@article {pmid42239166,
year = {2026},
author = {Ghadermazi, P and Emerson, JB and Olm, MR},
title = {ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42239166},
issn = {2692-8205},
abstract = {Strain-resolved metagenomics characterizes microbial communities at nucleotide-level resolution, enabling researchers to differentiate identical from closely related organisms and characterize population structure and gene content variation. Here we introduce ZipStrain, a program that performs highly accurate strain-resolved metagenomics over 500× faster than available methods while offering superior RAM management. Applied to a dataset of 2,754 samples spanning human populations, we identify a strain-sharing gradient across social relationships, reveal striking variation in clonal structure across bacteria and bacteriophage, and pinpoint genes whose nucleotide identity deviates from genome-wide expectations. ZipStrain is distributed as an open-source Python package and accompanying Nextflow pipeline at https://github.com/OlmLab/ZipStrain.},
}

@article {pmid42316154,
year = {2026},
author = {Seo, E and Kim, SH and Kwak, MJ and Hwang, JK and Mustafa, G and Chang, YS and Hoh, JK and Jeon, BH and Park, HK and Kim, Y},
title = {Gut dysbiosis associated with neonatal respiratory distress syndrome and biological plausibility of disease-specific probiotic intervention: a translational study.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08462-x},
pmid = {42316154},
issn = {1479-5876},
support = {202400000002957//College of Medicine, Hanyang University/ ; RS-2023-00255939//Korea Institute of Energy Technology Evaluation and Planning/ ; NSIT; RS-2025-16068814//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Neonatal respiratory distress syndrome (RDS) is among the most prevalent morbidities in late preterm and term infants. Although the gut-lung axis has been implicated in neonatal respiratory disease, the relationship between RDS and early gut microbiome composition remains poorly characterized. This study aimed to characterize gut microbiome alterations associated with RDS and surfactant replacement therapy (SRT), and to evaluate the biological plausibility of a disease-specific probiotic intervention.

METHODS: Two complementary cohorts were prospectively enrolled. In the clinical observational cohort (n = 45), fecal samples collected within 48 h of birth were analyzed by Nanopore 16S rRNA sequencing across three groups: infants without RDS (control group, n = 25), infants with RDS who did not receive SRT (RDS(S-) group, n = 7), and infants with RDS who received SRT (RDS(S+) group, n = 13). In the probiotic discovery cohort (n = 40), gut microbiota of infants without RDS (CON group, n = 17) and infants with RDS (RDS group, n = 23) were characterized by metagenomic sequencing and culturomics. Candidate probiotic strains were evaluated in a fermenter for intestinal microbiota model (FIMM) and a fecal microbiota transplantation (FMT) mouse model.

RESULTS: The RDS(S-) group exhibited depletion of beneficial taxa including Bifidobacterium and Lacticaseibacillus and enrichment of opportunistic pathogens including Enterococcus and Staphylococcus. Following SRT, gut microbial profiles partially shifted toward those of the control group. Limosilactobacillus fermentum SLAM_LAF05 and Bifidobacterium longum SLAM_BIL02 were identified as CON-enriched candidate probiotic strains through direct microbiome comparison and selected based on superior acid and bile tolerance and adhesion capacity. In the FIMM model, probiotic supplementation increased microbial diversity and suppressed opportunistic pathogens. In the FMT mouse model, probiotic supplementation was associated with upregulation of ZO-1, MUC2, and Reg3g, reduction of fecal calprotectin, and restoration of serum IgG levels.

CONCLUSIONS: This study provides an early translational characterization of RDS-associated gut dysbiosis and its partial resolution following SRT, and establishes proof-of-concept for a disease-specific probiotic approach. These findings offer a new perspective on the interplay between gut microbial dynamics and the early postnatal respiratory course, and provide a basis for future investigations into microbiota-targeted strategies in neonates with RDS.},
}

@article {pmid42316315,
year = {2026},
author = {Zebardast, A and Javadi, K},
title = {Human microbiome alterations in Epstein-Barr Virus infection: a systematic review.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00854-0},
pmid = {42316315},
issn = {1757-4749},
support = {724137379//Babol University of Medical Sciences/ ; },
abstract = {Epstein-Barr virus (EBV) is associated with several malignancies and immune-mediated conditions, but its relationship with human microbial communities remains incompletely understood. We systematically searched PubMed, Embase, and Scopus for human studies evaluating EBV-associated alterations in the microbiome. Because of substantial clinical and methodological heterogeneity, findings were synthesized narratively, and study quality was assessed using the ROBINS-I tool. Nine observational studies published between 2017 and 2025 were included, covering the oral cavity, nasopharynx, gut, gastric tissue, and subgingival plaque. EBV positivity or EBV-related clinical status was associated with niche-specific microbial shifts, including altered gut bacterial profiles, distinct microbial patterns in EBV-associated gastric cancer tissue, and enrichment of oral-associated pathobionts in nasopharyngeal carcinoma compartments. Alpha- and beta-diversity findings were inconsistent across studies. Overall, the evidence suggests context-dependent alterations in the microbiome in EBV-positive or EBV-related disease settings. However, these findings should be interpreted as EBV-associated rather than EBV-specific, particularly when EBV status overlaps with malignancy. The small observational evidence base, heterogeneous EBV-status definitions, methodological variability, and residual confounding limit causal inference. Larger longitudinal and standardized multi-omic studies are needed to clarify directionality, mechanisms, and clinical relevance.},
}

@article {pmid42316350,
year = {2026},
author = {Zhao, J and Su, Q and Wang, S and Li, Q and Chen, L and Kang, X and Xu, Q and Liu, C and Zhao, H},
title = {Differentiating hemorrhagic shock and organophosphate poisoning through integrated skin microbiome-metabolome signatures.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05276-1},
pmid = {42316350},
issn = {1471-2180},
support = {2024B04J0022//Guangzhou Science and technology planning project/ ; 82371901//National Natural Science Foundation of China/ ; 2023JC36//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; },
abstract = {Accurate determination of cause of death and estimation of postmortem interval (PMI) are critical yet challenging tasks in forensic science, particularly in cases with rapid demise and absence of obvious morphological abnormalities. We employed an integrative multi-omics approach to characterize postmortem microbial succession and metabolic alterations on facial skin in mouse models of hemorrhagic shock (HS) and organophosphorus poisoning (OP) across three decomposition stages: bloating (2 days), active decay (8 days), and advanced decay (16 days). Metagenomic profiling revealed significantly reduced α-diversity in HS compared with OP throughout all stages (p < 0.001), accompanied by stage-dependent compositional shifts, including early enrichment of Firmicutes in HS and Proteobacteria in OP. A total of 237 differential taxa were identified, with Providencia and Morganella predominating in OP, whereas Staphylococcus and Corynebacterium dominated bloating stage of HS. Untargeted metabolomics uncovered distinct cause-of-death-linked metabolites, notably elevated 2'-deoxycytidine-5'-diphosphate in early OP and persistent cholic acid/cholate accumulation in HS at later PMI. Functional analysis highlighted histidine and phosphate/phosphonate metabolism as key discriminatory pathways, exhibiting stage-specific oscillations and strong correlations with characteristic taxa. These findings demonstrate that skin-based metagenomic-metabolomic integration provides robust, mechanistically informed biomarkers for both PMI estimation and cause-of-death differentiation, offering a minimally invasive and temporally dynamic tool for forensic investigations.},
}

@article {pmid42316485,
year = {2026},
author = {Juma, NS and Shuaibu, A},
title = {Bioactive carbohydrates: a mini-review.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70835},
pmid = {42316485},
issn = {1097-0010},
abstract = {Bioactive carbohydrates, including dietary fibers, prebiotics and resistant starches, play emerging roles in gut health, metabolic regulation, as well as chronic disease prevention. This mini review systematically classifies these compounds, summarizes their mechanisms of action, and evaluates their current and potential applications in functional food development. It also identifies several critical gaps, for example: how structural properties (type, source, molecular characteristics) and non-short-chain fatty acid fermentation metabolites influence physiological outcomes, the challenge of maintaining stability and functionality during processing (heat and pH optimization), the need to investigate nano-carbohydrate systems and prebiotic delivery matrices for microbiota modulation, metabolite release, and bioavailability, and the optimization of resistant starch extraction and application to balance functional benefits with sensory quality and in vivo validation. Translational evidence gaps, regulatory frameworks, personalized nutrition, and microbiome-based therapeutics are also discussed as future priorities. Generally, this mini-review provides a brief overview of the role of bioactive carbohydrates in food and nutrition. © 2026 Society of Chemical Industry.},
}

@article {pmid42316492,
year = {2026},
author = {Epelde, F},
title = {The Microbiota-Gut-Brain Axis: A New Frontier in Precision Neuropsychopharmacology.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X438648260611062058},
pmid = {42316492},
issn = {1875-6190},
abstract = {INTRODUCTION: The gut microbiota has emerged as a relevant modulator of brain function, behavior, and treatment response through the microbiota-gut-brain axis. This bidirectional system may influence the pharmacokinetics and pharmacodynamics of psychotropic drugs, offering new perspectives for neuropsychopharmacology and precision psychiatry. The aim of this review was to synthesize current evidence on the mechanisms by which gut microbiota affects the absorption, metabolism, efficacy, and safety of neuroactive drugs, and to explore its clinical implications in psychiatric practice.

METHODS: A narrative review was conducted using preclinical and clinical studies published in recent years. Evidence was gathered from peer-reviewed articles indexed in PubMed, Scopus, and Web of Science, integrating findings from microbiology, neuroscience, pharmacology, and psychiatry. Particular attention was given to microbiota-drug interactions involving antidepressants, antipsychotics, mood stabilizers, and anxiolytics.

RESULTS: Gut microorganisms may modulate psychotropic drug effects through enzymatic biotrans-formation, alterations in host metabolic pathways, regulation of neurotransmitter systems, and modulation of immune and endocrine signaling. Differences in microbiota composition have been associated with variability in therapeutic response, tolerability, and adverse-effect profiles. Emerging evidence also suggests that microbiota-targeted strategies, including probiotics, prebiotics, and dietary interventions, may act as adjuvant approaches to improve efficacy and reduce side effects.

DISCUSSION: Although the microbiota-gut-brain axis represents a biologically plausible and clinically relevant determinant of psychotropic outcomes, current evidence remains heterogeneous and largely associative. Methodological variability, small sample sizes, and limited longitudinal data restrict translation into routine clinical practice. Microbiota-informed prescribing appears promising, but requires standardized multi-omics profiling, harmonized sampling procedures, and robust prospective validation.

CONCLUSION: Gut microbiota may play an important role in psychotropic drug outcomes and could support more personalized, effective, and safer psychiatric care. Further mechanistic studies and standardized clinical trials are needed before microbiota-informed prescribing can be reliably implemented.},
}

@article {pmid42316512,
year = {2026},
author = {Maeno, S and Kataoka, N and Matsutani, M and Yakushi, T},
title = {Discordance Between 16S rRNA Similarity and Genome-Based Species Boundaries in Gluconobacter.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70335},
pmid = {42316512},
issn = {2045-8827},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial ; Phylogeny ; *Gluconobacter/genetics/classification ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {The 16S rRNA gene is widely used for bacterial identification, but its resolving power is limited in several taxa. In the genus Gluconobacter, species boundaries remain unclear despite reliance on 16S-based classification. To examine these limitations, we analyzed all publicly available complete genomes (n = 12) together with curated 16S rRNA sequences and compared 16S rRNA sequences similarity with genome-based relatedness. Within the sampled complete genomes, 16S rRNA sequences were highly conserved and showed substantial overlap between intra- and interspecific similarities. In contrast, average nucleotide identity (ANI)-based divergence was pronounced: ANI values ranged from 79.7% to 100%, and G. oxydans included more than one genomic lineage. Notably, two strains (H24 and 1.637) showed higher ANI values (97.2%-97.4%) to G. thailandicus than to other G. oxydans strains. Even the hypervariable V4, V6, and V8 regions lacked clade-specific signatures, indicating limited species-level resolution within this group. Furthermore, type-strain 16S rRNA sequences of G. oxydans, G. frateurii, and G. japonicus show ≥ 99% similarity and are grouped within the same non-redundant representative in the SILVA NR99 database, indicating limited species-level resolution. These results demonstrate a clear mismatch between 16S rRNA sequences similarity and genomic structure in Gluconobacter. Genome-based criteria, supported by refined reference databases and validated gene markers, are essential for accurate taxonomy and microbiome-based analyses.},
}

*RNA, Ribosomal, 16S/genetics
*Genome, Bacterial
Phylogeny
*Gluconobacter/genetics/classification
DNA, Bacterial/genetics
Sequence Analysis, DNA

@article {pmid42316541,
year = {2026},
author = {Upadhyay, SK},
title = {Holobiont Plasticity Under Abiotic Stress: A Systems Biology Perspective on Plant-Bacteria-Fungi Interactions.},
journal = {Physiologia plantarum},
volume = {178},
number = {3},
pages = {e70971},
doi = {10.1111/ppl.70971},
pmid = {42316541},
issn = {1399-3054},
mesh = {*Stress, Physiological/physiology ; *Systems Biology ; *Plants/microbiology ; *Bacteria/metabolism ; *Fungi/physiology ; Plant Growth Regulators/metabolism ; Plant Roots/microbiology ; Rhizosphere ; Microbiota/physiology ; },
abstract = {Abiotic stress frequency and intensity are increasing, severely impacting plants' health, hence leading to significant crop yield losses (~20%-40% globally). In addition to modifying their genetic and physiological traits to increase stress tolerance, growing research revealed that plant-microbiome interaction plays a remarkable role in determining stress resilience. This review integrates physiological, ecological, and multi-omics data suggesting holobiont plasticity is an unifying paradigm for mechanistic understanding of stress-induced plant-microbe system reorganization. Abiotic stress causes rapid changes in plants' root metabolism and root exudate composition, which alter the release of organic acids, phenolics, osmolytes, and signaling compounds, which selectively change the microbial community's structure in the rhizosphere and endosphere. Microbial taxonomic diversity usually declines under stress conditions. Meanwhile, functional redundancy within the microbial communities is generally maintained or can increase. However, network connectivity may often remain stable or become stronger under stress, and the centrality of keystone taxa usually increases. These keystone microbes play a critical role in sustaining microbial community structure and function. Microbial regulation of phytohormones (such as auxin, ethylene, and abscisic acid), along with control of redox balance, osmotic adjustment, and nutrient cycling, improves plant water use, nutrient uptake, and root development. This often makes them more tolerant to stress by 15%-60% without increasing their biomass. Holobiont plasticity emerges as a quantifiable and potentially predictive characteristic of plant stress responses by integrating microbial network structure, functional gene profiles, metabolomic responsiveness, and host regulatory mechanisms. These responses function on ecological timescales (days to weeks), preceding the more gradual process of host genetic adaptation. This halobiont plasticity-based framework shows promising potential but requires validation under field conditions to prove its robustness and applicability. This opens new avenues for microbiome-assisted plant growth and development of a climate-resilient agricultural system.},
}

*Stress, Physiological/physiology
*Systems Biology
*Plants/microbiology
*Bacteria/metabolism
*Fungi/physiology
Plant Growth Regulators/metabolism
Plant Roots/microbiology
Rhizosphere
Microbiota/physiology

@article {pmid42316543,
year = {2026},
author = {Jia, L and Wang, H},
title = {Crohn's Disease Enteritis: Pathophysiological Mechanisms and Therapeutic Approaches.},
journal = {Scandinavian journal of immunology},
volume = {103},
number = {6},
pages = {e70129},
doi = {10.1111/sji.70129},
pmid = {42316543},
issn = {1365-3083},
mesh = {Humans ; *Crohn Disease/therapy/immunology/etiology ; Animals ; Intestinal Mucosa/immunology/pathology ; Gastrointestinal Microbiome/immunology ; Cytokines/metabolism ; Genetic Predisposition to Disease ; Intestinal Barrier Function ; *Enteritis/therapy/immunology ; Signal Transduction ; },
abstract = {Crohn's disease (CD) is a chronic, relapsing-remitting inflammatory condition of the gastrointestinal tract. This review provides a comprehensive analysis of the underlying pathophysiological mechanisms, highlighting the interplay between intestinal epithelial cells, dysregulated immune responses, gut microbiota and environmental triggers in CD. Key genetic susceptibilities (e.g., NOD2, ATG16L1, IL23R) and dysregulated T-cell signalling, particularly involving T-helper 1 (Th1) and T-helper 17 (Th17) pathways, are central to CD pathogenesis. The progression of the disease is driven by complex cytokine and chemokine networks (e.g., TNF-α, IL-6, IL-17), epithelial barrier dysfunction and microbial dysbiosis, all of which contribute to chronic inflammation and mucosal damage. Advanced models, including organoids and patient-derived xenografts, have elucidated these mechanisms, aiding in biomarker discovery and drug development. Diagnostic advancements such as capsule endoscopy, magnetic resonance enterography, faecal calprotectin and molecular assays enable precise characterization of CD phenotypes and activity. Therapeutic strategies now encompass targeted biologics that neutralize key cytokines, small-molecule Janus kinase (JAK) inhibitors that interrupt intracellular inflammatory signalling and emerging modalities targeting epithelial repair and microbiome restoration. Despite significant progress, challenges persist in managing refractory CD, including loss of response to biologics and fibrostenotic or fistulizing complications. Personalized approaches based on immunological profiling, microbiota composition and molecular diagnostics hold promise for more effective interventions. This review underscores the complexity of intestinal inflammation in CD and advocates for integrated, personalized strategies to improve patient outcomes.},
}

Humans
*Crohn Disease/therapy/immunology/etiology
Animals
Intestinal Mucosa/immunology/pathology
Gastrointestinal Microbiome/immunology
Cytokines/metabolism
Genetic Predisposition to Disease
Intestinal Barrier Function
*Enteritis/therapy/immunology
Signal Transduction

@article {pmid42316765,
year = {2026},
author = {Liang, L and Chen, S and Zhu, B and Huang, Y and Lu, X and Wang, S and Wang, W and Han, R and Zhou, J and Xiong, D and Li, H and Li, X and Ning, Y and Wu, F and Wu, K},
title = {Continuous Alterations in the Gut Microbial Landscape Associated With Suicidal Ideation in First-Episode Drug-naïve Major Depressive Disorder.},
journal = {CNS neuroscience & therapeutics},
volume = {32},
number = {6},
pages = {e70892},
pmid = {42316765},
issn = {1755-5949},
support = {2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; //Clinical Medical Research Institute/ ; GCAAL2022001//Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; },
mesh = {Humans ; *Major Depressive Disorder/psychology/microbiology ; *Gastrointestinal Microbiome/physiology ; *Suicidal Ideation ; Female ; Male ; Adult ; Dysbiosis/psychology ; Cohort Studies ; },
abstract = {BACKGROUND: Major depressive disorder (MDD) has been closely associated with gut microbiota dysbiosis; however, the role of the gut microbiota in the progression from depression to suicidal ideation (SI) remains unclear.

METHODS: We enrolled a well-characterized clinical cohort of first-episode, drug-naïve MDD patients, explicitly classified into those without SI (MDDNSI) and those with SI (MDDSI), and matched with healthy controls (HC) on demographic variables. A severity-ordered HC-MDDNSI-MDDSI framework was established to capture progressive microbial and functional shifts, and correlation analyses were used to evaluate their relationships with clinical symptoms and cognitive function.

RESULTS: We identified a group of taxa showing clear severity-related trends, with the potential pathogenic species Bacteroides stercoris and Bacteroides eggerthii increasing across the clinical spectrum, while seven species, including Faecalibacillus intestinalis and Dialister massiliensis, showed a steady decrease. Functional annotation indicated that several major metabolic pathways, such as the bacterial secretion system, weakened progressively with disease severity and formed stable microbe-pathway modules together with pathways involved in energy metabolism and signal transduction. These differential taxa and pathways showed strong associations with clinical features, with Bacteroides stercoris positively correlated with SI, whereas Bifidobacterium pseudocatenulatum displayed a negative association. In addition, mediation analysis further showed that Bacteroides stercoris indirectly influenced SI through the bacterial secretion system pathway, suggesting a meaningful mediating role in SI.

CONCLUSION: These results revealed progressive alterations in gut microbial composition and metabolic function associated with SI, indicating that gut dysbiosis serves as a potential biological marker for suicide risk in MDD.},
}

Humans
*Major Depressive Disorder/psychology/microbiology
*Gastrointestinal Microbiome/physiology
*Suicidal Ideation
Female
Male
Adult
Dysbiosis/psychology
Cohort Studies

@article {pmid42316807,
year = {2026},
author = {Chowdhury, MAH and Reem, CSA and Ashrafudoulla, M and Yoon, HJ and Ha, SD},
title = {Biofilm Formation and Spore-Mediated Persistence of Clostridium perfringens in Meat and Poultry Processing Environments and Their Implications for Control Strategies.},
journal = {Journal of food science},
volume = {91},
number = {6},
pages = {e71193},
pmid = {42316807},
issn = {1750-3841},
support = {//Chung-Ang University Young Scientist Scholarship in 2024/ ; //Chung-Ang University research grant in 2025/ ; },
mesh = {*Biofilms/growth & development ; *Clostridium perfringens/physiology/drug effects ; Animals ; *Spores, Bacterial/physiology ; *Meat/microbiology ; Poultry/microbiology ; *Food Handling ; Food Microbiology ; Food Contamination/prevention & control ; Food, Processed ; Anti-Bacterial Agents/pharmacology ; Quorum Sensing ; },
abstract = {Clostridium perfringens (C. perfringens) biofilms pose a persistent challenge in meat and poultry processing environments due to their structural resilience, spore-mediated survival and toxin-associated virulence. These biofilms readily develop on food-contact surfaces under typical processing conditions including organic residue accumulation, temperature fluctuations, and localized anaerobic niches, leading to increased tolerance to sanitation and thermal treatments. Mechanistically, biofilm resilience in C. perfringens is governed by the integration of sporulation processes, quorum sensing-regulated gene expression and extracellular polymeric substance (EPS) matrix formation, which collectively enhance stress tolerance, limit antimicrobial penetration, and facilitate persistence under fluctuating environmental conditions. The interaction between spore formation and EPS architecture further promotes survival during thermal processing and enables rapid re-establishment of biofilms following sanitation. This review synthesizes current knowledge on the formation and persistence of C. perfringens biofilms, key environmental drivers in meat and poultry processing systems and the mechanistic basis of their stress resistance and survival strategies. It also critically examines how these mechanisms influence the efficacy of existing intervention strategies. It further evaluates the limitations of conventional control strategies and highlights emerging approaches for biofilm prevention and control, including food-grade antimicrobials, surface engineering, enzymatic disruption, and microbiome-based interventions, with emphasis on their modes of action and applicability in industrial settings. Overall, this review provides a mechanistic and systems-level perspective to support the development of more effective biofilm control strategies in meat processing environments.},
}

*Biofilms/growth & development
*Clostridium perfringens/physiology/drug effects
Animals
*Spores, Bacterial/physiology
*Meat/microbiology
Poultry/microbiology
*Food Handling
Food Microbiology
Food Contamination/prevention & control
Food, Processed
Anti-Bacterial Agents/pharmacology
Quorum Sensing

@article {pmid42316904,
year = {2026},
author = {Saheb Sharif-Askari, N and Eladham, MW and Mdkhana, B and Sekar, P and Hafezi, S and Shakartalla, SB and Hachim, I and Saheb Sharif-Askari, F and Halwani, R},
title = {The Role of Fecal Microbiome Transplantation in Steroid Hyporesponsive Asthma.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70196},
doi = {10.1002/cph4.70196},
pmid = {42316904},
issn = {2040-4603},
support = {24010902170//University of Sharjah/ ; 25011103119//University of Sharjah/ ; 2401110399//University of Sharjah/ ; 24010903159//University of Sharjah/ ; ORF-RC-2026-0509//King Saud University/ ; },
mesh = {*Asthma/therapy/microbiology ; *Fecal Microbiota Transplantation ; Animals ; *Gastrointestinal Microbiome ; Humans ; Dysbiosis/therapy ; *Adrenal Cortex Hormones/therapeutic use ; },
abstract = {Asthma is a chronic inflammatory airway disease characterized by airflow obstruction, airway hyperresponsiveness, and structural remodeling. Corticosteroids remain the mainstay of asthma therapy; however, a substantial proportion of patients with severe disease develop steroid hyporesponsiveness, limiting therapeutic efficacy and increasing disease burden. Emerging evidence implicates the gut microbiome as a key regulator of systemic immune responses, with growing relevance to asthma pathogenesis and treatment responsiveness. In this study, we investigated whether gut microbiota dysbiosis contributes to steroid hyporesponsive lung inflammation and whether fecal microbiota transplantation (FMT) can restore steroid responsiveness. Using a steroid-hyporesponsive asthma model, we demonstrate that the disease is associated with significant gut microbial dysregulation, characterized by reduced microbial diversity and depletion of immunoregulatory taxa. FMT partially restored gut microbial diversity, normalized community structure, and selectively replenished beneficial commensal bacteria, including Akkermansia muciniphila and Faecalibacterium prausnitzii, while suppressing pathogenic taxa. Importantly, restoration of gut microbial balance was associated with attenuation of lung inflammation and improved steroid responsiveness. These findings support a functional gut-lung axis in steroid hyporesponsive asthma and identify modulation of gut microbiota as a potential therapeutic strategy. Incorporating microbiota-directed interventions such as FMT may represent a novel adjunct approach for the management of refractory steroid-hyporesponsive asthma.},
}

*Asthma/therapy/microbiology
*Fecal Microbiota Transplantation
Animals
*Gastrointestinal Microbiome
Humans
Dysbiosis/therapy
*Adrenal Cortex Hormones/therapeutic use

@article {pmid42317058,
year = {2026},
author = {Yue, R and Wen, Y and Zhao, S and Liu, X and Luo, L and Liu, Y and Zeng, L},
title = {Tea and digestive system health: integrating gut microbiota-involved ADME and personalized nutrition for gastrointestinal disorders intervention.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-34},
doi = {10.1080/10408398.2026.2684712},
pmid = {42317058},
issn = {1549-7852},
abstract = {The global burden of digestive diseases is escalating, marked by rising incidence and severity. Tea, a widely consumed beverage rich in polyphenols, offers a promising dietary intervention due to its demonstrated capacity to modulate gut microbiota, suppress inflammation, and enhance gastrointestinal barrier function. This review provides a systematic integration of the ADME characteristics of key tea compounds with their complex interplay with the gut microbiome, underscoring the central role of microbial biotransformation in mediating the health benefits of tea. We critically examine the specific protective mechanisms of tea against prevalent gastrointestinal disorders, including gastritis, gastric ulcers, inflammatory bowel disease, irritable bowel syndrome, constipation, and diarrhea. A major focus is placed on the pivotal impact of interindividual variability, shaped by host factors and distinct gut microbial metabolic phenotypes, on the outcomes of tea-based interventions. This synthesis thus advances a novel "component-microbiota-metabolite-host" axis as a unifying framework for understanding tea's pleiotropic mechanisms in gastrointestinal health. Beyond mechanistic insight, the review lays a conceptual foundation and proposes a translational roadmap for developing evidence‑based, personalized tea interventions aligned with precision nutrition.},
}

@article {pmid42317296,
year = {2026},
author = {Ahmad, R and Zobel, G and Hannaford, R and Maclean, P and Olson, T and Hurst, C and Bracegirdle, J and Young, W and Rettedal, E and Anderson, RC and Dalziel, JE},
title = {Social isolation during adolescence alters novel object recognition memory, brain and gut gene expression, and microbiota composition in a sex-specific manner.},
journal = {Brain, behavior, & immunity - health},
volume = {55},
number = {},
pages = {101284},
pmid = {42317296},
issn = {2666-3546},
abstract = {Adolescent social isolation is a known risk factor for anxiety and depression related disorders, yet its effects on brain-gut communication and potential sex differences remain unclear. We hypothesised that isolation would heighten anxiety- and depression-related behaviors and consequently impair memory in both sexes. To investigate this we exposed male (M) and female (F) rats to four weeks of social isolation beginning at 3 weeks of age and assessed behavior, brain and gut gene expression and microbiota, in single- (S) or pair-housed (P) animals. Contrary to our hypothesis, the results showed higher novel object recognition memory in socially-isolated females (FS vs FP). No isolation-induced changes in anxiety-related behaviours were detected in either sex. Social isolation in females (FS vs FP) increased expression of hippocampal Grik5 (glutamate receptor/memory/learning), and decreased expression of prefrontal cortex genes: Mbp, Mobp, Plp1 (neuroplasticity), Cnp (neuroprotection) and Tph2 (serotonin synthesis). There was a trend toward lower microbial diversity in socially-isolated females (FS vs FP). Although no behaviour change was detected in isolated males, amygdala c-Fos (neuronal activity) and prefrontal cortex Gabbr1 (inhibitory) expression were decreased. Il6r, Tgfb1, Tlr9 (immune-related) were increased in the colon (MS vs MP). In both sexes, social isolation increased Tph1 expression in the colon (FS vs FP; MS vs MP). These findings indicate sex-specific responses to adolescent social isolation, with females showing enhanced novel object recognition memory performance alongside changes in genes linked to neuroplasticity and memory, while males showed altered brain and gut gene expression linked to brain neuro-activity and gut-immune function.},
}

@article {pmid42317353,
year = {2026},
author = {Lohani, SC and Zhang, C and Mandal, S and Zhao, M and Cheng, Y and Ramer-Tait, AE and Li, Q},
title = {Fecal microbiota transplantation reduces inflammation and modulates gene expression in HIV-infected double humanized-BLT (dHu-BLT) mice on antiretroviral therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1773716},
pmid = {42317353},
issn = {1664-3224},
mesh = {Animals ; *Fecal Microbiota Transplantation ; *HIV Infections/therapy/immunology/microbiology/genetics/drug therapy ; Mice ; Humans ; *Inflammation/therapy/immunology ; Gastrointestinal Microbiome ; Disease Models, Animal ; *Anti-Retroviral Agents/therapeutic use ; Gene Expression Regulation ; },
abstract = {INTRODUCTION: Persistent immune activation and inflammation remain significant barriers to managing comorbidities in people living with HIV (PLWH) on suppressive antiretroviral therapy (ART). While ART substantially reduces plasma viral loads to an undetectable level, it fails to fully restore gut microbial homeostasis and prevent microbial translocation, a critical pathogenic contributor to systemic persistent immune activation and inflammation. To evaluate the potential of human fecal microbiota transplantation (FMT) as an adjunctive therapy to restore gut health and attenuate inflammation and immune activation in PLWH on ART, we utilized a double humanized-BLT (dHu-BLT) mouse model, featuring a functional human immune system and a human-like microbiome.

METHODS: Two groups of HIV-infected dHu-BLT mice were used in the study. One group received FMT in addition to ART, while the control group received ART alone. Using both a multi-omics approach (16S rRNA sequencing and RNA-seq) and an immune-based assay, we compared alterations in gut microbial composition, profiled transcriptomic changes in the intestinal tissue, and quantified markers of systemic immune activation and inflammation between the groups.

RESULT: FMT supplementation in ART-treated mice increased the relative abundance of beneficial bacteria and modulated the transcriptomic profile of both human- and murine-related genes. Notably, genes associated with cellular structure and tissue maintenance, including Mcpt4, were upregulated, along with the extracellular matrix organization pathway predicted as the most strongly activated pathway in the FMT-supplemented group compared to ART alone. In contrast, genes and signaling pathways associated with inflammation were downregulated. Importantly, the FMT-supplemented group exhibited a significant reduction of plasma inflammatory markers, including CD62E, sCD14, sCD163, and FABP2, relative to the ART alone group.

CONCLUSION: These results suggest that FMT may serve as a promising adjunctive strategy for mitigating systemic inflammation by improving gut health, thereby contributing to the reduction of comorbidities in PLWH on ART.},
}

Animals
*Fecal Microbiota Transplantation
*HIV Infections/therapy/immunology/microbiology/genetics/drug therapy
Mice
Humans
*Inflammation/therapy/immunology
Gastrointestinal Microbiome
Disease Models, Animal
*Anti-Retroviral Agents/therapeutic use
Gene Expression Regulation

@article {pmid42317363,
year = {2026},
author = {Blake, S and Mortara, L and Spada, S},
title = {Editorial: Microbiota-immune interactions: a new frontier in cancer treatment optimization.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1882251},
pmid = {42317363},
issn = {1664-3224},
}

@article {pmid42317531,
year = {2026},
author = {Thoenen, L and Giroud, C and Probst, C and Rouyer, L and Schandry, N and Schlaeppi, K},
title = {Customizable High-Throughput Chemical Phenotyping of Root Bacteria.},
journal = {Bio-protocol},
volume = {16},
number = {11},
pages = {e5710},
pmid = {42317531},
issn = {2331-8325},
abstract = {Chemical phenotyping is a fundamental technique to study the metabolic properties or chemical sensitivities of bacteria. Traditional methods such as dilution methods, discs, or gradient diffusion assays are labor-intensive, often have high material requirements, and are limited in scalability. High-throughput cultivation approaches based on 96-well plates scale efficiently to large numbers of samples. A stacker, when coupled with a plate reader system (often already available in most laboratories), greatly enhances assay scalability and robustness. Here, we describe a customized high-throughput, flexible, scalable, robust, and affordable method for the chemical phenotyping of bacteria. This liquid culture-based growth system allows screening many bacteria in parallel and in a replicated manner for their tolerance to various chemicals, including specialized metabolites of plants, antibiotics, or pesticides. Compared to commercial solutions, our approach offers high flexibility in experimental conditions while keeping costs for consumables low. Key features • Approach to determine tolerance of bacteria against diverse chemicals, including specialized plant metabolites. • Experimental platform where parameters like strains, media, chemicals, concentrations, or exposure time can be flexibly varied for bacterial phenotyping. • Coupling a stacker to a plate reader permits highly replicated and efficient screenings of large bacterial collections and numerous different compounds.},
}

@article {pmid42317759,
year = {2026},
author = {Jiya, N and Sha, SP and Khudai, W and Yadav, S and Sasane, R and Sah, SP and Ghatani, K and Sharma, A},
title = {Distinct bacterial and fungal communities linked to functional potential in fermented fish and vegetables.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1850075},
pmid = {42317759},
issn = {1664-302X},
abstract = {INTRODUCTION: Traditional fermented foods constitute a vital component of ethnic community diets; consequently, characterizing their specific food microbiome is essential for elucidating their nutritional, functional and health related attributes.

METHODS: In this study, targeted metagenomics was employed to investigate the bacterial and fungal compositions of fermented fish and vegetables from North Bengal, India. The functional predictions of the fermented food microbiomes was performed using PICRUSt2.

RESULTS AND DISCUSSION: High throughput sequencing of 16S rRNA and ITS genes revealed substantial differences in the diversity indices amongst the fermented fishes and vegetables. Fish samples were dominated by Pseudomonadota (23.05%), whereas vegetables were enriched in Bacillota (32.17%), with Psychrobacter and Aliivibrio prevalent in fishes and lactic acid bacteria including Levilactobacillus, Paucilactobacillus and Pediococcus dominant in vegetables. The fungal genera Bisifusarium belonging to Ascomycota and Cystobasidium affiliated to Basidiomycota, were abundant in the fermented fishes and vegetables, respectively. Functional predictions of bacterial and fungal communities revealed enhanced carbohydrate metabolism, biosynthesis pathways related to vitamins, short-chain fatty acids, organic acids, proteolytic enzymes and compounds contributing to organoleptic attributes in these fermented foods. The assessment of microbial communities associated with the traditionally fermented foods of North Bengal revealed the key microbial taxa involved in the fermentation process and their nutritional properties.},
}

@article {pmid42317762,
year = {2026},
author = {Joshi, G and Rani, S and Bharti, D and Panda, N and Chavan, P and Mathpal, S and Ramaiah, S and Anbarasu, A},
title = {The role of the gut microbiome in antibiotic-driven antimicrobial resistance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1856738},
pmid = {42317762},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is one of the most pressing threats to global health system. The human gut harbors a complex microbial ecosystem coordinated through mechanisms of metabolic interdependence. The gut microbiota plays a vital role in normal growth and physiological processes of the human body. It serves both as a target of antibiotic-mediated disruption and as a reservoir for the propagation of antimicrobial resistance genes. Although antibiotics remain indispensable for the treatment of bacterial infections, their broad ecological impact on the gut microbiota can undermine the microbial balance that protects the host against pathogen invasion and metabolic dysfunction. The gut microbiome also functions as a reservoir of antimicrobial resistance genes collectively termed the "resistome," which can be mobilised and transferred between commensal and pathogenic bacteria via horizontal gene transfer mechanisms such as conjugation, transformation, and transduction. This review examines the composition and functions of the human gut microbiota, the mechanism of antibiotic-induced gut dysbiosis, and the role of host factors like age, genetics, diet and immune status, on microbiome dynamics and AMR development. We further evaluate emerging methods for resistome characterisation, which include PCR, next-generation sequencing, functional metagenomics and artificial intelligence-driven tools. Finally, we discuss microbiome-targeted therapeutic strategies such as faecal microbiota transplantation (FMT), phage therapy, CRISPR-based therapies, and antimicrobial peptides for combating AMR and restoring gut microbial homeostasis. Overall, this review highlights that maintaining and re-establishing the integrity of the gut microbiome should be considered a fundamental component of antimicrobial stewardship strategies aimed at controlling AMR worldwide.},
}

@article {pmid42317866,
year = {2026},
author = {Alotaibi, W},
title = {Chrononutrition and cardiometabolic health: circadian timing as a dimension of precision nutrition.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1779033},
pmid = {42317866},
issn = {2296-861X},
abstract = {Cardiometabolic diseases, including obesity, type 2 diabetes mellitus (T2DM), hypertension, and cardiovascular disease (CVD), remain major global health challenges despite widespread adoption of evidence-based dietary guidelines. Traditional nutrition recommendations have largely focused on dietary composition and energy intake, with limited consideration of the timing of food consumption. Growing evidence indicates that metabolic processes are strongly regulated by circadian rhythms, suggesting that when food is consumed may be a critical but underappreciated determinant of cardiometabolic health. Chrononutrition, which examines the interaction between meal timing and the circadian system, has therefore emerged as an important area of research. This narrative review synthesizes human evidence linking chrononutrition to cardiometabolic outcomes, with a focus on obesity, insulin resistance and T2DM, lipid metabolism, and cardiovascular risk. Findings from observational studies, randomized clinical trials, and mechanistic investigations consistently demonstrate that eating later in the biological day or night is associated with impaired postprandial glucose regulation, reduced insulin sensitivity, altered lipid handling, and adverse cardiometabolic profiles, independent of dietary composition and total energy intake. In contrast, eating patterns aligned with endogenous circadian rhythms characterized by earlier energy intake and avoidance of late-night eating appear metabolically favorable. This review further situates chrononutrition within the framework of precision nutrition. While precision nutrition aims to explain interindividual variability in metabolic responses using genetic, metabolic, and microbiome-based approaches, circadian timing is rarely considered. Because metabolic capacity varies across the day-night cycle, failure to account for meal timing, chronotype, and circadian alignment may contribute to unexplained variability in dietary responses. Integrating chrononutrition into precision nutrition frameworks may therefore improve interpretation of metabolic phenotypes and enhance the personalization of dietary strategies. Finally, key research gaps are identified, highlighting the need for long-term, diverse human studies and time-resolved metabolic phenotyping to clarify the role of chrononutrition in cardiometabolic disease prevention.},
}

@article {pmid42317870,
year = {2026},
author = {Perillo, F and Mascaretti, F and Maragno, P and Amoroso, C and Oriani, E and Baeri, A and Pinco, P and Pozzi, L and Baldari, L and Caprioli, F and Ghidini, M and Strati, F and Facciotti, F},
title = {Preoperative malnutrition is associated with suppressed intratumoral T cell function and distinct tumor-associated microbiota in colorectal cancer: a prospective pilot study.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1802354},
pmid = {42317870},
issn = {2296-861X},
abstract = {INTRODUCTION: Cancer-related malnutrition significantly reduces therapeutic effectiveness, lowers chemotherapy tolerance, and impairs immunotherapy efficacy. Monitoring nutritional status using tools such as the Malnutrition Universal Screening Tool (MUST) may improve clinical outcomes. Malnutrition also profoundly affects immune system functions and gut microbiota composition. However, the relationship between pre-surgery nutritional status, anti-tumor immunity, and tumor-associated microbiota remains poorly understood.

METHODS: We prospectively enrolled 43 colorectal cancer (CRC) patients who underwent resection surgery between July 2017 and August 2021 at IRCCS Ca' Granda Ospedale Maggiore Policlinico in Milan. Patients were evaluated for biochemical, anthropometric, and nutritional profiles, as well as intratumoral immune phenotypes and tumor-associated microbiota. Tumor-associated microbiota analysis was performed in a subset of 8 patients (5 malnourished and 3 non-malnourished) for whom mucosal samples were available.

RESULTS: Malnutrition was associated with increased tissue-infiltrating neutrophils and altered T cell phenotypes, including reduced expression of effector-associated cytokines in conventional T-helper and iNKT cells. Gut microbiota analysis revealed significant associations between neutrophil lymphocyte ratio (NLR) and the bacterial genera Bacteroides, Prevotella, and Parabacteroides, suggesting a potential role for these microbes in shaping immune responses in malnourished individuals.

DISCUSSION: These findings suggest a link between malnutrition, gut microbiota composition, and suppressed anti-tumor immunity in CRC patients.},
}

@article {pmid42317872,
year = {2026},
author = {Singh, G and Singh, G and Shreya, and Kumari, A and Aran, KR},
title = {Nutrients and bioactive compounds as modifiers of neurodegenerative trajectories: molecular mechanisms, translational barriers, and precision nutrition.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1819432},
pmid = {42317872},
issn = {2296-861X},
abstract = {The Neurodegenerative diseases (NDs) such as Alzheimer's disease (AD), Parkinson's disease (PD), Multiple sclerosis (MS), and Amyotrophic lateral sclerosis (ALS) are a growing health burden across the world with minimal disease-modifying treatment and therapy. It is emerging that neurodegeneration is not only a progressive loss of neurons, but also a nutrient-sensitive systems-level dysfunction that takes the form of redox imbalance, chronic neuroinflammation, mitochondrial dysfunction, impaired proteostasis, and synaptic loss. The aging brain are more prone to metabolic vulnerability, and subclinical deficiencies in essential nutrients and bioactive dietary compounds may exacerbate cellular stress responses that contribute to disease progression. It summarizes the existing data on the effects of nutrients like vitamins, minerals, polyunsaturated fatty acids, and various phytochemicals in modulating neuronal homeostasis by regulating oxidative signaling, inflammatory cascades, mitochondrial resilience, autophagy, and synaptic plasticity. These nutrient-mediated effects collectively influence neuronal survival, synaptic integrity, and cognitive function by affecting disease susceptibility and progression. Additionally newer metabolites of the marine and microbiome act as new neuroactive agents. The evidence from in-vitro and preclinical models, translation to clinical benefit remains inconsistent due to heterogeneity in study design, bioavailability, blood- brain barrier penetration, dosing strategies and disease stage. This review highlights emerging potential of precision nutrition frameworks that integrate nutrigenomics, metabolomics, and microbiome interactions, and individualized metabolic profiling to enable context-dependent and stage-specific interventions. Moreover, conceptualizing neurodegeneration as a nutrient-sensitive, systems level disorder, propose a mechanistically informed and integrative approach that combine targeted nutritional strategies with pharmacological and lifestyle therapies to more effectively modify neurodegenerative trajectories.},
}

@article {pmid42317952,
year = {2026},
author = {Andafa, TW and Imoh, EC and Adekanmbi, SA},
title = {Artificial Intelligence Applied to the Brain-Gut Axis in Irritable Bowel Syndrome: Advancing Toward Clinical Translation.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e109142},
pmid = {42317952},
issn = {2168-8184},
abstract = {Irritable bowel syndrome (IBS) is one of the most common functional gut disorders affecting the global population, characterized by chronic abdominal pain and altered bowel habits in the absence of structural disease. The brain-gut-microbiota axis, a bidirectional network integrating central nervous system processing, enteric and autonomic function, immune signaling, and gut microbial ecology, provides a mechanistic framework that helps explain the substantial symptom heterogeneity and variable treatment response observed across patients. Artificial intelligence (AI) and machine learning (ML) approaches offer the ability to model complex, nonlinear relationships across high-dimensional biological datasets generated from this axis, including microbiome composition profiles, resting-state functional MRI connectivity matrices, multiomics data layers, and psychological and clinical feature sets. This narrative review evaluated primary human studies applying AI and ML to brain-gut axis data in IBS, identified through structured searches of PubMed/MEDLINE and Scopus supplemented by citation chaining, with literature included up to April 2026. Across microbiome profiling, neuroimaging, multiomics integration, and psychological feature modeling, ML approaches have demonstrated proof-of-concept performance for IBS classification and, in a smaller number of studies, for prediction of clinically meaningful outcomes, including cognitive behavioral therapy (CBT) response. A notable early signal is the integration of baseline microbiome and brain features to predict CBT response, with high reported discrimination, although these results are derived from small, single-center cohorts with only internal validation and should be regarded as hypothesis-generating. The current evidence base is limited by small single-center cohorts, reliance on internal validation, healthy-control comparators, limited external replication, and substantial overfitting and data-leakage risk in high-dimensional small-sample settings. AI and ML applications in IBS are promising but remain exploratory and are not yet suitable for routine clinical use. Clinical translation will require larger multicenter datasets, harmonized preprocessing pipelines, external validation, calibration reporting, and evaluation against clinically realistic comparators and decision points.},
}

@article {pmid42318010,
year = {2026},
author = {Yang, H and Wu, G and Liang, S and Zan, R and Chen, Y and Yuan, W and Chen, H and Huang, G},
title = {Millettia speciosa reprograms the lung proteome and suppresses CCL24-driven eosinophilic inflammation in allergic asthma.},
journal = {Frontiers in allergy},
volume = {7},
number = {},
pages = {1726706},
pmid = {42318010},
issn = {2673-6101},
abstract = {BACKGROUND: Asthma is a Th2-skewed inflammatory disorder characterized by eosinophilic infiltration, cytokine dysregulation, and airway remodeling. Emerging evidence highlights the role of immunometabolic pathways and the gut-lung axis in asthma pathogenesis.

METHODS: We investigate the therapeutic effects of Niudali (Millettia speciosa), a traditional Chinese medicinal herb, in an ovalbumin-induced mouse model of allergic asthma using high-resolution data-independent acquisition (DIA) lung proteomics integrated with cytokine profiling.

RESULTS: Niudali treatment significantly alleviated airway inflammation and eosinophilic infiltration. Proteomic analysis revealed 179 differentially expressed proteins (DEPs), with a notable finding that CCL24, a key eosinophil-recruiting chemokine, was completely suppressed in Niudali-treated mice but highly expressed in the asthma model. This highlights the central role of CCL24 inhibition in the mechanism through which Niudali mitigates eosinophil-mediated inflammation.Functional enrichment analyses revealed that Niudali modulates pathways involved in complement and coagulation cascades, lipid transport, antioxidant defense, and PPAR signaling, reflecting a shift toward immune resolution and metabolic homeostasis. Network analysis identified key hub proteins, including Alb, Apoe, Apoa1, Proc, and Serpina7, which orchestrate lipid metabolism, antioxidant functions, and immune regulation. The modulation of serpins, apolipoproteins, and extracellular space-related proteins suggests a broad immunometabolic reprogramming effect. Notably, this molecular signature aligns with the gut-lung axis paradigm, potentially reflecting microbiota-mediated modulation via short-chain fatty acids (SCFAs). Consistent with proteomic findings, bronchoalveolar lavage fluid (BALF) analyses showed significant reductions in IgE, IL-4, IL-5, and IL-6, further confirming suppression of Th2-mediated inflammation.

CONCLUSION: study provides proteomic evidence that Niudali treats asthma by disrupting the CCL24-eosinophil axis and rebalancing immunometabolic networks. These findings support Niudali as a promising candidate for gut-lung axis-targeted interventions in asthma and provide a systems-level framework for future microbiome metabolome integrated studies. While our findings suggest a potential link between these molecular changes and the gut-lung axis, this mechanism was not directly investigated in the present study and should therefore be considered hypothetical. Future studies incorporating microbiome and metabolomic analyses will be essential to clarify the role of gut-derived metabolites, including SCFAs, in mediating these effects.},
}

@article {pmid42318064,
year = {2026},
author = {Li, XT and Zhang, X and Liang, ZL and Jiang, Z and Huang, Y and Han, YQ and Tan, ZB and Ying-Liu, and Liu, ZH and Yin, HQ and Liu, SJ and Jiang, CY},
title = {A culturomics biobank decodes extremophile evolution and metabolism in acid mine drainage.},
journal = {Environmental science and ecotechnology},
volume = {32},
number = {},
pages = {100722},
pmid = {42318064},
issn = {2666-4984},
abstract = {Extreme environments such as acid mine drainage (AMD) host highly specialized microbial communities that drive profound biogeochemical cycles. Within these ecosystems, iron- and sulfur-metabolizing taxa catalyze mineral weathering, generating intense acidity and mobilizing heavy metals. However, more than 97% of these microorganisms remain uncultured "microbial dark matter," heavily restricting our understanding of extremophile metabolism and adaptation. Here we present the Microbial Biobank of AMD (mbAMD), a culturomics-derived collection of 652 isolates spanning 42 species-including 21 novel taxa-that achieves 86.7% coverage of the global AMD core microbiome. Functional validation demonstrates that 36 of these taxa possess active iron or sulfur metabolic capacities, including the discovery of the first pure cultures of acid-tolerant sulfate reducers. Comparative genomic analyses across these isolates reveal that extreme environmental adaptation is predominantly driven by pervasive horizontal gene transfer. Specifically, extremophiles preferentially acquire adaptive genes governing acid tolerance and metal resistance from phylogenetically proximal relatives rather than distant donors. These findings elucidate the modular evolutionary strategies of extremophiles and provide critical functional resources for advancing biohydrometallurgy and environmental bioremediation. This mbAMD resource will accelerate biohydrometallurgical process optimization and environmental bioremediation strategies while advancing evolutionary microbial ecology research.},
}

@article {pmid42318276,
year = {2026},
author = {Krithika, C and Sridhar, C and Santhanakrishnan, S and Mahendra, J and Sankari, L and Sivakumar, T},
title = {Salivary Biomarkers for Diagnosis and Monitoring of Thyroid Diseases: A Systematic Review of Current Evidence.},
journal = {Biomarker insights},
volume = {21},
number = {},
pages = {11772719261452222},
pmid = {42318276},
issn = {1177-2719},
abstract = {BACKGROUND: Thyroid hormones have a crucial impact on all physiological systems. Diagnosis of thyroid diseases using salivary biomarkers is an emerging discipline and requires consolidation of existing information.

AIMS: This systematic review is aimed at identifying and analyzing salivary biomarkers that are associated with thyroid diseases and evaluate their potential as diagnostic applicability as non-invasive indicators of thyroid dysfunction.

METHODOLOGY: Literature search was conducted in PubMed, Cochrane, EBSCO, ProQuest, and Google Scholar from date of inception to May 2025. Human observational studies, clinical trials, and diagnostic accuracy studies published in the English language, that related biomarkers in saliva to thyroid diseases were collected and analyzed for relevant information. The search resulted in 35 records, followed by PRISMA 2020 compliant screening which resulted in 9 records included for data synthesis. Data extraction, tabulation and Risk of Bias assessment was carried out by 2 independent reviewers.

RESULTS: Included studies suggest that FT3, amino acids, salivary metabolic profiling, glycan profiles, microbiome, and thyroid antibodies present in saliva could be putative and noninvasive biomarkers of diagnostic and prognostic importance.

CONCLUSION: Heterogeneity in study design and analytical techniques has limited definitive conclusions about said markers, necessitating future well-designed clinical studies for validation of these biomarkers for noninvasive thyroid screeing and diagnosis.},
}

@article {pmid42318277,
year = {2026},
author = {Wilding, MC and Shaffer, AD and Rapsinski, GJ and Johnson, M and Hilliam, Y and Williams, JV and Bomberger, JM and Stapleton, AL},
title = {Viral Detection and Clinical Disease Features in Pediatric Chronic Rhinosinusitis.},
journal = {Laryngoscope investigative otolaryngology},
volume = {11},
number = {3},
pages = {e70465},
pmid = {42318277},
issn = {2378-8038},
abstract = {OBJECTIVES: Chronic rhinosinusitis (CRS) results from complex host-environment interactions with microbiome dysbiosis and viral infections postulated to drive inflammation and anatomic remodeling. This study investigates the impact of viral presence on pediatric sinonasal disease and clinical outcomes.

METHODS: A prospective, case-control study with retrospective data collection was conducted at a single-institution tertiary children's hospital. Pediatric patients undergoing sinus surgery for CRS (cystic fibrosis [CF] and non-CF CRS groups) and a control group undergoing structural septoplasty were enrolled from 2018-2022. Sinus swabs were collected intraoperatively and during up to 3 years of follow-up. A 14-virus panel was run. 16S and custom amplicon sequencing and quantitative PCR assessed microbial profiles. Clinical and endoscopic data were recorded.

RESULTS: Sinonasal swabs were collected from 15 CF-CRS, 21 non-CF CRS, and 32 control patients during initial sinus surgery. At least one virus was detected in 30.9% of samples (n = 21/68): 18.8% (n = 6/32) in controls, 33.3% (n = 7/21) in non-CF, and 53.3% (n = 8/15) in CF. Human rhinovirus (HRV) was most common, comprising 45.8% (n = 11/24) of viral detections. Across study duration, viral-positive CRS individuals were 3.49 times more likely to report nasal drainage (95% CI: 1.59-9.25, p = 0.005) and 4.23 times more likely to exhibit discharge on endoscopy (95% CI: 1.40-12.81, p = 0.011) than viral-negative individuals. HRV-positive samples had decreased Corynebacterium prevalence (p = 0.025), increased Haemophilus prevalence (p = 0.052), and increased Pseudomonas relative abundance (p = 0.076) versus viral-negative samples.

CONCLUSION: Viral infections can exacerbate pediatric CRS by increasing nasal drainage and endoscopic discharge while promoting chronic inflammation and persistent disease.

LEVEL OF EVIDENCE: 4.},
}

@article {pmid42318308,
year = {2026},
author = {Yu, C and Dong, L and Zhang, R and Li, H and Shi, X and Wu, H and Zhou, W and Li, Y and Wei, WB},
title = {Causal Effects of Gut Microbiota and Associated Metabolites on Retinal Diseases and Visual Impairment: A Mendelian Randomization Study.},
journal = {Journal of ophthalmology},
volume = {2026},
number = {},
pages = {4233490},
pmid = {42318308},
issn = {2090-004X},
abstract = {BACKGROUND: Previous observational study findings have indicated a vital association between gut microbiota features and retinal diseases based on the "gut-retina" axis. However, whether their relationships underlie causal effects remains to be established.

METHODS: Instrumental variables of 211 gut microbiota taxa were obtained from a genome-wide association study (GWAS), and 28 gut-associated metabolites and pathways were included as exposures. A two-sample Mendelian randomization (MR) study was carried out to estimate gut microbiota effects on diabetic retinopathy (DR), early age-related macular degeneration (eAMD), retinal detachments and breaks (RDs/RBs), retinal vascular occlusion (RVO), disorders of the choroid and retina (D-C/R), and visual impairment. MR methods, including inverse variance weighted (IVW), MR‒Egger, weighted median, simple mode, and weighted mode methods, were used to investigate the causal relationship between gut microbiota features and various outcomes. Heterogeneity, pleiotropy, and stability tests of MR results were performed, and Bonferroni's correction was used to test the strength of the causal relationships between exposures and outcomes, as well as reverse and multivariable MR analyses.

RESULTS: Through MR analysis of 211 microbes and six clinical phenotypes, a total of 35 gut microbiome and 3 associated metabolites were found to be associated with various outcomes. Cochrane's Q test revealed that there was no significant heterogeneity between various single-nucleotide polymorphisms. In addition, no significant level of pleiotropy was found according to the MR‒Egger and MR-PRESSO global tests. After the Bonferroni-corrected test, Genus id.2041 (OR = 0.874, 95% CI: 0.816-0.936, p = 1.10e - 04, IVW) showed robust causality with D-C/R, which had a nominal association with multiple other retinal diseases as well. Seven exposure-outcome effects markedly remained valid when BMI or alcohol intake frequency was separately included in multivariable MR analyses. According to the results of reverse MR analysis, no significant causal effect of outcomes was found on gut microbiota. No significant heterogeneity of instrumental variables or horizontal pleiotropy was found.

CONCLUSION: We confirmed a potential causal relationship between some gut microbiota features and retinal diseases, thus providing new insights into the gut microbiota-mediated mechanism of retinopathy and indicating vital biomarkers for potential diagnostic, therapeutic, and prevention strategies.},
}

@article {pmid42318566,
year = {2026},
author = {Shetty, J and Hegde, NN and Hegde, MN},
title = {Mineral encapsulation of microorganisms in calcified oral biofilms: implications for immune dysregulation and vascular calcification.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1849108},
pmid = {42318566},
issn = {2673-4915},
abstract = {Oral biofilms represent highly organized microbial ecosystems embedded within extracellular matrices enriched with calcium and phosphate ions that promote the nucleation of calcium phosphate minerals, including hydroxyapatite. During plaque mineralization, microorganisms may become incorporated within calcium phosphate-protein matrices, forming mineralized microenvironments that facilitate microbial persistence while partially shielding pathogens from host immune surveillance. Hydroxyapatite crystals can also directly influence innate immune responses. Macrophages exposed to these particles exhibit altered polarization, impaired antigen presentation, and sustained low-grade inflammatory signaling accompanied by dysregulated tissue repair mechanisms. In biological fluids, calcium phosphate nanoparticles rapidly acquire a protein corona that modulates cellular uptake, biodistribution, and systemic interactions. These particles may disrupt intracellular calcium homeostasis, promote endothelial dysfunction, influence coagulation pathways, and contribute to vascular remodeling. We propose that calcium phosphate mineralization within oral biofilms encapsulates microbial cells within mineral-protein matrices that behave as protected reservoirs capable of systemic dissemination, immune modulation, and promotion of vascular calcification. This mineral encapsulation model provides a mechanistic framework linking opportunistic oral microorganisms with chronic inflammation and cardiovascular disease and suggests potential targets for therapeutic intervention.},
}

@article {pmid42318592,
year = {2026},
author = {Sun, Q and Ling, X and Zhang, Y and Yim, CC and Peng, Y and Yang, Y and Chan, HN and Zhang, X and Kam, KW and Chu, WK and Ip, P and Young, AL and Tsui, SK and Tham, CC and Pang, CP and Chen, LJ and Yam, JC},
title = {Association between secondhand smoke exposure and ocular microbiome changes in children.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100630},
pmid = {42318592},
issn = {2666-5174},
abstract = {PURPOSE: To investigate whether secondhand smoke (SHS) exposure alters the ocular surface microbiome (OSM) in children and to explore potential functional consequences.

METHODS: 432 children aged 3-18 years were enrolled, including 111 SHS-exposed and 321 unexposed controls. Conjunctival swabs were collected and analyzed by 16S rRNA gene sequencing targeting the V3-V4 region. Sequencing data were processed with Qiime2 and DADA2, and taxonomic classification was based on the SILVA 138 database. Alpha diversity and beta diversity were compared using t-tests and PERMANOVA. Differentially abundant taxa were identified using LEfSe, and predicted functional pathways were analyzed using PICRUSt2 with MetaCyc and KEGG annotation.

RESULTS: SHS-exposed children showed significantly altered alpha diversity (Chao1, Shannon, Simpson) and distinct beta diversity compared with controls. LEfSe analysis revealed enrichment of several phyla and genera, including Lactobacillus and Rubellimicrobium in controls, with no taxa enriched in SHS-exposed children. Functional prediction showed enrichment of metabolism pathways such as L-methionine salvage, biphenyl, heparin, and toluene degradation and immune-related pathways, including complement activation, T and B cell receptor signaling, MAPK, and TGF-beta pathways.

CONCLUSION: SHS exposure in children is associated with significant alterations in ocular surface microbial diversity, community structure, and predicted functional pathways related to environmental stress and immune signaling. These findings highlight the sensitivity of the pediatric OSM to SHS exposure and underscore the importance of minimizing environmental tobacco smoke to protect children's ocular health.},
}

@article {pmid42318955,
year = {2026},
author = {Oh, SY and Lee, J and Han, K and Ku, GY and Yoo, N},
title = {Risk of Metabolic Disease After Right- vs Left-Sided Colectomy for Colon Cancer: A Nationwide Cohort Study.},
journal = {Diseases of the colon and rectum},
volume = {},
number = {},
pages = {},
doi = {10.1097/DCR.0000000000004350},
pmid = {42318955},
issn = {1530-0358},
abstract = {BACKGROUND: The metabolic consequences of colon cancer surgery may vary by anatomic resection site, but direct comparisons of right- versus left-sided colectomy are limited.

OBJECTIVE: To compare the incidence of new-onset diabetes mellitus, hypertension, and dyslipidemia after right- versus left-sided colectomy for colon cancer.

DESIGN: Retrospective population-based cohort study.

SETTINGS: Nationwide data from the Korean Clinical Data Utilization for Research Excellence project, linking cancer registry, insurance claims, and health screening databases.

PATIENTS: Adults aged 30 years or older with histologically confirmed colon cancer who underwent colectomy between January 1, 2013, and December 31, 2019.

MAIN OUTCOME MEASURES: New-onset diabetes mellitus, hypertension, and dyslipidemia occurring after colectomy. Hazard ratios were estimated with Cox models adjusted for demographics, lifestyle factors, body mass index, waist circumference, Surveillance, Epidemiology, and End Results summary stage, and treatment; Fine-Gray subdistribution models accounted for the competing risk of death. Inverse probability of treatment weighting (IPTW) was used to address residual confounding.

RESULTS: Among 8,228 patients (mean [standard deviation] age, 58.8 [11.4] years; 4,633 [56.3%] male), 3,253 underwent right-sided and 4,975 underwent left-sided colectomy. During a median follow-up of 4.0 years (interquartile range, 2.5-5.8), 358 patients (4.4%) developed diabetes mellitus, 1,050 (12.8%) developed hypertension, and 1,167 (14.2%) developed dyslipidemia. Right-sided colectomy was associated with a 20% lower risk of incident dyslipidemia compared with left-sided colectomy (adjusted hazard ratio, 0.80; 95% confidence interval, 0.71-0.91; p = 0.005), with no significant differences for diabetes or hypertension.

LIMITATIONS: Observational design using administrative data limits causal inference; direct measurements of bile acids, microbiome composition, or inflammatory markers were unavailable; results from a Korean population may not be generalizable to other ethnic groups.

CONCLUSIONS: The anatomic laterality of colectomy was differentially associated with metabolic outcomes; right-sided resection was associated with a lower risk of incident dyslipidemia. These findings suggest that surgical laterality may inform postoperative metabolic risk stratification and support incorporating routine lipid monitoring into post-colectomy survivorship care. See Video Abstract.},
}

@article {pmid42319135,
year = {2026},
author = {Udayakumar, S and Pollock, J and Irungu, E and Muthoga, P and Adhiambo, W and Huibner, S and Kungu'u, M and Kabuti, R and Babu, H and , and Ngurukiri, P and Weiss, HA and Seeley, J and Abramsky, T and Beattie, TS and Kimani, J and Kaul, R},
title = {Genital Immune Correlates of Seroprevalent and Seroincident Herpes Simplex Type 2 Infection Among Women Who Sell Sex in Nairobi, Kenya.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {95},
number = {6},
pages = {e70273},
pmid = {42319135},
issn = {1600-0897},
support = {MR/R023182/1/MRC_/Medical Research Council/United Kingdom ; MR/R010161/1//European Union grant/ ; #PJT-180629//Canadian Institute of Health Research (CIHR)/ ; #PJT-156123//Canadian Institute of Health Research (CIHR)/ ; },
mesh = {Humans ; Female ; Kenya/epidemiology ; Adult ; *Herpesvirus 2, Human/immunology ; *Herpes Genitalis/immunology/epidemiology ; Cadherins/metabolism ; *HIV Infections/epidemiology/immunology ; Young Adult ; *Vagina/immunology/virology ; Antibodies, Viral/blood ; Prevalence ; Sex Workers ; Seroepidemiologic Studies ; Incidence ; },
abstract = {PROBLEM: Most Herpes simplex virus type 2 (HSV-2) infection is asymptomatic but increases the risk of HIV acquisition, possibly due to alterations in genital immunology. We examine associations of HSV-2 prevalence and incidence with epithelial barrier disruption.

METHOD OF STUDY: The study was nested within the longitudinal Maisha Fiti cohort of women who sell sex in Nairobi, Kenya. HSV-2 serostatus was assessed by Kalon HSV-2 IgG assay. Socio-behavioural characteristics were assessed by questionnaire and analysed by logistic regression. Immune factors (including soluble E-cadherin (sE-cad)) were assayed in cervicovaginal secretions by multiplex immunoassay, log-transformed and analysed through linear regression.

RESULTS: Among 731 HIV-negative participants, 414 (57%) were HSV-2 seropositive. These women were older (median age 35 vs 28 years; p < 0.001) and reported increased intravaginal washing (64 vs 56%; p = 0.027) than those who were HSV-2 seronegative. Genital sE-cad levels were similar, and IL-6 levels were lower in seropositive participants (1.15 vs 1.28 pg/mL, p < 0.01). Seroincidence was 10.7/100 person (95% CI: 7.3, 15.2) years among the 317 initially seronegative participants. Incident infection was associated with older age (31 vs 28 years, p = 0.001), increased number of clients (6 vs 4 clients/week, p = 0.005), and bacterial vaginosis (BV) (32 vs 15%, p = 0.009). Although women who acquired HSV-2 had higher sE-cad and lower MIP-3α levels, there was no association after controlling for Nugent score.

CONCLUSIONS: Subclinical epithelial barrier disruption is unlikely to be underpinning HIV acquisition in asymptomatic HSV-2 infection. There was no evidence of genital immune predictors of HSV-2 acquisition, whereas the vaginal microbiome is important.},
}

Humans
Female
Kenya/epidemiology
Adult
*Herpesvirus 2, Human/immunology
*Herpes Genitalis/immunology/epidemiology
Cadherins/metabolism
*HIV Infections/epidemiology/immunology
Young Adult
*Vagina/immunology/virology
Antibodies, Viral/blood
Prevalence
Sex Workers
Seroepidemiologic Studies
Incidence

@article {pmid42319242,
year = {2026},
author = {Papadopoulou, A and Tournas, G and Antsaklis, P and Daskalakis, G and Domali, E},
title = {Do Not Treat a Sequencing Report: Therapeutic Stewardship in Endometrial Microbiome Testing.},
journal = {American journal of therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1097/MJT.0000000000002175},
pmid = {42319242},
issn = {1536-3686},
}

@article {pmid42319359,
year = {2026},
author = {Ursu, Ș and Ciocan, RA and Ursu, CP and Moldovan, RC and Zaharie, F and Spârchez, Z and Moisoiu, T and Bărăian, AI and Pop, RS and Bodea, CI and Iuga, CA and Gherman, CD and Hajjar, NA},
title = {Metabolomic Profiling of Plasma Bile Acids in Resectable Gastric Cancer.},
journal = {Chirurgia (Bucharest, Romania : 1990)},
volume = {121},
number = {Ahead of print},
pages = {aop},
doi = {10.21614/chirurgia.3314},
pmid = {42319359},
issn = {1221-9118},
mesh = {Humans ; *Stomach Neoplasms/blood/surgery/pathology/diagnosis/metabolism ; *Bile Acids and Salts/blood ; Female ; Male ; Case-Control Studies ; Middle Aged ; *Biomarkers, Tumor/blood ; *Metabolomics/methods ; Aged ; Prognosis ; Neoplasm Staging ; Predictive Value of Tests ; Tandem Mass Spectrometry ; Liquid Chromatography-Mass Spectrometry ; Biomarkers/blood ; Chromatography, Liquid ; },
abstract = {Background: Gastric cancer (GC) is characterized by late-stage diagnosis and a lack of reliable non-invasive biomarkers. This study aims to investigate the plasma bile acid (BA) profile to enhance the understanding of GC metabolism and identify potential diagnostic and prognostic tools. Methods: In a case-control design, 62 GC patients (stages I III) and 70 matched controls were recruited. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), the concentrations of 48 metabolites in plasma were measured. Statistical analysis included univariate tests, principal component analysis, and linear discriminant analysis (LDA). Results: GC patients showed a significantly lower CA/CDCA ratio and alterations in secondary and conjugated bile acids, including TLCA, GLCA, TDCA, GDCA, and GUDCA, suggesting involvement of the gut liver microbiome axis. The ability to distinguish between groups was moderate (AUC = 0.731). Furthermore, BA levels were negatively correlated with tumor stage, tumor size, and systemic inflammatory markers (CRP, mGPS), while they were positively correlated with nutritional and hematological markers such as albumin and hemoglobin. Conclusions: Gastric cancer is associated with a distinct circulating BA profile that reflects not only tumor-related metabolic remodeling, but also systemic inflammation, nutritional status, and disease burden. The reduced CA/CDCA ratio and alterations in secondary and conjugated bile acids support the involvement of the gut-liver-microbiome axis in GC biology. Although BA profiling alone showed moderate diagnostic performance, its integration with conventional tumor markers, inflammatory indices, and clinico-pathological parameters may improve multimodal biomarker panels for noninvasive patient stratification, disease assessment, and future prognostic evaluation.},
}

Humans
*Stomach Neoplasms/blood/surgery/pathology/diagnosis/metabolism
*Bile Acids and Salts/blood
Female
Male
Case-Control Studies
Middle Aged
*Biomarkers, Tumor/blood
*Metabolomics/methods
Aged
Prognosis
Neoplasm Staging
Predictive Value of Tests
Tandem Mass Spectrometry
Liquid Chromatography-Mass Spectrometry
Biomarkers/blood
Chromatography, Liquid

@article {pmid42319373,
year = {2026},
author = {Shi, S and Liang, Y},
title = {Nutrition as a regulator of hematopoietic stem cell biology and transplantation.},
journal = {Current opinion in hematology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOH.0000000000000940},
pmid = {42319373},
issn = {1531-7048},
abstract = {PURPOSE OF REVIEW: Nutrition is increasingly recognized as a biologically active regulator of hematopoietic stem cell (HSC) function and transplant recovery. This review summarizes recent advances linking nutrient availability, metabolic signaling, and the gut-marrow axis to HSC maintenance and hematopoietic stem cell transplantation (HSCT) outcomes.

RECENT FINDINGS: Recent work supports a model in which nutrient sensing, glucose, amino acid and lipid metabolism, mitochondrial redox control, and microbiome-derived metabolites collectively shape HSC quiescence, regenerative capacity, immune recovery, and susceptibility to transplant-related complications. Dietary states such as caloric restriction, fasting, obesity, and high-fat diet exposure alter HSC behavior through metabolic, inflammatory, and niche-mediated pathways. In HSCT, nutritional status before and after transplantation appears to interact with mucosal injury, microbial disruption, graft-versus-host disease (GVHD), infection, and overall outcomes, although causal evidence remains limited.

SUMMARY: Nutrition should be viewed as more than a background component of supportive care in hematology. A better mechanistic understanding of how diet and metabolism influence HSC biology may help define biomarker-informed and clinically actionable nutritional strategies to improve transplant recovery.},
}

@article {pmid42319454,
year = {2026},
author = {Xie, M and Jie, Y},
title = {From Health to Disease: A Comprehensive Review of Ocular Surface Microbiota and Detection Methods in Dry Eye.},
journal = {Current microbiology},
volume = {83},
number = {8},
pages = {},
pmid = {42319454},
issn = {1432-0991},
support = {82371022//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; *Dry Eye Syndromes/microbiology/diagnosis ; Bacteria/genetics/classification/isolation & purification ; *Eye/microbiology ; Fungi/isolation & purification/genetics/classification ; Tears/microbiology ; },
abstract = {Dry eye disease (DED) is a prevalent and multifactorial condition that significantly impacts the ocular surface, characterized by symptoms of discomfort, visual disturbance, and tear film instability. Recent research has increasingly focused on the ocular surface microbiome (OSM) and its potential role in the pathogenesis and progression of DED. The OSM consists of a diverse community of microorganisms, including bacteria, fungi, and viruses, that interact with the host to maintain ocular surface health. Dysbiosis, or the imbalance of these microbial communities, has been linked to various ocular surface disorders, including DED. This review comprehensively summarizes the current understanding of the differences in OSM between healthy individuals and patients with different types of DED, such as aqueous-deficient dry eye, evaporative dry eye, and DED associated with autoimmune conditions. Additionally, it explores the detection methods used to study the OSM, highlighting the strengths and limitations of culture-based approaches, 16 S rRNA sequencing, metagenomic shotgun sequencing, and emerging technologies like 2bRAD-M. The review also outlines future research directions, emphasizing the need for advanced multi-omics approaches, personalized microbiome-based therapies, and longitudinal studies to further elucidate the role of the OSM in DED. By enhancing our understanding of the OSM composition and function, these insights may lead to innovative diagnostic and therapeutic strategies for managing DED.},
}

Humans
*Microbiota
*Dry Eye Syndromes/microbiology/diagnosis
Bacteria/genetics/classification/isolation & purification
*Eye/microbiology
Fungi/isolation & purification/genetics/classification
Tears/microbiology

@article {pmid42319657,
year = {2026},
author = {Shon, WJ and Kim, KA and Kim, JS and Kim, BG and Im, JP and Lee, HJ and Kim, SH and Kim, JW and Kang, HW and Kim, KW and Choi, JW and Cheon, DH and Kim, D and Choi, J and Kim, ES and Koh, SJ},
title = {Habitual Ultra-processed Food Intake Is Associated with Gut Dysbiosis and Pro-inflammatory Metabolite Profiles in Korean Patients with IBD.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {42319657},
issn = {1573-2568},
abstract = {BACKGROUND AND AIMS: Ultra-processed food (UPF) is increasingly consumed worldwide and may influence gut microbial ecology relevant to inflammatory bowel disease (IBD). However, patient-level multi-omics data remains scarce. We investigated whether habitual UPF intake is associated with specific microbiota and metabolite profiles in Korean patients with IBD.

METHODS: Dietary intake was assessed using a validated food frequency questionnaire, and food was categorized by the NOVA system. UPF intake was expressed as percent of energy, and 313 patients were stratified into UPF low (Q1-Q2) and UPF high (Q3-Q4). Fecal samples of 174 patients underwent 16S rRNA sequencing and untargeted metabolomics. Microbiome differences were tested using PERMANOVA for beta-diversity and Mann-Whitney U tests for taxa. Differential metabolites were defined by p < 0.05 and |fold change|≥ 1.5, followed by Reactome enrichment with FDR correction. Correlations among microbiota, metabolites, and UPF subgroups were examined using Spearman tests with Benjamini-Hochberg adjustment. Associations between UPF intake and clinical characteristics were analyzed using Spearman tests, η[2] from ANOVA and point-biserial correlation.

RESULTS: Microbial beta-diversity differed significantly between UPF low and UPF high participants. UPF high participants showed expansion of pro-inflammatory pathobionts (Escherichia-Shigella, Proteus, Parasutterella, Enterococcus, Fusobacterium, and Clostridium innocuum group) and depletion of anti-inflammatory commensals (Faecalibacterium, Butyricicoccus, Lachnospiraceae ND3007 group, and Bifidobacterium). Metabolomic profiling revealed enrichment of inflammatory pathways (phospholipid metabolism, eNOS/NO signaling, mitochondrial β-oxidation, FMO3-mediated TMA to TMAO, tryptophan catabolism) and reduction of anti-inflammatory metabolites (AHR ligands, BAAT-conjugated bile acids). Integrated analyses demonstrated significant correlations between dysbiotic taxa and inflammatory metabolites. Among NOVA-defined UPF subgroups, sugar-sweetened beverages, ready-to-eat dishes, and packaged snacks and confectioneries showed the strongest associations with these adverse signatures. Analysis of clinical characteristics showed trends between total UPF intake and inflammatory markers (WBC, CRP, fecal calprotectin), and association with upper gastrointestinal tract involvement in patients with CD. Subgroup analysis showed that sugar-sweetened beverage intake was significantly associated with CRP elevation and upper gastrointestinal involvement in patients with CD.

CONCLUSIONS: In IBD, higher UPF intake, particularly from specific NOVA-defined subgroups, is associated with gut dysbiosis and a pro-inflammatory metabolome, which in turn correlates with unfavorable clinical characteristics. These findings provide patient-based multi-omics evidence and underscore clinically relevant dietary targets for IBD management.},
}

@article {pmid42320152,
year = {2026},
author = {Bell, A and Ergas, SJ and Main, K and Rhody, N and Guttman, L},
title = {Performance of moving bed biofilm, periphyton, and halophyte biofilters in marine multi-trophic aquaculture systems.},
journal = {The Science of the total environment},
volume = {1045},
number = {},
pages = {181943},
doi = {10.1016/j.scitotenv.2026.181943},
pmid = {42320152},
issn = {1879-1026},
abstract = {Combining multi-trophic recirculating aquaculture system (MT-RAS) biofilter types leverages the strengths of different ecological biomes, benefits water treatment, resource recovery, economics, and environmental sustainability. The overall goal of this study was to determine the effects of different aquaculture biofilter combinations on MT-RAS. Three duplicate biofilter combinations were tested in a pilot scale MT-RAS with red drum (Sciaenops ocellatus): 1) periphyton with halophytes (P + H), 2) periphyton with moving bed biofilm reactors (P + M), and 3) periphyton only (P[2]). Experiments were performed in two trials (spring and summer) with four replicates. Water quality tests validated that NH3/NH4[+], NO2[-], NO3[-], and CO2 were below fish toxic limits for all biofilter combinations. Fish mortalities were low, with food conversion ratios between 1.1 and 2.0. In all trials, periphyton added dissolved oxygen (DO) to the water (at an average of +3.95 ± 6.52 mg/(L*d)), thus reducing energy costs. Periphyton was also found to include valuable lipid content (4.55 ± 2.24% of dry weight) with the detection of Ω-3 fatty acids. The P[2] trials maintained a stable alkalinity and pH balance. The M + P trials removed NH3/NH4[+] at a high rate; however, they also required more energy for DO. Edible sea purslane growth rates (1.0431 ± 0.3361 g/day/plant) were efficient in all P + H trials. The microbiome revealed abundance of Ignavibacterium bacteria, Navicula and Chlorella algae, Nitrospira, Nitrospirae, Nitrosospharota, and Nitrosoarchaeum nitrogen cyclers. Overall, periphyton biofilter combinations nitrify, denitrify, stabilize pH, photosynthesize, and produce oxygen and a value-added product.},
}

@article {pmid42320497,
year = {2026},
author = {Miller, SJ and Rogers, GB},
title = {What constitutes a healthy vaginal microbiome? Implications for intervention strategies.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101474},
doi = {10.1016/j.lanmic.2026.101474},
pmid = {42320497},
issn = {2666-5247},
}

@article {pmid42320590,
year = {2026},
author = {Zhang, JS and Lu, W and Zhu, H and Liang, Z and Chu, CH and Jakubovics, NS and Chen, Z and Yu, OY},
title = {Staging-Dependent Dysbiosis of Plaque Microbiota in Early Childhood Caries.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106846},
doi = {10.1016/j.jdent.2026.106846},
pmid = {42320590},
issn = {1879-176X},
abstract = {OBJECTIVES: The stage-specific ecological and functional microbial features of ECC remains poorly defined. This study aimed to characterize the lesion-associated microbiome and evaluate stage-specific microbial signatures of ECC.

METHODS: Paired supragingival plaque samples were collected from an active cavitated lesion (caries) and a spatially-matched intact surface (control) of 84 ECC-affected children aged 3 - 4 years. Lesions were classified by depth as enamel caries and dentine caries. Microbial profiles were generated by 16S rRNA sequencing and analysed for community diversity, structure, and differentially abundant taxa. PICRUSt2 was used for functional prediction.

RESULTS: Alpha diversity did not differ between caries and controls, but beta diversity revealed significant compositional separation. PERMANOVA identified disease status as the main driver of community variation, with disease staging as an additional significant factor. Caries lesions were enriched with classical and emerging cariogenic taxa, including Streptococcus mutans, Prevotella histicola, Prevotella salivae, Selenomonas sputigena, Scardovia wiggsiae, and Veillonella dispar. A 13-species panel distinguished caries from controls with an AUC of 0.85. Stratification by caries staging revealed pronounced dysbiosis confined to the dentine caries subgroup. Functional prediction suggested that dentine caries had a distinct inferred profile, with predicted enrichment of carbohydrate metabolism pathways, the phosphotransferase system, and the pentose phosphate pathway.

CONCLUSIONS: In ECC-affected children, plaque microbiome in carious lesions showed distinct compositional, ecological and functional alterations versus unaffected surfaces, with further dysbiosis driven by caries progression. Dentine caries featured a stage-specific consortium of cariogenic taxa and a predicted functional shift toward intensified carbohydrate uptake and fermentation, informing potential microbiome-targeted strategies for ECC management.

CLINICAL SIGNIFICANCE: The identified ecological progression of ECC offers key microbial biomarkers to inform microbiome-targeted preventive and therapeutic strategies, ultimately improving clinical outcomes in pediatric dentistry.},
}

@article {pmid42320750,
year = {2026},
author = {Siddiqui, S and Kahkasha, K},
title = {Gut-pancreas-metabolism axis: emerging anti-diabetic roles of gut-derived bioactive molecules.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113383},
doi = {10.1016/j.diabres.2026.113383},
pmid = {42320750},
issn = {1872-8227},
abstract = {The rising global burden of diabetes mellitus necessitates exploration of mechanisms beyond classical pancreatic dysfunction. The gut-pancreas-metabolism axis has emerged as a central regulatory network linking gut microbiota, enteroendocrine signaling, immune modulation, and pancreatic function in glucose homeostasis. Gut-derived bioactive metabolites, including short-chain fatty acids, bile acid derivatives, indole compounds, lipopolysaccharide fragments, and microbial peptides, significantly influence insulin secretion, insulin sensitivity, inflammation, and energy metabolism. These metabolites regulate key pathways such as AMP-activated protein kinase, PI3K/Akt signaling, G-protein-coupled receptor activation, and inflammatory cascades, thereby contributing to β-cell preservation and metabolic balance. Dysbiosis-associated shifts in microbial metabolite profiles are strongly associated with insulin resistance, impaired incretin responses, and chronic low-grade inflammation in type 2 diabetes. This review summarizes recent mechanistic advances in the gut-pancreas-metabolism axis and highlights the therapeutic potential of microbiota-derived bioactive compounds. Furthermore, it discusses emerging translational strategies, including probiotics, prebiotics, postbiotics, and dietary modulation of the gut microbiome, as adjunctive approaches for diabetes management. Targeting this axis provides promising opportunities for precision-based metabolic therapy in diabetes care.},
}

@article {pmid42320811,
year = {2026},
author = {Wang, Y and Wu, X and Deng, H and Yan, G and Xu, Z and Zhu, L},
title = {A high-molecular-weight polysaccharide from Polygonatum sibiricum inhibits distant tumor growth associated with gut microbiota remodeling and synergizes with αPD-1 therapy.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153116},
doi = {10.1016/j.ijbiomac.2026.153116},
pmid = {42320811},
issn = {1879-0003},
abstract = {BACKGROUND: Defined polysaccharide fractions can reshape the gut microbiome and influence systemic antitumor immunity. We investigated whether an operationally defined high-molecular-weight Polygonatum sibiricum polysaccharide fraction (PSP-H) enriched by 100 kDa ultrafiltration suppresses growth of subcutaneous MC38 tumors via microbiota-dependent mechanisms and potentiates anti-PD-1 therapy.

MATERIALS AND METHODS: PSP-H was isolated by cascade ultrafiltration and compared with a total polysaccharide extract (PSP-T) and lower-MW fractions. We profiled fecal metagenomes, serum metabolites, tumor molecular readouts (immunoblotting; HDAC activity), and immunity. Fecal microbiota transplantation (FMT) tested the microbiota dependence and sufficiency of PSP-H-remodeled communities to transfer the immunometabolic phenotype. Combination with anti-PD-1 (RMP1-14) was evaluated.

RESULTS: PSP-H showed minimal direct cytotoxicity while suppressing tumor growth, selectively enriching butyrate-producing taxa (e.g., Lachnospiraceae) and elevating serum butyrate and inosine, with TNF-α reduced. In vitro, butyrate enhanced T-cell IFN-γ/IL-2/granzyme-B, inhibited tumor HDAC activity, and counteracted IFN-γ-induced PD-L1; in vivo, PSP-H created a T-cell-activating milieu with adaptive STAT1/PD-L1 up-regulation. FMT recapitulated the key metabolite/cytokine signature. PSP-H + anti-PD-1 synergistically increased intratumoral CD8[+] T cells and yielded superior tumor control versus monotherapy.

CONCLUSION: PSP-H is a defined microbiota-modulating adjuvant that engages a microbiome-butyrate-immune axis to restrain subcutaneous tumors and sensitizes them to PD-1 blockade by converting systemic immunity while inducing targetable adaptive resistance.},
}

@article {pmid42320851,
year = {2026},
author = {Shen, S and Zhang, J and Qi, X},
title = {The role of short-chain fatty acids as key mediators of gut microbiota - host crosstalk in thyroid diseases.},
journal = {Autoimmunity reviews},
volume = {25},
number = {9},
pages = {104123},
doi = {10.1016/j.autrev.2026.104123},
pmid = {42320851},
issn = {1873-0183},
abstract = {The gut-thyroid axis has emerged as a pivotal area of research in endocrinology. Growing evidence suggests that gut microbiota (GM) dysbiosis is implicated in the pathogenesis of thyroid diseases. Short-chain fatty acids (SCFAs), key microbial metabolites, are proposed as critical mediators in this interplay, but a comprehensive synthesis of their roles is needed. This review provides an overview of the mechanisms and therapeutic potential of SCFAs in thyroid diseases. Patients with thyroid diseases commonly exhibit gut microbiota dysbiosis, characterized by reduced SCFA-producing bacteria and decreased systemic SCFA levels. Mechanistically, SCFAs regulate immune and metabolic homeostasis through G protein-coupled receptor signaling, histone deacetylase inhibition, mitochondrial metabolism, mTOR-S6K signaling, and intestinal barrier protection. Their deficiency may disrupt immune tolerance, promoting autoimmunity and tumor progression. However, current research remains largely correlative, with insufficient mechanistic evidence. SCFAs are central to gut-thyroid crosstalk. Targeting SCFA pathways through probiotics, prebiotics, or microbiota transplantation represents a promising therapeutic frontier. Future research must prioritize establishing causality using advanced models and validating these approaches in rigorous clinical trials to pave the way for personalized microbiome-based therapies for thyroid diseases.},
}

@article {pmid42321165,
year = {2026},
author = {Zhang, L and Lv, C and Guo, W and Fu, Q and Li, Y and Liu, X},
title = {Multi-omics insights into isovaleric acid effects on broiler performance, physiological health, and meat quality.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01053-0},
pmid = {42321165},
issn = {2055-5008},
support = {2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Isovaleric acid (IVA) has been shown to benefit gut health, but its effects on broiler meat quality remain unclear. A total of 864 broilers were assigned to control or 0.05%, 0.1%, or 0.2% IVA groups to evaluate the effects of IVA supplementation on performance, blood biochemistry, immunity, gut microbiota, metabolome, and meat quality. IVA increased average daily gain and, at some doses, feed intake and villus height, while reducing feed conversion ratio. It also lowered serum blood urea nitrogen at 21 and 42 days and modulated inflammatory and immune indices. IVA improved meat quality by increasing breast and leg muscle protein content at 42 days, reducing drip loss and shear force, and improving color parameters. Microbiome analysis showed that IVA reduced Ace index and altered bacterial and fungal β-diversity at 21 days, whereas at 42 days it increased bacterial Shannon index and shifted community composition, while fungal α-diversity remained largely unchanged. Metabolomics revealed marked changes in lipid and amino acid metabolism. Integrative analysis identified Collinsella, norank_f__Ruminococcaceae, and unclassified_f__Oxalobacteraceae as key taxa associated with beneficial muscle metabolites. These findings highlight a gut microbiota-metabolome-muscle axis contributing to improved broiler meat quality and inform nutritional interventions in poultry production.},
}

@article {pmid42321256,
year = {2026},
author = {Zhao, Y and Wang, Y and Bai, S and Tan, J and Niu, H and Zhang, A and Guo, G and Fang, L and Jiang, L},
title = {Reprogramming hydrogen metabolism for methane mitigation in dairy cows: mechanistic insights from polyphenols using meta-omics approaches.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01068-7},
pmid = {42321256},
issn = {2055-5008},
support = {JR25027//Beijing High-Level Innovation and Entrepreneurship Talent Program-Basic Research Talent Project/ ; 2023YFD1301801//National Key R&D Program of China/ ; BAIC05-2025//Beijing Livestock Industry Innovation Team/ ; },
abstract = {Enteric methane emissions from ruminants contribute significantly to agricultural greenhouse gases. Plant-derived phytochemicals such as grape seed proanthocyanidins (GSP) are promising natural antimethanogenic feed additives, yet their modes of action remain incompletely understood. This study aimed to comprehensively elucidate the microbiological and functional mechanisms underlying phytochemical-induced methane mitigation using integrative meta-omics. Both in vivo and in vitro experiments demonstrated that GSP supplementation significantly reduced methane emissions; in lactating dairy cows, GSP decreased methane emission intensity by 16.5% (g/kg energy-corrected milk). Metagenomic and metatranscriptomic analyses revealed a reprogramming of microbial communities, with decreased abundance and transcriptional activity of methanogenic archaea (e.g., Methanobrevibacter) and enhanced activity of alternative hydrogenotrophic bacteria (Selenomonas, Veillonella, Sharpea). Functionally, GSP elevated expression of genes involved in reductive acetogenesis (e.g., acsB), nitrate ammonification (narG, nrfA), and sulfate reduction (dsrA), thereby redirecting hydrogen flux away from methanogenesis. These shifts were accompanied by increased microbial carbohydrate metabolism and antioxidative responses. Our findings provide the first meta-omics-based mechanistic framework for understanding methanogenesis suppression by phytochemicals in ruminants. GSP modulates microbial composition and function to reroute reductant flows and suppress archaeal methanogenesis through enhanced bacterial electron sinks. This work highlights the potential of polyphenols to modulate the rumen microbiome for sustainable methane mitigation, supporting the development of next-generation feed additives.},
}

@article {pmid42321259,
year = {2026},
author = {Lu, CR and Hu, WP and Hsu, CH and Wang, CC and Chang, SS and Lin, YN and Lin, YK and Chung, WH and Chang, KC and Wang, JM and Cho, DY and Hsu, YY and Tsai, HH and Lai, ZL and Wang, YJ and Hsueh, PR and Lai, HY},
title = {Gut microbiome signatures discriminate deep vein thrombosis through machine learning and metabolic analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-55650-2},
pmid = {42321259},
issn = {2045-2322},
support = {DMR-113-007//China Medical University Hospital/ ; CMU113-N-11//China Medical University, Taiwan/ ; NSTC114-2314-B-039-053-MY2//National Science and Technology Council/ ; },
abstract = {Deep vein thrombosis (DVT) remains difficult to distinguish because of its often silent presentation and the limited specificity of current diagnostic tools. We aimed to evaluate whether integrating gut microbiome profiles with routine clinical data could enhance the classification performance for identifying DVT in a case-control cohort. Stool samples were collected from individuals with DVT (n = 58), coronary artery disease (CAD, n = 56), and healthy controls (HC, n = 500). Full-length 16S rRNA gene sequencing was used to characterize the gut microbiota at species-level resolution. A random forest classifier was trained using a nested cross-validation framework, with permutation importance and SHAP (Shapley additive explanations) analyses applied to assess model interpretability. Decision curve analysis (DCA) was employed to evaluate the discriminative value of the models in an independent test set. Following linear discriminant analysis (LDA) effect size (LEfSe) screening, 95 candidate microbial features were entered into a random forest framework. Features were reduced using mutual information filtering and embedded selection to retain the final 10 for DVT vs. non-DVT classification. The integrated microbial-clinical model demonstrated substantially improved discrimination compared with the clinical-only model, achieving higher ROC-AUC [0.947 (95% CI 0.870-0.991) vs. 0.874 (95% CI 0.794-0.941)] and PR-AUC [0.793 (95% CI 0.602-0.931) vs. 0.497 (95% CI 0.274-0.724)]. Importantly, the microbiome-derived signals were robustly associated with DVT risk after adjustment for clinical covariates. Functional prediction analysis indicated enrichment of vitamin K2 and lipopolysaccharide (LPS) biosynthesis pathways in DVT, suggesting potential microbial links to coagulation and inflammation, whereas healthy controls were predominantly enriched in NAD and tetrahydrofolate (THF) biosynthesis pathways. Together, these results demonstrate that microbiome-based classification provides complementary biological insights that distinguish DVT cases from controls.},
}

@article {pmid42321264,
year = {2026},
author = {Mtshali, A and Togo, AH and Kama, A and Letsoalo, M and Mzobe, G and Sivro, A and Garrett, N and Zondo, N and Mahomed, S and Archary, D and Ngcapu, S},
title = {Cervicovaginal microbiome diversity was not associated with mucosal pharmacokinetics of systemically delivered HIV broadly neutralizing antibodies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57511-4},
pmid = {42321264},
issn = {2045-2322},
support = {REF: TTK240315209308//National Research Foundation/ ; EDCTP Grant number: RIA2017S//European and Developing Countries Clinical Trials Partnership/ ; },
abstract = {Broadly neutralizing antibodies (bNAbs) are a promising HIV prevention strategy due to their potent antiviral activity and potential for long-acting protection. While the vaginal microbiome can influence mucosal immunity and the efficacy of topical interventions, its effect on the pharmacokinetics of systemically administered bNAbs remains unclear. Forty-two women were included in a retrospective analysis of the CAPRISA 012B clinical trial evaluating passive immunization for HIV prevention. Vaginal microbiota were profiled using 16 S rRNA gene sequencing and classified into three community state types (CSTs): CST I (Lactobacillus crispatus-dominated), CST III (Lactobacillus iners-dominated), and CST IV (diverse, non-Lactobacillus-dominated). Mucosal concentrations of CAP256V2LS were measured from Soft-cup[®] cervicovaginal fluid using the Meso Scale Discovery (MSD) platform with electrochemiluminescence (ECL) detection. Longitudinal analyses assessed CST stability, transitions, and associations with mucosal antibody pharmacokinetics. Lactobacillus-dominated CSTs were most frequent (CST I, 5.3%; CST III, 57.9%), whereas BV-associated CST IV subtypes were less common (CST IV-A, 2.6%; CST IV-B, 34.2%). Lactobacillus-dominated communities were generally stable, while high-diversity CST IV communities were more dynamic, with transitions toward Lactobacillus-dominated states observed over time. Despite these microbial shifts, mucosal bNAb kinetic patterns appeared broadly similar across CSTs. Within the limits of this exploratory analysis, we did not observe clear evidence of an association between CST composition and the timing or magnitude of mucosal bNAb accumulation. These observations were descriptive and not derived from inferential statistical or pharmacokinetic modelling analyses. In this exploratory sub-analysis, cervicovaginal microbiome composition was not clearly associated with differences in mucosal concentrations of systemically administered bNAbs. These findings suggest that systemic bNAb delivery may achieve measurable genital tract exposure across diverse vaginal microbial communities; however, larger studies incorporating inferential pharmacokinetic and immunological analyses are needed to confirm these observations and exclude subtle microbiome-associated effects.},
}

@article {pmid42321538,
year = {2026},
author = {Holmberg, SM and Schroeder, BO},
title = {Fatty diets disrupt mucus-microbiome-metabolite interactions to increase intestinal lipid uptake.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42321538},
issn = {2058-5276},
support = {2025-02844//Vetenskapsrådet (Swedish Research Council)/ ; 2021-06602//Vetenskapsrådet (Swedish Research Council)/ ; 2024-0100//Familjen Erling-Perssons Stiftelse (Erling-Persson Family Foundation)/ ; },
}

@article {pmid42321605,
year = {2026},
author = {Sun, Y and Tang, J and Ma, S and Maimaiti, A and Liu, J and Qiu, J and Ge, J},
title = {Stage-specific rhizosphere microbial succession is associated with nutrient cycling in the desert plant Leymus racemosus (Lam.) tzvelev.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09294-z},
pmid = {42321605},
issn = {1471-2229},
support = {XKLEAEEEO-03//Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organisms, College of Life Sciences, Xinjiang Agricultural University/ ; 23XJTRZW20//the Special Fund of the Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; },
abstract = {BACKGROUND AND AIMS: Plants regulate nutrient uptake and growth by recruiting rhizosphere microorganisms via root exudates. However, a systematic understanding of how the rhizosphere core and functional microbiota jointly regulate the dynamics of carbon, nitrogen, phosphorus, and potassium across the entire plant life cycle in desert ecosystems remains limited. In this study, we asked: how does the succession of rhizosphere bacterial communities align with stage-specific nutrient demands in the desert plant Leymus racemosus?

METHODS: We used 16 S rRNA high-throughput sequencing to analyze the rhizosphere bacterial communities and nutrient contents of the desert plant Leymus racemosus at three growth stages (seedling, flowering, maturity) in the Kalamaili Nature Reserve, Xinjiang, China. For each stage, ten 5 × 5 m quadrats (20 m apart) were established; 6-10 healthy plants were sampled per quadrat, and rhizosphere soil from each quadrat was pooled into one composite sample (n = 10 per stage).

RESULTS: Arthrobacter, identified as a core taxon, was associated with the stability of hydrolyzable nitrogen across all growth stages. Bacillus became the dominant genus during the flowering stage, based on correlation and functional prediction, it may contribute to nutrient supply, reflecting a potential "investment" strategy. At maturity, enhanced microbial cooperation (inferred from co-occurrence and correlation analyses) combined with reduced plant demand was associated with the accumulation of rhizosphere nutrients, possibly facilitating energy storage for subsequent growth. These findings provide a potential answer to our question, suggesting that the plant recruits distinct microbial alliances at different phenological phases-a persistent Arthrobacter-based system for nitrogen buffering, a transient Bacillus-enriched community for rapid nutrient mobilization at flowering, and a synergistic network at maturity for delayed nutrient accumulation.

CONCLUSIONS: This study reveals the developmental dynamics of rhizosphere bacterial community assembly and nutrient regulation in L. racemosus and provides a theoretical basis for further elucidating plant-microbe interactions in desert ecosystems. However, the proposed functional roles of specific taxa are primarily derived from correlation and predictive analyses; experimental validation (e.g., strain isolation, inoculation tests, and metabolomics) is needed to establish causality.},
}

@article {pmid42321612,
year = {2026},
author = {Nikparast, A and Sepehrinia, M and Zamanian, N and Razaz, JM and Tabatabaeyan, A and Hadi, S and Homayounfar, R},
title = {Adherence to the dietary index for gut microbiota and the 5-year incidence of metabolic dysfunction-associated steatotic liver disease in Iranian adults: a prospective cohort study.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-026-05036-5},
pmid = {42321612},
issn = {1471-230X},
abstract = {BACKGROUND: Diet is a key modulator of gut microbiota and may influence the development of metabolic dysfunction-associated steatotic liver disease (MASLD). The Dietary Index for Gut Microbiota (DI-GM) has been proposed to capture the overall capacity of diet to promote a favorable gut microbial profile. Prospective evidence linking DI-GM to MASLD risk remains limited.

METHODS: This prospective analysis included 5,058 adults without MASLD at baseline from the Monitoring of Metabolic Diseases Risk Factors in Tehran (MMRT) study. Dietary intake was assessed using a validated 125-item food frequency questionnaire. The five-year incidence of MASLD was evaluated using multivariable logistic regression models, and associations were expressed as odds ratios (ORs) with 95% confidence intervals (CIs). Subgroup analyses were conducted to assess potential effect modification. Sensitivity analyses examined the robustness of results after excluding participants with substantial weight gain and after additional adjustment for metabolic and dietary factors. Mediation analyses were performed to explore potential pathways underlying the observed associations.

RESULTS: Over five years of follow-up, 562 participants developed MASLD. Higher DI-GM scores were associated with a lower likelihood of incident MASLD. In the fully adjusted model, individuals in the highest quartile of DI-GM had 42% lower odds of MASLD compared with those in the lowest quartile (OR:0.58; 95%CI:0.42-0.80; P-trend < 0.01). Each one-standard-deviation increment in DI-GM score was associated with reduced odds of MASLD (OR:0.72; 95%CI:0.65-0.81;P-value < 0.001). The inverse association was more pronounced among women and participants aged ≥ 45 years (P-interaction < 0.01). Mediation analyses suggested that CAP, HOMA-IR, and serum vitamin D partially explained the association.

CONCLUSIONS: Greater adherence to a diet supportive of gut microbiota, as reflected by higher DI-GM scores, was associated with a lower five-year risk of MASLD. These findings highlight the potential role of microbiota-related dietary patterns in MASLD prevention.},
}

@article {pmid42321771,
year = {2026},
author = {Nielsen, DP and Holding, ML and Del Carlo, RE and Everson, KM and Ochsenrider, K and Simison, WB and Henderson, J and Dearing, MD and Hayes, JP and Frese, SA and Richards, LA and Ferguson, BS and Forbey, JS and Matocq, MD},
title = {Diet change reveals asymmetric response in gene expression and microbial composition across the digestive tract of two closely related herbivores.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-026-02658-9},
pmid = {42321771},
issn = {1741-7007},
abstract = {BACKGROUND: Understanding what shapes variation in organisms' capacity to utilize novel resources is essential to predicting how species will respond to environmental change. For herbivores, exposure to toxic phytochemicals in novel plants may limit persistence in new habitats. We investigated the behavioral, physiological, genetic, and microbial consequences of diet switching in two closely related species of rodent herbivores that each consume differentially toxic plants in their native habitat, and that maintain different dietary strategies (i.e., relative dietary specialist versus relative generalist).

RESULTS: In reciprocal laboratory feeding trials, we exposed wild-caught woodrats (genus Neotoma) to toxins characteristic of either familiar or novel plant secondary compounds. We measured changes in food and water intake, locomotor activity, gut microbial composition, and gene expression across the digestive tract following feeding trials. The dietary generalist responded minimally, but the specialist responded strongly when exposed to the novel diet. This response included behavioral and genetic components including increased water intake, reduction in locomotor activity, increased differential expression of detoxification genes, and a greater shift in gut microbial composition.

CONCLUSIONS: The dietary specialist exhibited a strong response to diet switching that corresponded with ecologically relevant shifts in behavior and physiology that would have negative fitness consequences. Although the dietary specialist had a strong genetic and microbial response to novel plant secondary compounds, this response would likely be insufficient to overcome the immediate challenge of exposure to novel dietary toxins in the wild. Our results underscore the link between feeding strategy and the capacity to shift to novel dietary resources in response to environmental change.},
}

@article {pmid42321864,
year = {2026},
author = {Wang, W and Huang, X and Wu, F and Liu, X},
title = {Identification of keystone taxa shaping biocrust formation and biodeterioration of limestone monuments in the Xiaoling Tomb of the Ming Dynasty.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42321864},
issn = {2524-6372},
support = {BK20250086//Basic Research Program of Jiangsu Province/ ; 32570139 and 32370105//National Natural Science Foundation of China/ ; },
abstract = {The limestone monuments of the Rectangular Tower in the Xiaoling Tomb of the Ming Dynasty, created in the mid-fourteenth century, are biodeteriorating from environmental exposure, resulting in the formation of black biocrusts. However, the microbiomes that shape biocrust formation and the biodeterioration processes involved remain unclear, significantly challenging the conservation of stone monuments at this archaeological site. Here, we systematically investigated the physicochemical properties and microbial communities of biocrusts to identify keystone taxa that shape their formation and biodeterioration. Physicochemical analysis indicated that biological crusts are associated with calcium mobilization and redistribution of the limestone monuments. Microscopy and spectroscopy indicated that microbial interactions with limestone promote the formation of biological crusts. Importantly, we observed the significant predominance of Cyanobacteria and/or Chloroflexi in biocrusts, suggesting that photosynthesis may be a crucial process in biocrust formation. Fungal communities in biocrusts were dominated by Ascomycota, Basidiomycota, and Chytridiomycota, while archaeal communities were dominated solely by Nitrososphaerota. Microbial co-occurrence network and correlation analyses identified 12 keystone taxa across 11 genera that shape biocrust formation. Importantly, Scytonema spp. could provide organic carbon and nitrogen for Spirosomaceae spp., and members of the classes Cyanobacteriia and Agaricomycetes, as well as the genera Setophaeosphaeria and Plectosphaerella, are likely the keystone taxa responsible for both biocrust formation and the associated biodeterioration. Additionally, two predominant ammonia-oxidizing archaeal families (i.e., Nitrososphaeraceae and Candidatus Nitrocosmicus) could support chemolithoautotrophic growth in the microbiome by oxidizing ammonia and fixing carbon dioxide. Together, these findings underscore the need for targeted conservation strategies to mitigate microbial biodeterioration of stone monuments during biocrust formation.},
}

@article {pmid42321912,
year = {2026},
author = {Zhou, M and Deng, Y and Huang, Y and Yu, C and Chen, X and Yang, Q and Liao, Y and Wang, S and Zhang, P and Chen, A and Ling, W and Chen, X and Li, J and Xue, H},
title = {Dietary index for gut microbiota, plasma metabolome, and risks of metabolic dysfunction-associated steatotic liver disease and other chronic liver diseases.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-026-01145-w},
pmid = {42321912},
issn = {1743-7075},
support = {82304130//National Natural Science Foundation of China/ ; SL2023A04J01145//Basic research project of Guangzhou Science and Technology Bureau/ ; },
abstract = {BACKGROUND: The dietary index for gut microbiota (DI-GM) is a newly proposed metric for assessing diet quality linked to gut microbiota. However, prospective evidence is scarce on the associations between DI-GM and adverse liver outcomes.

METHODS: The DI-GM was calculated by averaging the intakes of 12 foods and nutrients. Elastic net regression was performed to identify metabolites associated with DI-GM and metabolic signature reflecting higher adherence to DI-GM was constructed. Cox proportional hazards regression and mediation analyses were employed to explore the potential associations and mechanisms.

RESULTS: This prospective cohort study included 168,456 participants from the UK Biobank. Compared to participants with DI-GM scores of 0-3, those scoring ≥ 6 presented 22% lower risk of MASLD (HR = 0.78, 95% CI = 0.68-0.90). Metabolic signature for DI-GM and dietary index beneficial to gut microbiota (BDI-GM) were also inversely correlated with MASLD. Similar inverse correlations between DI-GM and BDI-GM and the risks of other chronic liver diseases were identified. Furthermore, phenotypic age, body mass index, metabolic score, inflammatory score, and metabolic signature significantly mediated the relationship between DI-GM and MASLD. No significant interactions were observed between DI-GM and polygenic risk score of hepatic steatosis, and the associations between DI-GM and adverse liver outcomes persisted regardless of genetic risk.

CONCLUSIONS: Higher adherence to DI-GM significantly correlates with reduced risks of MASLD and other chronic liver diseases, independent of genetic susceptibility. And the apparent mediating effects of five indices highlight the role of aging, obesity, metabolic disorders, inflammation, and metabolomic alterations in the association between DI-GM and MASLD. Further research is warranted to evaluate the utility of metabolic signatures in metabolic profile monitoring and risk stratification.

IMPACT AND IMPLICATIONS: This large-scale cohort study first demonstrates that higher adherence to a gut microbiota-beneficial diet (DI-GM) is associated with a lower risk of MASLD and other chronic liver diseases, independent of genetic susceptibility. The estimated population attributable fractions, while derived from observational data and requiring cautious interpretation, suggest that a substantial portion of liver disease cases in the study population might be linked to suboptimal DI-GM adherence. These findings underscore the importance of integrating gut microbiome health into public health strategies for liver disease prevention, offering a practical approach to reduce disease burden at both individual and population levels. The DI-GM-associated metabolic signature represents a candidate objective biomarker meriting evaluation in future studies for its potential in early risk assessment. Mediation analyses further reveal that a diet promoting healthy gut microbiota may reduce MASLD risk by maintaining gut microbiota homeostasis, decelerating biological aging, ameliorating obesity, attenuating metabolic disorders, alleviating inflammation, and altering metabolome. Collectively, this study generates important hypotheses and provides a rationale for future interventional research to determine whether promoting DI-GM-aligned diets can effectively reduce liver disease risk at the population level.},
}

@article {pmid42322129,
year = {2026},
author = {Usui, T and Yu, J and Frederickson, ME},
title = {For colonization success, should hosts and microbes travel alone, together, or swap partners along the way?.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71372},
pmid = {42322129},
issn = {1469-8137},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; GBM10635//Gordon and Betty Moore Foundation/ ; GBMF9536//Gordon and Betty Moore Foundation/ ; //University of Toronto/ ; },
abstract = {Microbiomes that enhance the performance of host plants are likely to be co-introduced with their host during colonization because of their intimate association. Yet, it is unclear how co-introduced microbes will impact host colonization, as both the microbiome and its effects could vary upon introduction into a new habitat. Using the duckweed Lemna japonica - a cosmopolitan, freshwater angiosperm - and its microbiome, we tracked the colonization of both plants and microbes during an experimental co-introduction in the wild. We tested how plant performance varied during colonization when plants were co-introduced with microbes from their home habitat or with microbes local to the introduced habitat. We found that plant performance was substantially reduced when plants were co-introduced with microbes from their home habitat (i.e. with microbes that are non-local to the introduced habitat), relative to hosts with a local microbiome. Moreover, negative impacts from the initial, non-local microbiome persisted for multiple host generations despite a rapid turnover in microbiome composition. Our results suggest that the initial microbiome plants are co-introduced and can leave lasting impacts on plant performance during colonization. Considering the identity of the co-introduced microbiome will therefore be critical to predicting plant colonization dynamics in an era of global change.},
}

@article {pmid42322204,
year = {2026},
author = {Moran, GP and McQuillan, A and Ho, GT and Whelan, RJ and Navas-López, VM and Lawrence, S and Rolandsdotter, H and Olen, O and Martín-de-Carpi, J and Sigall Boneh, R and Wine, E and Hussey, S},
title = {Modified Crohn's Disease Exclusion Diet and exclusive enteral nutrition (EEN) resolve oral dysbiosis in pediatric Crohn's disease: a prospective cohort study.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag107},
pmid = {42322204},
issn = {1536-4844},
support = {c/18/2//Children's Health Foundation/ ; },
abstract = {BACKGROUND AND AIMS: Changes to the oral microbiome have been reported in patients with Crohn's disease (CD). The aim of this study was to determine the characteristics and dynamics of the oral microbiome in children randomized to 1 of 2 nutritional treatments for CD.

METHODS: Participants (n = 54) in this randomized controlled trial (NCT02843100) received the Crohn's Disease Exclusion Diet (CDED) with either partial enteral nutrition (PEN; n = 28) or exclusive enteral nutrition (EEN; n = 26). The oral microbiome was assessed via swabs from the dorsum of the tongue and the buccal gingiva by 16S rRNA sequencing at 0, 2, 8, 14, 24, and 52 weeks.

RESULTS: There were no significant differences in primary or clinical outcomes between the 2 groups. Due to the COVID-19 pandemic, sampling by 24 weeks was limited to 34 participants. At week 0, moderate-severe disease activity (Pediatric Crohn's Disease Activity Index [PCDAI] > 30) was associated with decreased Porphyromonas, Haemophilus, Alloprevotella, Neisseria, and Bergeyella species and increased Actinomyces. As patients entered remission (PCDAI < 10), we observed a restoration in the abundance of these taxa. A modified oral dysbiosis index (MODI) was generated, capable of distinguishing mild from moderate-severe disease activity based on microbiome profiles. Dysbiosis decreased as treatment continued and patients entered remission. Patients on CDED exhibited more significant dysbiosis index changes at weeks 8-24, compared with the EEN group. Application of the index across published oral microbiome data sets validated its ability to discriminate health from CD.

CONCLUSION: Oral microbiome changes in pediatric CD reflect disease activity and parallel therapeutic response to CDED and EEN over time. Additional validation of the proposed dysbiosis index should be undertaken in adequately powered future studies.},
}

@article {pmid42322208,
year = {2026},
author = {Thi Dang, ND and Nguyen, MT and Nguyen, DS and Nguyen, QV},
title = {Wild guava (Psidium guajava L.) leaf extract: multifaceted effects on gut microbiota, gene expression, and metabolic regulation in a zebrafish model of type 2 diabetes.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/14786419.2026.2689480},
pmid = {42322208},
issn = {1478-6427},
abstract = {Wild guava (Psidium guajava L.) leaf extract shows promise for type 2 diabetes mellitus (T2DM) management through its effects on the gut microbiota, gene expression, and metabolism. This study examined the extract's effects on probiotic growth, gut microbiota, and diabetes-related gene expression in a zebrafish T2DM model. The extract enhanced probiotic growth of Lactobacillus casei, L. plantarum, and YC-381 by up to 33.11% in hyperglycaemic conditions. In diabetic zebrafish, it restored gut microbiota diversity, reduced pathogenic genera, and increased beneficial taxa like Leuconostoc and Bacillus. Functional analysis showed improved microbial polyphenol and lipid metabolism. The extract downregulated ACC1, normalised insulin receptor expression, reduced SGLT1, and moderately increased GLP1. Transcriptomic analysis revealed the homeostatic effects of the extract on metabolic pathways, in contrast to the pharmacological modulation of metformin. These results demonstrate the potential of wild guava leaf extract as a T2DM intervention through its effects on the microbiome-transcriptome-phenotype axis.},
}

@article {pmid42322288,
year = {2026},
author = {Silva, E and Santana Aguiar, MC and Vilhena Araújo, E and França, P and Berlinck, RGS and Ballester, AR and González-Candelas, L and Fill, T},
title = {Green Mold of Citrus: Recent Insights into Penicillium digitatum Pathogenicity and Biological Control Strategies.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c02943},
pmid = {42322288},
issn = {1520-5118},
abstract = {P. digitatum, the causal agent of citrus green mold, remains the most destructive postharvest pathogen of citrus worldwide. Recent advances have greatly expanded our understanding of the molecular dialogue between P. digitatum and citrus hosts, revealing coordinated virulence strategies involving cell wall-degrading enzymes, major facilitator superfamily transporters, transcription factors, and secondary metabolism, alongside host defenses mediated by phytohormones and specialized metabolites. This review integrates genomic, transcriptomic, metabolomic, and functional genetic discoveries, including CRISPR/Cas9 and Agrobacterium tumefaciens-mediated transformation, which have accelerated the characterization of fungal pathogenicity and host resistance. We further assess biological control as a sustainable alternative to chemical fungicides, emphasizing complementary mechanisms such as niche competition, antibiosis, volatile organic compound (VOC) production, biofilm formation, iron sequestration, lipopeptide synthesis, and induction of host defenses. In addition, we highlight microbiome-informed strategies and the design of synthetic microbial communities (SynComs) as promising next-generation approaches to enhance efficacy, stability, and ecological resilience in citrus postharvest disease management.},
}

@article {pmid42322355,
year = {2026},
author = {de Souza Menezes, JD and da Silva, MQ and Dos Santos, ER and de Carvalho, SRPVT and Faria, MAG and de Cássia Helú Mendonça Ribeiro, R and André, JC},
title = {Clinical potential of the gut microbiome in oncology: a scoping review of treatment response, toxicity and biomarker development.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {34},
number = {7},
pages = {},
pmid = {42322355},
issn = {1433-7339},
mesh = {Humans ; *Neoplasms/microbiology/therapy/drug therapy ; *Gastrointestinal Microbiome ; *Antineoplastic Agents/adverse effects/therapeutic use/administration & dosage ; Precision Medicine/methods ; Immunotherapy/methods/adverse effects ; Biomarkers, Tumor ; Biomarkers ; Treatment Outcome ; },
abstract = {PURPOSE: This scoping review aimed to systematically map and critically describe the current evidence on the role of the gut microbiome as a biomarker in oncology, including microbiome-based predictive models and microbial signatures associated with treatment response, toxicity and disease course, and to identify methodological gaps and challenges for clinical translation in precision medicine.

METHODS: This scoping review was conducted following the Joanna Briggs Institute (JBI) guidelines for scoping reviews and reported according to the PRISMA Extension for Scoping Reviews (PRISMA-ScR). The search was performed in five electronic databases (PubMed/MEDLINE, Web of Science, Scopus, SciELO, and LILACS) using a structured PICO strategy. Studies involving adult cancer patients undergoing systemic oncological therapies (including chemotherapy, immunotherapy and combined regimens), with gut microbiome analysis and the investigation, development or validation of microbiome-based biomarkers or predictive models, were included.

RESULTS: The literature demonstrates that specific microbial taxa significantly influence the efficacy of immunotherapies (e.g., AUCs up to 0.88 for ICI response prediction) and chemotherapies, and modulate toxicity (e.g., mucositis reduction from 47.1% to 25% with probiotics). Microbiome-based predictive models often outperform clinical markers (e.g., AUC of 0.88 vs. 0.50 in urothelial carcinoma), and variations in microbiota composition can predict disease progression. The literature mapping of the 20 included studies demonstrates that specific microbial taxa significantly influence the efficacy of immunotherapies (e.g., AUCs up to 0.88 for ICI response prediction) and chemotherapies. Regarding toxicity, while the review focuses on baseline biomarkers, exploratory intervention-based data were addressed, showing that a probiotic cocktail reduced Grade 3-4 oral mucositis from 47.1% to 25%. Furthermore, microbiome-based predictive models demonstrated enhanced discriminatory accuracy in predicting patient outcomes compared to standard clinical classification markers alone (e.g., achieving an Area Under the Curve [AUC] of 0.88 vs. 0.50 for clinical factors in urothelial carcinoma), though these models remain in early exploratory stages.

CONCLUSION: Overall, the evidence suggests a growing interest and potential for microbiome-based predictive models in oncology; however, their clinical translation remains limited by methodological heterogeneity, insufficient external validation, and incomplete mechanistic understanding.},
}

Humans
*Neoplasms/microbiology/therapy/drug therapy
*Gastrointestinal Microbiome
*Antineoplastic Agents/adverse effects/therapeutic use/administration & dosage
Precision Medicine/methods
Immunotherapy/methods/adverse effects
Biomarkers, Tumor
Biomarkers
Treatment Outcome

@article {pmid42322360,
year = {2026},
author = {Anderson, KL and Shipley, LA and Staudenmaier, AR and Galla, SJ and Forbey, JS},
title = {Influence of Plant Secondary Metabolites on intake, Detoxification Costs, and Microbial Communities in Deer.},
journal = {Journal of chemical ecology},
volume = {52},
number = {4},
pages = {},
pmid = {42322360},
issn = {1573-1561},
support = {1018967//USDA National Institute of Food and Agriculture, McIntire-Stennis Project/ ; 2437743//U.S. National Science Foundation/ ; OIA-1826801//U.S. National Science Foundation/ ; },
mesh = {Animals ; *Deer/microbiology/physiology/metabolism ; Herbivory ; *Plants/metabolism/chemistry ; Feces/microbiology ; Secondary Metabolism ; Glucuronic Acid/urine ; *Gastrointestinal Microbiome ; Bacteria/classification/metabolism/isolation & purification ; Inactivation, Metabolic ; },
abstract = {Plants available to wild herbivores, especially browsers, often contain plant secondary metabolites (PSMs). Herbivores have evolved behavioral, physiological, and microbial mechanisms for avoiding and detoxifying PSMs. The detoxification limitation hypothesis suggests that herbivores can reduce toxicity by consuming a mixture of PSMs to avoid overloading a particular detoxification pathway. Although this hypothesis has been examined for smaller mammalian hindgut-fermenters, less is known about responses to PSM mixtures in wild ruminants. To assess the role of host and microbial responses to PSM composition, we used controlled feeding trials to measure voluntary dry matter and PSM intake, urinary excretion of glucuronic acid (GA, a byproduct of PSM detoxification through conjugation), and the diversity and relative abundance of gastrointestinal bacterial families in the feces of two species of captive-raised deer (Odocoileus hemionus, O. virginianus). Deer were fed five mixtures of four purified PSMs that included two same-chemical class mixtures, two different-class mixtures, and one 4-way mixture of all chemicals. Overall, we found that PSM composition had minimal effect on intake, that GA was a consistent physiological biomarker of PSM intake regardless of PSM composition, and that dietary phenolics may influence microbial communities more than monoterpenes. Our results partially conformed to the detoxification limitation hypothesis, where deer consumed less of one same-class mixture (monoterpenes) than different-class mixtures. Our results point to the complexity of the interplay between different behavioral, physiological, and microbial mechanisms that can mediate the consequences of PSMs.},
}

Animals
*Deer/microbiology/physiology/metabolism
Herbivory
*Plants/metabolism/chemistry
Feces/microbiology
Secondary Metabolism
Glucuronic Acid/urine
*Gastrointestinal Microbiome
Bacteria/classification/metabolism/isolation & purification
Inactivation, Metabolic

@article {pmid42322403,
year = {2026},
author = {Tadros, M and Lemmon, B and Bhide, A and Digesu, A and Fernando, R and Khullar, V},
title = {Changes in Uropathogen Distribution in Relation to the COVID-19 Pandemic Timeline.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {42322403},
issn = {1433-3023},
abstract = {INTRODUCTION AND HYPOTHESIS: Recent research has shown that the COVID-19 virus changes the gastrointestinal microbiome as it is a bacteriophage [1], leading to immune dysregulation and bowel dysbiosis [2]. This creates an environment where opportunistic pathogens thrive while beneficial bowel flora diminish [3]. There is an association among the bowel, vaginal and bladder microbiomes where the bacteria from the bowel are found in the bladder [4]. Urinary tract infections (UTIs) are among the most common bacterial infections, typically caused by Escherichia coli (E. coli), Enterococcus faecalis (E. faecalis), Klebsiella spp, and Proteus mirabilis (P. mirabilis) in women [5]. Changes in the bowel microbiome lead to changes in the bladder microbiome [6]. We aimed to evaluate whether the composition of observed uropathogens differed across the different phases of the COVID-19 pandemic.

METHODS: This retrospective study analysed positive urine cultures from women before, during and after the COVID-19 pandemic. The leading three causative uropathogens with a count over 10[3] cfu/mL were reported.

RESULTS: There were 5543 positive cultures with pre-COVID-19 from 1 January 2019 to 30 January 2020, n = 204, during from 1 February 2020 to 4 May 2023, n = 2518, and after from 5 May 2023 to 1 February 2025, n = 2821. In total, 10,456 bacteria were identified. After May 2023, E. coli prevalence dropped from 27 to 21%, and Pseudomonas spp decreased from 6 to 2% (p value < 0.001). In contrast, Klebsiella spp incidence rose from 8 to 12%. Corynebacterium spp (p < 0.05) and Acinetobacter spp (p < 0.001) were increasingly isolated in symptomatic UTIs after May 2023.

CONCLUSIONS: The bacterial organisms found in urinary tract infections detected before and subsequent to the onset of COVID-19 have changed. This may reflect an interaction between changes in the bowel microbiome and pathological urinary tract infections.},
}

@article {pmid42322405,
year = {2026},
author = {Reasoner, SA and Francis, J and Gidney, M and Amponsah, A and Frainey, B and Schrepf, A and Kelly, AG and Ryden, AM and Crofford, LJ and Dmochowski, RR and Hadjifrangiskou, M and McKernan, LC},
title = {Urobiome Analysis in Interstitial Cystitis/Bladder Pain Syndrome Reveals Nuanced Differences Associated with Localized Pain.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {42322405},
issn = {1433-3023},
support = {K23DK118118/DK/NIDDK NIH HHS/United States ; P20DK123967/DK/NIDDK NIH HHS/United States ; F30AI169748//National Institute of Allergy and Infectious Diseases/ ; UL1TR002243/TR/NCATS NIH HHS/United States ; },
abstract = {INTRODUCTION AND HYPOTHESIS: Interstitial cystitis/bladder pain syndrome (IC/BPS) is a prevalent chronic pain syndrome associated with functional urinary disorders. IC/BPS symptoms can be localized to the pelvic-region or have co-occurring widespread pain. Importantly, response to treatment depends on pain localization phenotype. The etiology of IC/BPS remains elusive, and whether bacteria contribute to IC/BPS pathophysiology remains uncertain. We hypothesized that the urobiome does not differentiate phenotypic presentations of IC/BPS.

METHODS: We used urine samples collected from a longitudinal randomized controlled trial of psychotherapy for individuals with IC/BPS to study the association of the urobiome and IC/BPS symptoms over time. Individuals provided urine samples at baseline, posttreatment, and at 5 months. We performed a secondary analysis on urine samples applying 16S rRNA sequencing and assigned bacterial taxonomy to amplicon sequence variants (ASVs) to characterize the urobiome. We compared urobiome diversity and stability over time, their associations with IC/BPS symptoms, and relationships with pain localization.

RESULTS: As validation of this dataset, we noted a strong influence of menopausal status and recent urinary tract infection on the composition of the urobiome. We did not detect widespread differences in the urobiome that correlated with an individuals' pain localization or severity. Instead, we observed specific bacterial sequences that were altered in abundance in relation to symptomatology, such as reduced abundance of a Dialister ASV in persons with localized pelvic pain.

CONCLUSIONS: Together, this dataset advances our understanding of the urobiome in IC/BPS and sets the stage for future studies on the urobiome and IC/BPS symptoms.},
}

@article {pmid42322535,
year = {2026},
author = {De, R and Chakrabortty, S and Das, J and Chaudhary, P and Patra, R and Sardar, K and Nath, R and Pal, R and Debnath, B and Ashique, S},
title = {Hormonal Imbalance and Gut Dysbiosis: Emerging Perspectives in Women's Health.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42322535},
issn = {1867-1314},
abstract = {The gut microbiota plays a crucial function in reproductive well-being and is vital for maintaining fundamental physiological balance. This article surveys the mutual relationships between the gut flora and the female reproductive system, which are maintained through metabolic, immunological, and neuroendocrine mechanisms, thereby creating the gastrointestinal-reproductive axis. Dysbiosis, which results from an imbalance in microbial levels, has been related with reproductive diseases, such as polycystic ovary syndrome (PCOS), infertility, endometriosis, and pregnancy-related problems. Modulation of the gut microbiota via targeted synthetic materials, such as metformin, dietary phytocompounds, synbiotics, probiotics, and prebiotics, affects hormonal levels, glucose resistance, and monthly cycle regulation, showcasing favorable prospects for medical care. This review elucidates the molecular and cellular processes underlying gut-reproductive relationships and assesses the potential of microbiome-targeted medications as viable clinical approaches for enhancing fertility outcomes. Further attention should be devoted to determining the crosstalk between endometrial disruption, hormonal imbalance, and inflammation.},
}

@article {pmid42322766,
year = {2026},
author = {Wang, Y and Kim, E and Cui, J and Lee, Y and Zhang, G},
title = {Medium-chain inulin reshapes the gut microbiome-metabolome axis to counteract high-fat diet-induced obesity.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {159},
number = {},
pages = {158423},
doi = {10.1016/j.phymed.2026.158423},
pmid = {42322766},
issn = {1618-095X},
abstract = {BACKGROUND: Inulin, a natural dietary fiber, exerts diverse health benefits that are closely linked to its molecular structure. However, the biological activity of medium-chain inulin and its role in high-fat diet (HFD)-induced obesity remain poorly characterized.

OBJECTIVE: This study aimed to determine whether medium-chain inulin could alleviate high-fat diet (HFD)-induced obesity by modulating the gut microbiota and metabolome, thereby restoring metabolic homeostasis.

METHODS: Forty male C57BL/6 mice were fed either a standard chow diet or an HFD with 1%, 3%, or 5% medium-chain inulin (average degree of polymerization = 12) for 12 weeks. Body weight (BW), physiological indices, gut microbiota, and metabolome were analyzed to elucidate the underlying mechanisms. Short-chain fatty acids (SCFAs) were quantified by gas chromatography. Cecal microbiota and metabolome were analyzed using 16S rRNA sequencing and LC-MS/MS, respectively. Correlation and pathway analyses were conducted to identify key microbe-metabolite interactions.

RESULTS: Medium-chain inulin supplementation significantly reduced BW gain (by 16% and 20% at 3% and 5% doses, respectively), increased acetic and butyric acid levels, and improved serum and hepatic lipid profiles. It reshaped the gut microbiota by enriching Faecalibaculum, Bifidobacterium, Parasutterella, Clostridium_sensu_stricto_1, Bacteroides, Lactobacillus, and Akkermansia. Metabolomic analysis revealed elevated levels of eight key metabolites related to tryptophan metabolism and bile acid metabolism, correlating with improved metabolic indicators.

CONCLUSION: Medium-chain inulin alleviated HFD-induced obesity by remodeling the gut microbiome-metabolome axis and promoting SCFA production. These findings highlight its potential as a functional prebiotic candidate for obesity-related metabolic disorders.},
}

@article {pmid42322920,
year = {2026},
author = {Mateos-Hernandez, L and Wu-Chuang, A and Maitre, A and Rego, ROM and Denis-Abuin, L and Piloto-Sardiñas, E and Fernández-Ruiz, N and Maye, J and Aželytė, J and Banovi, P and Palinauskas, V and Obregon, D and Cabezas-Cruz, A},
title = {Natural antibodies induced by host gut microbiota modulate tick microbiota, inhibiting Borrelia colonization.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {4},
pages = {102674},
doi = {10.1016/j.ttbdis.2026.102674},
pmid = {42322920},
issn = {1877-9603},
abstract = {The gut microbiome undergoes natural selection pressure, likely because it can affect infection resistance by stimulating natural antibody (NAb) production, notably against the glycan Galα1-3Galβ1-4GlcNAc-R (α-Gal). In our study, we explored whether particular glycans, such as α-Gal, from specific host microbiota components could trigger NAbs that, once ingested by Ixodes ricinus ticks during the blood meal, are capable of cross-reacting with bacterial strains in the tick microbiota that share these glycans. Such interactions might alter the tick microbiota and reduce Borrelia afzelii colonization in ticks. When mice were orally administered various Escherichia coli strains, it triggered the stimulation of NAbs and resulted in strain-specific alterations in the tick microbiota. These changes effectively decreased Borrelia colonization in the tick vector. Additionally, vaccination with the glycan α-Gal induced notable shifts in the tick microbiota and similarly reduced Borrelia colonization. Reduced Borrelia colonization was associated with shifts in bacterial diversity, abundance, and microbial network properties. The study provides evidence that natural mechanisms, such as the production of NAb in response to the host gut microbiome, can modulate the microbiota of disease vectors and reduce pathogen colonization within the vector. These findings offer new insights into potential strategies for reducing the transmission of vector-borne diseases through modulation of the host gut microbiome.},
}

@article {pmid42323003,
year = {2026},
author = {Zhao, H and Tian, H and Nuerbieke, T and Ma, K and Li, W and Niu, X and Li, J and Ashby, CR and Chen, ZS and Zhou, T and Li, W and Li, D},
title = {Immunotherapy Resistance in Triple-Negative Breast Cancer: Mechanisms and Emerging Therapeutic Strategies.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {218690},
doi = {10.1016/j.canlet.2026.218690},
pmid = {42323003},
issn = {1872-7980},
abstract = {Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited treatment options and a poor prognosis. Immunotherapies, particularly immune checkpoint inhibitors (ICIs), have expanded the therapeutic options for TNBC. Despite the revolutionary breakthroughs in the treatment of TNBC, some patients still exhibit primary or acquired resistance to immunotherapy. A comprehensive understanding of the mechanisms of immunotherapy resistance is crucial for developing new strategies to overcome the resistance. In this review, we discuss the multifactorial resistance mechanisms to immunotherapy in TNBC, including tumor cell-intrinsic mechanisms (low tumor mutation burden, driver gene mutations, antigen presentation defect, and aberrant PD-L1 expression) and alterations in the tumor microenvironment (T cells, dendritic cells, cancer-associated fibroblasts, tumor-associated macrophages, mast cells, B cells, myeloid-derived suppressor cells, cytokines, hypoxia, metabolic reprogramming, neurological factors, ferroptosis, cuproptosis, and microbiome). Furthermore, we discuss strategies to overcome immunotherapy resistance (including combination of ICIs with other existing treatments and nanotechnology-assisted immunotherapy), and identify emerging biomarkers enabling the selection of patients who may benefit from immunotherapy. Therefore, our review provides insights into immunotherapy resistance mechanisms, developing novel therapeutic strategies, and guiding treatment plans.},
}

@article {pmid42323281,
year = {2026},
author = {Liang, Q and Lan, X and Wu, J and Wei, W and Li, L and Tang, X and Zhao, G and Guo, R and Jia, H},
title = {Precision culturomics enabled by unlabeled single-cell morphology and Raman spectra.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74582-z},
pmid = {42323281},
issn = {2041-1723},
support = {82401226//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M750502//China Postdoctoral Science Foundation/ ; },
abstract = {Selective enrichment of target bacteria from complex communities, such as the human microbiome, has remained a challenge. Here, we report precision single-cell culturomics based on label-free morphology, Raman spectrometry, and Laser-Induced Forward Transfer (LIFT) technology. This approach operates at the level of single microbial cells, many generations before these cells form visible colonies. We develop a machine learning-based framework that achieves species-level identification of single cells in complex microbiome and achieve selective culturing for or against specific bacteria in fecal or vaginal samples, and quantify some of the cellular components based on Raman spectra. Genomic analysis of single-cell cultures reveals that short-term antibiotic use promotes both pre-existing resistance and de novo mutations of gut commensals, alongside convergent evolution across species. Our precision culturomics method provides a powerful tool for morphological, metabolic, and genomic analysis of microbial phenotypic variations at the single-cell level in microbiome studies.},
}

@article {pmid42323320,
year = {2026},
author = {Wang, J and Yang, Y and Ru, Z and Zhang, Y and Xiong, X and Ding, Y and Yu, X and Ma, M and Su, W and Huang, Y and Yang, X and Liu, N and Wang, Y},
title = {Food-derived peptide RDP3 mitigates pyroptosis to enhance oral mucosal repair via the IL-2Rβ/PI3K axis.},
journal = {NPJ Regenerative medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41536-026-00487-6},
pmid = {42323320},
issn = {2057-3995},
support = {2025SKY021//the 2025 Innovation Fund of Graduate Student of Yunnan Minzu University/ ; 32360138//the National Natural Science Foundation of China/ ; 82404582//the National Natural Science Foundation of China/ ; 32301054//the National Natural Science Foundation of China/ ; 2024XKTDTS10//he First-Class Discipline Team of Skin & Mucosal Regenerative Medicine of Kunming Medical University/ ; 202301AS070036 and 202301AU070218//Programs of Yunnan Fundamental Research Project/ ; 202501AY070001-149, 202301AY070001-301, 202301AY070001-012, and 202301AY070001-165//Programs of Yunnan Applied Basic Research Project-Kunming Medical University Union Foundation/ ; YKKF2024003, 2022YKZY006 and 2025YKZY004//the Open Research Fund of Yunnan Characteristic Plant Extraction Laboratory/ ; L-2025003//High-level Health Technology Talent in Yunnan Province/ ; },
abstract = {Oral ulcers represent a prevalent mucosal disease with incompletely elucidated pathogenesis and a clinical deficiency in multifunctional therapeutics. This study investigates a food-derived peptide, RDP3, with tissue-penetrating capability, which significantly promotes repair of oral ulcer mucosal in vivo and in vitro in a low concentration (1 nM). This is the first time to report a food-origin peptide capable of accelerating oral ulcer mucosal repair. RDP3 can not only accelerate wound healing but also restore microbiome homeostasis. Mechanistically, RDP3 functions as a novel peptide-antagonist of the interleukin-2 receptor β subunit (IL-2Rβ; binding affinity KD = 0.99 μM). This interaction suppresses pathological PI3K signaling, thereby inhibiting NLRP3/GSDMD-mediated pyroptosis, reducing inflammation, and promoting mucosal regeneration. These findings position RDP3 as a promising multifunctional therapeutic candidate for oral ulcer treatment.},
}

@article {pmid42323381,
year = {2026},
author = {Berezkina, A and Rahn, T and Suchantke, M and Beck, KK and Espinoza, JP and Richter, C and Hentschel, U and Wall, M},
title = {Changes in bacterial community composition and antibiotic resistance profiles of coral-associated microbiota in the vicinity of Chilean salmon farms.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42323381},
issn = {2045-2322},
mesh = {Animals ; *Salmon ; Chile ; *Anthozoa/microbiology ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification/isolation & purification ; *Drug Resistance, Bacterial ; Aquaculture ; *Drug Resistance, Microbial ; },
abstract = {The extensive use of antibiotics in Chilean salmon farming raises concerns about harmful effects on benthic habitats, particularly the iconic cold-water coral (CWC) banks in semi-enclosed fjords. We collected specimens of the CWC Desmophyllum dianthus near and far from salmon farms in Comau Fjord, Chile, and investigated their associated bacterial community (metabarcoding, culturing) and screened bacterial isolates for their antibiotic resistance (15 antibiotics, including antibiotics common in Chilean salmon farming). The cultured bacterial isolates of D. dianthus showed a slight but significant increase in antibiotic resistance (near: 7.7 ± 0.47 vs. far: 6.3 ± 0.48). This was accompanied by a change in dominance in the randomly selected isolates, with Pseudoalteromonas and Shewanella dominating far and near, respectively. Metabarcoding also showed a shift in the dominant bacterial strains from SUP05 clade to Mycoplasma and a loss of Pseudoalteromonas strains near the salmon farm. Common antibiotics used in salmon farming, however, significantly reduced bacterial growth at the community level, and most bacterial isolates were also sensitive to these antibiotics, except for tilmicosin. This may provide a first indication of how salmon farms modify the microbiome of D. dianthus and underscores the need to expand such assessments in space and time.},
}

Animals
*Salmon
Chile
*Anthozoa/microbiology
*Microbiota/drug effects
Anti-Bacterial Agents/pharmacology
*Bacteria/drug effects/genetics/classification/isolation & purification
*Drug Resistance, Bacterial
Aquaculture
*Drug Resistance, Microbial

@article {pmid42323395,
year = {2026},
author = {Xu, R and Du, C and Gao, Y and Chen, K and Guo, J and Ma, J and Zhang, Y and Wang, Z and Sun, Z},
title = {Distinct rhizosphere microbiomes and metabolomes mediate Fusarium crown rot resistance across wheat cultivars.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01065-w},
pmid = {42323395},
issn = {2055-5008},
support = {2023YFD2300203//National Key Research and Development Program of China/ ; CARS301//National Wheat Industry Technology System/ ; SKLMB2442//Research Project from State Key Laboratory of Maize Bio-breeding/ ; PC2023B02006//Pinduoduo-China Agricultural University Research Fund/ ; },
abstract = {Soil-borne Fusarium crown rot (FCR) poses a major challenge to wheat production. Plants can recruit beneficial microbes through a "cry-for-help" strategy in response to pathogen attack, yet how different wheat genotypes modulate this response remains unclear. In FCR-affected wheat fields, we systematically investigated the interactions among wheat, pathogens, rhizosphere microbes, and metabolites using a combination of phenotypic assessment, molecular detection, and microbiome and metabolome profiling. Our results showed that wheat genotype and plant health jointly shaped rhizosphere microbial communities and metabolite profiles. Beneficial Bacillus species were key taxa in healthy rhizosphere communities, whereas the susceptible cultivar additionally relied on Pseudomonas to maintain plant health. In vitro assays and a pot experiment confirmed that these microbes antagonize the pathogen and enhance wheat performance, thereby alleviating FCR. Furthermore, the tolerant cultivar exhibited more complex rhizosphere microbial co-occurrence networks and harbored conserved taxa, such as Devosia. Microbe-metabolite interaction networks revealed strong associations between beneficial rhizosphere microbes (e.g., Bacillus and Pseudomonas) and specific metabolites, such as tritrans-heptacis-undecaprenyl phosphate, PE(14:1(9Z)/20:5(5Z,8Z,11Z,14Z,17Z)), and 1,2-Dioleoyl-sn-glycerol-3-phosphate. Collectively, our results provide novel evidence that rhizosphere metabolite-mediated plant-microbe interactions contribute to the suppression of soil-borne diseases.},
}

@article {pmid42323440,
year = {2026},
author = {Carboni, S and Macfarland, C and Cheves Hernandez, S and Buret, AG and Kutz, S and Melin, AD},
title = {Ecological and methodological insights from genetic and coprological profiling of gastrointestinal communities in wild howler monkeys.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57628-6},
pmid = {42323440},
issn = {2045-2322},
support = {RGPIN-2017-03782//Natural Sciences and Engineering Research Council of Canada/ ; 950-231257//Canada Foundation for Innovation and Canada Research Chairs/ ; },
abstract = {The gastrointestinal tract hosts a complex community of microorganisms and helminth parasites that collectively contribute to host health and fitness. Analysis of these communities provides insight into diverse aspects of host dietary ecology, immunity, nutrition, and host-parasite interactions. However, research methodologies, such as sample preservation and sequencing approach, can influence how we understand and characterize these features. Here, we profiled the gastrointestinal microbial and helminth communities in different groups of wild Costa Rican mantled howler monkeys (Alouatta palliata palliata). We compared samples stored in ethanol versus directly flash frozen, and contrasted conclusions drawn from 16S versus shotgun sequencing approaches. Bacterial, archaeal, and eukaryotic taxa associated with the digestion of plant material dominated the GI communities. Storage and sequencing methods influenced microbial profiles: ethanol-stored samples exhibited higher diversity than frozen samples, and 16S sequencing detected lower diversity than shotgun. Helminths were detected via coprological microscopy in 71% of individuals, whereas metagenomic detection was inconsistent. This study provides new data on the microorganisms and their putative digestive functions in the gut of a folivorous primate, and highlights the pros and cons of different methodological choices when profiling host-microbiome and host-parasite interactions.},
}

@article {pmid42323523,
year = {2026},
author = {Hatwar, N and Qureshi, A},
title = {Microbial Community and Enzymes for Biodeterioration of PVC Plastic Buried in Soil and Compost Environment.},
journal = {Current microbiology},
volume = {83},
number = {8},
pages = {},
pmid = {42323523},
issn = {1432-0991},
support = {UGC August 2021-Grant Number -191620062301//UGC/ ; },
mesh = {*Polyvinyl Chloride/metabolism/chemistry ; Biodegradation, Environmental ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/enzymology/isolation & purification ; Composting ; *Microbiota ; Soil/chemistry ; *Plastics/metabolism ; },
abstract = {Polyvinyl chloride (PVC) plastic films accumulate in the environment and cause ecological damage due to their persistent, high-density polymeric nature. To mitigate PVC pollution, a sustainable bioremediation approach needs to be designed. Biodegradation of PVC using pure bacterial cultures has been reported as a sustainable option. However, PVC biodegradation studies in the presence of a soil/compost indigenous microbiome have not been conducted. In the present study, attempts have been made to understand and show the biodeterioration and biodegradation of PVC under soil and compost burial conditions. The study revealed that the PVC films, when buried under soil and compost at different conditions (ambient, sun-exposed, and 37 °C conditions), resulted in gravimetric weight loss with CO2 release. Under soil burial at 37 °C, PVC films showed 13.32 ± 0.10% weight reduction with 9.9 ± 0.9% CO2 evolution in 90 days, whereas compost conditions resulted in 6.89 ± 0.11% weight reduction. Another unique feature of the study is the metagenomic profiling of PVC buried soil/compost microbiomes, which revealed Proteobacteria and Actinobacteria as dominant phyla with Bacillus, Staphylococcus, Streptomyces, Arthrobacter, and Exiguobacterium as predominant genera. Also, the bioinformatics analysis revealed that these microbes possess potential metabolic capability associated with PVC biodeterioration and biodegradation (laccases, peroxidases, and oxidoreductases). Overall, the novelty reflects integrating metagenomic, spectroscopic, and morphological characterization of buried PVC plastic and linking microbial community dynamics with their enzymatic machinery and physico-chemical transformations of PVC. These multi-analytical approaches provided mechanistic evidence that the soil/compost microbial community initiates the PVC biodegradation process, offering a scientific basis for designing sustainable plastic waste management and remediation practices.},
}

*Polyvinyl Chloride/metabolism/chemistry
Biodegradation, Environmental
*Soil Microbiology
*Bacteria/classification/genetics/metabolism/enzymology/isolation & purification
Composting
*Microbiota
Soil/chemistry
*Plastics/metabolism

@article {pmid42323568,
year = {2026},
author = {Alves, CPP and Pinto, OHB and Pappas, GJ and Mota, SS and Rahlff, J and Krüger, RH},
title = {Taxonomic and functional diversity of the microbiome associated with the freshwater sponge Metania sp. (Haplosclerida: Metaniidae) from the Brazilian Cerrado, a metagenomic approach.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42323568},
issn = {1471-2180},
mesh = {Animals ; Brazil ; *Porifera/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Fresh Water/microbiology ; *Archaea/classification/genetics/isolation & purification ; Symbiosis ; Phylogeny ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Sponges, the oldest metazoans on the planet, have an evolutionary history shaped by symbiotic associations with microorganisms. Although well studied in marine sponges, these associations are poorly understood in freshwater species. This study explored the taxonomic diversity and functional potential of the microbiome of the freshwater sponge Metania sp. and its distinction from the surrounding water, using a metagenomic approach. The samples were collected in the Brazilian Cerrado.

RESULTS: Taxonomic assignment identified 17 phyla, including bacterial and archaeal, with 19 sequence variants successfully assigned to the species level. Bacteria comprised 16 phyla, with a predominance of Pseudomonadota, Actinomycetota, and Bacteroidota in both microbiomes. The sponge microbiome is distinct from the water microbiome (PERMANOVA; F = 21.6, p = 0.04), sharing only 27% of the identified taxa. Functional prediction resulted in 7,201 KEGG Orthologs (KOs), assigned to 117 significantly enriched metabolic pathways. Although 95 pathways are shared, differential abundance analysis identified 1,024 KOs more abundant in the sponge microbiome and 1,275 in the water. The presence of bacterial defense systems such as CRISPR-Cas in the sponge microbiome suggests a crucial role in protecting against phages while maintaining symbiosis. In contrast, the water microbiota is enriched with pathways linked to environmental adaptation, such as secondary metabolite biosynthesis and pollutant degradation. Although the water microbiome harbored 1.3 times more biosynthetic gene clusters (BGCs), the sponge microbiome also demonstrated biotechnological potential for producing secondary metabolites, especially antimicrobial.

CONCLUSIONS: These findings demonstrate that the freshwater sponge Metania sp. hosts a complex and functionally specialized microbial community that plays fundamental roles in adaptation, nutrition, and defense, highlighting the critical importance of symbiotic associations for the host.},
}

Animals
Brazil
*Porifera/microbiology
*Microbiota/genetics
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Fresh Water/microbiology
*Archaea/classification/genetics/isolation & purification
Symbiosis
Phylogeny
Metagenome
RNA, Ribosomal, 16S/genetics
Biodiversity
Sequence Analysis, DNA

@article {pmid42323575,
year = {2026},
author = {Abitew, YA and Reyer, H and Oster, M and Haas, VP and Schmid, M and Sommerfeld, V and Chien, YH and Camarinha-Silva, A and Bennewitz, J and Rodehutscord, M and Wimmers, K and Ponsuksili, S},
title = {Divergent jejunal cis- and trans-eQTLs and their microbiome associations following a diet lacking mineral phosphorus supplements in laying hens.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42323575},
issn = {1471-2164},
mesh = {Animals ; *Chickens/genetics/microbiology ; *Quantitative Trait Loci ; *Jejunum/metabolism/microbiology ; Female ; MicroRNAs/genetics ; *Dietary Supplements ; *Phosphorus/metabolism/deficiency ; Diet ; Genome-Wide Association Study ; *Gastrointestinal Microbiome ; Minerals ; },
abstract = {BACKGROUND: Phosphorus (P) utilization is a complex trait influenced by numerous genetic variants. The jejunum is the primary site of P absorption in poultry. Therefore, identifying the genetics that regulate transcription in jejunum may help uncover key regulators of P homeostasis. We performed a genome-wide association study using the expression of jejunal mucosa transcripts (88 miRNAs, 65 mRNAs). These transcripts were selected from our previous studies due to their association with P utilization and related pathways. In total, the trial comprised 400 laying hens from two high-yielding strains, Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL), fed a diet lacking mineral P supplements and exogenous microbial phytase to stimulate adaptive mechanisms.

RESULTS: In total, 114 miR-eQTLs (microRNA expression quantitative trait loci) were detected at a false discovery rate (FDR) of less than 5%, including 56 miR-eQTLs in the LB strain and 58 miR-eQTLs in the LSL strain. Lohmann Brown contained 23 cis and 35 trans loci, with the most significant cis-eQTL targeting miR-146b. In the LSL strain, a cis-eQTL cluster for miR-203a was present on chromosome 5. Similarly, 123 mRNA-eQTLs (94 in LB and 29 in LSL) were identified at the 5% FDR threshold. The genetic regulation of key genes involved in mineral binding and mineral transport, including CALB1 and SLC34A2, in LB hens was predominantly driven by strong cis-eQTL. In contrast, gene expression in LSL hens was largely modulated by trans-eQTLs, with CALM1 being the only gene under significant cis-regulation. Furthermore, correlation analysis with the gut microbiome revealed that the expression of cis-regulated CALB1 is significantly positively associated with the abundance of Lactobacillus species.

CONCLUSIONS: Our findings reveal that LB and LSL hens exhibit distinct genetic architectures contributing to maintain mineral homeostasis. Genetic differences between the two strains influence the transcriptional response of key mineral transporter genes and miRNAs under a low-P diet. These divergent host genetic strategies are also associated with distinct gut microbiota profiles, highlighting interactions between host genetics, gene expression, and the microbiome in P utilization.},
}

Animals
*Chickens/genetics/microbiology
*Quantitative Trait Loci
*Jejunum/metabolism/microbiology
Female
MicroRNAs/genetics
*Dietary Supplements
*Phosphorus/metabolism/deficiency
Diet
Genome-Wide Association Study
*Gastrointestinal Microbiome
Minerals

@article {pmid42323579,
year = {2026},
author = {Ghaeli, Z and Aghdam, R and Eslahchi, C},
title = {Evaluating microbial network inference methods: moving beyond synthetic data with reproducibility-driven benchmarks.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06510-3},
pmid = {42323579},
issn = {1471-2105},
abstract = {BACKGROUND: Microbial network inference is an essential approach for revealing complex interactions within microbial communities. However, the lack of experimentally validated gold standards presents a significant obstacle in evaluating the biological accuracy of inferred networks. This study delivers a comprehensive comparative assessment of six widely used microbial network inference algorithms on four diverse real-world microbiome datasets alongside computationally generated samples, including synthetic, noisy, and bootstrap-derived variants. Our evaluation framework extends beyond conventional synthetic benchmarking by emphasizing reproducibility-focused assessments grounded in biologically realistic perturbations.

RESULTS: Our analysis reveals that bootstrap resampling and low-level noisy datasets (≤10% perturbation) effectively preserve the key statistical properties of real microbiome data, serving as reliable proxies for assessing algorithmic consistency. Conversely, synthetic datasets generated via the widely used SPIEC-EASI method exhibit substantial divergence from real data. Notably, several algorithms fail to distinguish between structured and random networks, highlighting a lack of structural sensitivity and the limitations of overreliance on synthetic benchmarks.

CONCLUSIONS: This study provides critical insights for the microbiome research community, emphasizing the need for more reliable and broadly applicable approaches to network evaluation. We propose a benchmarking framework that prioritizes real-data-derived perturbations and mandates rigorous statistical validation of synthetic datasets. Our findings highlight the importance of robustness and reproducibility analyses as complementary evaluation criteria for microbial network inference methods when validated biological ground truth is unavailable.},
}

@article {pmid42323699,
year = {2026},
author = {Kawahara, E and Morimoto, K and Islam, MS and Yamada, H and Sekiguchi, T and Morita, M and Mitsuyama, J and Morinaga, Y},
title = {Live nontypeable Haemophilus influenzae exacerbates respiratory syncytial virus-associated lower airway inflammation.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03774-4},
pmid = {42323699},
issn = {1465-993X},
support = {24K23308//Japan Society for the Promotion of Science/ ; 23K27639//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract disease in infants and immunocompromised adults, and secondary bacterial infections are recognized as important contributors to disease severity. Recent microbiome studies have shown that Haemophilus influenzae is frequently co-detected in severe RSV cases and ranks among the bacteria most closely correlated with disease severity; however, its causal role and underlying mechanisms remain unclear. Here, we used a murine model to examine the manner in which H. influenzae influences RSV-associated airway inflammation.

METHODS: We established a murine respiratory infection model by infecting mice with RSV and subsequently intratracheally inoculating them with live, ultraviolet (UV)-killed, or heat-killed nontypeable H. influenzae (NTHi). Body weight, viral and bacterial loads, bronchoalveolar lavage fluid (BALF) cytokine levels, and immune cell populations were analyzed.

RESULTS: Live NTHi inoculation following RSV infection induced severe lower airway inflammation, characterized by pronounced body weight loss and lung injury along with increased CD8[+] T-cell accumulation and enhanced interleukin (IL)-6 inflammatory mediator production in BALF. Additionally, CD8[+] T-cell depletion modestly attenuated body weight loss, altered the recruited innate immune cell composition, and reduced BALF IL-6 levels. However, RSV-infected mice inoculated with UV- or heat-killed NTHi exhibited CD8[+] T-cell accumulation without developing body weight loss, which suggested that CD8[+] T-cell accumulation alone may be insufficient to drive full disease manifestation. In contrast to that observed for non-viable NTHi, live NTHi induced robust neutrophil recruitment along with strong production of inflammatory mediators. Additionally, BALF IL-6 levels showed a strong negative correlation with body weight; hence, IL-6 was identified as a potential marker associated with disease severity.

CONCLUSIONS: This mouse model shows that pulmonary inoculation of live NTHi after RSV infection induces severe lower airway inflammation partially involving CD8[+] T cells and that IL-6 is a potential biomarker associated with disease severity. Overall, this study suggests a novel pathological role for NTHi in the exacerbation mechanism of secondary bacterial infection in RSV infection.},
}

@article {pmid42324060,
year = {2026},
author = {Thomas, P and Sindel, B and Winter, G},
title = {Diversity, Composition and Resilience of the Root Microbiome of Tomato Plants in a Hydroponic Rockwool System.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70380},
doi = {10.1111/1758-2229.70380},
pmid = {42324060},
issn = {1758-2229},
support = {//Australian Government/ ; },
mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Plant Roots/microbiology ; *Microbiota ; *Hydroponics ; *Bacteria/classification/genetics/isolation & purification ; Fungi/classification/isolation & purification/genetics ; Biodiversity ; Soil Microbiology ; Trichoderma/physiology ; },
abstract = {In hydroponic horticulture, where soil is replaced by a sterile artificial substrate, attention to microorganisms is primarily focused on the suppression of plant pathogens and the application of potentially beneficial organisms. This study examined the ecology of the root microbiome of tomato plants which were grown to maturity in a hydroponic rockwool system and then treated with a Trichoderma-based biocontrol product. The bacterial community was species-rich but was dominated by a small number of Alphaproteobacteria, Gammaproteobacteria and Bacteroidia species. The fungal community was less diverse and consisted almost exclusively of Ascomycota and Rozellomycota species. Biocontrol treatment did not have a significant effect on bacterial diversity, but the microbiome composition changed distinctly over the period of sampling in both treated and untreated plants. These results support the view that mineral substrates in a hydroponic system can support a complex and resilient root microbiome. Understanding the microorganisms that thrive in this unique environment may help identify effective biological treatments, and enable the development of rockwool-specific practices for monitoring, protecting and promoting plant health.},
}

*Solanum lycopersicum/microbiology/growth & development
*Plant Roots/microbiology
*Microbiota
*Hydroponics
*Bacteria/classification/genetics/isolation & purification
Fungi/classification/isolation & purification/genetics
Biodiversity
Soil Microbiology
Trichoderma/physiology

@article {pmid42324270,
year = {2026},
author = {Ma, Y and Yang, M and Xu, A and Zhao, X and Dong, X and Li, W and Tu, H and Guo, Y and Song, Z and Wu, X},
title = {Characterization of gut microbiome signatures in metabolic dysfunction associated steatotic liver disease.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01059-8},
pmid = {42324270},
issn = {2055-5008},
support = {K20230085//Healthy Zhejiang One Million People Cohort/ ; 2020E10004//Zhejiang Key Laboratory of Intelligent Preventive Medicine/ ; 2019R01007//the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2020C03002//Cancer Center, Zhejiang University and Key Research and Development Program of Zhejiang Province/ ; },
abstract = {This cross-sectional study compared the gut microbiota between metabolic dysfunction associated steatotic liver disease (MASLD) patients and healthy controls. A total of 1401 participants, including 392 MASLD patients and 1009 healthy controls, were enrolled from one project site of the Healthy Zhejiang One Million People Cohort (HOPE) between January 2022 and June 2023. Shotgun metagenomic sequencing was conducted to compare the composition and functional profiles of the gut microbiome between MASLD patients and healthy controls. Compared to the control group, MASLD patients exhibited significant alterations in both alpha and beta diversity, along with reduced connectivity and robustness of the gut microbial network. We identified significant changes in the abundance of 12 microbial strains between the two groups with two strains (t_SGB4749 and t_SGB4753) enriched and ten strains depleted in MASLD patients. In comparison to the control group, MASLD patients demonstrated distinct differences in the genomic potential related to increased glycolysis, decreased pyruvate metabolism, and elevated lipopolysaccharide (LPS) biosynthesis in both metagenomic functional profiling and single-strain genome analysis. These findings suggest that alterations in specific microbial strains and metabolic pathways may contribute to MASLD pathogenesis.},
}

@article {pmid42324373,
year = {2026},
author = {Sharata, EE and Bakry, T and Mohamed, H and Mohyeldin, RH and Rofaeil, RR and Hemeida, RAM and Kotb, ASM and Abdelnaser, M},
title = {Ulcerative colitis: from molecular pathophysiology to management and the emerging role of natural and pharmacological drug candidates.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42324373},
issn = {1432-1912},
abstract = {Ulcerative colitis (UC) is a chronic, relapsing, immune-mediated inflammatory disease of the colonic mucosa that imposes a substantial and growing global health burden. The pathophysiological basis of UC encompasses a multifactorial interplay among genetic predisposition, dysregulated innate and adaptive immune responses, gut microbiome dysbiosis, epithelial barrier dysfunction, and environmental triggers. Despite considerable advances in therapeutic strategies over the past two decades ranging from aminosalicylates and corticosteroids to biologic agents targeting TNF-α, integrins, and the IL-12/23 axis, as well as small molecule modulators such as JAK inhibitors and sphingosine-1-phosphate receptor agonists-a substantial proportion of patients either fail to achieve remission or experience loss of response over time, underscoring the continued need for novel therapeutic approaches. This comprehensive review systematically addresses the definition, epidemiology, socioeconomic burden, and unmet clinical needs in UC. The molecular and cellular underpinnings of the disease are discussed in depth, including the roles of key signaling pathways, pattern recognition receptors, cytokine networks, and the gut-immune interface. Clinical features, diagnostic criteria, endoscopic and histological scoring systems, and validated disease activity indices are also described. Current pharmacological therapies are reviewed with regard to mechanisms of action, pivotal clinical trial data, and safety profiles. Emerging investigational strategies including precision biologic agents, next-generation small molecules, microbiome-based therapeutics, and cell and gene therapy approaches are evaluated within a translational framework. A curated synthesis of experimental models of UC induction in rodents is presented, followed by structured tabular summaries of selected naturally derived bioactive compounds and pharmacological drug candidates that have demonstrated protective efficacy in preclinical models of UC. Compounds were selected for tabular inclusion on the basis of three prespecified criteria: (i) availability of at least one peer-reviewed in vivo study conducted in a validated experimental colitis model (DSS, TNBS, and acetic acid); (ii) a clearly described and mechanistically plausible basis of action relevant to UC pathophysiology; and (iii) representation across the principal mechanistic clusters identified in this review. Application of these criteria to the studies included in the final review yielded 29 naturally derived bioactive compounds (Table 1) and 26 pharmacological drug candidates (Table 2) for structured synthesis.},
}

@article {pmid42324435,
year = {2026},
author = {Chien, PY and Cheng, WC and Hung, CC and Tu, CY and Hsia, TC and Cho, DY and Hsueh, PR and Lai, ZL and Shen, YC and Lin, YC},
title = {Smoking-associated modulation of gut microbiota shapes response to immune checkpoint inhibitors in non-small cell lung cancer.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00262-026-04463-3},
pmid = {42324435},
issn = {1432-0851},
support = {C1110812016-2//China Medical University Hospital/ ; },
abstract = {BACKGROUND: Smoking status has been associated with differences in immune checkpoint inhibitor (ICI) efficacy in non-small cell lung cancer (NSCLC), though the underlying mechanisms remain unclear. This prospective cohort study evaluated whether smoking-related changes in the gut microbiota are linked to ICI response.

METHODS: Baseline fecal samples from 225 patients with NSCLC were analyzed using full-length 16S rRNA sequencing. Microbial composition, predicted functional features, and clinical variables were examined in relation to treatment response and progression-free survival (PFS). Associations with treatment response were assessed using multivariable ordinal logistic regression. PFS was evaluated using Kaplan-Meier analysis and the log-rank test.

RESULTS: Smoking was associated with selected taxon-level microbial differences despite no significant differences in alpha or beta diversity. Compared with never-smokers, smokers exhibited reduced abundance of Bifidobacterium longum and enrichment of Gram-negative taxa. Functional prediction indicated increased potential for lipopolysaccharide, Kdo₂-lipid A, and lipid IVA biosynthesis in smokers. Predicted lpxM abundance, encoding a lipid A myristoyltransferase, was positively correlated with the Gram-negative bacterial fraction. Moreover, increased abundance of lpxM-linked Gammaproteobacteria was associated with improved ICI response in the NSCLC cohort. Conversely, lower B. longum abundance was associated with favorable ICI response and prolonged PFS.

CONCLUSIONS: These results indicate that smoking-related gut microbial alterations, particularly reduced B. longum abundance, are associated with enhanced ICI efficacy in NSCLC, supporting a role for the gut microbiota in smoking-associated differences in immunotherapy outcomes.},
}

@article {pmid42324448,
year = {2026},
author = {Patatian, A and Ngari, C and Durand, C and Romain, D and Guéré, C and Vie, K and Poulet, V and Percoco, G and Seyer, D},
title = {Development of an ex vivo skin model for quantitative recovery and preservation of donor-specific human microbiota.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05316-w},
pmid = {42324448},
issn = {1471-2180},
abstract = {BACKGROUND: Through multi-omics approaches, our understanding of skin microbiota has substantially advanced. However, the development of reliable and physiologically relevant experimental models would greatly accelerate progress in microbiome-targeted science. Most investigations of skin microbiota rely on in vitro 2D models or reconstructed epidermis colonized with a limited number of strains, which do not reflect the complexity and the spatial microbial organization observed on in vivo skin. To overcome these limitations, we developed a model based on perfused human skin explants (Perfex model), that enables the transfer of complex bacterial communities from human volunteers onto ex vivo skin.

RESULTS: After quantitative validation of recovered microbial DNA by qPCR from volunteers (V1-V2-V3) and corresponding inoculated explants (MV1-MV3), 16S rRNA gene sequencing was performed to assess whether microbiota transfer influenced community structure and diversity. No statistically significant differences in alpha-diversity were observed between original and transferred microbiota at the genus level, suggesting that the transfer procedure did not substantially alter overall community diversity. Clustering analysis revealed distinct grouping of samples according to donor origin, indicating that donor-specific microbial signatures were largely maintained on the explants after 48 hours. Control samples formed separate clusters, suggesting minimal background signal and supporting the absence of cross-contamination. These observations indicate that the model enables clear discrimination between the endogenous microbiota of the explants and the transferred microbiota, supporting the integrity of the experimental conditions. Beta-diversity analysis based on Bray-Curtis supported these findings. Across samples, microbial communities were characterized by the recurrent presence of common skin-associated genera such as Cutibacterium, Staphylococcus, and Corynebacterium. Histological analyses demonstrated preserved tissue architecture, while immunostaining revealed modulation of selected innate immune markers consistent with a localized skin response to microbial transfer.

CONCLUSIONS: The Perfex model enables transfer of donor-specific skin microbiota to ex vivo human skin while preserving tissue integrity over short-term culture. This model provides a human-relevant platform for studying host-microbiota interactions under controlled conditions and for preclinical evaluation of microbiome-targeted therapies and dermo-cosmetic treatments.},
}

@article {pmid42324499,
year = {2026},
author = {Ye, X and Yue, M and Lee, S and Li, A and Wang-Erickson, AF and Forno, E and Eddens, T and Shaikh, N and Chen, W},
title = {Dual-transcriptomic analysis of human nasal transcriptome and microbiome reveals host-bacteria associations in symptomatic respiratory infection.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13054-6},
pmid = {42324499},
issn = {1471-2164},
support = {KL2TR001856/TR/NCATS NIH HHS/United States ; 184862//Merck Investigator Studies Program/ ; S10OD028483/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The human nasopharynx is colonized by a diverse community of commensal microbiota linked to many respiratory diseases, yet their associations with the host remain unclear.

RESULTS: In this study, we introduced a dual-transcriptomics analysis strategy, which can characterize the host transcriptome and microbiome from nasal samples simultaneously. We applied this workflow to a local SARS-CoV-2 cohort with 76 asymptomatic infected patients, among whom 52 (68.42%) developed symptomatic infection during a 1-week follow-up period. Nasal swabs were collected from all 76 patients at enrollment and from 73 patients at one-week later follow-up. We detected a median of 8.94% reads that did not map to the human genome across all 149 samples, among which around half (median 49.68%) were successfully mapped to microbiome genome. Meta-transcriptomic analysis detected significantly higher SARS-related coronavirus loads in samples from the symptomatic group at enrollment (P = 0.004), and both groups showed decreased loads one week later (symptomatic, P = 0.001; asymptomatic, P = 0.035). Compared with benchmarking 16 S rRNA sequencing on 53 samples, our computational strategy showed high correlation of relative abundance in all top 20 genera (median Rho = 0.90, Pmax < 0.001). A total of 670 bacteria species were identified to show a relative abundance ≥ 0.01% in at least 10% samples. Differential abundance analysis identified 76 species (DASs) from six phyla with significantly decreased abundance in samples from the symptomatic group (log2(fold change or FC) < -1 and adjusted P < 0.05) compared to the asymptomatic group at enrollment. Integrating these symptom-associated DASs with host's gene expression using an expression quantitative trait bacteria (eQTB) model, we found 45 symptom-associated DASs identified at enrollment were significantly associated with one to 14 genes (adjusted P < 0.05). GSEA showed a series of symptom-associated DASs were significantly correlated with pathways related to olfactory function, keratinocyte differentiation, and DNA methylation.

CONCLUSIONS: In summary, our dual-transcriptomic analysis strategy effectively characterized host-microbiome associations, offering insights into microbial contributions to respiratory diseases.},
}

@article {pmid42324596,
year = {2026},
author = {Patel, D and Lain, AD and Vijayaraghavan, A and Faghih-Mirzaei, N and Mweetwa, MN and Wang, M and Beck, T and Posma, JM},
title = {Microbial Named Entity Recognition and Normalisation for AI-assisted Literature Review and Meta-Analysis.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag418},
pmid = {42324596},
issn = {1367-4811},
abstract = {MOTIVATION: Manual curation of biomedical literature is slow and error-prone and while large language models trained on general texts have shown to be useful for text summarisation, these methods lack the domain-specific expertise required to perform this task accurately. Here we describe the creation of the first microbiome-specific text corpus, use this to train deep learning algorithms for named-entity recognition (NER) and entity linking (EL), and demonstrate their use to meta-analyse microbiome literature.

RESULTS: The training and validation set (n = 1,410) contained a total of 90,150 annotations (both long form and abbreviations). Using the gold-standard test set (n = 288), with an inter-annotator agreement rate of 99.52% for NER and 88.31% for EL, the trained models were evaluated and our fine-tuned BioBERT model achieved an F1-score of 96% for NER surpassing a rule- and dictionary-based annotation pipeline (94%). For EL the accuracy obtained by the deep learning models greatly surpassed that of the pipeline (91% vs 69%). Evaluated across the entire available literature (n = 6,927) across 14 domains, our models annotate an entire full-text document in only 7 seconds.

AVAILABILITY: All codes are available for automatic annotation and model training, with instructions on how to deploy the model on new text, from GitHub and Zenodo. The redistributable, annotated training set and unannotated test set are made available from Zenodo with the redistributable, human-labelled test set hosted as benchmark on Codabench for NER only and NER+EL for evaluation. The annotated documents for all available literature are hosted separately at Zenodo.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42324602,
year = {2026},
author = {Lauer, JM and Leng, Y and Chembe, M and Henderson, S and Parkerson, D and Chibesa, K and Moono, A and Fink, G and Rockers, PC and Locks, LM},
title = {Gut Microbiome and Environmental Enteric Dysfunction Are Unchanged by 18 Months of Small-Quantity Lipid-Based Nutrient Supplementation among Young Children in Lusaka, Zambia.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-25},
doi = {10.1017/S0007114526107818},
pmid = {42324602},
issn = {1475-2662},
abstract = {Small-quantity lipid-based nutrient supplements (SQ-LNS) have been shown to improve growth, development, and survival among young children in low-resource settings. One hypothesized pathway is through improvements in intestinal health, including modulation of the gut microbiome and reductions in environmental enteric dysfunction (EED). This study examined the effects of SQ-LNS on the gut microbiome and markers of EED and systemic inflammation among young children in Lusaka, Zambia. We conducted intention-to-treat analyses of 302 children aged 27-35 months in a 2x2 cluster-randomized trial. Serum biomarkers of EED (soluble CD14, intestinal fatty acid binding protein) and inflammation (alpha-1-acid glycoprotein, C-reactive protein) were assessed in 240 children via the Multiple-Micronutrient and Environmental Enteric Dysfunction Assessment Tool (MEEDAT). Differences by SQ-LNS assignment were assessed using unadjusted and adjusted ordinary least squares regression models. Rectal swab samples from 299 children underwent 16S rRNA gene sequencing. Taxonomic profiles were visualized using stacked bar plots, alpha diversity was quantified using Shannon diversity indices, and beta diversity was assessed using non-metric multidimensional scaling based on Bray-Curtis dissimilarity matrices. We found that SQ-LNS had no significant effect on EED or inflammation biomarkers and was not associated with differences in gut microbiome alpha diversity, beta diversity, or overall microbial community composition. In exploratory analyses, Enterococcus abundance was lower among children receiving SQ-LNS. Overall, 18 months of SQ-LNS supplementation was not associated with broad changes in intestinal health among young Lusakan children. These findings suggest that the benefits of SQ-LNS operate through pathways other than intestinal health, such as improved nutrient availability.},
}

@article {pmid42324603,
year = {2026},
author = {Yu, J and Meng, J and Shi, Z and Zou, J and Lai, Z},
title = {Cross-kingdom microbiome interactions along the gut-lung axis: immune-microecological coordination, shared mechanisms, and disease-context dependence in respiratory disorders.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2689168},
doi = {10.1080/19490976.2026.2689168},
pmid = {42324603},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung/microbiology/immunology ; Animals ; Bacteria/classification/genetics/metabolism ; Fungi ; Dysbiosis/microbiology/immunology ; Asthma/microbiology/immunology ; Pulmonary Disease, Chronic Obstructive/microbiology/immunology ; Bacteriophages ; *Lung Diseases/microbiology ; },
abstract = {Cross-kingdom dysbiosis of the gut microbiome along the gut-lung axis has emerged as a key driver of chronic and acute respiratory diseases. Beyond bacteria, the intestinal mycobiome and virome, including bacteriophages, shape mucosal immunity and metabolism through partially overlapping but non-redundant pathways. In this Review, we synthesize rapidly expanding evidence that fungi, bacteria, and phages in the gut form an integrated network that may influence susceptibility, inflammatory tone, and therapeutic responsiveness across asthma, chronic obstructive pulmonary disease (COPD), acute respiratory distress syndrome (ARDS), and lung cancer via the gut-lung axis. We first summarize how cross-kingdom communities in the intestine are organized and interact, highlighting a tripartite framework centered on pathogen-associated molecular pattern-pattern recognition receptor (PAMP-PRR) circuits, the short-chain fatty acid (SCFA)-regulatory T-cell axis, and tryptophan-indole-aryl hydrocarbon receptor (AHR) signaling. We then compare how these shared axes are differentially perturbed across asthma, COPD, ARDS, and lung cancer, using these disorders as representative but non-sequential disease contexts along a conceptual gradient of immune-microecological disruption. Finally, we discuss how dietary modulation, pre-/pro-/postbiotics, mycobiome- and virome-targeted strategies, and phage-based approaches could be rationally combined to restore gut-derived immunometabolic circuits and improve respiratory outcomes. By integrating cross-kingdom ecology with mucosal immunology, this Review provides an integrative interpretive framework suggesting that gut microbiome-targeted strategies may help refine prevention, stratification, and adjunctive treatment approaches in selected respiratory disease contexts.},
}

Humans
*Gastrointestinal Microbiome
*Lung/microbiology/immunology
Animals
Bacteria/classification/genetics/metabolism
Fungi
Dysbiosis/microbiology/immunology
Asthma/microbiology/immunology
Pulmonary Disease, Chronic Obstructive/microbiology/immunology
Bacteriophages
*Lung Diseases/microbiology

@article {pmid42324618,
year = {2026},
author = {Hernandez, JB and Abiodun, M and Hayer, SS and Dickson, T and Ayayee, P and Clayton, JB},
title = {Mapping the metagenomic landscape: combined shotgun sequencing and quantitative PCR to profile gut metagenome-assembled genomes in marmosets following treatment with a broad-spectrum antibiotic cocktail.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2687925},
doi = {10.1080/19490976.2026.2687925},
pmid = {42324618},
issn = {1949-0984},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Metagenome/drug effects ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Callithrix/microbiology ; Metagenomics ; Shotgun Sequencing ; Real-Time Polymerase Chain Reaction ; Genome, Bacterial ; Feces/microbiology ; },
abstract = {Broad-spectrum antibiotics are invaluable tools for treating pathogenic infections, but their sustained use can contribute to changes in gut microbiome membership and the emergence of antimicrobial resistance. While these unintended side effects are independently well documented, the relationship between them has seldom been investigated. To address this, we quantified the effects of 28-d antibiotic cocktail exposure on metagenome-assembled genomes and antibiotic resistance genes in common marmosets using a custom whole-genome shotgun sequencing pipeline and quantitative polymerase chain reaction assays. We observed contrasting genus-level reductions in Bifidobacterium abundance and Fusobacterium growth, both during antibiotic treatment and a 2-week post-treatment period. Total bacterial abundance was not significantly affected by antibiotics, likely due to the presence of antibiotic-resistant opportunists. Genes for vancomycin resistance and multidrug efflux pumps were identified in metagenome-assembled genomes of an unclassified Sarcina sp. and Escherichia coli, respectively, and were accompanied by increased abundance of these species during treatment. Additionally, we detected 11 dysregulated metagenomic pathways related to carbohydrate metabolism, including 2 pathways relevant to short-chain fatty acid production, following antibiotic exposure. This study provides insights into the species-dependent emergence of antimicrobial resistance mechanisms in non-human primates following antibiotic exposure that could be relevant for antibiotic therapies and resistance management.},
}

Animals
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Metagenome/drug effects
*Bacteria/genetics/drug effects/classification/isolation & purification
*Gastrointestinal Microbiome/drug effects/genetics
*Callithrix/microbiology
Metagenomics
Shotgun Sequencing
Real-Time Polymerase Chain Reaction
Genome, Bacterial
Feces/microbiology

@article {pmid42325052,
year = {2026},
author = {Esteban, DJ and Conrad, B and Cullinan, A and Luong, S and Albaum, J and Wilk, V},
title = {Tryptophan Metabolism and Aryl-Hydrocarbon Receptor Agonists in the Gut Microbiome of People With Myalgic Encephalomyelitis/Chronic Fatigue Syndrome.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70333},
doi = {10.1002/mbo3.70333},
pmid = {42325052},
issn = {2045-8827},
mesh = {Humans ; *Fatigue Syndrome, Chronic/microbiology/metabolism ; *Tryptophan/metabolism ; *Receptors, Aryl Hydrocarbon/agonists/metabolism ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Female ; Adult ; Male ; Middle Aged ; Metabolomics ; },
abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating chronic disease with unknown biological basis and no cure. Microbiome dysbiosis has been reported in people with ME/CFS but its relevance to pathophysiology is unknown. Gut microbes are an important source of tryptophan metabolites that activate the aryl hydrocarbon receptor (AHR), a regulator of homeostatic and inflammatory genes. Dysregulated activation of AHR contributes to pathophysiology of several neuroimmune and chronic diseases but its role in ME/CFS has not been investigated. The purpose of this study was to investigate the production of tryptophan metabolites and AHR agonists by gut microbes of people with ME/CFS. We found lower diversity and altered microbiome community structure in people with ME/CFS and changes in the subcommunity of microbes that correlated with tryptophan metabolites. Using targeted metabolomics we identified nine metabolites elevated in the stool of people with ME/CFS, including three AHR agonists. Stool ex vivo cultures were tested for their capacity to activate AHR in a reporter cell line and by qPCR. AHR activation did not differ between people with ME/CFS and controls, however, we detected elevated agonist activity in people with neurocognitive symptoms, regardless of underlying disease. These findings are consistent with previous work revealing changes in the gut microbiome of people with ME/CFS and adds further support to alterations in tryptophan metabolism associated with the disease. Altered AHR activity by gut microbial metabolites may be a common mechanism contributing to neurocognitive symptoms in diseases including ME/CFS.},
}

Humans
*Fatigue Syndrome, Chronic/microbiology/metabolism
*Tryptophan/metabolism
*Receptors, Aryl Hydrocarbon/agonists/metabolism
Feces/microbiology/chemistry
*Gastrointestinal Microbiome
Female
Adult
Male
Middle Aged
Metabolomics

@article {pmid42325131,
year = {2026},
author = {Valentine, GC and Bobetsis, YA and Shayo, BC and Milgrom, P and Madianos, PN},
title = {Periodontitis and Adverse Pregnancy Outcomes: Mechanistic Evidence.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70134},
pmid = {42325131},
issn = {1600-0765},
support = {K23HD105929//National Institute of Child Health and Human Development/ ; },
abstract = {Periodontal diseases, including both gingivitis and periodontitis, occur commonly among pregnant individuals. Both gingivitis and periodontitis are associated with adverse pregnancy outcomes (APOs) such as early pregnancy loss, preterm birth, preeclampsia, low birth weight, and stillbirth. This review highlights that the strongest mechanistic evidence linking periodontal diseases with APOs involves the domains of systemic inflammation, including increased pro-inflammatory cytokines and activation of matrix metalloproteases associated with preterm labor, and microbial translocation involving hematogenous dissemination of periodontopathic bacteria to the fetoplacental unit. Yet, other mechanistic domains remain underexplored, including maladaptive myelopoiesis with alterations of neutrophil activity, immune player trafficking with autoantibody development, masticatory dysfunction-diet interactions that may further increase risk of critical vitamin and nutritional deficiencies related to both periodontitis and APOs, and functional dysregulation of the oral microbiome including generation of nitric oxide that could impact pregnancy outcomes. Additionally, specific underlying vulnerabilities unique to pregnancy such as increased hormone production such as progesterone and cortisol likely impact the risk of periodontal diseases in pregnancy. By delving into these critical mechanistic domains, this review reveals both current understanding and critical areas for future research to overcome deficits in knowledge pertaining to how periodontal diseases in pregnancy lead to APOs. Elucidating these novel insights can promote scientific advancement, facilitate the development of novel interventions that prevent and/or treat periodontal diseases in pregnancy, and concurrently improve the lives and well-being of pregnant individuals and their children worldwide.},
}

@article {pmid42325215,
year = {2026},
author = {Conner, L and Tuladhar, L},
title = {The Aging Vaginal Microenvironment: A Communication Toolkit.},
journal = {Acta microbiologica Hellenica},
volume = {71},
number = {2},
pages = {},
pmid = {42325215},
issn = {2813-9054},
abstract = {BACKGROUND: The vagina undergoes important changes across the life course that are shaped not only by hormonal transitions but also by shifts in the vaginal microbial environment. Despite growing interest in the vaginal microbiome, research has disproportionately centered reproductive-aged populations, leaving the aging vagina comparatively understudied.

OBJECTIVE: This article examines the aging vagina through a life-course lens, with emphasis on microbial and clinical transitions associated with midlife and older adulthood.

KEY CONTENT: The article highlights menopause-related changes and approaches for reducing stigma and missed clinical opportunities. Particular attention is given to menopause-related declines in estrogen, reduced glycogen availability, increased vaginal pH, and accompanying changes in microbial balance, as well as their relationship to dryness, irritation, genitourinary symptoms, and susceptibility to adverse outcomes. The article also provides health professionals with a practical educational framework for symptom recognition, patient communication, vaginal health assessment, menopause-related education, stigma reduction, and prevention of missed clinical opportunities.

CONCLUSIONS: Positioning the aging vagina within life-course and microbial-health frameworks can strengthen prevention, improve symptom recognition, and support more ageinclusive, informed, and responsive care for older women.},
}

@article {pmid42325301,
year = {2026},
author = {Zhang, Y and Li, M and Fan, Z and He, F and Li, X and Wang, S and Wei, W},
title = {Plant-based diet quality is associated with esophageal mucosa-associated microbiome profiles and disease severity in a high-risk Chinese population.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2682962},
pmid = {42325301},
issn = {2000-2297},
abstract = {BACKGROUND: Esophageal squamous cell carcinoma (ESCC) remains a major public health challenge in China. Diet is a modifiable risk factor, and the esophageal mucosa-associated microbiome may contribute to esophageal disease progression. However, population-based evidence integrating plant-based diet quality, esophageal microbiome profiles anddisease severity remains limited.

METHODS: We conducted a cross-sectional study including 236 participants undergoing upper gastrointestinal screening in Linzhou, a high-risk region for ESCC. Dietary intake was assessed using a food frequency questionnaire, and plant-based diet indices, including the overall plant-based diet index (PDI), healthful plant-based diet index (hPDI) and unhealthful plant-based diet index (uPDI), were calculated. Esophageal mucosal swabs were profiled by 16S rRNA gene sequencing. Associations among diet indices, microbiome features, and esophageal disease severity were evaluated using regression and risk stratification models.

RESULTS: Higher hPDI was inversely associated with esophageal disease severity, whereas higher uPDI were positively associated. Higher hPDI was associated with greater relative abundance of Rothia and Prevotellaceae-related taxa, whereas higher uPDI was associated with enrichment of Streptobacillus and Fretibacterium. Integrating dietary indices with microbiome features modestly but consistently improved risk stratification beyond epidemiological factors alone (e.g. AUC for the combined hPDI-microbiome model was 0.93, 95%CI: 0.89-0.98).

CONCLUSIONS: Healthful and unhealthful plant-based diet patterns showed opposite associations with esophageal disease severity and distinct mucosa-associated microbiome profiles, supporting an exploratory diet-microbiome framework for ESCC risk stratification.},
}

@article {pmid42325367,
year = {2025},
author = {Zhang, R and Gu, X and Zhang, H and Guo, Y and Cao, B},
title = {Long COVID: current research and future directions.},
journal = {Infectious diseases & immunity},
volume = {5},
number = {4},
pages = {260-271},
pmid = {42325367},
issn = {2693-8839},
abstract = {Long coronavirus disease (COVID) is defined as the continuation or development of new symptoms three months after the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and that last for at least two months, with no other explanation for their cause. This disease includes various clinical manifestations that affect multiple organ systems, such as complications in respiratory, cardiovascular, neurological, and musculoskeletal systems. The most commonly reported symptoms include fatigue, cognitive dysfunction, dyspnea, and chest pain; however, the prevalence and severity of these symptoms vary greatly among individuals. The underlying mechanisms of long COVID are complex and multifaceted, encompassing viral persistence, immune system dysfunction, mitochondrial abnormalities, endothelial impairment, and alterations in the microbiome. Further, long COVID has imposed a significant burden on individuals, healthcare systems, and the economy by impairing an individual's quality of life and functional capacity, thereby increasing costs and demand for care and rehabilitation services. This review summarizes the definition, phenotypes, mechanisms, and current treatment advancements of long COVID and highlights specific research directions for future investigation.},
}

@article {pmid42325370,
year = {2025},
author = {Liu, S and Guo, Y and Wang, FS},
title = {Viral persistence in long COVID: Research advances and treatment strategies.},
journal = {Infectious diseases & immunity},
volume = {5},
number = {4},
pages = {272-288},
pmid = {42325370},
issn = {2693-8839},
abstract = {Although the coronavirus disease 2019 (COVID-19) pandemic has ended, the enduring health impacts of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continue to garner global attention, as approximately 10% of patients develop long COVID (post COVID-19 condition). The epidemiological characteristics and symptoms of long COVID have been reported, and various pathogenic hypotheses have been proposed. Recent evidence suggests that SARS-CoV-2 nucleic acids or fragments persist in some patients post-infection and that these are correlated with long COVID symptoms. This review focuses on clinical studies linking SARS-CoV-2 persistence to long COVID symptoms, and explores the relationship between viral persistence and other etiological hypotheses, such as immune dysregulation, vascular issues, coagulation dysfunction, microbiome dysbiosis, brainstem/vagus nerve signaling dysfunction, and latent virus reactivation. Futhermore, treatment strategies for long COVID are proposed based on current clinical trials of antiviral and immune modulation therapies. Understanding the role of viral persistence in long COVID pathogenesis is critical for developing targeted therapies and improving clinical management of this debilitating condition.},
}

@article {pmid42325378,
year = {2026},
author = {Molina, NM and Pérez-Prieto, I and Tenorio, CM and Gámiz-Aguilera, M and Sola-Leyva, A and Salas-Espejo, E and Andrés-León, E and Vargas, E and Canha-Gouveia, A and Leonés-Baños, I and Gonzalvo, MC and Fontes, J and Castilla, JA and Altmäe, S},
title = {The impact of vasectomy on the seminal microbiome: possible implications and source of microbes.},
journal = {Human reproduction open},
volume = {2026},
number = {3},
pages = {hoag043},
pmid = {42325378},
issn = {2399-3529},
abstract = {STUDY QUESTION: Does vasectomy alter the seminal microbiome, and what proportions of seminal microorganisms originate from the urinary and upper reproductive tract?

SUMMARY ANSWER: Vasectomy is associated with modest shifts in the seminal microbial community structure, where inter-individual variability prevails, and the semen shares over 60% of bacterial communities with urine, suggesting an influence of the urinary tract and upstream genitourinary compartments on the seminal microenvironment.

WHAT IS KNOWN ALREADY: The semen harbours a polymicrobial community whose origin is not fully understood. Also, the effect of vasectomy, a common sterilization procedure, on seminal microenvironment is not clear. Recent studies with a limited sample size suggest that part of the seminal microbiome may derive from the upper genital tract, and that vasectomy may alter seminal microbial composition, potentially revealing testicular or epididymal microbial contributions.

STUDY DESIGN SIZE DURATION: This prospective cohort study including 82 men undergoing vasectomy, with paired semen and urine samples collected before and 3 months after the procedure.

Paired semen and urine samples were collected pre- and post-vasectomy. The seminal and urine microbiome was analysed by sequencing the V4 hypervariable region of the 16S rRNA gene. Amplicon sequence variants were decontaminated using rigorous negative-control-based methods. Microbial diversity, taxonomic composition, and differential abundance were assessed, and functional profiles were predicted using PICRUSt2.

More than 60% of seminal bacterial genera were also present in urine, indicating substantial overlap. Vasectomy significantly altered β-diversity; however, the effect was small, and several predicted functional pathways were detected, including lipid metabolism. Although some genera differed between pre- and post-vasectomy samples, these did not remain significant after false discovery rate (FDR) correction. These findings should be interpreted considering the prevailing inter-individual variability and shared urinary-seminal taxa.

LARGE SCALE DATA: The 16S rRNA gene sequencing data have been uploaded to the SRA database under BioProject ID PRJNA1355064.

The main limitations of the study are the use of 16S rRNA gene sequencing, which limits species-level resolution, the lack of repetitive sampling, and the absence of absolute bacterial load quantification. Also, the functional pathway analyses present predictive estimates from the sequencing data rather than from direct measurements of the microbial metabolic activity.

Vasectomy may induce subtle changes in the seminal microenvironment by modifying microbial composition and metabolic functions, as indicated by these exploratory analyses. Nevertheless, our study findings should not be interpreted as evidence against vasectomy, rather as novel information to better understand the dynamics of the seminal microbiome. Whether the microbial changes have any effect on the male urogenital health requires further research.

This work was supported by projects ENDORE (SAF2017-87526-R); Endo-Map (PID2021-12728OB-I00), and ROSY (CNS2022-135999), funded by MICIU/AEI/10.13039/501100011033 and by FEDER, EU; I.L.-B. and C.M.T. are supported by the FPU22/03045 grant and FPU23/01576, awarded by MCIN/AEI/10.13039/501100011033, respectively; additionally, S.A. obtained a mobility grant for senior researchers to do a research stay abroad funded by the Spanish Ministry of Science, Innovation and Universities (ref. PRX24/00372); I.P.-P. and A.S.-L. were supported by Becas Fundación Ramón Areces para Estudios Postdoctorales-Convocatorias XXXVI-XXXV para Ampliación de Estudios en el Extranjero en Ciencias de la Vida y de la Materia; A.S.-L. is supported by the Estonian Research Council (grant no. PSG1082); funding for open access charge: Universidad de Granada / CBUA. The authors declare no competing interests.},
}

@article {pmid42325392,
year = {2026},
author = {Cao, J and Jin, Y and Zhang, L},
title = {Integrating metabolomics and microbiome analysis to unravel the plum blossom signature of premium Jiuqu Hongmei tea.},
journal = {Food chemistry: X},
volume = {37},
number = {},
pages = {104072},
pmid = {42325392},
issn = {2590-1575},
abstract = {Jiuqu Hongmei (JQHM), a Chinese tea, features plum blossom aroma. However, its quality is often compromised by raw material and processing variability, and the chemical and microbial basis of this aroma remains unclear. To address this gap, integrated multi-omics assessed JQHM across grades. High grades showed enriched beneficial microbiota and critical aroma compounds, which synergistically formed a floral-fruity profile. Conversely, lower grades exhibited microbial dysbiosis and elevated theabrownins linked to sensory deterioration. Correlation networks revealed microbial regulation of metabolic pathways, deciphering the microbial-metabolite nexus governing the plum blossom signature and moving beyond empirical observations. By integrating metabolomics and microbiome analysis, this study uniquely demonstrates that the synergistic enrichment of specific beneficial taxa directly orchestrates the biosynthesis of key aroma compounds (linalool, geraniol, and methyl salicylate). This multi-omics strategy provides a mechanistic blueprint for precision quality control in JQHM production and establishes a paradigm for dissecting flavor formation in fermented foods.},
}

@article {pmid42325435,
year = {2026},
author = {Liu, C and Zhu, Z and Lin, H and Bush, WS and Jenq, RR and Cominelli, F and Pillai, JA and Haines, JL and Zhu, X and Xu, R and Williams, SM and Cheng, F and Zhang, L},
title = {The gut-brain axis in Alzheimer's disease: early detection, microbial metabolites, mechanisms, and therapeutic opportunities.},
journal = {Frontiers in molecular biosciences},
volume = {13},
number = {},
pages = {1735332},
pmid = {42325435},
issn = {2296-889X},
abstract = {Alzheimer's disease (AD), the leading cause of dementia worldwide, imposes a growing clinical and societal burden, yet no therapies have been proven to alter its progression despite decades of intensive research. As traditional targets have yielded limited success, attention has shifted to modifiable upstream pathways, notably the gut-brain axis, a bidirectional system linking gut microbiota with CNS function. Emerging evidence indicates that microbial dysbiosis may influence key processes leading to AD, including neuroinflammation, amyloid and tau pathology, and cognitive decline. While microbiome composition is associated with AD, it remains unclear at which stage-preclinical, mild cognitive impairment (MCI), or AD dementia-these differences first arise, or how specific risk bacteria and metabolites contribute to progression. The precise roles of these microbes and metabolites in AD pathology or brain resilience also remain poorly understood, and few microbiome-targeted treatments have been validated in humans. Existing reviews often overlook host-specific factors that influence microbiome composition and confound associations with AD. To bridge these gaps, we summarize human studies published in the past 5 years. The literature suggests that gut microbial changes may precede clinical symptoms, with consistent dysbiosis observed in AD patients. We adopt a microbiome-centered perspective emphasizing bacteria-driven and metabolite-driven mechanisms, each playing distinct yet complementary roles in neural and bloodstream pathways. These pathways offer potential targets for microbiome-based prevention and treatment but require more human validation. Future studies should leverage longitudinal, multi-omics approaches and artificial intelligence (AI) tools while rigorously accounting for confounders to improve early detection and develop personalized therapies for AD.},
}

@article {pmid42325450,
year = {2026},
author = {Giriraj, A and Bhat, A and Sabat, S},
title = {Lactobacillus spp. from the Human Gut Microbiota as a Therapeutic Tool in Controlling MRSA-Induced Sepsis.},
journal = {Indian journal of microbiology},
volume = {66},
number = {3},
pages = {677-687},
pmid = {42325450},
issn = {0046-8991},
abstract = {Over the past few years, sepsis, characterized by an exaggerated response to infection, has emerged as a significant global cause of mortality. The rise in antibiotic-resistant strains underscores the necessity to explore alternative approaches beyond antibiotics, which is the conventional treatment. Recent investigations into the human gut microbiome propose considering it as a potential therapeutic alternative. The study was performed on 10 blood samples infected with Staphylococcus aureus ATCC 25923 by treating it with different concentrations of partially purified protein isolated from Lactobacillus spp. Proteins were isolated and purified using a lysis buffer followed by 35-40% ammonium sulphate precipitation and dialysis. The protein efficacy was measured via cytotoxicity and cell viability assays such as MTT and dye exclusion assay. The 1:8 and 1:10 S. aureus-to-protein ratio was found to be highly effective in controlling and inhibiting the growth of S. aureus. A statistical analysis by ANOVA determined the effect of age and gender on the blood cells infected with 1:8 and 1:10 S. aureus-to-protein samples. The results represent the concentration of protein added to the transfected sample reduced the damage by protecting the systemic immune cells. This overview specifically examines potential proteins within the human gut microbiome that may regulate S. aureus-induced sepsis. This investigative study is an advantage as gut microbiome used can be a novel therapeutic focus to mitigate over activation of inflammasomes during sepsis.},
}

@article {pmid42325463,
year = {2026},
author = {Dobhal, S and Kaushik, M and Manhas, PL and Kumar, A and Naithani, P and Gupta, P and Kaushik, H and Naithani, M and Omar, BJ and Kothari, A and Uniyal, A and Mathuria, YP and Kohli, H and Manhas, HS and Gairolla, J},
title = {Crossroad Between Gut Microbiome and Ischemic Stroke: Underlying Pathways and Therapeutic Possibilities.},
journal = {Indian journal of microbiology},
volume = {66},
number = {3},
pages = {553-573},
pmid = {42325463},
issn = {0046-8991},
abstract = {Stroke is a cerebrovascular condition that has emerged as the major cause of death globally, among other non-communicable diseases, due to its pathophysiological complexity and varied etiologies. Ischemic stroke (IS) represents the most prevalent subtype accounting for more than 70% of all stroke cases worldwide. The gut microbiome is considered the most abundant pool of microorganisms, which release metabolic products that facilitate gut-brain signaling. Despite advancements, the precise processes by which gut microbes influence stroke pathogenesis are not entirely understood. This review explores the immunomodulatory impact of gut-derived metabolites in IS, with a focus on short-chain fatty acids (SCFAs) and other bioactive substances. A comprehensive literature search was undertaken using MeSH terms such as gut microbiome, ischemic stroke, cerebral ischemia, brain infarction, intestinal flora, and gut-brain axis. We address how metabolites such as short-chain fatty acids produced by gut bacteria influence the host's immune system, which in turn affects the activity of neural networks linked to atherosclerosis, a major underlying mechanism of IS. Furthermore, this review also looks at new research opportunities and highlights evidence from studies conducted on humans and animals.},
}

@article {pmid42325564,
year = {2026},
author = {Ping, Y and Peng, Y and Sun, J and Xiang, J and Wang, P and Shen, Y and Xia, J and Dang, C and Lu, J and Xue, D},
title = {Geographic transplantation promotes the growth of Atractylodes macrocephala by restructuring the rhizosphere microbial community.},
journal = {iScience},
volume = {29},
number = {7},
pages = {116350},
pmid = {42325564},
issn = {2589-0042},
abstract = {This study systematically elucidated the microecological mechanisms underlying Atractylodes macrocephala geoherbalism via integrated transplantation experiments across China's four major producing regions. Data showed that soil from Pan'an significantly enhanced the accumulation of bioactive compounds in A. macrocephala sourced from Bozhou. 16S rRNA gene sequencing revealed that geographic transplantation significantly restructured the rhizosphere microbial community and markedly increased its α-diversity. Functional metabolic analysis indicated that transplantation to Pan'an regulated various pathways and enhanced secondary metabolism in the rhizosphere microbiome. Co-occurrence network analysis revealed 11 upregulated keystone genera that potentially promoted secondary metabolism in A. macrocephala, and were positively correlated with root growth and bioactive compound accumulation. These results demonstrate that direct soil nutrient supply, microbiome-mediated C/N metabolism remodeling, and resource reallocation collectively drive A. macrocephala geo-authenticity. It will lay the groundwork for the use of microbiome biofertilizers and the cross-regional eco-cultivation of geo-authentic herbs.},
}

@article {pmid42325613,
year = {2026},
author = {Komati, A and Mandava, K and Anand, A},
title = {Decoding type 5 diabetes using spatial omics: microarchitectural and molecular mechanisms of malnutrition-associated diabetes.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1822644},
pmid = {42325613},
issn = {1664-2392},
mesh = {Humans ; *Malnutrition/complications/metabolism ; Animals ; Gastrointestinal Microbiome ; },
abstract = {This review advocates for the formal recognition of Type 5 Diabetes Mellitus, a distinct, neglected form of non-autoimmune, lean diabetes predominantly affecting low-income and middle-income populations with a history of early-life malnutrition. Characterized by impaired insulin secretion amid preserved insulin sensitivity, this phenotype exhibits unique microarchitectural alterations within pancreatic islets and is strongly linked to malnutrition-induced epigenetic reprogramming and gut microbiota dysbiosis. Recent advancements in spatial omics technologies have illuminated region-specific gene expression, inflammatory pathways, and cellular remodeling in pancreatic tissue, offering novel insights into its pathophysiology. Despite its global prevalence, especially in resource-constrained settings, Type 5 diabetes remains underdiagnosed and poorly understood, hindering the development of tailored diagnostic criteria and therapeutic strategies. This review synthesizes current epidemiological, mechanistic, and molecular evidence, emphasizing the imperative for establishing standardized classification, research collaborations-including the formation of the IDF Type 5 Diabetes Working Group-and region-specific management protocols. Recognizing this disease entity is critical for advancing health equity, improving clinical outcomes, and guiding future research in metabolic disease frameworks.},
}

Humans
*Malnutrition/complications/metabolism
Animals
Gastrointestinal Microbiome

@article {pmid42325748,
year = {2026},
author = {Liu, X and Xu, Y and Yu, J},
title = {Perioperative gut microbiota homeostasis and its interactions with anesthetic agents: recent advances.},
journal = {American journal of translational research},
volume = {18},
number = {5},
pages = {3901-3915},
pmid = {42325748},
issn = {1943-8141},
abstract = {The perioperative period is a critical and acute phase during which host-microbiota interactions play an essential role in determining susceptibility to anesthetic exposure and post-surgical stress. Immune homeostasis, gut barrier integrity, and metabolic regulation, as well as gut-brain and gut-liver axis, are highly dependent on the gut microbiota. However, this microbial ecosystem is disrupted during the perioperative period due to the combined effects of fasting, bowel preparation, surgical stress, hemodynamic alterations, and antibiotic and opioid use. Growing evidence has linked perioperative dysbiosis to a wide range of adverse outcomes, including infectious complications, anastomotic leakage, postoperative ileus, organ dysfunction, and perioperative neurocognitive disorders. Meanwhile, anesthetic and analgesic agents do not act in isolation from this ecosystem; rather, they engage in a bidirectional chemical interaction with the microbiota. These interactions can alter microbial structure and metabolite profiles, thereby influencing host metabolic processes, while microbial activity, in turn, affects drug disposition, immune response, and neuroinflammation. In this review, we first describe the vulnerability of gut microbiota homeostasis during the perioperative period and its associated clinical consequences. We subsequently elaborate on the mechanistic framework of anesthetic-microbiota crosstalk, highlighting pathways involving vascular, epithelial, immune and neural signaling. Then, we summarize emerging evidence demonstrating that different anesthetic and analgesic regimens generate discrete microbiota-metabolite signatures, which may underlie intersubject differences in postoperative recovery trajectories. Finally, we describe perioperative microbiota-targeted strategies, including probiotics and synbiotics, postbiotics and microbial consortia, nutritional optimization, and microbiome-based customization of anesthetic and analgesic protocols. Collectively, existing data suggest that preserving and actively modulating gut microbiota homeostasis represents a promising yet underexplored strategy for improving the safety of anesthesia and postoperative outcomes.},
}

@article {pmid42325817,
year = {2025},
author = {Chung, HC and Ni, Y and Gaynanova, I},
title = {Sparse Semiparametric Discriminant Analysis for High-dimensional Zero-inflated Data.},
journal = {Journal of machine learning research : JMLR},
volume = {26},
number = {},
pages = {},
pmid = {42325817},
issn = {1532-4435},
abstract = {Sequencing-based technologies provide an abundance of high-dimensional biological data sets with highly skewed and zero-inflated measurements. Despite the computational efficiency and high interpretability offered by linear classification methods, the violation of underlying distribution assumptions, driven by high skewness and zero inflation, results in invalid classification rules and interpretations. Furthermore, existing data transformation methods addressing these violations introduce ambiguity, rendering the final model and classification performance contingent on the specific transformation employed. To tackle these challenges, we propose a novel semiparametric framework for discriminant analysis based on the truncated latent Gaussian copula model. This model accommodates skewness and zero inflation, and its estimation procedure ensures robustness against data transformations. To facilitate model interpretability, we incorporate ℓ 1 sparsity regularization and establish the consistency of the classification directions in high-dimensional settings. We validate our approach using human gut microbiome, breast cancer microRNA, and single-cell RNA sequencing data, highlighting its superior classification accuracy and robustness to data transformations.},
}