we identified 86 485 riboswitches across 12 916 genomes (92.6%), representing 23 metabolite-sensing classes, with six dominant classes accounting for ~70% of all riboswitch hits. Riboswitch composition varied significantly across ecosystems, but variance partitioning showed this structure is driven primarily by phylogeny: phylum explained 25.5% of compositional variance, whereas the fraction uniquely attributable to ecosystem after conditioning on taxonomy was only 2.2%. Overall riboswitch distributions reflect both phylogenetic and ecological influences, highlighting their role in shaping metabolite-responsive regulatory strategies across microbial life.},
}

*Riboswitch
Animals
*Ecosystem
*Phylogeny
*RNA, Untranslated/genetics/metabolism
*Microbiota/genetics
Humans
Bacteria/genetics/classification/metabolism

@article {pmid42954653,
year = {2026},
author = {Busturia, I and Martín-Cardoso, H and Domingo, C and Garcia-Molina, A and San Segundo, B},
title = {Decoding microbial diversity in roots of rice plants under flooded conditions: influence of the host genotype, root compartment, and mycorrhizal association.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0167126},
doi = {10.1128/aem.01671-26},
pmid = {42954653},
issn = {1098-5336},
abstract = {UNLABELLED: Rice is a vital staple for more than half of the world's population, uniquely adapted to grow under flooded conditions. Our current understanding of root-associated microbiomes in rice plants under flooded conditions (anaerobic rice) is, however, limited. While rice plants are capable of establishing symbiotic associations with arbuscular mycorrhizal (AM) fungi, also under flooded conditions, little is known about the impact that mycorrhizal associations might have on the root microbiome. Here, we used metagenomic sequencing to characterize the root-associated microbiomes of cultivated rice grown under flooded conditions. The root endosphere and rhizosphere compartments were found to harbor distinct microbial communities, with bacterial taxa comprising approximately 95% of the total microbial community. At the phylum level, the root bacteriome was primarily composed of Pseudomonadota (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria), followed by Actinomycetota. The fungal microbiome was dominated by Ascomycota (Sordariomycetes, Eurotiomycetes, and Dothideomycetes) and Basidiomycota. Both root compartment and host genotype significantly influenced microbiome composition, with most genotype-specific recruitment occurring at the species level. These associations were further reshaped in plants pre-inoculated with the AM fungus Rhizophagus irregularis. Co-occurrence networks revealed a genotype-dependent effect in the complexity of microbial taxa in mycorrhizal rice plants. Key microbial species primarily involved in methane production and nutrient cycling (e.g., phosphate-solubilizing bacteria and nitrogen-cycling bacteria) residing in roots of flooded rice were identified. Functional analysis of gene abundance related to those microbial communities revealed compartmentalization, with nutrient-cycling bacteria being more prevalent at the endosphere. Overall, this study demonstrated that the rice genotype, root compartment, and mycorrhizal condition shape the root microbiome in rice plants, ultimately influencing holobiont dynamics in flooded rice fields.

IMPORTANCE: Plant roots harbor a large diversity of microorganisms that strongly influence plant health and improve stress tolerance. Among them, root colonization by arbuscular mycorrhizal (AM) fungi enhances mineral nutrition and mitigates environmental stress. Although most rice cultivated worldwide is grown under anaerobic conditions (flooded fields), investigation of microbial communities inhabiting root-associated compartments of flooded rice, including AM fungi, has received only little attention. Here, we demonstrated that the rice genotype, root compartment, and mycorrhizal condition markedly influence the microbiome in roots of rice plants in flooded conditions, thus illustrating the potential of the rice plant to shape its root-associated microbiome. Differential root-associated microbiomes of commercial rice varieties include microbes primarily associated with methane production and nutrient cycling. Elucidation of factors influencing root-associated microbiomes in flooded rice systems, including their association with AM fungi, offers practical guidance for exploiting root-associated microbial communities for sustainable rice cultivation while reducing reliance on agrochemicals.},
}

@article {pmid42954768,
year = {2026},
author = {Debnath, D},
title = {The gut-ovary axis in polyendocrine metabolic ovarian syndrome: Mechanisms, microbiome dysbiosis, and emerging therapeutic strategies.},
journal = {International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijgo.71478},
pmid = {42954768},
issn = {1879-3479},
abstract = {Polycystic ovary syndrome (PCOS), recently termed polyendocrine metabolic ovarian syndrome (PMOS), is a heterogeneous endocrine-metabolic disorder characterized by reproductive, metabolic, and hormonal disturbances. Increasing evidence suggests that interactions between the gut microbiota and host physiology may be relevant to PMOS through pathways involving intestinal barrier function, inflammation, insulin sensitivity, steroid hormone metabolism, bile acid signaling, and gut-brain-ovary communication. This narrative review synthesizes current human and preclinical evidence on the gut-ovary axis in PMOS, with particular emphasis on microbial dysbiosis, proposed mechanistic pathways, microbiome-related metabolic and endocrine interactions, and emerging therapeutic approaches. Human studies generally report associations between altered microbial composition and metabolic or reproductive features of PMOS, although findings vary considerably according to population characteristics, bodyweight, diagnostic criteria, sequencing methods, and analytical approaches. Experimental studies provide additional support for potential roles of microbial metabolites, intestinal permeability, immune signaling, and metabolic pathways, but these mechanisms have not been established as causal in humans. Microbiome-targeted interventions, including probiotics, prebiotics, synbiotics, and dietary approaches, show potential, whereas fecal microbiota transplantation remains largely experimental. Conventional metabolic therapies, including glucagon-like peptide-1 receptor agonists, should be considered separately from microbiome-targeted approaches. Overall, the gut-ovary axis represents a promising framework for understanding the systemic features of PMOS, but substantial heterogeneity, limited longitudinal human evidence, and underrepresentation of diverse populations currently limit translation into clinical practice.},
}

@article {pmid42954932,
year = {2026},
author = {Plisko, OL and Chapel, VS and Sekela, JJ and Talbert, JA and Townsend, SD and Zemel, BS and Wu, GD and R Redinbo, M},
title = {Human milk oligosaccharides are distinctly processed by early life gut microbial sialidases.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748788},
doi = {10.1080/19490976.2026.2748788},
pmid = {42954932},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry/metabolism ; *Oligosaccharides/metabolism/chemistry ; *Neuraminidase/metabolism/genetics/chemistry ; Infant ; Adult ; Lactose/analogs & derivatives/metabolism ; *Bacteria/enzymology/genetics/classification ; Metagenome ; },
abstract = {The infant gut microbiome in early life is shaped by numerous factors, including feeding method. Exclusively breastfed and formula-fed infants exhibit distinct microbiome compositions. While these effects are well-established, the underlying mechanisms that drive these differences are not fully understood. Here, we examine the removal of sialic acid from human milk oligosaccharides (HMOs) influenced by human microbial sialidases in early life. We identify 351 and 214 unique sialidase sequences from adult and infant microbiome metagenomes, respectively, and characterize a diverse, representative set in vitro using sialylated HMOs normally present in human breastmilk. We find these proteins exhibit distinct abilities to metabolize 3'- and 6'-sialyllactose, which are the most abundant sialylated HMOs in breastmilk, and distinctly process other more complex substrates, as well. We provide structural insights into these functional differences by pinpointing active site features uniquely present in efficient enzymes and show that these results extend to activities on complex mixtures of sialylated HMOs purified from human breastmilk. Finally, we demonstrate in human clinical data that distinct profiles of sialidase-encoding bacterial taxa are observed in breastfed and formula-fed infants at 1 and 4 months of age, prior to the introduction of solid foods. Together, these findings show that specific bacterial sialidases are influential in shaping the early gut microbiome, data that may improve the supplementation of infant formulas for enhanced developmental outcomes.},
}

Humans
*Milk, Human/chemistry/metabolism
*Oligosaccharides/metabolism/chemistry
*Neuraminidase/metabolism/genetics/chemistry
Infant
Adult
Lactose/analogs & derivatives/metabolism
*Bacteria/enzymology/genetics/classification
Metagenome

@article {pmid42955029,
year = {2026},
author = {Stevens, T and Salani, M},
title = {The Crossroads Between the Kidney and Gastrointestinal Disorders: Core Curriculum 2026.},
journal = {American journal of kidney diseases : the official journal of the National Kidney Foundation},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.ajkd.2026.08.005},
pmid = {42955029},
issn = {1523-6838},
abstract = {The kidney and gastrointestinal (GI) tract are closely linked through a bidirectional system involving complex interactions called the gut-kidney axis. Within this system, alterations in the gut microbiome can promote progression of chronic kidney disease (CKD) while uremic toxins from advanced kidney dysfunction can adversely affect intestinal health. Incretin hormones, particularly glucagon-like peptide 1 (GLP-1), play an important role in this gut-kidney signaling and will be explored here. We also examine how this physiology helps explain the connection between GI illness and IgA nephropathy, along with the kidney manifestations seen in inflammatory bowel disease. Furthermore, we will review how CKD and end-stage kidney disease increase the risk of GI disease and complicate its management, and how CKD therapies affect GI symptoms. In this AJKD Core Curriculum, we use a case-based format to illustrate the intricate interplay between the kidneys and the GI tract.},
}

@article {pmid42955175,
year = {2026},
author = {de Lima Núñez, TA and de Moraes, RS and de Cerqueira Júnior, JCN and Ribeiro, D and Reyes, RPR and Andreatti Filho, RL and Melchert, A and Guimarães-Okamoto, PTC and Okamoto, AS},
title = {Constructing a Perspective of Probiotic Bacteria in the Management of Urinary Tract Infection in Cats: A Scoping Review.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42955175},
issn = {1867-1314},
abstract = {Feline lower urinary tract disease (FLUTD) and urinary tract infections (UTIs) pose a significant clinical challenge in companion animal medicine. Increasing antimicrobial resistance and emerging insights into the feline urinary microbiome highlight the potential of probiotic-based therapeutic strategies. However, the scope and quality of existing evidence in feline medicine remain unclear. This study aimed to systematically map and characterize the literature on probiotic microorganisms (particularly Lactobacillus spp. and Bifidobacterium spp.) in feline urinary health, identifying research domains, evidence gaps, and future priorities. A scoping review identified peer-reviewed studies addressing FLUTD, urinary microbiota, antimicrobial resistance, and probiotic interventions. Studies were categorized into four domains: clinical burden, microbiome evidence, clinical probiotic evidence, and mechanistic probiotic evidence. Fifty-three studies met inclusion criteria. The main finding of this review is that there is limited to no direct evidence on the use of probiotics for the management of FLUTD or UTIs in cats: only nine studies addressed probiotics (clinical probiotic evidence: n = 5; mechanistic probiotic evidence: n = 4), and no randomized controlled trials specifically assessing probiotic efficacy in cats were identify. Most literature focused on clinical burden (n = 37), comprising epidemiological surveys and antimicrobial resistance reports, whereas microbiome investigations were limited (n = 7). The high prevalence of Escherichia coli and increasing antimicrobial resistance underscore the need for alternative strategies. Addressing this gap through well-designed clinical trials in cats is essential before probiotic-based strategies can be recommended to improve both clinical outcomes and animal welfare in feline patients.},
}

@article {pmid42955188,
year = {2026},
author = {Saqr, A and Mohamed, ME and Staley, C and Onyeaghala, G and Vo, D and Remmel, RP and Teigen, L and Guan, W and Oetting, WS and El-Rifai, R and Dorr, CR and Gupta, K and Matas, AJ and Israni, AK and Jacobson, PA},
title = {Microbiome-Mediated Pharmacokinetics and Informed Dosing of Mycophenolate in Kidney Transplantation.},
journal = {Clinical pharmacokinetics},
volume = {},
number = {},
pages = {},
pmid = {42955188},
issn = {1179-1926},
support = {5R01AI140303//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND AND OBJECTIVES: The gut microbiome contributes to interindividual variability in drug pharmacokinetics; however, its role in guiding dose adjustments remains unclear. Mycophenolic acid (MPA), the active metabolite of the immunosuppressant mycophenolate mofetil (MMF), exhibits high pharmacokinetic variability, potentially linked to microbial activity. This study aimed to characterize the gut microbiome effect on MPA pharmacokinetics and determine if these effects necessitate dose modifications.

METHODS: In 84 kidney transplant recipients, plasma and urine concentration-time profiles for MPA and its glucuronide metabolites were characterized using population pharmacokinetic modeling in NONMEM[®]. Stool samples were collected within 2 days of pharmacokinetic sampling for microbiome shotgun metagenomic sequencing. Machine learning was used to identify microbial species associated with pharmacokinetic variability. The impact of these species and clinical covariates was evaluated using full fixed-effect modeling. Simulations were conducted to assess the effect of microbial relative abundance on MPA therapeutic target attainment across various MMF doses.

RESULTS: Five bacteria were associated with the magnitude or duration of enterohepatic circulation (EHC). High relative abundance of Eubacterium callanderi increased EHC and MPA exposure by 29-63%, requiring a 17% lower MMF dose. Conversely, high Faecalibacterium SGB15315 abundance reduced EHC and MPA exposure by 13-26%, requiring a 50-75% higher dose. While Gemmiger formicilis and Eisenbergiella tayi prolonged EHC by >100% and Anaerostipes caccae decreased it by 30%, these taxa did not clinically impact therapeutic target attainment.

CONCLUSION: We identified several stool microbial species affecting MPA pharmacokinetics. Specifically, Eubacterium callanderi and Faecalibacterium SGB15315 may identify patients who require additional therapeutic drug monitoring or possible dose modifications to reach target concentrations.

CLINICAL TRIAL REGISTRATION: Clinicaltrials.gov, NCT04953715.},
}

@article {pmid42955203,
year = {2026},
author = {Sagawa, T and Hirakawa, M and Nagashima, H and Fujikawa, K},
title = {Gut Microbiome Signatures and Immune Checkpoint Inhibitor Response in Gastrointestinal Cancers: Reproducibility and Translational Readiness.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42955203},
issn = {1534-6269},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Neoplasms/drug therapy/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects/immunology ; Reproducibility of Results ; Translational Research, Biomedical ; },
abstract = {PURPOSE OF REVIEW: Gut microbial features have been associated with immune checkpoint inhibitor (ICI) outcomes, but whether these signatures are robust across gastrointestinal (GI) tumor types, treatment regimens, and populations remains uncertain. This critical narrative review assesses human evidence, experimental mechanisms, longitudinal sampling, and the criteria needed for clinical implementation.

RECENT FINDINGS: A gastric cancer cohort showed different response-associated microbial features for immunotherapy alone, chemotherapy alone, and combined treatment. Cross-cancer strain-resolved analyses found that signature transportability was strongly conditional on matching ICI regimens. A large primary liver cancer cohort analyzed 315 patients and 777 serial samples and explored a baseline score derived from on-treatment species selection; later samples were available only in a selected subgroup, complicating interpretation. Experimental studies link selected microbes and metabolites with antitumor immunity, but these mechanistic findings do not establish therapeutic efficacy in humans. Fecal microbiota transplantation (FMT) studies in melanoma demonstrate feasibility yet do not establish benefit in GI malignancies. Stool profiles may not represent mucosal or tumor-adjacent communities in upper GI cancer. No stool microbiome signature is currently validated to select ICI therapy in GI oncology. Meaningful translation requires standardized assays, non-ICI comparators to establish treatment-effect prediction, strict separation of discovery and external validation, prospectively handled missingness, and randomized clinical-utility studies.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Neoplasms/drug therapy/microbiology/immunology
*Gastrointestinal Microbiome/drug effects/immunology
Reproducibility of Results
Translational Research, Biomedical

@article {pmid42955208,
year = {2026},
author = {Shen, WH and Zheng, LP and Zhou, JQ and Wang, JW},
title = {Exploring endophytic actinomycetes from Shiraia fruiting bodies to enhance fungal hypocrellin A biosynthesis.},
journal = {Bioresources and bioprocessing},
volume = {13},
number = {1},
pages = {},
pmid = {42955208},
issn = {2197-4365},
support = {82073955//National Natural Science Foundation of China/ ; 81773696//National Natural Science Foundation of China/ ; 900520246116//Start-up Funding for Research of Jiangsu Medical College/ ; },
abstract = {The medicinal fruiting bodies of Shiraia harbor diverse microbial communities that are increasingly recognized as important regulators of fungal secondary metabolism. While endophytic bacteria and fungi associated with Shiraia have recently attracted considerable attention, the diversity and functional roles of endophytic actinomycetes remain largely unexplored. Here, we combined culture-dependent isolation with high-throughput 16 S rRNA amplicon sequencing to investigate the endophytic actinomycete community associated with Shiraia fruiting bodies. A total of 28 actinomycete isolates representing four genera were recovered, with Streptomyces being the predominant culturable genus. Functional screening identified the native endophyte S. pseudogriseolus A6 as the most effective elicitor of fungal hypocrellin A (HA) biosynthesis. Genome analysis revealed abundant carbohydrate-active enzymes and 27 secondary metabolite biosynthetic gene clusters, indicating a strong genetic potential for fungal colonization and metabolite-mediated communication. Co-cultivation with live strain A6 markedly enhanced both intracellular and extracellular HA accumulation without significantly affecting fungal biomass. Under the optimized co-cultivation conditions, total HA production reached 296.0 mg/L, representing a threefold increase over the monoculture control. Furthermore, A6 coordinately upregulated the expression of HA biosynthetic genes and metabolite transport genes. This study provides the first characterization of endophytic actinomycetes associated with Shiraia fruiting bodies and identifies actinomycete elicitors capable of stimulating fungal HA biosynthesis. These findings expand current knowledge of the Shiraia microbiome and highlight endophytic actinomycetes as promising microbial resources for enhancing fungal perylenequinone production.},
}

@article {pmid42955256,
year = {2026},
author = {Bastaminejad, S and Bakhtiyari, S and Heidari, A and Ebrahimi, E},
title = {Gut microbiota as a key player in diabetes mellitus: mechanisms, dysbiosis, and emerging interventions.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42955256},
issn = {1874-9356},
abstract = {The gut microbiome has emerged as a critical regulator of metabolic and immune homeostasis, with significant implications for diabetes mellitus. This narrative review synthesizes findings from selected landmark original investigations published from 2000 to 2026, examining the role of the gut microbiome in both type 1 diabetes (T1D) and type 2 diabetes (T2D). As a narrative rather than a systematic review, this synthesis does not follow a registered protocol or an exhaustive, reproducible search strategy. Observational studies frequently report dysbiosis, characterized by reduced microbial diversity and altered taxa, as a feature of both prediabetes and diabetes, correlating with poor glycemic control and complications, although the specific taxa and dysbiotic signatures implicated vary across geographically and ethnically distinct populations, indicating that dysbiosis is not a uniform, population-invariant hallmark of disease. Mechanistic studies highlight pathways such as short-chain fatty acid production, immune modulation, and gut barrier integrity, which mediate microbial effects on insulin sensitivity and glucose metabolism, with short-chain fatty acid (SCFA) signaling and gut barrier integrity identified as the most significant pathways driving these effects. Interventional approaches, including probiotics, prebiotics, dietary modifications, fasting, exercise, and bariatric surgery, show preliminary, proof-of-concept potential to reshape the microbiome and improve diabetic outcomes, although none of these interventions has yet been validated in large-scale, adequately powered, multi-center randomized controlled trials with hard clinical endpoints, and none should be regarded as an established treatment. Notably, T1D research emphasizes autoimmune interactions, while T2D focuses on metabolic dysfunction. Despite advances, challenges like establishing causality and addressing inter-individual variability persist. This review underscores the microbiome's therapeutic promise pending confirmation in the larger trials outlined above, and advocates for personalized, multi-omics-driven strategies to enhance diabetes management.},
}

@article {pmid42955320,
year = {2026},
author = {Martin-Loeches, I and Povoa, P and Robba, C and Bandera, A and Guglielmi, A and Citerio, G},
title = {Ventilator-associated pneumonia after traumatic brain injury: a timing-sensitive ecological framework of neuroimmune-pulmonary vulnerability.},
journal = {Intensive care medicine},
volume = {},
number = {},
pages = {},
pmid = {42955320},
issn = {1432-1238},
abstract = {BACKGROUND: Ventilator-associated pneumonia (VAP) is frequent after traumatic brain injury (TBI), but its biological meaning and outcome impact remain incompletely defined. Traditional models emphasise mechanical ventilation, aspiration, colonisation, endotracheal tube biofilm, and hospital pathogens. These mechanisms remain essential, but they do not fully explain the early clustering, heterogeneous susceptibility, changing bacteriology, and variable mortality effect observed after TBI.

MAIN TEXT: Severe brain injury creates an early vulnerable host state through impaired consciousness and airway protection, neuroimmune dysregulation, autonomic and endocrine activation, altered pulmonary immune surveillance, and, in many patients, extracranial trauma, shock, transfusion, or thoracic injury. These processes interact with ventilation, antibiotic pressure, and rapid respiratory microbiome disruption. Early VAP may reflect abrupt loss of control after injury and intubation, whereas late VAP may reflect persistent or secondary failure driven by biofilm maturation, antibiotic selection, multidrug-resistant pathogens, and intensive care unit (ICU)-acquired immune dysfunction. Clinically, VAP consistently prolongs ventilation, ICU stay, antibiotic exposure, and resource use, while its independent effect on mortality is phenotype- and context-dependent.

CONCLUSIONS: This model proposes a timing-sensitive ecological framework in which established mechanisms may converge early and with particular clinical intensity after severe TBI, creating a vulnerable host-microbe state that may lower the threshold for clinically apparent infection. Future studies should distinguish isolated TBI from polytrauma, compare TBI with other acute brain injuries and non-neurological ventilated populations, and incorporate dynamic immune, microbial, and trajectory-based outcomes.

HIGHLIGHTS: VAP after TBI should be viewed as a timing-sensitive interaction between ventilator exposure and early host vulnerability, not as a distinct disease entity or as a pneumonia pathway unique to traumatic brain injury. The TBI-focused contribution lies in the early convergence of otherwise non-unique mechanisms: impaired airway control, aspiration risk, neuroimmune-endocrine activation, treatment exposure, dysbiosis, and extracranial injury burden, rather than in any single TBI-specific mechanism. Isolated TBI and TBI with polytrauma are biologically different phenotypes and should be separated in future studies. Early and late VAP may represent different phases of loss of pulmonary host-microbe containment; this distinction is probabilistic rather than TBI-specific in itself and requires validation in TBI-stratified cohorts. Mortality remains clinically relevant but context-dependent; VAP more consistently modifies recovery trajectory, ventilator dependence, ICU stay, antibiotic exposure, and possibly neurological recovery.},
}

@article {pmid42955366,
year = {2026},
author = {Ketehouli, T and Trub, MR and Goss, EM and Martins, SJ},
title = {Pseudomonas spp.-based synthetic microbial community effects on nutrient dynamics in citrus plants under induced dysbiosis.},
journal = {Planta},
volume = {264},
number = {6},
pages = {},
pmid = {42955366},
issn = {1432-2048},
support = {2022-68015-36721//National Institute of Food and Agriculture/ ; },
mesh = {*Pseudomonas/physiology ; Rhizosphere ; *Citrus/microbiology/metabolism ; *Microbiota ; Soil Microbiology ; *Dysbiosis/chemically induced ; Nutrients/metabolism ; Potassium/metabolism ; Streptomycin/pharmacology ; Anti-Bacterial Agents/adverse effects/pharmacology ; Plant Roots/microbiology ; },
abstract = {A targeted Pseudomonas-based synthetic microbial community reshaped rhizosphere bacterial communities and altered potassium partitioning under stress conditions, suggesting a potential role in mitigating antibiotic-induced dysbiosis. Sustainable agriculture primarily relies on biological practices to improve crop yield and resilience. Synthetic bacterial communities (SynComs) are a promising approach to promote plant growth; however, their effectiveness in situ is influenced by interactions with native microbial ecosystems and by environmental stressors, such as low pH and antibiotic use. In this context, beneficial microorganisms like Pseudomonas may enhance nutrient availability and mitigate antibiotic-induced dysbiosis by supporting microbial community reassembly and functional stability, thereby improving plant health. This study evaluated the effects of a Pseudomonas-based SynCom on nutrient accumulation and rhizosphere microbial dynamics in citrus plants subjected to streptomycin-induced dysbiosis and low-pH conditions. Selected Pseudomonas strains, chosen for their compatibility and adaptability to low-pH conditions, and through whole-genome sequencing, were applied at equal concentrations (OD600 = 0.1). SynCom treatment increased Chloroflexota abundance in the rhizosphere while reducing Actinomycetota and Pseudomonadota after 24 days. By Day 45, the abundance of Actinomycetota decreased, with slight increases in the other two phyla. At the genus level, SynCom application reduced the abundance of Pseudomonas and Agrobacterium, while enriching the Klebsiella community. Plants treated with SynCom under stress exhibited a 25% increase in leaf potassium levels, accompanied by a 29% decrease in root potassium (essential for stomatal regulation, osmotic adjustment, and photosynthetic efficiency, which are fundamental to tree growth and stress resilience) levels. Overall, our findings demonstrate that a targeted Pseudomonas-based SynCom can reshape rhizosphere communities and improve nutrient dynamics under abiotic stress, highlighting its potential as a sustainable strategy to mitigate antibiotic-induced dysbiosis and enhance citrus resilience.},
}

*Pseudomonas/physiology
Rhizosphere
*Citrus/microbiology/metabolism
*Microbiota
Soil Microbiology
*Dysbiosis/chemically induced
Nutrients/metabolism
Potassium/metabolism
Streptomycin/pharmacology
Anti-Bacterial Agents/adverse effects/pharmacology
Plant Roots/microbiology

@article {pmid42955378,
year = {2026},
author = {Gschwendtner, S and Maison, N and Illi, S and von Mutius, E and Rosenboom, I and Tümmler, B and Dittrich, AM and Weckmann, M and Abdo, M and Waschki, B and Kopp, MV and Hansen, G and Brinkmann, F and Rabe, K and Schaub, B and Schloter, M and , },
title = {Exploratory analysis of nasal and gut microbial community structure in preschool children with recurrent wheeze.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42955378},
issn = {1432-184X},
mesh = {Humans ; *Respiratory Sounds/etiology ; *Bacteria/classification/isolation & purification/genetics ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Pilot Projects ; Cross-Sectional Studies ; Female ; Infant ; Male ; *Nose/microbiology ; *Gastrointestinal Microbiome ; Recurrence ; *Microbiota ; DNA, Bacterial/genetics ; },
abstract = {Early-life wheezing has been associated with microbial alterations along the gut-airway axis, yet few studies have examined bacterial communities in both compartments within the same children. This cross-sectional exploratory pilot study (n=25) characterized nasal and stool bacterial communities in children aged 1-4 years with recurrent wheeze and healthy controls using 16S rRNA gene metabarcoding. Across participants, nasal and stool bacteriomes were highly individualized and taxonomically diverse. Overall richness, evenness, and global community composition did not differ significantly between healthy controls and children with recurrent wheeze in either compartment. Nasal communities in the recurrent-wheeze group showed greater within-group dispersion, although the comparison did not reach the conventional significance threshold (p=0.054). Exploratory distance-based stratification identified a subgroup with nasal profiles farther from the healthy-control centroid; these profiles had lower richness and evenness, higher Moraxella abundance, and lower abundances of Prevotella spp., Alloprevotella, and Veillonella. No statistically supported genus-level differences were detected in stool samples. Community-assembly and co-occurrence analyses yielded group-specific descriptive patterns in both compartments. Different sets of cross-compartment correlations passed the multiple-testing threshold in healthy controls and children with recurrent wheeze, including correlations of stool Lactococcus with several nasal taxa in the recurrent-wheeze group. Because these analyses were performed in small groups, they are considered hypothesis-generating. These findings identify nasal microbial heterogeneity and exploratory differences in community organization in preschool children with recurrent wheeze, while providing no evidence for causal or Moraxella-driven effects. Larger longitudinal studies with functional measurements are required for validation.},
}

Humans
*Respiratory Sounds/etiology
*Bacteria/classification/isolation & purification/genetics
Child, Preschool
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Pilot Projects
Cross-Sectional Studies
Female
Infant
Male
*Nose/microbiology
*Gastrointestinal Microbiome
Recurrence
*Microbiota
DNA, Bacterial/genetics

@article {pmid42955504,
year = {2026},
author = {Catalogna, A and Agostoni, C and Barni, S and Canani, RB and Carucci, L and Ciliberti, L and Coppola, S and Corsello, A and Milani, GP and Mori, F and Nocerino, R and Pinto, BS and Spolidoro, GCI and Giovannini, M and Munblit, D},
title = {Breast Milk and Allergic Disease Development: Immunological Factors Associated with Eczema, Food Allergy and Wheezing/Asthma.},
journal = {Current allergy and asthma reports},
volume = {26},
number = {1},
pages = {},
pmid = {42955504},
issn = {1534-6315},
mesh = {Humans ; *Milk, Human/immunology ; *Food Hypersensitivity/immunology ; Female ; *Eczema/immunology ; *Respiratory Sounds/immunology ; *Asthma/immunology ; Infant ; Cytokines/metabolism ; *Hypersensitivity/immunology ; },
abstract = {PURPOSE OF REVIEW: Human milk (HM) contains a diverse array of immunological, microbial, and metabolic bioactive factors that may influence early immune maturation and allergic disease susceptibility. This narrative review examines current evidence linking major HM bioactives with eczema, food allergy, and wheezing/asthma, integrating mechanistic findings with human observational and clinical data.

RECENT FINDINGS: Transforming growth factor-β (TGF-β), secretory IgA (sIgA), human milk oligosaccharides (HMOs), cytokines, fatty acids, short-chain fatty acids, the HM microbiome, and extracellular vesicles have all been implicated in pathways relevant to epithelial integrity, microbial colonization, and immune tolerance. However, associations with allergic outcomes are heterogeneous and frequently context dependent. Findings vary according to lactation stage, maternal characteristics, infant susceptibility, microbial exposures, and outcome definition. Mechanistic evidence is often stronger than prospective clinical evidence, and no individual HM component or bioactive profile has yet emerged as a reproducible predictor of allergy protection. Current evidence supports viewing HM as a dynamic maternal-milk-infant biological network rather than as a source of isolated protective factors. Future studies should integrate repeated HM sampling, rigorous allergic phenotyping, and multi-omic approaches to distinguish causal mediators from biomarkers of maternal or infant biology.},
}

Humans
*Milk, Human/immunology
*Food Hypersensitivity/immunology
Female
*Eczema/immunology
*Respiratory Sounds/immunology
*Asthma/immunology
Infant
Cytokines/metabolism
*Hypersensitivity/immunology