@article {pmid42288255,
year = {2026},
author = {Fonacier, L and Mawhirt, S and Stern, H and Roellke, E and Singer, S and Hunt, A and Lio, P},
title = {Precision medicine in atopic dermatitis: Present and future.},
journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2026.06.006},
pmid = {42288255},
issn = {1534-4436},
abstract = {Atopic dermatitis (AD) is a chronic, multifactorial inflammatory skin disease characterized by barrier dysfunction, immune dysregulation, genetic predisposition, and environmental factors, including microbiome and allergens. As more is learned about its pathophysiology, treatment evolves using precision medicine-leveraging phenotype, endotype, biomarkers, disease severity, and response predictors, molecular profiling, and omics. Oral and topical corticosteroids may be effective and most accessible, but their use has been associated with various adverse effects. Cyclosporine also has proven efficacy for moderate to severe AD but is an immunosuppressive and is typically reserved for short-term therapy because of its prominent adverse effects. The advent of systemic and topical biologics and small molecule therapies targeting key cytokines involved in the pathogenesis of AD-namely, cytokines interleukin (IL)-4 (dupilumab), IL-13 (tralokinumab and lebrikizumab), and IL-31 (nemolizumab), and Janus kinase inhibitors has revolutionized treatment of moderate to severe AD. Although biomarkers defining distinct molecular endotypes are now available to use for precision targeting, such tools are not yet widely accessible or sufficiently validated for routine clinical use. Thus, in current practice, treatment decisions can use a combination of biomarkers, if possible, phenotype-based patterns, and observable constellations of age, disease distribution, morphology, barrier integrity, pruritus predominance, and associated comorbidities.},
}

@article {pmid42497997,
year = {2026},
author = {Srisanoi, K and Tiwari, A and Srinivasan, M},
title = {Changes in the oral microbiota among dentate, edentate, and complete denture-wearing older adults: A systematic review and meta-analysis.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106927},
doi = {10.1016/j.jdent.2026.106927},
pmid = {42497997},
issn = {1879-176X},
abstract = {OBJECTIVE: This systematic review investigated differences in the oral microbiome among dentate older adults, edentate older adults, and older adults wearing complete dentures (CDs).

DATA AND SOURCES: Online databases (PubMed, Embase, and the Cochrane Library) were systematically searched. The last search update was on 16[th] April 2026.

STUDY SELECTION AND METHODS: Studies were eligible if they reported on oral microbiome outcomes in older adults (≥65 years) who were dentate or edentate (with and without CDs). Meta-analyses were performed for studies comparing edentate versus dentate individuals and for studies evaluating pre- and post-CD insertion.

RESULTS: Fifteen studies (descriptive analysis: n = 10; meta-analysis: n = 5) were included from 444 identified records. Two studies reported lower microbial diversity and distinct microbial patterns in edentate individuals, with or without CDs, compared with dentate individuals. Two studies reported that individuals with denture stomatitis exhibited different microbial patterns from healthy CD wearers, suggesting microbial dysbiosis. The meta-analysis revealed that Porphyromonas gingivalis (p < 0.001), Tannerella forsythia (p < 0.001), Treponema denticola (p < 0.001), and Prevotella intermedia (p < 0.001) were less prevalent in edentate than dentate individuals. While Porphyromonas gingivalis (p = 0.002) and Tannerella forsythia (p = 0.006) increased during short-term follow-up after CD insertion. Risk of bias ranged from low to moderate.

CONCLUSIONS: The review concluded that edentate older adults had a distinct oral microbiome when compared with dentate older adults. Denture stomatitis in CD wearers was associated with microbial dysbiosis. The review further found that P. Gingivalis and T. Forsythia may reappear transiently in edentate older adults rehabilitated with CDs.

CLINICAL SIGNIFICANCE: In older adults, CD therapy requires consistent follow-up with an emphasis on maintaining optimal mucosal health and denture hygiene. Although longitudinal evidence on changes in species associated with periodontitis remains limited, the prevention and management of denture stomatitis-associated dysbiosis should be prioritized because it may contribute to inflammaging.},
}

@article {pmid42498043,
year = {2026},
author = {Kaki, D and Kore, U and Talari, A and Komati, A and Garlapati, C and Dondra, T and De, S and Mandava, K},
title = {Modern approaches to gut microbiome investigation: Sequencing, culturomics, metabolomics, and beyond.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107636},
doi = {10.1016/j.mimet.2026.107636},
pmid = {42498043},
issn = {1872-8359},
abstract = {The human gut microbiome is a complex and constantly evolving community of trillions of microorganisms that are crucial to various aspects of health and disease. It impacts digestion, metabolism, immune function, neurological processes, and vulnerability to illnesses. Recent technological advancements in biology and engineering have transformed microbiome research, allowing for more detailed analysis of microbial composition, functions, and interactions with the host. This review offers a thorough overview of both current and emerging methods for studying the gut microbiome, including sample collection techniques, culture-based approaches like culturomics and microfluidics, as well as culture-independent methods such as 16S rRNA sequencing, shotgun metagenomics, and the integration of multi-omics approaches like metabolomics, proteomics, and transcriptomics. It also discusses innovative tools including single-cell genomics, spatial transcriptomics, and microbiome-on-a-chip platforms, which hold promise for revealing host-microbe interactions at unprecedented levels of detail. The review underscores the importance of combining biological insights with engineering innovations particularly microfluidics and organ-on-a-chip models to recreate gut environments that mimic physiological conditions. Additionally, it explores the potential of artificial intelligence and machine learning in analyzing data and developing predictive models for personalized microbiome-based diagnostics and therapies. Acknowledging challenges such as microbial diversity, environmental sensitivity, and technical hurdles, this review aims to guide researchers in choosing optimal tools to study the gut microbiota, deepen mechanistic understanding, and translate findings into clinical applications that enhance human health.},
}

@article {pmid42498165,
year = {2026},
author = {Senthamarai, S and Sarala, G and Sivasankari, S and Naveen, P},
title = {Comment on "Polypharmacy is Associated with Altered Gut Microbiota Diversity in Older Post-Stroke Inpatients".},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {103619},
doi = {10.1016/j.clnesp.2026.103619},
pmid = {42498165},
issn = {2405-4577},
}

@article {pmid42498366,
year = {2026},
author = {Li, A and Li, M and Xu, W and Zhang, Y and Yin, S and Yu, Y and Zheng, S and Hu, Y and Song, M},
title = {Association between gut microbiota composition and liver dysfunction in school-aged children exposed to triclosan.},
journal = {Journal of environmental sciences (China)},
volume = {167},
number = {},
pages = {308-316},
doi = {10.1016/j.jes.2025.10.026},
pmid = {42498366},
issn = {1001-0742},
mesh = {*Triclosan/toxicity ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Endocrine Disruptors/toxicity ; Child ; *Environmental Pollutants/toxicity ; *Environmental Exposure/statistics & numerical data ; Liver/drug effects ; Phenols/toxicity ; },
abstract = {Growing epidemiological evidence implicate endocrine-disrupting chemicals (EDCs) in the development of liver dysfunction across populations. However, the effects of mixed EDC exposure on children's liver function remains critically limited. This study investigated the association between co-exposure to three prevalent EDCs - bisphenol S, triclosan (TCS), and methylparaben - and liver function, as measured by the aspartate aminotransferase/alanine aminotransferase ratio (AST/ALT), in school-aged children. Using g-computation and Bayesian kernel machine regression, we found consistent positive associations between the EDCs mixture and elevated AST/ALT levels, with TCS emerging as the primary contributor. Stratification by median TCS exposure revealed significant gut microbiota compositional differences between high- and low-exposure groups. Mediation analysis identified Desulfovibrio as a key microbial mediator, explaining 48.5 % of the TCS-associated effect on AST/ALT. Our findings suggest that EDC co-exposure, particularly to TCS, may promote subclinical liver injury in children, potentially mediated through gut microbiome alterations. These results highlight the need for longitudinal studies to confirm these associations and elucidate the underlying mechanisms.},
}

*Triclosan/toxicity
Humans
*Gastrointestinal Microbiome/drug effects
*Endocrine Disruptors/toxicity
Child
*Environmental Pollutants/toxicity
*Environmental Exposure/statistics & numerical data
Liver/drug effects
Phenols/toxicity

@article {pmid42498611,
year = {2026},
author = {Singh, DP and Ryan, E and Clarke, G and Cryan, JF},
title = {Forever chemicals, the microbiome, and brain health: towards therapeutics.},
journal = {Trends in pharmacological sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tips.2026.06.010},
pmid = {42498611},
issn = {1873-3735},
abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent xenobiotics linked to neurodevelopmental, neurodegenerative, and neurological disorders. PFAS-induced gut microbiota remodelling may disrupt gut-brain signalling, thereby affecting brain functions and behaviour. Integrating microbiome endpoints (diversity, taxonomic shifts, and metabolic configuration) into PFAS research provides a framework to elucidate toxicodynamic mechanisms and to inform the development of targeted, mechanism-based therapeutic strategies.},
}

@article {pmid42498637,
year = {2026},
author = {Dhanasekaran, S and Dhaneesh, KV},
title = {Molecular mechanisms of heavy metal-induced cancer: Insights from animal models and human implications.},
journal = {Toxicology and industrial health},
volume = {},
number = {},
pages = {7482337261469287},
doi = {10.1177/07482337261469287},
pmid = {42498637},
issn = {1477-0393},
abstract = {Heavy metals and metalloids, including arsenic (As), cadmium (Cd), chromium (Cr), nickel (Ni), lead (Pb), and mercury (Hg), are well-recognised human carcinogens, and the molecular mechanisms underlying their carcinogenicity are incompletely characterised. In this review, we critically discuss and synthesise the available evidence on how heavy metals and metalloids contribute to cancer development by inducing ROS, oxidative stress, DNA damage, mitochondrial dysfunction, endoplasmic reticulum stress, and alterations in apoptotic regulators such as p53, Bax, and Bcl-2. Metal-specific differences in genotoxic versus cytotoxic mechanisms and assessing endogenous protective responses, including metallothionein sequestration, antioxidant pathways, and chelation, are included. An extended analysis of the toxicodynamics of metal mixtures is also made, focusing on a realistic but underexplored exposure scenario. Co-occurring metal combinations, such as As-Cd-Cr-Pb, produce endpoint-specific interaction profiles that pose a greater risk for neurological and genotoxic effects than for renal endpoints and cardiovascular effects, depending on the binary combination. Cd and As co-exposure produces synergistic DNA damage 3-5 times greater than predicted from single-metal effects through concurrent p53 dysfunction and ROS overload. Evaluation of the role of gut microbiome interactions in modulating metal bioavailability and carcinogenic potential, limitations of traditional animal models for mixture risk assessment, and emerging technologies, including single-cell sequencing, CRISPR-based functional genomics, and organ-on-chip platforms that may resolve current knowledge gaps, are included.},
}

@article {pmid42498870,
year = {2026},
author = {Ganguly, D and Choudhury, A and Deka, H and Sarmah, J and Majumdar, S and Mahanti, K and Hoque, N and Ghosh, S},
title = {Emerging and targeted therapeutic strategies in colorectal cancer: molecular mechanisms and clinical perspectives.},
journal = {Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {42498870},
issn = {1699-3055},
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide, driven by complex genetic, epigenetic, and environmental factors. Despite advances in conventional treatments such as surgery, chemotherapy, and radiotherapy, therapeutic resistance and disease recurrence continue to limit long-term outcomes. This review provides a comprehensive overview of emerging and targeted therapeutic strategies in CRC, with emphasis on their molecular basis and clinical relevance. The key pathways involved in CRC pathogenesis, including the adenoma-carcinoma sequence, microsatellite instability, and CpG island methylator phenotype, are discussed to highlight their roles in disease progression and therapeutic targeting. Recent advances in targeted therapies, particularly those directed against vascular endothelial growth factor and epidermal growth factor receptor, along with the expanding role of immunotherapy, are critically examined. In addition, novel approaches such as gene- and RNA-based therapies, microbiome modulation, nanotechnology-driven drug delivery systems, and precision medicine strategies based on multi-omic profiling are explored. Despite these developments, the challenges including tumor heterogeneity, therapeutic resistance, and limitations in drug delivery and biomarker identification remain significant. Future perspectives emphasize the integration of molecular profiling and innovative therapeutic platforms to enable more personalized and effective treatment strategies. Collectively, these advances highlight a shift toward precision oncology for improved management of colorectal cancer.},
}

@article {pmid42498984,
year = {2026},
author = {Zhang, W and Xu, S and Yu, H and Wang, YY and Liu, J and Carpentier, S and Zheng, SJ},
title = {TR4-triggered recruitment of suppressive rhizomicrobiome enhances Fusarium wilt resistance in banana.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71464},
pmid = {42498984},
issn = {1469-8137},
support = {NSFC32161143001//National Natural Science Foundation of China/ ; NSFC32302424//National Natural Science Foundation of China/ ; D23033//International Atomic Energy Agency, under project "An Integrative Approach to Enhancing Disease Resistance Against Fusarium Wilt (Foc TR4) in Banana-Phase II/ ; YNWR-YLXZ-2018-018//Yunling Scholar Programme of the Yunnan Provincial Government/ ; },
abstract = {Fusarium wilt of banana threatens banana production world-wide. Although beneficial rhizomicrobiomes are linked to disease resistance, whether resistant cultivars systemically recruit disease-suppressive rhizomicrobiomes after pathogen challenge remains unclear. Using a split-root system combined with rhizomicrobiome transfer, we tested whether systemically recruited rhizomicrobiomes from different cultivars after pathogen challenge could alter disease development in a susceptible cultivar. Rhizosphere soil suspension from the pathogen-challenged highly resistant cultivar GCTCV119 was the only donor treatment that significantly reduced the disease index in the susceptible recipient cultivar Guijiao No. 1. This effect was associated with pathogen-induced enrichment of absolute bacterial abundance and absolute Bacillus abundance in the rhizosphere of GCTCV119, whereas such enrichment was not observed in the other donor cultivars. A syncom of seven Bacillus strains from the GCTCV119 rhizosphere most effectively reduced (by 90.20%) the disease index by the induction of plant resistance. Soil incubation showed that pathogen-induced D-sorbitol accumulation in GCTCV119 significantly increased total bacterial abundance and Bacillus abundance, and reduced the disease index. This study highlights pathogen-triggered rhizomicrobiome reshaping, higher absolute bacterial abundance, and the suppressive role of Bacillus as key features linked to disease resistance in banana, providing insights into microbiome-mediated disease suppression.},
}

@article {pmid42499215,
year = {2026},
author = {Haworth, S and Esberg, A and Eriksson, L and Ahmed, H and Mack, CI and Noerman, S and Nordin, E and Egert, B and Hanhineva, K and Landberg, R and Brunius, C and Johansson, I},
title = {Salivary Dipeptides and Microbiota Multiomics Biomarkers of Caries.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345261466143},
doi = {10.1177/00220345261466143},
pmid = {42499215},
issn = {1544-0591},
abstract = {Dental caries is a prevalent disease shaped by dietary and metabolic interactions between the host and oral microbiota. While separate microbiome and metabolome profiling have improved the understanding of caries etiology, integrated multiomics approaches remain underutilized. We aimed to identify salivary biomarkers of caries experience in a cross-sectional study combining microbiome, metabolome, sugarome, and diet, oral, and demographic information in 217 healthy Swedish adolescents and young adults. Participants underwent clinical examination, dietary assessment, and saliva analysis using full-length 16S rRNA gene sequencing, untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics, and 2-dimensional gas chromatography-MS (GC×GC-MS)-based sugar profiling. Caries signs and restorations were summarized as decayed and filled surfaces including enamel caries. Associations between caries experience, demographics, and omics measures were evaluated using a nested cross-validated linear-regression framework with inner-loop feature selection and outer-loop performance assessment, emphasizing effect-direction stability and reproducibility across cross-validation models. Selected OMICs features were then integrated using orthogonal partial least-squares (OPLS) modeling. Three salivary dipeptides (Ser-Pro, Phe-His, and Thr-Gly) showed robust inverse associations with caries experience. Several cariogenic taxa, including Streptococcus mutans, Streptococcus sobrinus, Lactobacillus gasseri, and selected Actinomyces and Prevotella species, were positively associated with caries experience, whereas Veillonella rogosae, Stomatobaculum sp. HMT-097, and other taxa as well as 5 bacteria-predicted enzymes were associated with lower caries experience. Dietary variables and salivary sugars showed no consistent associations with caries experience. An integrated OPLS model incorporating demographics, microbiota composition, microbial-predicted enzymes, and metabolomics explained 41% of the variation in caries (R[2] = 0.41) with a cross-validated predictive ability of 30% (Q[2] = 0.30). This saliva-based multiomics framework revealed coherent microbial and metabolic signatures of caries experience. The Ser-Pro dipeptide showed the strongest inverse association and warrants validation in longitudinal cohorts to establish temporal precedence and clinical utility as a novel caries biomarker.},
}

@article {pmid42499231,
year = {2026},
author = {Simons, S and van Goudoever, H and Vlieg-Boerstra, B},
title = {Recruitment Challenges in Mother-Infant Research: Factors Associated With Low Enrollment and Inclusion in the Synbio-Breast Study.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e2358274},
pmid = {42499231},
issn = {2314-6141},
support = {WO 17.186//OLVG research/ ; },
mesh = {Humans ; Female ; Infant ; Adult ; *Patient Selection ; Breast Feeding ; *Milk, Human/microbiology ; Mothers ; },
abstract = {BACKGROUND: An optimal early-life environment is crucial for child health, with human milk and the infant microbiome playing central roles. The Synbio-Breast study investigates how maternal diet contributes to the synbiotic composition of human milk in atopic women. Despite increasing societal interest in this topic, recruitment proved challenging.

OBJECTIVE: The aim of this study is to quantify and analyze factors associated with low enrollment and inclusion rates and to explore strategies for improving recruitment in future mother-infant studies.

METHODS: Enrollment and inclusion rates and temporal trends were assessed using linear regression models, whereas associations between facilitating factors-including involvement of the PhD student, recruitment strategy, lactation meetings, and attendance at the Nine Months Fair-and enrollment were assessed using logistic regression models.

RESULTS: Of the 681 women screened, 215 expressed willingness to participate. Despite multiple efforts and adaptations to enhance engagement, enrollment remained low. After adjusting for the COVID-19 period, only recruitment conducted by the PhD student via email-without personal contact through a healthcare professional-was significantly associated with lower odds of enrollment. Of the 215 enrolled participants, 75 were ultimately included (11% of all screened women). Key reasons for exclusion were partial breastfeeding (30.0%), antibiotic use (22.1%), and loss of interest (19.3%).

CONCLUSION: Strict inclusion and exclusion criteria contributed to substantial low enrollment and inclusion rates in the Synbio-Breast study. Successful recruitment in mother-infant research requires more than logistical organization; it depends on personalized engagement built on existing relationships of trust. Moreover, studies that offer no direct health benefit to participants-such as the Synbio-Breast study-tend to have inherently lower uptake, underscoring the need for tailored and relationship-based recruitment strategies.},
}

Humans
Female
Infant
Adult
*Patient Selection
Breast Feeding
*Milk, Human/microbiology
Mothers

@article {pmid42499417,
year = {2026},
author = {Basch, L and Gopu, A and Welp, H and Mukarram, M and Imokhai, PO and Huynh, K and Amin, S and Jacobs, R},
title = {Developing Three-Dimensional (3D) Skin Models to Study the Interaction Between the Skin Microbiome and Immune Cells in Chronic Wounds.},
journal = {Cureus},
volume = {18},
number = {7},
pages = {e113304},
pmid = {42499417},
issn = {2168-8184},
abstract = {Developing three-dimensional (3D) skin models provides a physiologically relevant platform to investigate the dynamic interactions between the skin microbiome and immune cells in chronic wounds, offering insights into delayed healing, persistent inflammation, and microbial dysbiosis. Traditional in vitro models fail to replicate the complex architecture of human skin and its immune-microbiome crosstalk, motivating the development of biomimetic systems that incorporate stratified epidermal layers, dermal fibroblasts, and innate immune components such as macrophages and neutrophils. Engineered 3D skin constructs inoculated with wound-associated microbiota, including Staphylococcus aureus, Pseudomonas aeruginosa, and Cutibacterium acnes, can reveal how biofilm formation, quorum sensing, and microbial metabolites influence immune cell recruitment and cytokine secretion. Dysregulated immune responses within these models, characterized by excessive interleukin-1 beta, tumor necrosis factor alpha, and reactive oxygen species production, mirror aspects of the inflammatory milieu observed in nonhealing wounds and highlight candidate pathways for therapeutic intervention. The incorporation of patient-derived immune cells into 3D co-culture systems further enables personalized modeling of wound-healing deficiencies and antimicrobial-resistance patterns. Applications of 3D skin models extend to the development of antibiofilm agents, immune-modulating therapies, and microbiome-targeted interventions. It is important to emphasize that the current evidence base is predominantly preclinical and in vitro; accordingly, these platforms should be viewed as a promising foundation for advancing precision-medicine approaches to chronic wound management, contingent on rigorous cross-laboratory and clinical validation.},
}

@article {pmid42499440,
year = {2026},
author = {Yaşar Bilge, NŞ and Perez Brocal, V and Kaşifoğlu, T and Bilge, U and Kaşifoğlu, N and Moya, A and Dinleyici, EÇ},
title = {Alterations in gut microbiota composition in adult patients with familial Mediterranean fever: a pilot case-control study.},
journal = {Turkish journal of medical sciences},
volume = {56},
number = {3},
pages = {801-807},
pmid = {42499440},
issn = {1303-6165},
mesh = {Humans ; *Familial Mediterranean Fever/microbiology/drug therapy ; Pilot Projects ; Adult ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Prospective Studies ; Feces/microbiology ; Colchicine/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; },
abstract = {BACKGROUND/AIM: Although familial Mediterranean fever (FMF) is a monogenic disease, recent evidence suggests that the gut microbiota may play a role in its pathogenesis or phenotypic expression. We conducted a pilot exploratory study to evaluate the intestinal microbiota composition in patients with FMF and compare it to that of healthy controls.

MATERIALS AND METHODS: In this prospective cohort study, 10 adult patients with FMF receiving colchicine and 10 age- and sex-matched healthy controls were enrolled. Fecal samples were collected and stored at -80 °C until DNA extraction. The V3-V4 region of the 16S rRNA gene was amplified and sequencing was performed.

RESULTS: Alpha and beta diversity metrics were largely similar between FMF patients and the control group, except for the Chao 1 index, which was significantly reduced in the FMF group (p < 0.05), indicating lower species richness. Taxonomic analysis revealed differences in gut microbiota composition, notably an increased abundance of Eggerthella at the genus level. At the species level, Eggerthella sinensis and Eggerthella lenta were more prevalent in FMF patients.

CONCLUSION: Our findings reveal distinct gut microbiota alterations in FMF patients, characterized by reduced microbial richness and particularly enrichment of Eggerthella, including E. lenta. These findings suggest a possible association between gut microbiota alterations and FMF. The small sample size of this study is a limitation, but further longitudinal studies with treatment-naïve patients, alongside functional analyses of microbial metabolites, are warranted to elucidate causal relationships and inform microbiome-based diagnostic or therapeutic strategies in FMF.},
}

Humans
*Familial Mediterranean Fever/microbiology/drug therapy
Pilot Projects
Adult
Case-Control Studies
Female
*Gastrointestinal Microbiome/genetics
Male
Prospective Studies
Feces/microbiology
Colchicine/therapeutic use
RNA, Ribosomal, 16S/genetics
Middle Aged

@article {pmid42499495,
year = {2026},
author = {Altaher, H and Al-Mashhadani, M and Usman, R and Ghelani, H and Jan, RK},
title = {Infliximab-linked gut microbiome signatures as candidate treatment response biomarkers in pediatric inflammatory bowel disease: a systematic review.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1877033},
pmid = {42499495},
issn = {1663-9812},
abstract = {BACKGROUND: Infliximab (IFX) is a chimeric monoclonal antibody against tumor necrosis factor-alpha (TNF-α) that is widely used for induction and maintenance therapy in pediatric inflammatory bowel disease (IBD), yet its effects on the developing intestinal microbiome and treatment response remain unclear.

OBJECTIVE: To systematically synthesize evidence on IFX-associated microbiome changes in pediatric IBD and evaluate microbiome features linked to treatment response.

METHODS: A systematic review was conducted following the PRISMA 2020 guidelines. PubMed, Scopus, Embase, and CENTRAL were searched from database inception until March 2026, and our results were synthesized narratively.

RESULTS: Of the 945 records identified, 13 studies met the inclusion criteria, comprising 242 pediatric patients. Findings for alpha diversity were variable across studies. In contrast, beta-diversity patterns, taxonomic profiles, and functional analyses more consistently showed positive IFX-associated microbial changes. Responders to treatment more frequently showed enrichment of beneficial taxa, including Faecalibacterium, Subdoligranulum, and Bifidobacterium, while non-responders exhibited a tendency towards dysbiotic microbial signatures, evidenced by increased levels of Gammaproteobacteria and Candida. Functional and metabolomic studies suggested beneficial shifts in bile-acid metabolism, short-chain fatty acid-related pathways, and inflammatory signaling post IFX treatment. Clinical and biochemical improvements with IFX were consistently reported; however, these improvements were not always accompanied by uniform recovery of overall microbial diversity.

CONCLUSION: In pediatric IBD, IFX is more consistently associated with shifts in microbial composition and function than with broad increases in overall microbial diversity. Further large, standardized studies are warranted to refine the role of microbiome features in biologic treatment stratification.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251133625, identifier CRD420251133625.},
}

@article {pmid42499533,
year = {2026},
author = {Shaer, NA and Al-Abbas, NS},
title = {In silico dysbiosis-associated neuroprotective metabolite insufficiency in Alzheimer's disease.},
journal = {Open medicine (Warsaw, Poland)},
volume = {21},
number = {1},
pages = {20261484},
pmid = {42499533},
issn = {2391-5463},
abstract = {Perturbation of oral and gut microbiomes has been implicated in alzheimer's disease (AD) along the oral-gut-brain axis; however, the extent of global community restructuring may differ between niches. The present work constitutes a computational interrogation of 16S rRNA profiles from eight-month-old APP/PS1 and wild-type mice, characterizing oral and gut community structure and predicted functional capacity through PICRUSt-driven, KEGG-anchored pathway inference. Comparative taxonomic interrogation disclosed patterns consistent with ectopic occurrence, whereby classically oral genera (Fusobacterium, Streptococcus) were preferentially enriched within intestinal assemblages and gut-typical genera (Muribaculum, Paramuribaculum) emerged as prominent constituents of the oral microbiota in APP/PS1 mice. These cross-niche enrichment patterns, together with significant oral community separation but non-significant gut beta-diversity separation by ANOSIM, were accompanied by predicted decrements in 85 orally enriched enzymes distributed across 25 KEGG pathways, approximately 40 % of which were associated with the biosynthesis of metabolites with reported neuroprotective properties, including glutathione, acetyl-CoA, succinate, malate, formate, lactate, acetate, and monoterpenoids. Systems-level synthesis of these predictions indicated convergent perturbation of antioxidant defenses, bioenergetic circuitry, and one-carbon metabolism, plausibly reflecting metabolic choke points that may favor cognitive deterioration. Although the oral microbiome showed significant inter-cohort separation, the gut microbiome did not, indicating that gut changes are best viewed as taxon-specific shifts within an otherwise stable community. These observations support a hypothesis-generating framework in which oral dysbiosis, selective gut alterations, and cross-niche enrichment patterns are linked to computationally inferred neuroprotective metabolite insufficiency, highlighting specific taxa, enzymes, and pathways as candidates for biomarker and microbiome-targeted therapeutic development in AD.},
}

@article {pmid42499542,
year = {2026},
author = {Liegenfeld, SC and Stuermer, EK and Pelzer, N and Nathrath, C and Krueger, N and Geissen, M and Dittmer, M},
title = {Microbial volatile organic compounds and olfactory receptors in wound malodor.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1833939},
pmid = {42499542},
issn = {2235-2988},
mesh = {Humans ; *Volatile Organic Compounds/metabolism/analysis ; *Receptors, Odorant/metabolism ; *Odorants/analysis ; *Olfactory Receptor Neurons/metabolism ; *Halitosis/microbiology/metabolism ; *Wounds and Injuries/microbiology ; Animals ; },
abstract = {Wound odor is a common symptom in patients with chronic wounds. Malodorous wounds can result in embarrassment, anxiety, and, therefore, in social isolation of the patient. Current treatment options are limited and focused on masking the odor. Current approaches to wound odor management have notable limitations and fail to adequately address existing therapeutic needs. Wound odor is multifactorial, with a major contribution from volatile organic compounds (VOCs) emitted by microorganisms and necrotic tissue. Several VOCs have been identified as key drivers of malodor, such as short-chain fatty acids, dimethyl-trisulfide, specific alcohols, ketones, and aldehydes. These compounds are detected by the human olfactory system, including olfactory receptors (ORs) expressed on olfactory sensory neurons (OSNs). The human olfactory system comprises more than 400 ORs, which enable the detection of a vast array of odorants, however only a small fraction of these receptors has been deorphanized. This systematic review will evaluate therapeutic clinical strategies addressing malodor and compile current knowledge on VOCs that cause wound odor and the ORs associated with their detection. It summarizes the existing evidence on deorphanized ORs that detect these VOCs in malodorous wounds and outlines experimental mechanisms of deorphanization. Identifying wound-odor-associated VOCs and their corresponding ORs provides a framework for novel therapeutic strategies, such as antagonizing the OR to suppress odor perception. This may directly improve the quality of life of patients with chronic malodorous wounds, particularly in malignant wounds and palliative care.},
}

Humans
*Volatile Organic Compounds/metabolism/analysis
*Receptors, Odorant/metabolism
*Odorants/analysis
*Olfactory Receptor Neurons/metabolism
*Halitosis/microbiology/metabolism
*Wounds and Injuries/microbiology
Animals

@article {pmid42499545,
year = {2026},
author = {Chen, K and Lin, J and Zhang, Y and Liu, Y and Yang, X and Yang, X},
title = {Gut microbiota and serum metabolic profiles in patients with sepsis-induced cardiomyopathy and their association with the disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1811654},
pmid = {42499545},
issn = {2235-2988},
mesh = {Humans ; *Cardiomyopathies/etiology/blood/microbiology/metabolism ; *Sepsis/complications/blood/microbiology ; *Gastrointestinal Microbiome ; Female ; Male ; Prospective Studies ; *Metabolome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Dysbiosis ; Aged ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; China ; Biomarkers/blood ; },
abstract = {BACKGROUND: The pathogenesis of sepsis-induced cardiomyopathy (SIC) remains unclear, and the lack of effective treatment options results in high mortality rates. There may be interactions between gut microbiota dysbiosis, serum metabolic changes, and SIC; however, research in this area is limited. This study aims to provide a theoretical basis for targeted interventions to improve the gut microbiome, thereby enhancing cardiac function and prognosis in patients with SIC.

METHODS: This prospective cohort study enrolled 48 septic patients admitted to the intensive care unit (ICU) of a tertiary general hospital in Ningxia, China, between March 2024 and March 2025. Patients were stratified into SIC (n=28) and SEPSIS (n=20) groups. Age- and sex-matched healthy controls (HC, n=10) were also recruited. Fecal samples from all three groups were analyzed via 16S rRNA gene amplicon sequencing, and serum samples from the SIC and SEPSIS groups were analyzed via LC-MS-based untargeted metabolomics. Spearman's correlations linked microbial and metabolic alterations to echocardiographic parameters and myocardial injury markers.

RESULTS: Compared with the SEPSIS and HC groups, the SIC group presented significant differences in both the α and β diversity of the gut microbiota (all P<0.05). Compared with that in the SEPSIS group, the Bacillota/Bacteroidota ratio was significantly lower in the SIC group (P<0.05); compared with the SEPSIS and HC groups, the SIC group presented significantly increased abundances of genera such as Parabacteroides and Clostridium innocuum group and significantly decreased abundances of genera such as Oscillospiraceae_UCG-003 and Lachnospiraceae_UCG-004 (all P<0.05). Forty-nine differential metabolites were identified (VIP≥1, P<0.05): hippuric acid, estrone glucuronide, and TMAO were elevated, while 15-deoxy-Δ12,14-prostaglandin J2 was reduced in the SIC group (all P<0.05). Differential genera/metabolites correlated strongly with SIC diagnostic indicators: e.g., Parabacteroides positively correlated with estrone glucuronide, hippuric acid, and GLS, and negatively with LVEF.

CONCLUSION: Gut microbiota dysbiosis differs between patients with Sepsis-induced cardiomyopathy and healthy individuals or patients with sepsis. Additionally, the serum metabolic profile changes in SIC patients differ from those in patients with sepsis, and these characteristic changes are significantly associated with clinical indicators related to the diagnosis of SIC.},
}

Humans
*Cardiomyopathies/etiology/blood/microbiology/metabolism
*Sepsis/complications/blood/microbiology
*Gastrointestinal Microbiome
Female
Male
Prospective Studies
*Metabolome
Middle Aged
RNA, Ribosomal, 16S/genetics
Dysbiosis
Aged
Metabolomics
Bacteria/classification/genetics/isolation & purification
Feces/microbiology
China
Biomarkers/blood

@article {pmid42499636,
year = {2026},
author = {Ying, J and Fang, Z and Zhang, C and Liu, X and Cui, J and Li, Z and Tang, J},
title = {Crosstalk Between Parkinson's Disease and Colorectal Cancer: Genetic Mechanisms, Gut Microbiota, and Therapeutic Insights.},
journal = {Health care science},
volume = {},
number = {},
pages = {},
pmid = {42499636},
issn = {2771-1757},
abstract = {This review summarizes the potential genes involved in both Parkinson's disease (PD) pathogenesis and colorectal cancer (CRC) carcinogenesis, focusing on the oncogenic mechanisms that may arise from PD gene dysfunctions. By investigating genes such as PRKN, PINK1, and DJ-1, which influence pathways primarily related to oxidative stress, mitophagy, cell cycle regulation, and inflammation, this review provides insight into how PD genes may contribute to CRC tumorigenesis through interactions with gut microbes such as Bacillus subtilis and Clostridium butyricum. This review highlights a mechanistic bridge between neurodegeneration and cancer centered on mitochondrial dysfunction, mitophagy, and inflammation. The convergence of molecular mechanisms and gut microbiota in PD and CRC highlights promising avenues for microbiome-targeted interventions alongside genetic and molecular approaches to advance novel diagnostic and therapeutic strategies for these two diseases. Importantly, therapeutic strategies should be considered in a holistic manner, as interventions for one disease may influence the course of another, and probiotics represent a unique modality with the potential to confer preventive and therapeutic benefits across both conditions.},
}

@article {pmid42499655,
year = {2026},
author = {Schultz, J and Romanenko, A and Rosado, AS},
title = {Culturable bacterial diversity and genome-encoded metabolic potential in Al Wahbah Crater's volcanic soils, Saudi Arabia.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1867957},
pmid = {42499655},
issn = {1664-302X},
abstract = {The growing demand for sustainable biotechnological solutions has intensified interest in microorganisms inhabiting understudied and environmentally constrained ecosystems. Volcanic systems create ecological niches shaped by geochemical and physicochemical stressors, yet the culturable bacteria in many remain poorly characterized. Here, we investigated the culturable bacterial fraction in the soils of Al Wahbah Crater (Saudi Arabia), an underexplored volcanic ecosystem, and evaluated its members' hydrolytic enzyme production and the genome-encoded metabolic potential of the most-promising isolates. Using multiple media and incubation conditions, we isolated bacterial strains from three crater soil types, identifying 65 representative isolates through 16S rRNA gene sequencing. The culture collection was dominated by Bacillota, particularly Bacillus spp., reflecting selective pressures typical of mineral-rich, saline soils. All isolates were screened for six hydrolases: cellulase, xylanase, amylase, protease, lipase, and gelatinase. Twenty-three strains exhibited activities for all six, while only one (Paenibacillus sp. AWC54) showed no detectable enzymatic activity. Cellulase activity was most prevalent (61/65 isolates), followed by xylanase (59/65), amylase (57/65), protease (48/65), lipase (35/65), and gelatinase (31/65). Five high-performing strains, Bacillus spizizenii AWC2, B. cereus AWC16, B. vallismortis AWC57 and AWC81, and B. haynesii AWS14, were selected for whole-genome sequencing and genome mining. Genome annotations revealed diverse carbohydrate-active enzyme repertoires including glycoside hydrolases, glycosyl transferases, and polysaccharide lyases, as well as multiple biosynthetic gene clusters predicted to encode antimicrobial and antifungal metabolites. Together, these findings establish Al Wahbah Crater as a cultivable regional reservoir of metabolically versatile bacteria and provide a curated strain collection and genomic framework for future ecological, evolutionary, and biotechnological investigations of volcanic microbiomes in the Arabian Peninsula.},
}

@article {pmid42499657,
year = {2026},
author = {Yi, H and He, W and Ma, Z and Qiu, X and Ren, L and Liang, X},
title = {Tumour tissue-associated microbiome differences between colonic adenoma and carcinoma revealed by 5R 16S rRNA sequencing of formalin-fixed paraffin-embedded tissues: a case-control study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1880194},
pmid = {42499657},
issn = {1664-302X},
abstract = {Tumour-associated microbiota directly colonise lesion sites and interact with the local immune microenvironment, yet their compositional shifts during the adenoma-to-cancer transition remain poorly characterised, particularly in archival tissue. Using five-region 16S ribosomal RNA (5R 16S rRNA) sequencing with a four-category contamination control framework, we compared tumour-associated microbiomes in formalin-fixed paraffin-embedded (FFPE) tissues from 25 colonic tubular adenoma and 25 colon cancer patients in a case-control design. Alpha diversity was significantly reduced in the colon cancer group across three indices (Shannon, Simpson, and Pielou's evenness), reflecting shifts in community evenness rather than overall species loss. Beta diversity analysis, however, revealed no significant differences in global community composition between groups (ANOSIM: R = 0.026, p = 0.106; PERMANOVA: R [2] = 0.024, p = 0.137), indicating that observed compositional differences are taxon-specific rather than community-wide. Across four independent statistical methods (ANCOM-BC2, LEfSe, Mann-Whitney U test, and Fisher's exact test), Bacteroides caccae and Prevotella intermedia were consistently enriched in colon cancer tissue, suggesting compositional shifts in the tumour-associated microbiome that may be associated with colorectal carcinogenesis. Within the colon cancer group, Alistipes finegoldii abundance showed a negative correlation with tumour diameter across all colon cancer samples (Spearman r = -0.520, p = 0.008; n = 25, including 20 samples at the detection limit as tied ranks; only 5 samples had detectable abundance); given the very limited number of detectable samples, this finding should be regarded as strictly exploratory and requires prospective validation. These findings demonstrate that tumour-associated microbiome profiling in archival FFPE tissue is feasible under a rigorous contamination control framework, and provide preliminary evidence for taxon-specific compositional differences during colonic adenoma-to-carcinoma progression. The identified candidate taxa warrant prospective validation in larger cohorts and mechanistic investigation to clarify their roles in colon carcinogenesis.},
}

@article {pmid42499659,
year = {2026},
author = {Ning, L and Chen, Z and Gao, H and Tan, Z and Quan, X and Kong, L and Chen, X},
title = {Dynamic remodeling of the gut microbiome and host responses after myocardial infarction revealed by longitudinal metaproteomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1826248},
pmid = {42499659},
issn = {1664-302X},
abstract = {The gut microbiota is increasingly recognized as a key regulator of cardiovascular health; however, its functional dynamics following myocardial infarction (MI) remain poorly defined. While traditional sequencing approaches focus on microbial composition, they cannot capture real-time functional activity. In this study, we established a rat model of MI via permanent ligation of the left anterior descending artery and collected fecal samples from MI and sham-operated cohorts at baseline and Days 2, 7, and 14 post-surgery. High-resolution metaproteomics was applied to quantify microbial and host proteins, integrating functional annotation, differential expression, and weighted gene co-expression network analysis (WGCNA). We observed an acute, generalized decline in microbial diversity at Day 2 across both groups, indicative of a physiological response to surgical stress. Crucially, MI-specific divergence emerged during the subacute phase (Day 7) and persisted into recovery (Day 14). At Day 7, functional perturbations peaked in the MI group, significantly involving carbohydrate metabolism, nucleotide biosynthesis, and oxidative stress pathways, accompanied by taxonomic shifts including the depletion of Akkermansia and enrichment of Odoribacter and Muribaculum. Concurrently, host-derived proteins displayed time-dependent alterations in lipid catabolism and redox regulation. WGCNA revealed co-regulated protein modules linked to MI status and the recovery phase, reflecting highly synchronized host-microbiome responses. This time-resolved metaproteomic study demonstrates that following initial surgical stress, MI triggers dynamic, stage-specific alterations in gut microbial function and coordinated host responses, providing mechanistic insights into the gut-heart axis and suggesting potential microbiota-targeted strategies to promote post-MI recovery.},
}

@article {pmid42500045,
year = {2026},
author = {Wen, Z and Wei, YH and Zhu, HY and Song, L and Han, DY and Guo, LC and He, CJ and Guo, ZX and Han, PJ},
title = {Integrated microbiome and metabolome analyses reveal spatial heterogeneity of medium-temperature Daqu and its potential impact on simulated strong-flavor baijiu fermentation.},
journal = {Food chemistry: X},
volume = {38},
number = {},
pages = {104225},
pmid = {42500045},
issn = {2590-1575},
abstract = {Medium-temperature Daqu (MTD) exhibits pronounced spatial heterogeneity between its surface (QS) and inner (QI) portions, yet their functional differences remain poorly understood. This study compared physicochemical properties, metabolites, and species-level microbial communities of QS and QI and evaluated their impacts on simulated strong-flavor Baijiu (SFB) fermentation. QS exhibited higher saccharification and liquefaction activities and higher counts of lactic acid bacteria and yeasts, whereas QI was enriched in thermophilic molds and volatile compounds. Thirty-two microbial biomarkers differentiated QS and QI, and QS showed a more complex microbial co-occurrence pattern. Simulated fermentation revealed early bacterial divergence followed by convergence to Acetilactobacillus jinshanensis. During mid-to-late fermentation, QI showed higher levels of acids and esters than QS. Collectively, QS was mainly associated with substrate conversion and early fermentation initiation, whereas QI was more closely associated with flavor development during later fermentation stages. These findings provide valuable insights into MTD optimization and SFB quality control.},
}

@article {pmid42500106,
year = {2025},
author = {Kanchanapoomi, K and Thaipisuttikul, I and Nitayanon, P and Srisuwatchari, W and Pacharn, P and Visitsunthorn, N and Jirapongsananuruk, O},
title = {Distinct Nasal Microbiome Profiles and Prediction Model for Allergic Rhinitis, Nonallergic Rhinitis, and Healthy Children.},
journal = {World journal of otorhinolaryngology - head and neck surgery},
volume = {},
number = {},
pages = {},
pmid = {42500106},
issn = {2589-1081},
abstract = {OBJECTIVES: Adult studies reported differences in nasal microbiota composition among patients with allergic rhinitis (AR), nonallergic rhinitis (NAR), and healthy controls (HCs), whereas pediatric data remain limited. This study compared the nasal microbiomes of children with AR, NAR, and HC, investigated factors influencing these microbiomes, and developed a predictive model to differentiate these conditions based on microbiome data.

METHODS: Nasal swab samples were collected from children with AR, NAR, and HC. Microbial characterization was performed using 16S rDNA sequencing to analyze bacterial composition. Relevant demographic data and influencing factors were collected.

RESULTS: Sixty participants (median age 6.3 [4.3-8.4] years, 51.6% males) were categorized into AR (n = 24), NAR (n = 14), and HC (n = 22). Significant differences in alpha and beta diversity were observed among groups (p < 0.01 and p < 0.05, respectively). The AR and NAR groups exhibited lower Pielou's evenness than HC (FDR-adjusted p < 0.01 and p = 0.02, respectively). Compared to HC, the AR group showed a higher abundance of Escherichia-Shigella, Negativicoccus, and Campylobacter. In contrast, Dolosigranulum was enriched while the Enterobacteriaceae family was depleted in the NAR group. Household pets and breastfeeding duration significantly influenced nasal microbiome diversity regardless of the disease groups. A prediction model of nasal microbial distribution for AR, NAR, and HC identified 14 taxa critical for distinguishing these groups (accuracy of 0.83).

CONCLUSION: This pilot study identified preliminary differences in nasal microbiome diversity and composition among children with AR, NAR, and HC. Differential microbial abundances may reflect distinct rhinitis phenotypes. However, these findings are hypothesis-generating and require validation in larger, independent cohorts.},
}

@article {pmid42500187,
year = {2026},
author = {Andrade, CP and Marconi, C and da Silva, MG and de Carvalho, NS},
title = {Descriptive analysis of genital colonization across gestational trimesters in pregnant women with different obstetric histories.},
journal = {Revista brasileira de ginecologia e obstetricia : revista da Federacao Brasileira das Sociedades de Ginecologia e Obstetricia},
volume = {48},
number = {},
pages = {},
pmid = {42500187},
issn = {1806-9339},
mesh = {Humans ; Female ; Pregnancy ; Prospective Studies ; Case-Control Studies ; Adult ; *Vagina/microbiology ; *Ureaplasma/isolation & purification ; *Pregnancy Trimesters ; *Mycoplasma hominis/isolation & purification ; *Pregnancy Complications, Infectious/microbiology/diagnosis ; Young Adult ; *Ureaplasma Infections/diagnosis ; Premature Birth/microbiology ; },
abstract = {OBJECTIVE: The aim of this study was to assess the Ureaplasma parvum variation of genital colonization during pregnancy with an exploratory approach among women with term and preterm birth histories.

METHODS: Prospective case-control study of 24 pregnant women with history of full-term pregnancy and 26 pregnant women with history of prematurity whose endpoint was to assess the colonization pattern of these agents with a vaginal/cervical sample collected at the beginning of each trimester of gestation. Collected data: sociodemographic characteristics, previous diseases, gynecological and obstetric history, and microorganisms in vaginal secretion samples by real-time polymerase chain reaction (PCR).

RESULTS: The overall number of cases positive for at least one microorganism was 18 (36.0%). A significantly higher positivity rate was observed in the second and third trimesters in both study groups compared with the first trimester (p<0.001). The microorganisms identified in the vaginal environment were Ureaplasma parvum (66.6%), Mycoplasma hominis (16.7%), and both (16.7%), and the frequency of both these microorganisms was comparable in both groups at each pregnancy trimester (p for all = nonsignificant), but with a difference between the trimesters. Prematurity in the current pregnancy occurred in a single case (6.7%) in a pregnant woman without history of prematurity in the previous pregnancy (p=1.00).

CONCLUSION: The most frequently identified microorganism was Ureaplasma parvum, and the overall incidence of positive cases including all microorganisms was 36.0%. Although Ureaplasma parvum was the most frequently identified microorganism, the sample was not powered to assess its association with prematurity.},
}

Humans
Female
Pregnancy
Prospective Studies
Case-Control Studies
Adult
*Vagina/microbiology
*Ureaplasma/isolation & purification
*Pregnancy Trimesters
*Mycoplasma hominis/isolation & purification
*Pregnancy Complications, Infectious/microbiology/diagnosis
Young Adult
*Ureaplasma Infections/diagnosis
Premature Birth/microbiology

@article {pmid42500245,
year = {2026},
author = {Chen, AS and Nguyen, LH and Gray, B and Williams, K and Gurung, J and Canha, L and McGoldrick, J and Hubbard, J and Khalili, H},
title = {Specific carbohydrate diet versus Mediterranean diet in adult patients with mild to moderate ulcerative colitis: a randomized controlled-feeding trial.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1838160},
pmid = {42500245},
issn = {2296-861X},
abstract = {BACKGROUND AND AIMS: This pilot randomized controlled-feeding trial compared the effect of Specific Carbohydrate Diet (SCD) and Mediterranean diet (MeD) in mild to moderate ulcerative colitis (UC).

METHODS: Seventeen adults were randomized to a 6-week SCD (n = 8) or MeD (n = 9) intervention. Primary outcome was change in partial Mayo Clinic score (pMCS).

RESULTS: The study was discontinued early due to significant dropout (n = 9, 52.9%). There was no significant between-group differences observed for pMCS change (SCD, -0.8; MeD, -1.3; p = 0.499) or secondary outcomes. Exploratory metagenomic analysis revealed enrichment of Parasutterella excrementihominis in SCD at week 10.

CONCLUSION: In this pilot trial, SCD and MeD showed no difference in therapeutic effects for patients with mild to moderate UC. However, the study was limited by a significant drop out in both arms.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier NCT04398550.},
}

@article {pmid42500251,
year = {2026},
author = {Xiong, P and Wang, B and Liu, Y and Wang, Z and Huang, X and Guo, J},
title = {Reframing glucolipid metabolic disorders through the lens of the oral microbiome: from pathophysiological mechanisms to translational potential.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1819765},
pmid = {42500251},
issn = {2296-861X},
abstract = {With the rising prevalence of metabolic diseases, their comorbidity is increasingly common. Glucolipid metabolic disorders (GLMD) constitute a major health challenge associated with increased cardiovascular risk and mortality. Despite many advances in disease mechanisms and therapeutic strategies, the metabolic disease burden remains substantial. Routine clinical practice still lacks straightforward approaches for identifying individuals at elevated risk, and the challenge of effectively preventing and controlling GLMD has become an urgent clinical problem. Significant gaps remain in our understanding of metabolic disease. Advances in high-throughput sequencing and omics technologies have expanded the research perspective, shifting attention from organ-centered pathology toward microecological and metabolic networks, elucidating the interactions between the oral microbiota and host metabolism. As the second largest microbial community after the gut microbiota, the oral microbiome provides an integrative lens for examining GLMD-related microbial signatures, plausible mechanistic pathways, and translational opportunities, including inflammation, taste signaling, nitric oxide metabolism, and microbial translocation. This review aims to clarify the relationship between the oral microbiome and GLMD, outline characteristic microbial alterations in metabolic diseases, and summarize the plausible mechanisms linking oral microorganisms with metabolic homeostasis. Current evidence indicates partially recurrent microbial patterns across GLMD-related conditions, but no universal oral microbial signature has been established. Building on recent findings, we conclude by outlining the methodological requirements for evaluating the clinical utility of oral microbiome-based markers and interventions, and further discuss the value of oral microbiota in disease prediction, risk assessment, and individualized intervention. We also summarize the key limitations and challenges in the field and outline directions for future prevention and control of GLMD based on oral microecology.},
}

@article {pmid42500360,
year = {2026},
author = {Heneberg, P},
title = {From infection to cholangiocarcinoma: Why opisthorchiids break these rules.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101517},
pmid = {42500360},
issn = {2352-7714},
abstract = {BACKGROUND: Helminth infections are among the most prevalent causes of chronic inflammation in humans, but only a small subset of these infections is causally linked to cancer. This discrepancy challenges the long-standing assumption that chronic inflammation is intrinsically carcinogenic and suggests that additional constraints govern inflammation-driven tumorigenesis in parasitic diseases.

OBJECTIVES: This review aims to explain why most helminths fail to induce malignancy despite long-term inflammatory host responses, and why opisthorchiid liver trematodes represent a rare and informative exception. We seek to integrate primary experimental, epidemiological, and pathological evidence into a unified conceptual settings applicable to helminth-associated cancers.

KEY FINDINGS: We introduce the concept of a "pro-oncogenic inflammation threshold," proposing that carcinogenesis emerges only when multiple dimensions converge simultaneously: sustained inflammatory intensity and quality, prolonged exposure, genotoxic stress, tissue-specific vulnerability, and permissive environmental cofactors. Most helminths remain below this threshold because of evolutionary selection that favors host survival, the absence of direct genotoxins, and effective immunoregulatory mechanisms. In contrast, opisthorchiids exceed this threshold through chronic mechanical injury to bile ducts, secretion of genotoxic and mitogenic metabolites, synergy with dietary nitrosamines, perturbation of the biliary microbiome, and failure of reparative homeostasis.

CONCLUSIONS: Helminth-induced cancers represent a neglected category of tropical disease that remains poorly integrated into global oncology strategies because of disciplinary fragmentation and a mutation-centric cancer paradigm. Setting helminth-associated carcinogenesis in a One Health context highlights actionable prevention opportunities at the human-animal-environment interface. Chronic helminth-induced inflammation is therefore a conditional, rather than universal, driver of cancer.},
}

@article {pmid42500484,
year = {2026},
author = {Wang, J and Xu, J and Fu, P and Li, J and Tang, B and Zhang, Y and Zeng, Z and Fu, Y},
title = {Bacillus amyloliquefaciens ART9 modulates the growth of Radix serratulae Chinensis through rhizosphere microbiome reprogramming and root transcriptomic regulation.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1891133},
pmid = {42500484},
issn = {1664-462X},
abstract = {OBJECTIVE: Continuous cropping obstacles and heavy chemical fertilizer use constrain Radix serratulae chinensis cultivation. This study evaluates the optimal concentration of plant growth-promoting rhizobacterium Bacillus amyloliquefaciens ART9 and investigates its underlying mechanisms via rhizosphere microbiome and host transcriptome analyses.

METHODS: Seedlings were treated with ART9 suspensions at OD600 of 0.4, 0.6, and 1.0. Growth parameters, soil nutrient contents, rhizosphere bacterial communities, and root transcriptomic profiles were assessed to compare treatment effects.

RESULTS: The OD600 0.6 treatment yielded the best performance, increasing plant height, stem diameter, and SPAD value by 48.56%, 14.09%, and 12.42%, respectively, over the control, and raising soil available nitrogen, phosphorus, and potassium by 177%, 179%, and 168%. Rhizosphere microbiota were significantly enriched with beneficial genera, notably Bacillus, Pseudomonas, and Sphingomonas. Transcriptomics revealed prominent enrichment in phenylpropanoid biosynthesis (map00940), plant hormone signal transduction (map04075), and circadian rhythm-plant (map04712) pathways. Upregulated genes included JAZ, ABF, PYL, PP2C, SPA1_2, and HY5, indicating coordinated regulation of hormone and light signaling.

CONCLUSION: ART9 systematically promotes growth of Radix serratulae chinensis by reshaping the rhizosphere microbiome and modulating hormone/light signaling pathways, supporting its development as a sustainable biofertilizer for medicinal plant production.},
}

@article {pmid42500581,
year = {2026},
author = {Wei, Z and Cai, J and Wang, S and Li, Y and Luo, L and Chen, J and Li, F and Nie, H and Gong, K and Cai, M},
title = {The Intratumoral Microbiota in Breast Cancer: Roles in Progression, Immunity, and Therapy.},
journal = {Oncology research},
volume = {34},
number = {8},
pages = {9},
pmid = {42500581},
issn = {1555-3906},
mesh = {Humans ; *Breast Neoplasms/microbiology/immunology/therapy/pathology ; Female ; *Microbiota/immunology ; Tumor Microenvironment/immunology ; Disease Progression ; Animals ; Immunotherapy/methods ; Prognosis ; },
abstract = {Breast cancer (BC) remains a leading cause of cancer-related mortality worldwide, and accumulating evidence suggests that tumor-associated microbiota may contribute to disease heterogeneity beyond host genetic and immune determinants. Advances in sequencing and multi-omics technologies have uncovered a reproducible intratumoral microbiome in BC, with distinct compositional patterns associated with molecular subtypes, clinicopathological features, and clinical outcomes. Alterations in specific microbial taxa have also been linked to tumor immune status, metastatic potential, and therapeutic sensitivity, underscoring their potential value in disease stratification and prognostic assessment. Although breast tissue represents a low-biomass environment, multiple studies employing stringent contamination control strategies have confirmed the reliability of these microbial signals. Experimental evidence further demonstrates that intratumoral microbes are functionally active components of the tumor microenvironment (TME), influencing tumor progression and metastasis through immune modulation, inflammatory signaling, and metabolic or hormonal reprogramming, while also shaping responses to chemotherapy and immunotherapy. This review summarizes current knowledge on the compositional features, functional mechanisms, and clinical relevance of the BC intratumoral microbiome, highlights methodological challenges in low-biomass profiling, and discusses future directions for translating these findings into clinically actionable strategies. The aim of this review is to systematically evaluate the role of the intratumoral microbiome in breast cancer pathogenesis and treatment, and to propose a framework for translating current findings into clinical practice.},
}

Humans
*Breast Neoplasms/microbiology/immunology/therapy/pathology
Female
*Microbiota/immunology
Tumor Microenvironment/immunology
Disease Progression
Animals
Immunotherapy/methods
Prognosis

@article {pmid42500599,
year = {2026},
author = {Ai, X and Liu, R and Lv, Y and Chen, L and Duan, R and Ma, X and Li, L and Ding, H and Shen, H and Hu, Y and Zhu, X and Zhang, Y},
title = {Functional signatures of the gut microbiome in middle-aged regular runners: insights from a metagenomic study.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1826138},
pmid = {42500599},
issn = {1664-042X},
abstract = {INTRODUCTION: Exercise influences host metabolism and inflammation, but its functional effects on the gut microbiome in middle-aged populations remain unclear. This study used shotgun metagenomics to investigate the associations between long-term endurance running and the gut microbial ecosystem and its functional potential in middle-aged adults.

METHODS: We conducted a cross-sectional analysis comparing 33 middle-aged regular runners with 33 sedentary controls. No significant differences in age, BMI, dietary intake between groups. Fecal samples underwent metagenomic sequencing at an average depth of 10.97 Gb per sample. Following stringent quality control, taxonomic profiling, diversity analyses, and differential abundance testing were performed. Functional potential was annotated using GO, eggNOG, KEGG, CARD, VFDB, and CAZy databases.

RESULTS AND DISCUSSION: The gut microbiota of middle-aged regular runners (RG, n = 33) and sedentary controls (CG, n = 33) was compared using metagenomic sequencing. No significant differences were observed between the two groups in terms of age, BMI, or self-reported dietary patterns. Although no significant differences in α-diversity or β-diversity were found, taxonomic profiling revealed differences in microbial community composition between the groups. Runners exhibited an increased relative abundance of carbohydrate-fermenting and short-chain fatty acid (SCFA)-producing species, including Prevotella copri, Lachnospira eligens, and Collinsella intestinalis. KEGG functional analysis revealed enrichment of genes associated with antibiotic biosynthesis pathways in runners, whereas the control group was enriched in genes related to lipid metabolism and xenobiotic degradation. The total abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs) was significantly lower in runners. Carbohydrate-active enzyme (CAZy) profiling further indicated that runners harbored higher abundances of carbohydrate-binding modules and glycosyltransferase families, while controls were enriched in complex polysaccharide-degrading enzymes. Nonetheless, the cross-sectional design, qualitative dietary assessment, residual sex imbalance, and lack of metabolomic validation limit causal inference. Longitudinal intervention studies incorporating metabolomic analyses are warranted to confirm these associations and elucidate the directional adaptation of the gut microbiota to long-term regular exercise.},
}

@article {pmid42500607,
year = {2026},
author = {Ding, T and Hu, W and Qi, X and Zhang, Y and Wang, H},
title = {Advances in Helicobacter pylori-mediated oncogenic signaling pathways in gastric cancer: From pathological evolution to clinical application prospects (Review).},
journal = {Oncology letters},
volume = {32},
number = {3},
pages = {408},
pmid = {42500607},
issn = {1792-1082},
abstract = {Helicobacter pylori (H. pylori) infection constitutes a principal risk factor for gastric cancer (GC), however, the intricate oncogenic mechanisms underlying this association are not fully elucidated. The present review provides a comprehensive synthesis of the molecular pathways driving H. pylori-mediated gastric carcinogenesis, with a focus on core oncogenic signaling cascades including NF-κB, MAPK, Janus kinase/STAT and PI3K/AKT, as well as epigenetic regulatory mechanisms such as DNA methylation and non-coding RNAs. By integrating insights from single-cell sequencing and microbiome research, the crosstalk between H. pylori and the gastrointestinal microbiota is dissected, alongside their combined impact on the tumor microenvironment. Additionally, the present review summarizes key H. pylori virulence factors, most notably cytotoxin-associated gene A and vacuolating cytotoxin A, and delineates their functional contributions to tumor progression. The role of gastric stem cells in tumorigenesis and the reprogramming of their intrinsic signaling pathways are also elaborated. From a clinical standpoint, current progress in the identification of molecular diagnostic biomarkers, therapeutic targets and immunotherapeutic approaches is highlighted based on these mechanistic discoveries. Overall, the present review seeks to integrate basic research findings with clinical practice, providing valuable insights into promising directions for the early diagnosis and precision therapy of GC.},
}

@article {pmid42500671,
year = {2026},
author = {Kaźmierczak-Siedlecka, K and Wiśniewski, P and Kucharski, R and Stachowska, E and Makarewicz, W},
title = {Immunologically-based nutritional status assessment amongst preoperative colorectal cancer patients - does it link to TNM stage.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1869012},
pmid = {42500671},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/pathology/immunology/surgery/diagnosis ; Female ; *Nutritional Status ; Neoplasm Staging ; Male ; *Nutrition Assessment ; Middle Aged ; Aged ; Prognosis ; Preoperative Period ; *Malnutrition/diagnosis ; Lymphatic Metastasis ; },
abstract = {INTRODUCTION: Disease-related malnutrition can develop in colorectal cancer (CRC) patients, negatively affecting postoperative clinical outcomes. Nutritional status should be assessed using standardised tools and laboratory parameters to identify malnourished patients and introduce personalised, targeted dietary interventions based on epigenetics, immunologically-related aspects, and gut microbiome. The primary aim of this study is to analyse the immunonutritional status of CRC patients in the preoperative period. The secondary aim is to assess the link between albumin-to-globulin ratio (AGR), prognostic nutritional index (PNI), and TNM staging.

PATIENTS AND METHODS: This study initially included 21 patients with histopathological confirmation of CRC qualified for surgical resection of the tumour. Immunologically-related nutritional status parameters, i.e., AGR and PNI, were calculated for selected 12 patients. The optimal cut-off value of PNI was determined, allowing patients to be divided into two independent groups: PNI-low and PNI-high. The link between AGR, PNI, and TNM was analysed.

RESULTS: TNM classification of the 12 selected participants revealed that most participants classified as T3 (67%), lymph node metastasis was identified in 50% of patients, and there were no distant metastases. Among selected patients, the analysis of mean values of immunological laboratory tests showed that they were within the normal range, except for lymphocyte levels, which were reduced (22.03 ± 7.31%). The optimal cut-off value was set at 51.74 for PNI; thus, patients were accordingly divided into PNI-low and PNI-high groups (<51.74, 34% of cases; ≥51.74, 66%, respectively). PNI-low was initially associated with more advanced cases (based on T assessment) compared to PNI-high (100% versus 75%; respectively); however, it failed to reach statistical significance (p = 0.515; effect size 0.2889; CI 95%, CI = 0.0110-7.5681). Therefore, this finding should be interpreted with caution. Lymph node metastasis was found more often in the PNI-high group than in the PNI-low group.

CONCLUSIONS: Overall concentrations of albumin and total protein were not decreased in CRC patients; however, these parameters allow calculation of AGR and PNI. The link between PNI-low and locally advanced cases of CRC based on T assessment can potentially exist; nevertheless, it should be confirmed with more clinical data. Lymph node metastasis was more often observed in the PNI-high group. This status is also related to higher levels of AGR. A PNI-low value is more related to local than distant pathological processes associated with CRC.},
}

Humans
*Colorectal Neoplasms/pathology/immunology/surgery/diagnosis
Female
*Nutritional Status
Neoplasm Staging
Male
*Nutrition Assessment
Middle Aged
Aged
Prognosis
Preoperative Period
*Malnutrition/diagnosis
Lymphatic Metastasis

@article {pmid42500836,
year = {2026},
author = {Mohabbat, M and Nouri, M and Arazi, H},
title = {mTOR-Gut Microbiome Interaction in Aging: Fusobacterium nucleatum, Resistance Training and Multi-nutrient Supplementation Effects in Aged Male Rats.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {14},
pages = {e72129},
doi = {10.1096/fj.202504395R},
pmid = {42500836},
issn = {1530-6860},
mesh = {Animals ; Male ; Rats ; *Aging/physiology/metabolism ; *Fusobacterium nucleatum/physiology ; *TOR Serine-Threonine Kinases/metabolism/genetics ; Rats, Wistar ; *Dietary Supplements ; *Gastrointestinal Microbiome/physiology ; *Resistance Training ; *Physical Conditioning, Animal/physiology ; Insulin-Like Growth Factor I/metabolism ; Muscle, Skeletal/metabolism ; Signal Transduction ; },
abstract = {We investigated the mTOR pathway in relation to gut microbiome composition and Fusobacterium nucleatum (Fn) in aged male Wistar rats undergoing resistance exercise and multi-nutrient supplementation. Thirty-five male rats (OC, YC, OS, OR, ORS; n = 7/group) underwent 8-week moderate-intensity resistance training and/or supplementation (Lactobacillus plantarum, Bifidobacterium bifidum, vitamin D, leucine). Muscle samples were analyzed by RT-PCR and Western blot; fecal DNA by 16S rRNA sequencing (p < 0.05). Finding revealed significant increases in the mTOR/IGF-1/S6K1 protein content and gene expression in the ORS group compared to OS and OR groups (mTORC1: ORS vs. OR, p = 0.011; ORS vs. OS, p < 0.001; IGF-1: ORS vs. OR, p = 0.008; ORS vs. OS, p = 0.001), which showed only mild increases. The F/B ratio decreased in all intervention groups, with ORS reaching levels comparable to YC (p = 0.207). Resistance training alone did not significantly affect Fn, but the ORS group had the lowest Fn levels, comparable to YC (p = 0.069) and significantly lower than OR and OS (p = 0.001). The study provides novel evidence that combined resistance training and multi-nutrient supplementation (L. plantarum, B. bifidum, vitamin D, leucine) upregulates mTOR/IGF-1/S6K1 signaling and reduces Fusobacterium nucleatum in aged male rats. The ORS group outperformed either intervention alone; Fn correlates strongly with S6K1 (r = -0.85) and IGF-1 (r = -0.81), supporting the gut-muscle axis as a therapeutic target for sarcopenia.},
}

Animals
Male
Rats
*Aging/physiology/metabolism
*Fusobacterium nucleatum/physiology
*TOR Serine-Threonine Kinases/metabolism/genetics
Rats, Wistar
*Dietary Supplements
*Gastrointestinal Microbiome/physiology
*Resistance Training
*Physical Conditioning, Animal/physiology
Insulin-Like Growth Factor I/metabolism
Muscle, Skeletal/metabolism
Signal Transduction

@article {pmid42501008,
year = {2026},
author = {Verma, B and Kumar, R and Sharma, A and Kumar, N and Khan, Z and Ashique, S and Rani, R and Parihar, VS and Antal, S and Mumtaz, and Anand, A},
title = {Targeting the microbiota-gut-brain axis in neurodegeneration: Zebrafish-based investigations.},
journal = {Neurodegenerative disease management},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/17582024.2026.2705869},
pmid = {42501008},
issn = {1758-2032},
abstract = {The microbiota-gut-brain axis (MGBA) is a bidirectional signaling pathway regulated by the gut microbiome and the central nervous system (CNS). Moreover, MGBA is crucial for normal growth, development, and physiology of the brain and gut of the host; dysfunction in MGBA has been closely linked with the development of neurological disorders. Gut dysbiosis and its metabolites modulate barrier permeability and cause gastrointestinal tract (GIT) inflammation, which is followed by an increase in pro-inflammatory cytokines, immune cell infiltration into the brain, and vagus nerve dysfunction, resulting in neuroinflammation and neuronal defects in the brain, as well as some other behavioral defects. In this review, we will discuss the molecular and neurobehavioral properties of Zebrafish as a research model to study MGBA, as well as current discoveries in humans, highlighting the vital role of MGBA in neuropathological conditions. Using Zebrafish as a genetic model in combination with in vivo imaging technology may suggest some novel mechanisms for the interaction between gut microbiota and CNS, particularly in the case of neurological disorders including Alzheimer's disease (AD), Parkinson's disease (PD) and autism spectrum disorder (ASD). A comprehensive literature search was conducted using electronic databases including PubMed, Scopus, Web of Science, and Google Scholar.},
}

@article {pmid42501070,
year = {2026},
author = {Zhang, C and Fukushima, T and Tsuchiya, Y and Ochi, E},
title = {Effects of exercise on gut microbiota in patients with cancer: a scoping review.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {34},
number = {8},
pages = {},
pmid = {42501070},
issn = {1433-7339},
mesh = {Humans ; *Neoplasms/therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; },
abstract = {BACKGROUND: Cancer and its treatments, such as chemotherapy, radiotherapy, endocrine therapy, and targeted therapy, often cause systemic effects, including inflammation, immune suppression, metabolic changes, and gastrointestinal toxicity. These complications are increasingly believed to be related to gut microbiota disorders, which play a crucial role in maintaining balance within the human body. In healthy individuals, exercise appears to have a beneficial influence on this microbial community. Yet how it influences the microbiota in cancer patients remains unclear.

OBJECTIVE: This scoping review aimed to summarize the current observational evidence on the relationship between exercise and gut microbiota in individuals with cancer. The focus was on microbial diversity, bacterial composition, and research gaps in the current evidence.

METHODS: We conducted a scoping review following the PRISMA-ScR guideline. The protocol was prospectively registered on the Open Science Framework (Registration ID: hn92y). Relevant peer-reviewed English-language studies were searched in PubMed, CINAHL, Cochrane Library, and Web of Science up to January 4, 2025. Reviews, case reports, and conference abstracts were excluded.

RESULTS: Six observational studies (three cross-sectional and three prospective cohorts) met the inclusion criteria after screening 2,814 records. The studies involved both adult and pediatric patients with breast, colorectal, gynecological, and hematologic cancers. Exercise, physical activity, or cardiorespiratory fitness was generally associated with differences in microbial diversity and selected bacterial taxa, including potentially beneficial taxa such as Faecalibacterium, Roseburia, and Akkermansia, and inflammation-related taxa such as Enterococcus. However, wide differences in cancer types, exercise formats, timing, and microbiome analysis methods, together with small sample sizes and limited follow-up, made comparison difficult.

CONCLUSION: Preliminary evidence suggests that exercise, physical activity, and cardiorespiratory fitness are associated with microbial diversity and selected potentially beneficial bacterial taxa in individuals with cancer. However, the current evidence is limited by observational study designs, small sample sizes, and methodological heterogeneity. Future studies should use standardized exercise protocols, randomized controlled designs, and advanced multi-omics approaches to clarify the functional significance of exercise-related microbiota changes.},
}

Humans
*Neoplasms/therapy/microbiology
*Gastrointestinal Microbiome/physiology
*Exercise/physiology

@article {pmid42501334,
year = {2026},
author = {Alsaadi, AI and Wehkamp, L and Pothakamury, AA and Yahia, MS and Prasad, P and Gilloteau, C and Sadler, J and Smith, JD and Jenkins, BC and Diven, GS and Bornhäuser, J and Mekdoud, T and Tian, S and Rosenstiel, P and Schreiber, S and Bisanz, JE and Aden, K and McReynolds, MR},
title = {Tracing NAD[+] metabolism uncovers adaptive coordination between host and microbiome during colitis.},
journal = {Cell reports},
volume = {45},
number = {8},
pages = {117730},
doi = {10.1016/j.celrep.2026.117730},
pmid = {42501334},
issn = {2211-1247},
abstract = {Host-microbiota metabolic interactions critically regulate nicotinamide adenine dinucleotide (NAD[+]) homeostasis, and their disruption is increasingly linked to chronic diseases, including inflammatory bowel disease (IBD). However, it remains unclear whether NAD[+] dysregulation in IBD arises from impaired production, enhanced consumption, or both. Using multi-omics approaches and stable isotope-labeled NAD[+] precursors administered via intravenous infusion in a murine model of dextran sulfate sodium (DSS)-induced colitis, we mapped tissue- and lumen-specific NAD[+] metabolism under inflammatory stress. Our results reveal tissue-specific rewiring of NAD[+] metabolism, with increased flux through the salvage pathway compensating for reduced de novo NAD[+] synthesis from tryptophan. In parallel, microbial de novo NAD[+] production was elevated, highlighting a cooperative host-microbiota response to inflammatory stress. These findings demonstrate differential regulation of NAD[+] biosynthesis during acute colitis and underscore the dynamic interplay between host and microbial metabolism in maintaining NAD[+] homeostasis under inflammatory conditions.},
}

@article {pmid42501338,
year = {2026},
author = {van de Ven, JJI and Amatngalim, GD and Garssen, J and Netea, MG and Perdijk, O},
title = {Microbial imprinting of the airway epithelium.},
journal = {Cell reports},
volume = {45},
number = {8},
pages = {117705},
doi = {10.1016/j.celrep.2026.117705},
pmid = {42501338},
issn = {2211-1247},
abstract = {The airway epithelium forms the frontline interface between the external environment and the respiratory system and is constantly exposed to microbes and their constituents. Epidemiological and preclinical evidence increasingly highlights an important role for microbial factors in shaping long-term respiratory health by maintaining immune homeostasis and modulating exacerbations in chronic inflammatory diseases. Here, we argue that these durable effects are likely due to "imprinting" events at the epithelial interface. Emerging evidence indicates that microbes can functionally imprint the airway epithelium through metabolic and epigenetic reprogramming, thereby shaping subsequent responses to microbial and inflammatory stimuli. We propose a conceptual framework of epithelial imprinting comprised of four categories: differentiation, tolerance, priming and trained immunity. This framework provides an important foundation for the mechanistic dissection of epithelial memory in the airways and highlights novel therapeutic opportunities to harness microbial factors to modulate respiratory health.},
}

@article {pmid42501555,
year = {2026},
author = {Zhu, T and Sha, Y and Wang, Q and Yang, H and Liu, T},
title = {Gut microbiota and polycystic ovary syndrome: Pathogenesis and novel therapeutic approaches.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128643},
doi = {10.1016/j.micres.2026.128643},
pmid = {42501555},
issn = {1618-0623},
abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder in women that is characterized by a complex pathogenesis involving multiple mechanisms, including hyperandrogenism, ovulatory dysfunction, insulin resistance (IR), and chronic inflammation. Recent studies have demonstrated that the gut microbiota acts as an important metabolic regulator and may play a pivotal role in the onset and progression of PCOS. Patients with PCOS frequently exhibit gut microbiota dysbiosis, which is characterized by reduced microbial diversity, decreased levels of beneficial bacteria, increased levels of pathogenic bacteria, and altered metabolic byproducts. This imbalance may contribute to IR and ovarian dysfunction by activating the toll-like receptor 4/nuclear factor kappa B inflammatory pathway, inducing oxidative stress, and disrupting Wnt/β-catenin signaling. The Wnt/β-catenin signaling pathway, a key regulator of follicular development, is frequently aberrantly activated in PCOS. In this narrative review, we summarize the recent advances in understanding the roles of the gut microbiota and the Wnt/β-catenin signaling pathway in the pathogenesis of PCOS. To this end, we conducted a comprehensive literature search across PubMed, Web of Science, Embase, and Cochrane Library databases, covering publications from January 2012 to March 2026. Ninety-eight articles were included after screening. We further explored therapeutic strategies based on microbiome modulation and signaling pathway targeting, including probiotics, traditional Chinese medicine, ginsenosides, puerarin, fecal microbiota transplantation, and nanoparticle-based ginseng-derived exosomes, thereby providing novel insights into potential therapies for PCOS.},
}

@article {pmid42501556,
year = {2026},
author = {Bhuyan, B},
title = {Enhancing crop productivity under stress through plant growth-promoting bacterial consortia: Relevance to sustainable development goals.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128641},
doi = {10.1016/j.micres.2026.128641},
pmid = {42501556},
issn = {1618-0623},
abstract = {Abiotic and biotic stresses significantly threaten global food security and agricultural sustainability. Achieving the United Nations Sustainable Development Goals (SDGs), particularly SDG 2 (Zero Hunger), SDG 6 (Clean Water and Sanitation), SDG 12 (Responsible Consumption and Production), SDG 13 (Climate Action), and SDG 15 (Life on Land), requires sustainable agricultural approaches. Recently, plant growth-promoting bacterial (PGPB) consortia have emerged as an effective strategy for enhancing crop productivity under stress conditions. These microbial communities improve plant growth through mechanisms such as nitrogen fixation, phosphate solubilization, phytohormone production, siderophore secretion, ACC deaminase activity, induction of systemic resistance, while enhancing nutrient uptake, antioxidant activity, osmotic regulation, and stress-responsive signalling pathways, thus improving plant health and productivity. Compared with single-strain inoculants, consortia provide synergistic effects that enhance rhizosphere colonization, microbial survival, and plant-microbe interactions, thus contributing to the achievement of the SDGs. Recent advances in modern tools such as metagenomics, metatranscriptomics, metabolomics, and machine learning for predictive microbiome modelling, as well as field-level engineering approaches such as encapsulation technologies, biochar-based carriers, seed coating, and root microbiome editing, have accelerated the development of efficient microbial formulations for sustainable agriculture. This review discusses the potential of PGPB consortia as a sustainable solution for boosting crop productivity under stress. The integration of consortia into modern agricultural practices can play a crucial role in supporting resilient farming systems and advancing the global SDG agenda. This review highlights the key limitations, challenges, and research gaps associated with PGPB consortia, as well as future prospects for enhancing crop productivity.},
}

@article {pmid42501557,
year = {2026},
author = {Zhao, Y and Wen, X},
title = {Rhizosphere arginine accumulation recruits Pseudomonas for maize salt tolerance via a lignin pathway modulated by a NAC-family gene.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128645},
doi = {10.1016/j.micres.2026.128645},
pmid = {42501557},
issn = {1618-0623},
abstract = {Soil salinization severely threatens global food security by reducing agricultural productivity. While root-associated microbiota are known to enhance plant adaptation to environmental stress, the metabolic and molecular mechanisms governing maize-microbe interactions under salt stress remain largely unclear. In this study, we integrated microbiome and metabolome profiling of field-grown maize and demonstrated that salt stress induces arginine accumulation, which in turn enriches Pseudomonas in both the rhizosphere and root compartments. Subsequent greenhouse experiments combined with transcriptomic analysis suggested that Pseudomonas modulates a NAC-family gene, thereby contributing to lignin biosynthesis and root cell wall thickening. This structural reinforcement reduces root Na[+] influx and ultimately alleviates salt stress in maize. Collectively, our findings establish a mechanistic framework for understanding plant-microbiome crosstalk and highlight promising strategies for engineering microbiomes to enhance crop resilience in saline environments.},
}

@article {pmid42501709,
year = {2026},
author = {Cheng, B and Jiang, J and Guo, G and Zhang, W and Chen, G},
title = {Multi-scale machine learning reveals the effects of sulfur species on sludge anaerobic fermentation: Bridging macroscopic performance and microscopic molecular mechanisms.},
journal = {Water research},
volume = {305},
number = {},
pages = {126524},
doi = {10.1016/j.watres.2026.126524},
pmid = {42501709},
issn = {1879-2448},
abstract = {Sulfur-mediated chemical regulation has emerged as an attractive strategy for enhancing sludge anaerobic fermentation (AF). However, the non-linear influence of diverse sulfur species on AF performance, and their cross-scale interactions with microbiomes and functional genes, remain poorly understood. Therefore, this study developed a multi-scale machine learning (ML) framework that integrates MacroML for AF performance prediction and MicroML for mechanistic microbiome-gene interpretation, using thiosulfate-mediated AF as a representative sulfur-regulated system. At the macroscopic level, support vector regression (SVR) exhibited superior predictive robustness for short-chain fatty acids (SCFAs) (R[2]-test = 0.94) and biogas (R[2]-test = 0.89) using multiple sulfur species and operational conditions as inputs. MacroML interpretation analysis identified H2S (>3000 ppm), thiosulfate (∼650 mg S/L), sulfite (3.0-3.5 mg S/L), sulfide (120-140 mg S/L), and sulfate (20-30 mg S/L) as determinants for increasing SCFA production, whereas biogas production required low thiosulfate (<200 mg S/L), sulfate (< 10 mg S/L), sulfide (10-20 mg S/L), sulfite (< 2.0 mg S/L), and H2S (< 2500 ppm). At the microscopic scale, a graph embedding-enhanced random forest (GE-RF) model (R[2]-test = 0.72-0.89) revealed that sulfur metabolism was associated with a metabolic shift toward acidogenesis, as indicated by the enrichment of core taxa (e.g., Proteiniphilum, Aminobacterium), higher expression of acidogenic genes (e.g., buk, ptb), and increased abundance of electron transfer chain components (e.g., aprA/B, COQ4). Concurrently, sulfur exposure (e.g., thiosulfate, sulfide, H2S) was associated with inhibition of terminal methanogenic enzymes (i.e., mcr and mtr) and a potential weakening of Methanothrix-centered functional modules, which may collectively contribute to reduced biogas production. This work provides a robust, data-driven roadmap for deciphering sulfur-mediated biochemical pathways and facilitates precision operational control in sludge AF systems.},
}

@article {pmid42493595,
year = {2026},
author = {Nagao, I and Kim, HJ},
title = {Engineering human Gut-on-a-Chip culturomics for predictive pharmacomicrobiomics of first-pass metabolism.},
journal = {npj biomedical innovations},
volume = {3},
number = {1},
pages = {},
pmid = {42493595},
issn = {3005-1444},
support = {24KJ0651//Japan Society for the Promotion of Science Research Fellowship for Young Scientists/ ; 1R33CA286797//NIH NCI IMAT program/ ; },
abstract = {For orally administered drugs, intestinal first-pass metabolism influences systemic exposure and accounts for inter-individual pharmacokinetic differences. However, the mechanistic roles of gut microbiome-mediated biotransformation and patient-specific intestinal variability remain underrepresented in current regulatory frameworks. This Perspective explores how human-relevant culturomics platforms, including Gut-on-a-Chip microphysiological systems, allow for quantitative analysis of host-microbiome-drug interactions. We also discuss the potential of predictive intestinal ecosystem models for personalized pharmacomicrobiomics and next-generation translational drug development.},
}

@article {pmid42493609,
year = {2026},
author = {Yang, Y and Li, N and Zhou, L and Gong, S and He, Z and Tang, S and Ni, J and Liu, Y and Chan, JWY and Or, BPN and Lam, SP and Zhang, J and Chan, PKS and Chen, Z and Wong, SH and Mok, VCT and Chan, NY and Chau, SWH and Lai, CKC and Scheperjans, F and Wang, J and Huang, B and Wing, YK},
title = {Gut Microbiome in Depression with and without REM Sleep Behavior Disorder.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {42493609},
issn = {1476-5578},
support = {18190221//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 05162876//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; C4044-21G//Research Grants Council, University Grants Committee (RGC, UGC)/ ; },
abstract = {Major depressive disorder (MDD) is a risk factor for neurodegeneration, yet its heterogeneity makes identifying at-risk subtype challenging. Notably, MDD frequently co-occurs with REM sleep behavior disorder (RBD), a specific prodrome of α-synucleinopathy. It remains unclear whether comorbid MDD + RBD reflects a benign antidepressant effect, or higher neurodegenerative risk. Given growing recognition of gut-brain axis in neuropsychiatry, we aimed to delineate microbial signatures of MDD + RBD. We employed a four-group case-control design (N = 420) comprising 124 healthy controls (HC); 80 MDD without RBD features (MDD-only); 82 MDD + RBD; and 134 iRBD without psychiatric disease. All participants underwent clinical evaluation and provided fecal samples for metagenomic sequencing. Random Forest model was used to distinguish MDD + RBD, and further assessed in a validation dataset of 65 participants with MDD + RBD (n = 31) and MDD-only (n = 34). MDD + RBD exhibited prodromal neurodegenerative features, including elevated total likelihood ratio of prodromal Parkinson's Disease, olfactory deficits, and subtle motor signs. The microbial composition in MDD + RBD differed from HC and MDD-only, while resembling iRBD. Taxonomically, MDD + RBD exhibited an iRBD-like dysbiosis (e.g., enriched Akkermansia muciniphila, Ruthenibacterium lactatiformans; depleted Faecalibacterium prausnitzii), alongside depression-associated shifts (e.g., Streptococcus parasanguinis and Actinomyces oris). Functionally, MDD + RBD showed attenuated capacity of B‑vitamin biosynthesis and polysaccharides degradation, mirroring iRBD. The Random Forest machine-learning model distinguished MDD + RBD in older adults from MDD-only with an AUC of 0.73 in cross-validation and 0.79 in the validation dataset. MDD + RBD may represent a biologically distinct depression subtype associated with potential neurodegenerative risk. Gut microbiome provides a candidate approach for potential risk stratification in psychiatric populations.},
}

@article {pmid42493633,
year = {2026},
author = {Rock, R and Zhang, S and Noecker, C and Turnbaugh, PJ},
title = {Eggerthella lenta: metabolism, pathogenesis and therapeutic implications.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42493633},
issn = {1740-1534},
abstract = {Despite a tremendous body of literature on environmental Actinomycetota, their role in the human gut remains poorly understood. In this Review, we highlight the representative species Eggerthella lenta, which has emerged as a major player in the gut microbiota and is increasingly amenable to mechanistic dissection. We discuss the unique metabolic niche of this asaccharolytic obligate anaerobe, including growth on amino acids and short-chain fatty acids, versatile anaerobic respiratory capacity, and the extensive biotransformation of endogenous, diet-derived and pharmaceutical small molecules. E. lenta is associated with a wide range of chronic diseases in humans and sufficient to exacerbate disease in preclinical models, prompting a renewed consideration of the pathogenic potential of this common member of the gut microbiota. Further mechanistic dissection coupled with the development of microbiome-editing tools is essential to understand E. lenta and its multifaceted contributions to gut microbial ecology and host pathophysiology.},
}

@article {pmid42493753,
year = {2026},
author = {Pielak, RM and Butler, DC},
title = {The Role of Skin Surface pH in Age Associated Pruritus: Mechanistic and Clinical Insights.},
journal = {American journal of clinical dermatology},
volume = {},
number = {},
pages = {},
pmid = {42493753},
issn = {1179-1888},
abstract = {Skin aging is characterized by progressive structural and biochemical changes that impair epidermal barrier function, alter the cutaneous microbiome, and predispose to chronic pruritus. Epidermal thinning, reduced lipid synthesis, and slowed barrier repair increase transepidermal water loss and vulnerability to irritation. Concurrently, age-related disruption of the acid mantle leads to elevation of skin surface pH, impairing acid-dependent lipid-processing enzymes while enhancing serine protease activity. These changes disrupt lamellar organization, weaken stratum corneum cohesion, and further compromise barrier integrity. Elevated pH and barrier dysfunction also reshape the skin microbiome. These changes favor alkalinity-tolerant and proinflammatory species while reducing protective commensals, thereby reinforcing inflammation and sensory irritation. Barrier impairment, dysbiosis, and pH-driven protease activation converge with neuroimmune dysregulation to sensitize peripheral nerves and promote chronic itch. Important contributors include kallikrein-protease-activated receptor-2 (PAR2) signaling and cytokines such as interleukin-31. This review highlights the pH-protease-itch axis as a unifying framework for pruritus in aging skin and discusses restoration of physiological acidity as a rational therapeutic strategy.},
}

@article {pmid42493771,
year = {2026},
author = {Yi, Y and Xie, F and Xia, C and Li, J and Zhao, P and Liu, M and Ma, X and Chen, J},
title = {Hypertension and gut microbial hydrogenases: a comparison of hydrogen metabolism and etiology.},
journal = {Medical gas research},
volume = {16},
number = {4},
pages = {352-358},
doi = {10.4103/mgr.MEDGASRES-D-25-00128},
pmid = {42493771},
issn = {2045-9912},
mesh = {*Hydrogenase/metabolism/genetics ; *Hydrogen/metabolism ; *Hypertension/microbiology/etiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; },
abstract = {JOURNAL/mgres/04.03/01612956-202612000-00006/figure1/v/2026-07-23T200825Z/r/image-tiff Hypertension is a prevalent chronic condition and serves as a significant risk factor for numerous cardiovascular and cerebrovascular disorders. Gut microbiota dysbiosis has been considered to contribute to the pathogenesis of hypertension. It has been reported that a large majority of gut microbiota possess genes encoding hydrogenases. These hydrogenases are involved in the alteration of gut microbiota in non-infectious colitis, suggesting a potential link between microbial hydrogen metabolism and disease onset. This study aims to explore the relationship between hydrogenase expression patterns in the gut microbiome and the incidence of hypertension. In this study, publicly available gut microbiome metagenomic data were used to comprehensively analyze the expression patterns of hydrogenases in the gut microbiota of hypertensive patients. Compared with the control group, a 2.3-fold increase in electron bifurcating [FeFe] group A3 hydrogenases (P = 0.0299), a 55.6% decrease in [NiFe] group 1d hydrogenases (P = 0.0097), increased hydrogen-sensing hydrogenases and decreased hydrogen-uptake hydrogenases in the hypertension group. The main difference between the two groups is reflected in the abundance of [NiFe] hydrogenase subtypes. After eliminating the effects of factors such as age, sex, and lifestyle, significant differences in the abundance of [FeFe] group A3, [NiFe] group 1d, and [NiFe] group 1c were observed between the two groups, suggesting that these three indicators could serve as potential biomarkers for diagnosing the onset of hypertension. Additionally, Mendelian randomization analysis showed a protective effect of hydrogen metabolism against hypertension (odds ratio = 0.72, 95% confidence interval: 0.61-0.85, P < 0.001). Our study advances the understanding of microbiome-mediated mechanisms in hypertension by demonstrating an association between hydrogenase expression dynamics and blood pressure regulation, providing a foundation for future microbiome-based diagnostic and therapeutic strategies.},
}

*Hydrogenase/metabolism/genetics
*Hydrogen/metabolism
*Hypertension/microbiology/etiology/metabolism
Humans
*Gastrointestinal Microbiome

@article {pmid42493800,
year = {2026},
author = {Van Den Bossche, T and Wolf, M and Armengaud, J and Arntzen, MØ and Benndorf, D and Figeys, D and Grenga, L and Hettich, RL and John, NS and Jagtap, P and Jehmlich, N and Kleiner, M and Kunath, BJ and Li, L and Lipton, M and Mesuere, B and Neely, BA and Ning, Z and Pedersen, AL and Perez-Riverol, Y and Rajan, J and Schallert, K and Seifert, J and Uzzau, S and Verschaffelt, P and Wilmes, P and Vizcaíno, JA and Martens, L and Heyer, R},
title = {The need for standardization and improved open (meta)data practices in metaproteomics.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42493800},
issn = {2049-2618},
mesh = {*Proteomics/standards/methods ; Computational Biology/methods ; *Microbiota ; Metadata ; Humans ; Multiomics ; Reproducibility of Results ; },
abstract = {Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices. Video Abstract.},
}

*Proteomics/standards/methods
Computational Biology/methods
*Microbiota
Metadata
Humans
Multiomics
Reproducibility of Results

@article {pmid42493801,
year = {2026},
author = {Van Den Bossche, T and Grenga, L and Alves, G and Arntzen, MØ and Benndorf, D and Brauer, M and Figeys, D and Henry, C and Hettich, RL and Heyer, R and Jagtap, PD and Jehmlich, N and Kleiner, M and Li, L and Mesuere, B and Pabst, M and Pandhal, J and Pope, PB and Seifert, J and Trautwein-Schult, A and Verschaffelt, P and Wilmes, P and Armengaud, J and Kunath, BJ},
title = {The Metaproteomics Initiative: five years of community-driven progress.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42493801},
issn = {2049-2618},
mesh = {*Proteomics/methods ; *Microbiota ; Humans ; Metagenomics ; },
abstract = {The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative's organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities. Video Abstract.},
}

*Proteomics/methods
*Microbiota
Humans
Metagenomics

@article {pmid42494129,
year = {2026},
author = {Wang, X and Akanyibah, FA and Zhang, P and Zhou, X and Zhang, M and Mao, F},
title = {Geniposide Alleviates Inflammatory Bowel Disease by Regulating Intestinal Flora and Arginine Metabolism and Inhibiting the NF-κB Pathway Through Targeting Anxa5.},
journal = {Mediators of inflammation},
volume = {2026},
number = {1},
pages = {e6231832},
doi = {10.1155/mi/6231832},
pmid = {42494129},
issn = {1466-1861},
support = {SH2024047//Zhenjiang Key Research and Development Plan (Social Development)/ ; SSF202410//Key Research and Development (Social Development) Projects of the Innovation Special Fund of Danyang/ ; 242102310081//Henan Province 2024 science and technology development plan/ ; KFKT23005//Open topic at the university level of Shangqiu Medical College in 2023/ ; K202423//Suqian Natural Science Fund Project/ ; K2024015//Key Project of Health Commission of Jiangsu Province/ ; JSDW202241//Jiangsu Provincial Medical Key Discipline Cultivation Unit/ ; },
mesh = {Animals ; Mice ; *NF-kappa B/metabolism ; *Arginine/metabolism ; Mice, Inbred BALB C ; *Inflammatory Bowel Diseases/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Iridoids/therapeutic use/pharmacology ; RAW 264.7 Cells ; *Annexin A5/metabolism ; Signal Transduction/drug effects ; Male ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including Crohn's and ulcerative colitis (UC), is a chronic gut inflammation thought to be caused by gut microbial causes and immune system dysfunction. Geniposide (GEN) is a natural compound shown to prevent IBD; however, its mechanism of modifying the gut microbiome, regulating arginine metabolism, and inhibiting the nuclear factor kappa B (NF-κB) pathway by targeting Annexin A5 (Anxa5) remains unexplored.

METHODS: This study examined the regulation of intestinal immunity, gut microbiota, metabolites, and associated activities and pathways, as well as the NF-κB pathway by GEN in a BALB/c mouse model of IBD. The mouse macrophage cell line (RAW264.7) was further utilized to investigate the role of GEN on the macrophage-arginine metabolism and the Anxa5 axis. qRT-PCR, Western blotting, hematoxylin and eosin (H&E), immunohistochemistry (IHC), immunofluorescence (IF), fecal 16S rDNA sequencing, and UHPLC/Q-TOF-MS were used to evaluate the treatment effect of GEN. Drug target sequencing and small interfering RNA (siRNA) were used to establish the target molecule of GEN.

RESULTS: GEN therapy improved colon and spleen tissues, decreased the disease activity index, helped mice maintain their weight, elevated anti-inflammatory cytokines and tight junction proteins, and decreased proinflammatory cytokines. GEN modulated the quantity of dysfunctional metabolites and enhanced the structure and diversity of the gut microbial community. GEN restored the underpopulated genera Enterorhabdus, Rikenella, Anaerotruncus, and Alistipes, regulating arginine metabolism mediated by G-guanidinobutyrate in RAW264.7 cells and the gut mucosa to protect the colon. GEN targeted Anxa5, enhancing its expression in both animal models and RAW264.7 cells. Following Anxa5 knockdown, cyclooxygenase-2 (COX-2) expression increased, along with the activation of NF-κB pathway-related proteins in RAW264.7 cells. GEN reduced the levels of NF-κB pathway-related proteins in both RAW264.7 cells and animal models.

CONCLUSION: GEN mitigated colitis by regulating the intestinal microbiota and arginine metabolism and inhibiting the NF-κB pathway via targeting Anxa5.},
}

Animals
Mice
*NF-kappa B/metabolism
*Arginine/metabolism
Mice, Inbred BALB C
*Inflammatory Bowel Diseases/drug therapy/metabolism
*Gastrointestinal Microbiome/drug effects
*Iridoids/therapeutic use/pharmacology
RAW 264.7 Cells
*Annexin A5/metabolism
Signal Transduction/drug effects
Male

@article {pmid42494203,
year = {2026},
author = {Hafez-Ghoran, S and Taktaz, F and Sang, S},
title = {Germination as a Strategy to Enhance the Bioactivity of Whole Grains: Phytochemical Remodeling and Health Implications.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {4},
pages = {e70574},
doi = {10.1111/1541-4337.70574},
pmid = {42494203},
issn = {1541-4337},
support = {//United States Department of Agriculture/ ; 2018-67001-28265//National Institutes of Food and Agriculture/ ; 2021-67017-33337//National Institutes of Food and Agriculture/ ; R01DK143583/NH/NIH HHS/United States ; },
mesh = {*Germination ; *Phytochemicals/analysis/chemistry ; Humans ; *Whole Grains/chemistry ; Nutritive Value ; },
abstract = {Consumption of microgreens, sprouts, and baby leaves is rapidly increasing, driven by consumer demand for nutrient-dense, minimally processed, and functional foods. Germination has emerged as a powerful biological strategy to enhance the nutritional quality and bioactivity of cereals and pseudocereals. The transition from dormancy to sprouting activates endogenous metabolic pathways that promote the accumulation of vitamins and diverse phytochemicals while reducing antinutritional compounds such as phytic acid. These changes are particularly relevant in the context of growing demand for gluten-free and clean-label food systems. This review evaluates recent advances in cereal and pseudocereal germination, with a focus on changes in whole-grain phytochemical composition and their implications for health-related outcomes. We discuss both shared phytochemicals, including γ-aminobutyric acid, phenolics, flavonoids, carotenoids, tocopherols, phytosterols, and policosanols, as well as grain-specific metabolites such as alkylresorcinols, avenanthramides, avenacosides, benzoxazinoids, hordatines, 3-deoxyanthocyanins, and γ-oryzanols. Emerging nonthermal pretreatments before germination and post-germination interventions may modify phytochemical profiles and could influence bioaccessibility or biological activity; however, their health benefits require further validation. Evidence from preclinical and limited human studies indicates that germination enhances grain bioactivity and may support glycemic regulation, lipid metabolism, inflammatory responses, and gut microbiome function. Collectively, these findings position germinated grains as promising ingredients for next-generation functional foods, while underscoring the need for standardized, mechanistic, and translational research to fully realize their potential.},
}

*Germination
*Phytochemicals/analysis/chemistry
Humans
*Whole Grains/chemistry
Nutritive Value

@article {pmid42494246,
year = {2026},
author = {Pang, Z and Yu, P},
title = {From genotype to microbiome function: a gene-metabolite-microbiome pathway shaping plant nutrient acquisition.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71457},
pmid = {42494246},
issn = {1469-8137},
}

@article {pmid42494273,
year = {2026},
author = {Ventura, EF and Corriger, J and Omer, H and Bodinier, M and Haller, D and Hertz, T and Larsen, M and Collado, MC},
title = {Microbiota Signatures in Early Life and Their Association With Food Allergy: A Systematic Review.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70433},
pmid = {42494273},
issn = {1398-9995},
support = {CEX2021-001189-S-20-1//Spanish Ministry of Science and Innovation and the European Social Fund Plus (ESF+)/ ; CEX2021-001189-S//Spanish Government MCIN/AEI to the Center of Excellence Accreditation Severo Ochoa/ ; //European Grant (Physiological and Ecological impact of pre- and probiotic interventions in relation to food allergy in early-life, EcoBIOTIC)/ ; //ERA-HDHL/ ; PCI2021-122059-2A//Programación Conjunta Internacional (PCI)/ ; ANR-17-HDIM-0002//EarlyFOOD/ ; ANR-20-CE15-0032//EcoBIOTIC/ ; FKZ 01EA2207//German Federal Ministry of Research, Technology and Space (BMFTR)/ ; },
abstract = {Food allergy (FA) is increasing worldwide, and early life may be a critical window for immune training. We systematically reviewed observational human studies linking early-life microbiota (infant, maternal, environmental, or extraintestinal) profiled using culture-based and/or culture-independent methods (including sequencing-based approaches) to subsequent FA or food sensitization outcomes in infants, children, and adolescents up to 18 years of age. PubMed, Web of Science Core Collection, Embase, Scopus, and LILACS were searched from database inception to March 2026. Inclusion required microbiota sampling during pregnancy or childhood and clinically ascertained FA/sensitization; non-human studies and studies without sequencing or clinical outcomes were excluded. Risk of bias was assessed using QUIPS. Owing to heterogeneity, we performed narrative synthesis. Forty studies were included (n = 6530 participants; 2077 cases). Across cohorts, cases were associated with lower diversity, early beta-divergence (1-6 months), neonatal enrichment of Proteobacteria (Pseudomonadota)/Enterobacteriaceae and selected taxa (Clostridium, Streptococcus, Sutterella), and depletion within the first year of Bifidobacterium, Blautia, and butyrate producers (Roseburia, Faecalibacterium). Functional profiles often suggested delayed maturation and reduced short-chain fatty acid capacity. Evidence was limited by moderate risk of bias, residual confounding, and heterogeneous outcome definitions. These findings support distinct early-life microbial configurations associated with FA susceptibility versus tolerance, informing mechanism-based prevention. Trial Registration: PROSPERO CRD420251234739.},
}

@article {pmid42494431,
year = {2026},
author = {Voermans, B and Prange, K and Bruin, S and Acherman, Y and Zaura, E and Nieuwdorp, M and Gerdes, V},
title = {Oral-gut strain sharing after Roux-en-Y gastric bypass: A canonical oral microbiome signature in the gut linked to hepatic and glycemic remodeling.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2693432},
pmid = {42494431},
issn = {2993-3935},
abstract = {Roux-en-Y gastric bypass (RYGB) induces durable weight loss and metabolic improvement, but the role of oral microbiota in shaping postsurgical gut ecology and metabolic outcomes is unclear. We examined whether RYGB promotes transfer and expansion of oral strains in the distal gut and how these relate to hepatic and glycemic health. In 25 patients from a longitudinal RYGB cohort, paired oral and fecal samples were collected before and 12 months after surgery. We examined the presence, abundance, and structure of cohort-specific canonical oral strains in the gut, and assessed α/β-diversity, cross-site correlations, and clinical associations using univariate tests and linear models. Machine-learning models evaluated the prognostic value of oral canonical strains for hepatic and glycemic outcomes. Oral taxon richness increased after RYGB, while Shannon diversity and individual signatures remained stable. In the gut, canonical oral strains expanded: shared oral-gut strains and their summed abundance rose significantly, converging into a reproducible post-RYGB niche. Abundance and fold change of oral-canonical strains associated with FIB-4, ASAT and fasting glucose, and predictive models suggested a prognostic signal for fasting glucose, TBF% and HbA1c. RYGB is associated with reproducible, strain-level enrichment of oral microbiota in the gut, with links to hepatic and glycemic outcomes.},
}

@article {pmid42494439,
year = {2026},
author = {Coote, E and Patel, N and Vijayanarayanan, R},
title = {The oral‒gut axis in periodontal disease: a systematic review of the associated human evidence of its mechanisms and implications for patient care.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2705699},
pmid = {42494439},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontal diseases may influence systemic health through the oral-gut axis, with three mechanistic pathways proposed. Periodontitis-associated gut dysbiosis has been repeatedly observed and may plausibly extend to effects on drug metabolism, yet the literature on periodontitis-associated dysbiosis and that on its potential effects on medicine pharmacokinetics have not previsouly been bridged.

OBJECTIVE: To synthesise the available human evidence for each of the three pathways with a distinct focus on the interventional evidence, and to position the evidence to its clinical context alongside downstream outcomes and the implications for patients and clinicians. Our secondary aim was to connect the dysbiosis and pharmacokinetic literatures in a hypothesis-generating section.

DESIGN: This systematic review was registered on PROSPERO. PubMed and Scopus were searched and eligibility restricted to human studies.

RESULTS: A total of 76 studies were included following full-text assessment by two independent reviewers. Across the three pathways, the human evidence was placed in clinical context with its downstream outcomes. Direct evidence that periodontitis modeifies drug response in humans was not identified, however, we were able to provide a hypothesis-generating section that identifies four drug classes for which a periodontitis-mediated modification of drug response would be most clinically relevant.

CONCLUSIONS: The oral-gut axis is a biologically plausible but, currently, under-evidenced route from periodontal disease to systemic and pharmacological outcomes. Future reserach should prioritise prospective comparative pharmacokinetic studies in periodontitis-affected popualtions and field-wide standardisation of methodology across oral-gut microbiome research.},
}

@article {pmid42494618,
year = {2026},
author = {Zhao, M and Huang, B and Chen, J and Li, J and Zhu, Z and Zhu, G and Hu, J and Li, F and Feng, J},
title = {Mechanism of Action and Therapeutic Potential of Sulforaphane in Skeletal Muscle Diseases: Molecular Pathways and Precision Medicine.},
journal = {Food science & nutrition},
volume = {14},
number = {7},
pages = {e72154},
pmid = {42494618},
issn = {2048-7177},
abstract = {Sulforaphane (SFN), a bioactive isothiocyanate abundant in cruciferous vegetables, has attracted growing interest as a potential nutraceutical intervention for skeletal muscle disorders. This narrative review synthesizes preclinical and early clinical evidence on the mechanisms and therapeutic applicability of SFN in ICU-acquired weakness, diabetic myopathy, sarcopenia, and exercise-induced muscle damage. SFN modulates skeletal muscle pathophysiology through four interconnected axes: regulation of protein homeostasis via mTOR-associated signaling and suppression of ubiquitin-proteasome-mediated catabolism; upregulation of oxidative stress defenses through Nrf2-driven antioxidant enzyme induction; attenuation of inflammatory networks via NF-κB inhibition and promotion of M2 macrophage polarization; and metabolic reprogramming through AMPK-mediated mitochondrial biogenesis and enhanced insulin sensitivity. Preclinical data suggest preliminary protective effects on respiratory and locomotor muscle; however, clinical translation remains uncertain. Several randomized controlled trials have failed to demonstrate significant effects on Nrf2 target genes or metabolic stress biomarkers, and bioavailability varies markedly across formulations and individuals. Heterogeneous responses across muscle fiber types, an undefined therapeutic window, and interindividual variability in gut microbiota-mediated conversion further complicate clinical application. To address these challenges, we propose a conceptual "Sulforaphane Precision Medicine Framework" integrating molecular biomarkers, gut microbiome profiling, and dynamic delivery systems to guide personalized intervention. While SFN shows promise as an adjunctive therapy, standardized formulations, refined patient stratification, and rigorous phase III trials are essential before routine clinical adoption can be recommended.},
}

@article {pmid42494654,
year = {2026},
author = {Dicksion, CA and Chao, DN and Rickmeyer, JD and Bess, EN},
title = {A Validated LC-MS/MS Method for Quantifying Phenolic Acids, Lignans, and Enterolignans from Human Fecal Samples.},
journal = {ACS nutrition science},
volume = {1},
number = {4},
pages = {356-366},
pmid = {42494654},
issn = {3067-6037},
abstract = {The human gut is home to numerous small molecules that impact health. Three prominent classes of molecules in this environment are phenolic acids, lignans, and enterolignans, which have been linked to anti-inflammatory and antioxidant effects as well as protection from cancer, cardiovascular disease, and neurodegeneration. The abundance of these molecules in the intestine as well as their biological significance motivated the development and validation of the LC-MS/MS method reported herein, which provides a simple, robust, and high-throughput approach to simultaneously quantify a 22-membered panel of phenolic acids, lignans, and enterolignans in human fecal samples. Facile sample preparation and a short analytical time (5 min per sample, compared to similar methods that range from 7.8-28 min) allow for high throughput. A 16-fold increase in sensitivity allows for quantitation of lignans that are often not detected via existing methods.},
}

@article {pmid42494770,
year = {2026},
author = {Woolsey, B and Sen, K},
title = {Dietary approaches to support cognition in older adults: a systematic review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1869091},
pmid = {42494770},
issn = {2296-861X},
abstract = {BACKGROUND: Older adults, particularly those residing in long-term care, experience disproportionate rates of cognitive decline and Alzheimer's disease (AD). While isolated nutrient supplementation has demonstrated limited clinical efficacy, comprehensive whole-food dietary patterns may offer significant neuroprotective benefits through complex nutrient synergy. This systematic review evaluates the efficacy of the Mediterranean, Nordic, Okinawan, and plant-based dietary approaches in mitigating cognitive decline and reducing dementia risk in older populations.

METHODS: The study protocol was prospectively registered with the International Prospective Register of Systematic Reviews (PROSPERO) under the registration ID CRD420261349593. Conducted in accordance with PRISMA 2020 guidelines, a systematic search of PubMed, Web of Science, CINAHL, and ScienceDirect was performed to identify peer-reviewed articles published between January 2021 and the present. Eligible studies included randomized controlled trials (RCT), prospective cohort studies, and longitudinal studies evaluating the impact of whole-food dietary patterns on cognitive outcomes in adults aged 60 and older.

RESULTS: Out of 622 initial records, 16 articles met all inclusion criteria. The synthesized evidence demonstrates that high adherence to these comprehensive dietary patterns is consistently associated with improved memory, enhanced executive function, and a reduced incidence of AD. These cognitive improvements are driven by interconnected physiological mechanisms, including reduced systemic inflammation, improved vascular integrity, favorable shifts in the gut microbiome, and optimized circulating endocannabinoid profiles. Additionally, the magnitude of these benefits is frequently modulated by individual biological factors, such as sex and APOE genotype.

CONCLUSION: Whole-food dietary patterns provide an effective, evidence-based framework for preserving cognitive resilience compared to single-nutrient interventions. Integrating these nutrient-dense diets into public health initiatives and long-term care settings offers a powerful strategy for neuroprotection, highlighting the need to advance personalized nutrition strategies in future clinical trials.},
}

@article {pmid42494846,
year = {2026},
author = {Mthembu, TP and Hlongwane, NL and Salawu-Rotimi, A and Hadebe, K and Pierneef, R},
title = {Metagenomic analysis of fecal and environmental microbiota in rural mixed livestock farming systems in South Africa.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1828785},
pmid = {42494846},
issn = {2235-2988},
mesh = {Animals ; South Africa ; *Feces/microbiology ; *Metagenomics ; *Livestock/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Environmental Microbiology ; *Microbiota ; Cattle ; Soil Microbiology ; Phylogeny ; Metagenome ; Swine ; Sheep ; Biodiversity ; Water Microbiology ; Rural Population ; },
abstract = {In South African rural areas, farmers often practice mixed extensive livestock farming, facilitating microbial exchange among and between animal species and their environment. The composition and transmission potential of microbiomes between animals and their environments in these smallholder livestock systems remain largely unexplored, creating a gap in understanding how mixed-livestock farming affects gut and environmental microbiomes. Shotgun metagenomics was used to uncover the fecal and environmental microbiota in smallholder mixed livestock systems, aiming to understand microbiome transfer within these systems. A total of 111 samples were collected in KwaZulu-Natal and Eastern Cape provinces of South Africa, including 76 fecal samples from cattle, goats, sheep, pigs, and chickens; 18 soil samples; and 17 water samples. Taxonomic analysis of the sequencing data identified Proteobacteria as the dominant phylum across most hosts, except that pigs were dominated by Firmicutes. Moraxellaceae and Pseudomonadaceae were the differentiating families between monogastrics and ruminants. Although microbial diversity differences were significantly attributed to the host, genera such as Acinetobacter, Chryseobacterium, Flavobacterium, Pedobacter, and Pseudomonas were consistently found across all animal and environmental hosts. Cattle shared more genera with the environment than other animal species. Opportunistic pathogens, including Enterococcus spp., Escherichia coli, and Clostridium spp., were found across all the livestock species, and were highest in chickens. Additionally, some pathogens were detected in water but none in soil, suggesting water as a potential medium for pathogen transmission. The microbial exchange between livestock and their surroundings highlights the permeability of host-environment boundaries in smallholder systems.},
}

Animals
South Africa
*Feces/microbiology
*Metagenomics
*Livestock/microbiology
*Bacteria/classification/genetics/isolation & purification
*Environmental Microbiology
*Microbiota
Cattle
Soil Microbiology
Phylogeny
Metagenome
Swine
Sheep
Biodiversity
Water Microbiology
Rural Population

@article {pmid42494872,
year = {2026},
author = {Quirino-Vela, LM and Mayoral-Chávez, MA and Matías-Cervantes, CA and Pérez-Cervera, Y and García-Montalvo, IA and Alpuche, J},
title = {The unified cardiometabolic disease continuum: mechanistic stages of a single pathophysiological process.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1897556},
pmid = {42494872},
issn = {1664-2392},
mesh = {Humans ; *Cardiovascular Diseases/physiopathology/metabolism ; *Diabetes Mellitus, Type 2/metabolism/physiopathology ; Animals ; Biomarkers/metabolism ; *Metabolic Diseases/physiopathology ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM), atherosclerotic cardiovascular disease (ASCVD), heart failure with preserved ejection fraction (HFpEF), metabolic dysfunction-associated steatotic liver disease (MASLD), hypertension, and chronic kidney disease (CKD) share risk factors and may represent endpoints of a pathophysiological cardiometabolic continuum. We analyzed data suggesting these phenotypes arise along a unified cardiometabolic disease (UCD) continuum with distinct stages, biomarkers, and therapeutic targets.

METHODS: A structured narrative review was conducted using PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar. Searches combined terms for mechanistic drivers (visceral adipose tissue, ceramides, lipotoxicity, NF-κB/NLRP3 signaling, gut microbiota, TMAO, adipokines, endothelial dysfunction, epicardial fat, metabolic flexibility) and clinical endpoints. Priority was given to peer-reviewed translational studies, major outcome trials, and consensus statements published between 2017-2026.

RESULTS: Current evidence supports a mechanistic framework in which visceral adipose tissue dysfunction and ectopic lipid accumulation, progressing through ceramide-mediated lipotoxicity, NF-κB/NLRP3-driven inflammation, gut microbiome-derived endotoxemia and TMAO, adipokine dysregulation, endothelial dysfunction, epicardial fat-mediated cardiac remodeling, impaired metabolic flexibility, and a cardiorenal amplification loop. Stage-specific mediators (e.g., ceramides, NLRP3, TMAO, leptin-adiponectin ratio) serve as biomarkers. The benefits of GLP-1 receptor agonists, SGLT2 inhibitors, and finerenone across T2DM, ASCVD, HFpEF, MASLD, and CKD reflect pharmacologic modulation of this continuum.

DISCUSSION: Data support a UCD model where T2DM, ASCVD, MASLD, HFpEF, hypertension, and CKD are manifestations of a progressive pathophysiological continuum. Framing these conditions as stages of a continuum informs risk stratification, biomarker development, and mechanism-guided therapy, providing a framework for designing trials targeting the continuum rather than individual endpoints.},
}

Humans
*Cardiovascular Diseases/physiopathology/metabolism
*Diabetes Mellitus, Type 2/metabolism/physiopathology
Animals
Biomarkers/metabolism
*Metabolic Diseases/physiopathology
Gastrointestinal Microbiome

@article {pmid42495133,
year = {2026},
author = {Joo, MK and Tak, J and Ha, S and Yoon, KS and Namgoong, JM and Kim, HO},
title = {The gut resistome as a potential determinant of immunotherapy response: antibiotics, immunometabolism, and precision oncology.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1835588},
pmid = {42495133},
issn = {1664-302X},
abstract = {Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, yet their efficacy can be compromised by systemic antibiotic exposure and the resulting disruption of the gut microbiome. Across several tumor types, antibiotic use near the initiation of ICI therapy has frequently been associated with reduced progression-free and overall survival. Emerging data suggest that, beyond taxonomic shifts, antibiotic exposure is often accompanied by expansion of the gut resistome, the collective pool of antibiotic resistance genes. Antibiotic-associated dysbiosis and resistome enrichment are linked to alterations in short-chain fatty acid production, bile acid signaling, and microbial purine metabolism, pathways known to shape antigen presentation, T-cell differentiation, and immune tone. Accordingly, gut resistome profiling should be considered an emerging candidate biomarker. Potential strategies to restore a favorable gut ecosystem include dietary modulation, microbiome-based therapies such as probiotics or fecal microbiota transplantation, and emerging anti-resistance approaches designed to limit resistome expansion. Together, these findings support a resistome-centered framework for patient stratification and microbiome-targeted interventions in precision immune-oncology.},
}

@article {pmid42495134,
year = {2026},
author = {Qu, J and Wu, Y and Qi, H and Chen, L and Luo, Y and Wang, Y and Zhang, Q},
title = {From assembly inference to co-occurrence organization: conservation contexts are associated with gut bacterial variation in the endangered Gymnocypris przewalskii.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1875592},
pmid = {42495134},
issn = {1664-302X},
abstract = {INTRODUCTION: Conservation programs increasingly rely on in-situ and ex-situ interventions to prevent the loss of endangered species; however, it remains unclear whether such interventions preserve host-associated microbial organization. Understanding how conservation contexts influence gut microbiome structure and function is therefore essential for evaluating their ecological effectiveness.

METHODS: We analyzed gut bacterial communities of the endangered high-altitude fish Gymnocypris przewalskii across wild, in-situ conservation, and ex-situ conservation contexts using 16S rRNA gene sequencing. Analyses included host morphometric covariate assessment, alpha- and beta-diversity statistics, co-occurrence network analysis, PICRUSt2-based functional prediction, and null-model-based community assembly inference.

RESULTS: Gut bacterial communities were consistently dominated by Proteobacteria, with Firmicutes, Bacteroidetes, Actinobacteria, and Chloroflexi as secondary taxa. Alpha diversity showed no significant differences among groups, whereas beta diversity revealed modest but significant compositional shifts associated with conservation context, independent of multivariate dispersion and host morphometric traits. Functional predictions indicated shifts in pathways related to carbohydrate, energy, lipid, amino acid, terpenoid, polyketide metabolism, secondary metabolite biosynthesis, and xenobiotic degradation. Co-occurrence networks exhibited context-dependent restructuring: wild communities showed highest connectivity and positive interactions, in-situ networks were most modular and sparsest, and ex-situ communities showed the highest proportion of negative interactions. Null-model analyses indicated dominance of stochastic processes across all groups, with highest drift and stochasticity in in-situ populations, while ex-situ communities showed stronger deterministic influence and homogeneous selection.

DISCUSSION: These results demonstrate that conservation contexts are associated not only with taxonomic turnover but also with functional potential shifts, altered co-occurrence topology, and changes in community assembly processes. Within the constraints of an observational and site-confounded design, our findings suggest that microbiome-informed conservation assessment should move beyond diversity metrics and incorporate compositional, functional, network, and assembly-based perspectives when evaluating conservation outcomes in endangered aquatic hosts.},
}

@article {pmid42495136,
year = {2026},
author = {Gewirtz, MA and Zhang, Y and Vaidy, N and Redekar, NR and Minerva, N and Haddad, JA and Oringher, JL and Afruza, R and Chakraborty, M and Menkart, MG and Gopalakrishna, H and Hercun, J and Lack, J and Kleiner, DE and Lionakis, MS and Koh, C and Heller, T},
title = {Chronic hepatitis D infection is associated with distinguishing microbial and functional features in the gut microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1851892},
pmid = {42495136},
issn = {1664-302X},
abstract = {BACKGROUND: The microbiome of patients with hepatitis D virus (HDV) has yet to be characterized. This study aims to (1) characterize gut microbial composition in HDV, (2) determine its functional profile, (3) identify microbial species that contribute to changes in pathway expression, and (4) correlate the changes in the gut microbiome with clinical markers of disease severity.

METHODS: Cross-sectional analyses of 35 HDV-infected patients and 32 healthy controls (HCs) were performed. DNA and RNA were isolated from stool and sequenced by shotgun-sequencing. Microbial and functional profiles were compared between the HDV-cohort and HCs to identify disease-specific alterations to the gut microbiome. Clinical metadata were used to identify correlations with disease severity.

RESULTS: There were significant changes in the composition of the gut microbiome in HDV-infected patients as compared with HCs, spanning multiple bacterial phyla. Expression of 194 pathways was significantly increased in the HDV group. Pathways that were upregulated in the HDV cohort were related to amino acid and carbohydrate biosynthesis or involved important metabolic cofactors and carriers. Several microbial species, including Bacteroides fragilis, Cateibacterium mitsuokai, and Faecalibacterium prausnitzii, were identified as contributing to the differentially expressed pathways. Four genera correlated with hepatic venous pressure gradient (HVPG).

CONCLUSION: There are significant differences in microbial composition between HDV and HCs, several of which are found to be altered in other liver diseases. Upregulated pathways suggest a broader dysregulation of energy metabolism, even in early disease. These findings provide insight into pathways that may lead to liver disease progression in HDV.},
}

@article {pmid42495138,
year = {2026},
author = {Pang, Y and Chen, Y and Huang, Q and You, F and Fang, R and Geng, M and Ke, X and Tang, J and Ling, J and Cheng, Y and Zhao, C and Deng, X and Guo, J and Miao, C},
title = {Temperature regulation mechanisms of diapause in Coridius chinensis revealed by multi-omics integration: coordinated responses of Brain-Gut-Fat Body.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1810191},
pmid = {42495138},
issn = {1664-302X},
abstract = {Diapause in Coridius chinensis is a complex survival strategy that enables them to survive under prolonged cold stress. To elucidate the mechanisms of temperature regulation during diapause, we conducted multi-omics analyses, including gut metagenomics, brain transcriptomics, and fat body metabolomics, under both normal (25 °C) and diapause conditions (4 °C). Gut microbiome analysis revealed an extreme polarization during diapause, dominated by the endosymbionts Pantoea endophytica (52%) and Rickettsia bellii (47.4%), while functional microbiota such as Pantoea and Dietzia were significantly reduced. This shift suggests a trade-off where microbial metabolic diversity is sacrificed in favor of intracellular symbionts that may regulate host mitochondrial activity and suppress energy consumption. Brain transcriptomic analysis indicated a downregulation of neural signaling pathways related to feeding suppression, stress resistance, and circadian rhythm regulation. Fat body metabolomics identified the coordinated activation of 13 core pathways that link energy storage with stress adaptation, with dynamic changes ranging from rapid stress responses (0-300 AU) to energy storage dominance (300-500 AU), and finally to a state of homeostasis (>500 AU). Notably, dysregulated choline metabolism was significantly correlated with necrotic features (r = 0.78, p < 0.001), while catecholamine biosynthesis derived from tyrosine emerged as a corrective pathway, revealing the mechanistic link between metabolic flexibility and survival. Adults primarily utilize plants within the Cucurbitaceae, Fabaceae, and Solanaceae families as hosts, underpinned by long-standing folk traditions in specific localities regarding their dietary consumption or therapeutic application.},
}

@article {pmid42495144,
year = {2026},
author = {Yoon, SH and Lew, LC and Park, YH and Rather, IA},
title = {Identification and functional characterization of lactic acid bacteria with probiotic potential for alleviating premenstrual syndrome symptoms.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1866966},
pmid = {42495144},
issn = {1664-302X},
abstract = {INTRODUCTION: Premenstrual syndrome (PMS) is a relatively widespread disorder associated with cyclical hormonal oscillations and disruptions in microbial homeostasis, particularly involving β-glucuronidase -producing bacteria that facilitate estrogen reabsorption. This study aimed to isolate, identify and functionally characterize probiotic strains from the vaginal microbiota of healthy Korean women in order to evaluate their potential in mitigating PMS-associated pathophysiology.

MATERIALS AND METHODS: A total of 12 isolates, named as KVS strains, were evaluated for their probiotic potential, including antimicrobial, enzyme inhibitory, and anti-adhesive activities associated with PMS. These isolates were further evaluated for adhesion capacity, survival under acidic conditions, auto-aggregation ability, inhibition of β-glucuronidase activity, antimicrobial activity, and suppression of Gardnerella vaginalis adhesion to HeLa cells.

RESULTS AND DISCUSSION: Several KVS strains, such as KVS001, KVS002, KVS004, KVS006, and KVS008 showed strong probiotic potential, adhesion capacity, high auto-aggregation rates, and survival in acidic conditions. In addition, these strains showed high antimicrobial activity and significantly suppressed β-glucuronidase activity, suggesting a mechanism for reducing estrogen recirculation. Moreover, many isolates effectively inhibited G. vaginalis adhesion to HeLa cells, indicating strong potential to counteract dysbiosis-associated PMS triggers. Collectively, the findings identify multiple KVS strains as promising probiotic candidates with multifunctional mechanisms relevant to PMS alleviation, supporting their prospective development as health-functional foods or therapeutic agents targeting microbiome-mediated hormonal modulation.},
}

@article {pmid42495148,
year = {2026},
author = {Cagle, R and Proll, S and Minot, SS and Purcell, H and Zhu, W and Djukovic, D and Liu, C and Fiedler, T and DeMeules, M and Mielcarek, M and Srinivasan, S and Raftery, D and Wu, M and Pergam, SA and Fredricks, DN},
title = {Acute gastrointestinal graft-versus-host disease is associated with reductions of secondary bile acids following allogeneic hematopoietic cell transplantation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818647},
pmid = {42495148},
issn = {1664-302X},
abstract = {INTRODUCTION: Allogeneic hematopoietic cell transplantation (HCT) can cure hematologic malignancies, but 30-70% of recipients experience acute graft-versus-host disease (GvHD). GvHD is associated with perturbations in the gut microbiome. Bile acids are host derived compounds that are transformed by gut bacteria and bind to specific host cell receptors, informing our hypothesis that changes in bile acid-metabolizing gut bacteria alter bile acid levels to affect gut physiology and immunity during GvHD.

METHODS: In a longitudinal case-control study of patients with and without acute gut GvHD, we characterized bile acid concentrations and the gut microbiome in stool.

RESULTS: Primary and conjugated bile acid levels were similar regardless of gut GvHD status, but endogenous secondary bile acid concentrations were associated with gut GvHD (p = 0.009). We observed 4.4-fold lower levels of endogenous secondary bile acids in GvHD, particularly lithocholic acid and derivatives (p = 0.004/padjusted = 0.02, fold change (FC) = 0.23). There was a 100-fold lower median abundance (p = 0.002 and FC < 0.01) and 20-fold lower median diversity of bacterial bile acid 7α-dehydroxylation (bai) genes (p = 0.0007 and FC < 0.05) in patients with GvHD.

DISCUSSION: This provides evidence that acute gut GvHD patients are deficient in microbial bai genes that make secondary bile acids.},
}

@article {pmid42495540,
year = {2026},
author = {Chen, Y and Lai, Y and Liu, Z and Zhang, K and Zheng, J and Lu, S and Huang, Z},
title = {The adaptation of the gut microbiome to social environmental changes in an Asian langur.},
journal = {iScience},
volume = {29},
number = {8},
pages = {116779},
pmid = {42495540},
issn = {2589-0042},
abstract = {Social environments profoundly impact social animals' gut microbiome. Understanding such effects is critical for evaluating population fitness and conservation. Employing 16S rRNA and metagenomic sequencing, we investigated the gut microbiome of the endangered white-headed langur (Trachypithecus leucocephalus) to clarify its potential adaptive strategies to social environmental changes. Distinct differences were observed among social groups: the all-male group was enriched in Bacillota and showed stronger cellulose degradation potential, which might be associated with greater cellulose intake and higher cortisol and T3 levels; mixed-sex group was enriched in Actinomycetota, Pseudomonadota, and non-carbohydrate metabolism genes, possibly due to more young leaves consumption and reproductive needs. Alpha male replacement also shaped gut microbiome: the third alpha male period had highest Bacteroidota and lowest metabolic genes abundance, potentially related to improved food quality during this period. These preliminary findings highlight gut microbial adaptation to social environments in the studied population, providing implications for the conservation of this endangered species.},
}

@article {pmid42495752,
year = {2026},
author = {Anjum, N and Ahmed, Z and Anjum, F and Liaqat, S},
title = {Efficacy of prebiotics, probiotics, and postbiotics on depression: a systematic review and meta-analysis of randomized controlled trials.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/1028415X.2026.2703621},
pmid = {42495752},
issn = {1476-8305},
abstract = {BACKGROUND: Depression is a global health issue linked to gut-microbiota-dysbiosis, which influences brain function through the gut-brain axis. Dietary biotics offer a promising therapeutic avenue.

OBJECTIVE: This systematic review and meta-analysis aimed to evaluate the efficacy of biotic interventions in managing depression.

METHODOLOGY: Five databases were searched for randomized controlled trials (RCTs) from 2016 to 2024. 27 RCTs with a control group and standard depression rating scales were included. Data extraction and risk-of-bias assessment were conducted independently by two reviewers, with certainty-of-evidence appraised using GRADE. Meta-analyses employed standardized mean differences, with subgroup analyses by intervention duration (short: <6 weeks, medium: 6-12 weeks, and long: >12 weeks), respectively.

RESULTS: Probiotic interventions showed no significant effects in short and medium-duration subgroups (6 and 12 studies, respectively), both of which demonstrated substantial heterogeneity. A significant effect was observed in the long-duration subgroup (2 studies) with no observed heterogeneity, although based on limited evidence. Prebiotic interventions showed no significant effects, while postbiotic interventions demonstrated no clear effects across durations, with variable heterogeneity. Sensitivity analyses were generally consistent with the main findings. Overall certainty of evidence was rated as moderate due to inconsistency across studies.

CONCLUSION: Probiotics administered over longer durations may be associated with improvements in depressive symptoms, although this finding is based on limited evidence. Evidence for prebiotic and postbiotic interventions remains inconclusive. Overall, substantial heterogeneity was observed across studies, and findings should be interpreted cautiously. Further well-designed randomized controlled trials are needed to clarify the effects of microbiome-targeted interventions in depression.},
}

@article {pmid42495760,
year = {2026},
author = {Hou, J and Li, Y and Lin, S and Liu, Q and Zheng, H and Liu, W and Wang, Y and Peng, L and Wang, Z},
title = {Gut‑liver‑kidney axis: A systems biology framework for understanding and treating chronic kidney disease (Review).},
journal = {International journal of molecular medicine},
volume = {58},
number = {4},
pages = {},
doi = {10.3892/ijmm.2026.5937},
pmid = {42495760},
issn = {1791-244X},
mesh = {Humans ; *Systems Biology/methods ; *Renal Insufficiency, Chronic/therapy/metabolism/pathology ; *Liver/metabolism/pathology ; *Kidney/metabolism/pathology ; Animals ; *Gastrointestinal Microbiome ; Signal Transduction ; },
abstract = {Chronic kidney disease (CKD) is traditionally studied through an organ‑centric paradigm, despite its frequent coexistence with intestinal dysbiosis and metabolic dysfunction‑associated steatotic liver disease, which confers a 38% increased CKD risk. Multi‑organ crosstalk along the gut‑liver‑kidney axis remains inadequately addressed in current guidelines. The present study aimed to establish the gut‑liver‑kidney axis as an integrated systems biology framework for understanding CKD progression and to translate this framework into diagnostic, therapeutic and clinical trial strategies. The present review aimed to combine mechanistic summaries with systems biology perspectives, including weighted gene co‑expression network analysis, Bayesian causal inference and ordinary differential equation‑based dynamic modeling, to map bidirectional signaling across microbial, metabolic, inflammatory and hemodynamic dimensions, with diabetic kidney disease (DKD) as the principal exemplar. The axis operates through anatomically and molecularly defined positive feedback loops in which gut dysbiosis drives barrier failure and endotoxemia, amplifying hepatic lipotoxicity and bile acid dysregulation, precipitating renal tubular injury and fibrosis. This self‑perpetuating cycle, sustained by uremic toxin signaling, dysregulated peroxisome proliferator‑activated receptor/farnesoid X receptor (FXR)/Takeda G protein‑coupled receptor 5 (TGR5) pathways and trained immunity (a persistent hyperinflammatory state of innate immune cells driven by epigenetic and metabolic reprogramming), is most pronounced in DKD. Microbiome‑targeted interventions and FXR/TGR5 modulators are as the most clinically advanced axis‑directed strategies, though most remain at preclinical or early‑phase stages. Reframing CKD as gut‑liver‑kidney axis dysfunction enables systems‑level mechanistic integration, precision diagnostics through composite microbiome‑metabolomic signatures, and adaptive trial designs targeting upstream pathology, providing a foundation for incorporating axis‑based approaches into future CKD management.},
}

Humans
*Systems Biology/methods
*Renal Insufficiency, Chronic/therapy/metabolism/pathology
*Liver/metabolism/pathology
*Kidney/metabolism/pathology
Animals
*Gastrointestinal Microbiome
Signal Transduction

@article {pmid42496089,
year = {2026},
author = {Schweichhart, J and de Paula, CCP and Kreidlová, V and Vrba, J and Šorf, M and Sirová, D},
title = {Fungi Associated With Freshwater Zooplankton Are Taxon-Specific, Temporally Dynamic and Reflect Allochthonous Inputs.},
journal = {Molecular ecology},
volume = {35},
number = {14},
pages = {e70436},
doi = {10.1111/mec.70436},
pmid = {42496089},
issn = {1365-294X},
support = {23-06429S//Grantová Agentura České Republiky/ ; },
mesh = {Animals ; *Zooplankton/microbiology ; *Fresh Water/microbiology ; *Fungi/classification/genetics ; Sequence Analysis, DNA ; Rotifera/microbiology ; Ecosystem ; DNA, Fungal/genetics ; Copepoda/microbiology ; Phylogeny ; },
abstract = {The associations between microbes and planktonic invertebrates in freshwater ecosystems are considered key ecological interactions. However, our understanding of the structure, taxonomic specificity, and environmental drivers of zooplankton microbiomes remains poor. Here, we present the results of a field study using ITS1-amplicon sequencing that assesses the structure of fungal assemblages associated with three zooplankton groups (Cladocera, Copepoda and Rotifera) inhabiting the same water column during a single growing season. Compared with fungal communities in the surrounding water, zooplankton-associated assemblages showed higher genus richness, particularly in Copepoda and Rotifera, but lower diversity and evenness. We identified 190 fungal genera spanning eight phyla, dominated by fast-growing yeasts that thrive in nutrient-rich environments and are commonly associated with soil, leaf litter and decaying wood. The taxonomic identity of the zooplankton emerged as the main factor shaping fungal assemblages, followed by spore size and precipitation. Fungal sequences in zooplankton samples were largely derived from taxa typically linked to soils and plants, and the community composition shifted after precipitation events, consistent with terrestrial inputs to the lake. No fungal taxa were found exclusively in zooplankton guts, suggesting that these associations are transient and trophic rather than colonising. Taken together, these patterns indicate that zooplankton feed on suspended fungal cells or spores, many of which originate from surrounding terrestrial habitats. This suggests an overlooked pathway connecting land and freshwater ecosystems, highlighting terrestrial fungi as an under-recognised component of freshwater trophic linkages.},
}

Animals
*Zooplankton/microbiology
*Fresh Water/microbiology
*Fungi/classification/genetics
Sequence Analysis, DNA
Rotifera/microbiology
Ecosystem
DNA, Fungal/genetics
Copepoda/microbiology
Phylogeny

@article {pmid42496113,
year = {2026},
author = {Piperni, E and Blanco-Míguez, A and Mengoni, C and Piccinno, G and Punčochář, M and Ren, J and Segata, N and Asnicar, F and Poole, AC},
title = {Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0076326},
doi = {10.1128/spectrum.00763-26},
pmid = {42496113},
issn = {2165-0497},
abstract = {Resistant starch (RS) can confer benefits for the gut microbiome and host cardiometabolic health. However, different types of resistant starch can differentially affect gut microbiome composition and functional capacity, especially given interindividual variability in responses, thus limiting the application of resistant starch in dietary strategies. We used shotgun metagenomics to perform a secondary analysis of samples collected during a previously reported randomized clinical trial to determine the effects of dietary supplementation with two types of resistant starch (RS2 and RS4) and a digestible starch (control) on the gut microbiome. Both resistant starch types induced distinct but transient alterations in the gut microbial community. RS2 enriched the keystone degrader, Ruminococcus bromii, and Blautia glucerasea, whereas RS4 favored Parabacteroides distasonis and known but uncharacterized microbial species such as a Lachnospiraceae bacterium. Moreover, we detected strain-level differences in the response of Bifidobacterium adolescentis to resistant starch. Microbial functional profiling revealed an enhanced capacity for complex carbohydrate utilization following resistant starch intake, including increased abundance of specific α-amylases, glycoside hydrolases, starch utilization systems, and other currently uncharacterized genes. Identifying the bacterial strains and genes that respond to different RS types will help to more accurately predict who will benefit from a given RS type. Our findings demonstrate that RS2 and RS4 differentially shape microbial ecology and metabolic capacity and provide a foundation for microbiome-informed personalization of resistant starch-based dietary interventions.IMPORTANCEDietary intake influences human health by modulating metabolism, partly by shaping the microbiota inhabiting the gut. Resistant starch (RS), a dietary fiber, is associated with metabolic improvements. While previous research has explored how RS alters the gut microbiome, RS comprises five types with differing physical and chemical characteristics, and the distinct impacts of each type on the microbiome and host health have not been fully characterized, particularly using high-resolution approaches such as shotgun metagenomics. In this secondary analysis of samples from a longitudinal crossover intervention study, we link dietary supplementation with RS2 and RS4 with distinct and transient changes in the composition and functional potential of the human gut microbiome. Specifically, we identify species that increase in abundance with each RS type, accompanied by increases in genes and pathways involved in complex carbohydrate utilization. The findings support the development of precision nutrition strategies utilizing RS supplementation to improve metabolic health.This study is registered with ClinicalTrials.gov as NCT05743790.},
}

@article {pmid42496154,
year = {2026},
author = {Zhang, J and Cai, L and Wang, L and Zhang, L and Meng, N and Chen, A and Ma, Q},
title = {Marine antifouling biocide 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one disrupts sediment microbiome structure and function: insights from absolute quantification and enzyme activity dynamics.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0081926},
doi = {10.1128/aem.00819-26},
pmid = {42496154},
issn = {1098-5336},
abstract = {The organic booster biocide DCOIT (4,5-dichloro-2-n-octyl-4-isothiazolin-3-one) is widely used in marine antifouling systems, yet its ecological impacts on sediment microbiomes remain poorly understood. Here, we integrated absolute quantitative 16S rRNA gene sequencing, metagenomics, and enzyme activity assays to examine microbial responses to DCOIT exposure (0-50 μg/g sediment) over 30 days. DCOIT induced oxidative stress and bioenergetic impairment, accompanied by reduced microbial activity and inhibition of key enzyme-mediated processes involved in organic matter turnover and nitrogen transformation. Absolute quantification revealed a compensatory increase in total microbial abundance by Day 30, despite persistent diversity loss and community restructuring. Metagenomic analysis showed that DCOIT disturbed functional potentials related to carbon and nitrogen cycling. Kordiimonas, Aliikangiella, and Neptuniibacter emerged as potential contributors to nitrogen transformation, whereas Marinobacter was more closely associated with potential DCOIT transformation. DCOIT exposure also enriched adaptive traits, including chemotaxis, motility, quorum sensing, and biofilm regulation, and was accompanied by increased multidrug efflux systems and heavy metal resistance determinants. Our findings provide novel insights into the ecotoxicological risks of isothiazolinone biocides and highlight the potential for DCOIT to undermine sediment ecosystem functions and microbial habitat health. Given its extensive application, this study emphasizes the need to consider the microbial ecological consequences of DCOIT accumulation in seafloor environments.IMPORTANCEDCOIT is widely used in marine antifouling coatings and can accumulate in benthic sediments, yet its effects on sediment microbiomes remain poorly defined. This study shows that DCOIT disrupts microbial energy status, enzyme activities, community structure, and nitrogen-cycling functions while selecting for adaptive traits and resistance-related determinants. By integrating absolute quantification, metagenomics, and enzyme assays, our work demonstrates that DCOIT poses microbial ecological risks beyond toxicity to macroorganisms and should be considered in assessments of antifouling biocides.},
}

@article {pmid42496155,
year = {2026},
author = {Maldarelli, GA and Marino, J and Lee, JR and Westblade, LF and Hovan, M and Douglass, C and Davidson, E and Longman, RS and Satlin, MJ},
title = {Enteric Microbiome Features that Contribute to Gram-Negative Bloodstream Infections in Hematopoietic Cell Transplant Recipients Colonized with Fluoroquinolone-Resistant Enterobacterales.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag376},
pmid = {42496155},
issn = {1537-6613},
abstract = {BACKGROUND: Hematopoietic cell transplant (HCT) recipients colonized with fluoroquinolone-resistant Enterobacterales (FQRE) frequently develop bloodstream infection (BSI) from their colonizing FQRE strains while receiving fluoroquinolone prophylaxis during neutropenia. However, enteric microbiome features that contribute to this increased BSI risk are unknown.

METHODS: 16S ribosomal RNA gene sequencing and quantitative cultures were performed on stool samples collected before and after the initiation of levofloxacin prophylaxis during a single-center prospective study of patients undergoing HCT. Enteric microbiome features were compared between FQRE-colonized and non-colonized patients and between FQRE-colonized patients who did and did not develop FQRE BSI.

RESULTS: We evaluated samples from 26 participants colonized with FQRE pre-HCT (nine developed FQRE BSI) and 69 not colonized with FQRE (none developed FQRE BSI). FQRE-colonized participants had a higher median baseline relative abundance of Enterobacterales (4.7% vs.0.3%) and Bacteroidales (14.3% vs. 0.5%) than non-colonized participants. After starting levofloxacin prophylaxis, the relative abundance of Enterobacterales declined in all but one HCT recipient without FQRE colonization, but increased in approximately one-third of participants with FQRE, including those who subsequently developed FQRE BSI. Among FQRE-colonized HCT recipients, there were no significant differences in FQRE colonization density or microbial diversity or composition between those who did and did not develop FQRE BSI.

CONCLUSIONS: FQRE-colonized HCT recipients have a distinct microbiome composition compared to HCT recipients without FQRE colonization and frequently have an expansion of Enterobacterales during levofloxacin prophylaxis that precedes FQRE BSI. Additional studies of FQRE-colonized HCT recipients are needed to clarify microbiome risk factors for FQRE BSI.},
}

@article {pmid42496300,
year = {2026},
author = {Ntais, C and Chatziprodromidou, IP},
title = {Antimicrobial Resistance as a Global Public Health Challenge: Epidemiological Burden, Bioethical Dimensions and Emerging Therapeutic Strategies.},
journal = {Infectious disease reports},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/idr18040070},
pmid = {42496300},
issn = {2036-7430},
abstract = {BACKGROUND/OBJECTIVES: Antimicrobial resistance (AMR) is a major global public health threat, compromising prevention and treatment of infectious diseases. This narrative review examines AMR as a multifactorial and transnational crisis through epidemiological, One Health, social and bioethical perspectives, and discusses emerging non-antibiotic preventive and therapeutic strategies.

METHODS: PubMed and Scopus were searched using terms related to AMR, epidemiology, public health, surveillance, One Health, bioethics, equity and alternative therapies. Peer-reviewed medical and public health articles were considered, together with selected reports from international organizations and public health agencies.

RESULTS: AMR is driven by inappropriate antibiotic use in human medicine, livestock, aquaculture and agriculture, combined with weaknesses in infection prevention, stewardship, environmental control and surveillance. Epidemiological evidence shows a substantial global burden, marked regional inequalities in resistance patterns, surveillance capacity and policy response, and major consequences, including increased mortality, prolonged hospitalization, rising healthcare costs and disproportionate effects on vulnerable populations. Key bioethical concerns include collective responsibility, equitable access to effective treatment, stewardship, global justice and intergenerational accountability. Emerging non-antibiotic strategies vary in translational maturity: vaccines and selected microbiome-based interventions have preventive or supportive roles in defined settings, bacteriophage therapy is used mainly in compassionate or specialized contexts, and many antimicrobial peptides and nanotechnology-based platforms remain experimental or early translational.

CONCLUSIONS: AMR requires coordinated global action grounded in One Health, strong public health systems, integrated surveillance, responsible antimicrobial use and sustained innovation. Effective containment must also address social inequalities, ethical stewardship, equitable access to diagnostics and treatment, and responsibility toward future generations.},
}

@article {pmid42496597,
year = {2026},
author = {Montanari, S and Hartmann, M and Nesler, A and Giovannini, O and Longa, CMO and Perazzolli, M},
title = {Choline pelargonate treatments decreased downy mildew and powdery mildew symptoms with negligible effects on grapevine phyllosphere microorganisms.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag082},
pmid = {42496597},
issn = {1574-6941},
abstract = {Grapevine is an important crop worldwide, but most cultivars are susceptible to downy mildew and powdery mildew. This study aimed to evaluate the efficacy of choline pelargonate (CP) against grapevine downy mildew and powdery mildew under controlled and field conditions, and to assess its effects on phyllosphere microorganisms. CP decreased the severity of both pathogens under greenhouse and field conditions. In greenhouse trials, 16 mM CP showed efficacy comparable to copper and sulfur applied at label-recommended concentrations as reference fungicides in organic viticulture. CP showed direct inhibitory activity against both pathogens, and slightly induced defense-related grapevine genes (CHIT-3, OSM-2, and PR-1). Field experiments corroborated the efficacy of CP against powdery mildew and downy mildew severity on leaves and bunches. Microbial community analysis revealed that plant compartment, vineyard location, and sampling time were key drivers of microbial community structure, while treatments showed negligible effects on microbial alpha-diversity and beta-diversity of grapevine leaves and bunches. CP treatment partially modified the relative abundances of some bacterial and fungal taxa, while reference fungicides caused broad changes across multiple genera. CP showed promising antifungal activity with minimal effects on phyllosphere microorganisms, supporting its potential as a sustainable disease management approach that preserves indigenous microbial communities.},
}

@article {pmid42496608,
year = {2026},
author = {Küper, K and Kittler, S and Peh, E and Hirnet, J and Hetterich, J and Kopp, JS and Plötz, M and Rohn, K and Müsken, M and Fruth, A and Pees, M},
title = {Salmonella-specific phages from captive bearded dragons (Pogona vitticeps): Temperate traits and temperature-dependent variability in inhibition across isolates.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag188},
pmid = {42496608},
issn = {1365-2672},
abstract = {AIMS: Zoonotic infections with Salmonella spp. transmitted from reptiles to humans are an increasing concern due to the growing number of documented cases and the close contact between humans and reptiles. Reptiles, such as bearded dragons (Pogona vitticeps), frequently carry Salmonella enterica asymptomatically as part of their intestinal microbiota.Given the rise of antibiotic-resistant Salmonella strains in reptiles, bacteriophages (phages) may provide a targeted and sustainable alternative for preventing reptile-to-human transmission.

METHODS AND RESULTS: Seventeen phages were isolated from ten of eighteen faecal samples collected from bearded dragons. Seven of these phages were selected for further analyses. Host range assays on 41 S. enterica and nine non-Salmonella isolates revealed a narrow spectrum: phages infected up to 63.4% of Salmonella isolates and lysed one non-Salmonella strain. Planktonic killing assays at 25 °C and 37 °C showed pronounced bacterial growth reduction, with 8 of 12 significant inhibitions observed at 37 °C. Phage cocktails generally showed stronger inhibition than individual phages. Electron microscopy and whole-genome sequencing identified six Myovirus-like and one Siphovirus-like phage, all temperate with integrase or transposase genes despite lytic activity.

CONCLUSIONS: This study expands knowledge of S. enterica-specific phages from reptiles, detailing host specificity, morphology and genomic features. While in vitro results are promising, in vivo efficacy may be influenced by host physiology, immunity and microbiome interactions. The predominance of temperate phages may limit direct therapeutic use, though low lysogeny rates in related phages and genetic engineering advances may enable future applications.},
}

@article {pmid42496748,
year = {2026},
author = {Manda, T and Hwarari, D and Dzinyela, R},
title = {Phosphorylation networks as regulatory hubs in plant stress signaling: kinase dynamics, crosstalk, and network plasticity.},
journal = {Plant cell reports},
volume = {45},
number = {8},
pages = {},
pmid = {42496748},
issn = {1432-203X},
mesh = {Phosphorylation ; *Signal Transduction ; *Stress, Physiological/physiology ; *Protein Kinases/metabolism ; Protein Processing, Post-Translational ; *Plants/metabolism ; Plant Proteins/metabolism/genetics ; },
abstract = {Agriculture faces significant limitations from climate change, soil degradation, and a wide range of abiotic and biotic stresses that continually threaten global food security. Although transcriptional and hormonal regulatory networks have been extensively studied, post-translational modifications (PTMs), particularly phosphorylation, remain comparatively underexplored despite their central role in rapid stress signaling. In this review, we synthesize recent advances in phosphoproteomics, kinase network mapping, and systems biology to highlight phosphorylation as a key regulatory hub in plant stress responses. Drawing from both model species and crops, we emphasize major kinase families, including MAPKs, CDPKs, RLKs, and SnRK1/TOR, which translate calcium signatures, reactive oxygen species (ROS) waves, and cellular energy status into precise physiological outputs. We also discuss how multi-omics integration, precision breeding, synthetic biology, and microbiome engineering can leverage phosphorylation dynamics to advance climate-smart agriculture. By outlining phosphorylation networks as functional regulators, this work underscores their translational potential for developing resilient crops that can maintain yield under environmental extremes.},
}

Phosphorylation
*Signal Transduction
*Stress, Physiological/physiology
*Protein Kinases/metabolism
Protein Processing, Post-Translational
*Plants/metabolism
Plant Proteins/metabolism/genetics

@article {pmid42496816,
year = {2026},
author = {Kumari, A and Koli, VK and Singh, NA},
title = {Diversity and antibiotic profile of Enterobacterales spp. bacteria from Red-naped ibis.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {42496816},
issn = {1612-9210},
support = {918/(CSIR-UGC NET JUNE 2018//University Grants Commission/ ; },
abstract = {Antibiotic resistance in wildlife is an emerging concern, as birds can serve as reservoirs and vectors for resistant bacteria. In this study, we investigated the diversity of bacteria belonging to the Enterobacterales order and their antibiotic resistance patterns in the unexplored Red-naped ibis (Pseudibis papillosa). It is a resident wading bird species in western India, i.e., Udaipur city, Rajasthan. It inhabits a wide range of environments, including urban areas, wetlands, agricultural fields, and fallow lands. Fecal samples (n = 45) were collected and a total of 60 bacterial isolates were analyzed for bacterial diversity and bacteria were characterized using biochemical, molecular, methods. Interestingly, four novel bacterial taxa from this host species were identified, i.e., Enterobacter mori, Enterobacter soli, Citrobacter freundii, and Leclercia adecarboxylata. Notably, E. mori and E. soli were reported for the first time in this bird species globally. Antibiotic susceptibility testing revealed high levels of multidrug resistance, with 40% of isolates resistant to at least three classes of antibiotics. Notably, resistance to clinically important antimicrobials, including the third-generation cephalosporin cefotaxime and reduced susceptibility to the carbapenem imipenem, was observed, raising concerns for spread of antibiotic resistance bacteria. Resistance to linezolid (100%) and rifampicin (100%) was also observed across isolates, consistent with the intrinsic resistance of Gram-negative bacteria to these agents. Our findings reported the presence of antibiotic-resistant bacteria in wild bird species which may contribute to the spread of antibiotic resistance through their fecal deposits and pose a serious risk to the health of humans and wild animals.},
}

@article {pmid42496932,
year = {2026},
author = {Kumar, A and Dakal, TC and Parveen, K and Bhushan, R and Dhabhai, B and Parveen, A and Yadav, P and Tandon, R},
title = {Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.},
journal = {Biochemical genetics},
volume = {},
number = {},
pages = {},
pmid = {42496932},
issn = {1573-4927},
support = {BT/RLF/Re-entry/38/2017//Department of Biotechnology, India Department of Biotechnology (DBT), Government of India/ ; },
abstract = {Integrating high-throughput sequencing with phylogenetic analysis now spans everything from single genes to long-read pangenomes and metagenomes, yet practitioners still face fragmented, tool-centric guidance. This review revisits algorithms, tools, and workflows for sequence and phylogenetic analysis in the NGS-based omics era, with a focus on comparative performance and scenario-driven decision-making. We first organise classical approaches to tree reconstruction - distance methods, maximum parsimony, maximum likelihood, and Bayesian inference - around core criteria of consistency, efficiency, robustness, and computational cost. We then examine multiple sequence alignment strategies, contrasting progressive, consistency-based, and structure-aware algorithms (such as MAFFT variants and T-Coffee family tools) with segment-based and incremental approaches (for example DIALIGN, anchored domains, and local updates) and alignment-free representations based on k-mers, absent words, and related statistics. For inference, we compare heuristic engines optimised for ultra-large alignments (FastTree, VeryFastTree, online tree optimisation) with full ML frameworks (IQ-TREE, RAxML-NG) and Bayesian platforms for time-scaled phylogenies and phylodynamics (MrBayes, BEAST family). We explicitly discuss trade-offs in accuracy, memory, scalability, and uncertainty support, and show how GPU-enabled implementations change the feasible design space. Beyond these core components, we address current trends that strongly influence method choice: long-read assemblies and pangenomes; data quality issues, contamination, recombination, and horizontal gene transfer; phylogenetic placement and alignment-free screening in metagenomics; and real-time pathogen surveillance using Nextstrain-style workflows. A dedicated section covers workflow management and containerisation (Snakemake, Nextflow, Docker/Singularity) together with benchmarking datasets and FAIR reporting, positioning reproducible pipelines as a first-class requirement rather than an afterthought. To make the review directly actionable, we provide a methodological checklist, a decision framework figure mapping input data to recommended strategies, and a large comparative table summarising algorithmic principles, best use cases, strengths, limitations, scalability, uncertainty support, and reproducibility notes for widely used tools. Applications in infectious disease genomics, oncology, and microbiome research illustrate how these choices translate into biological and clinical insight in practice.},
}

@article {pmid42497015,
year = {2026},
author = {Ma, D and Uhlemann, AC and Abrams, JA and Freedberg, DE},
title = {Clinical and Culture-Based Predictors of Gut Microbiome Alpha Diversity at the Time of ICU Admission.},
journal = {Critical care explorations},
volume = {8},
number = {7},
pages = {e1455},
doi = {10.1097/CCE.0000000000001455},
pmid = {42497015},
issn = {2639-8028},
mesh = {Humans ; *Intensive Care Units/statistics & numerical data/organization & administration ; Female ; Retrospective Studies ; *Gastrointestinal Microbiome/physiology ; *Sepsis/microbiology/drug therapy ; Male ; Middle Aged ; Aged ; Anti-Bacterial Agents/therapeutic use ; Vancomycin-Resistant Enterococci/isolation & purification ; },
abstract = {OBJECTIVES: Microbiome-based therapies to improve gut colonization resistance are being developed for the ICU, but their efficacy may depend on the baseline gut microbiome at ICU admission. We sought to identify clinical predictors of alpha diversity at ICU admission.

DESIGN: Retrospective reanalysis of a randomized clinical trial (NCT03865706).

SETTING: Single-center ICU.

PATIENTS: ICU patients with sepsis as the primary diagnosis who were receiving broad-spectrum antibiotics and could be enrolled within 24 hours of ICU admission.

INTERVENTIONS: None.

MEASUREMENTS AND MAIN RESULTS: Demographic and clinical characteristics for medical ICU patients with sepsis were recorded during a previously published randomized clinical trial. Deep rectal swabs were collected within 24 hours of ICU admission and sequenced to describe alpha diversity (Shannon index) and cultured for vancomycin-resistant Enterococcus (VRE). Patients were organized into tertiles of Shannon diversity (low, middle, high) with a primary outcome of a lower Shannon tertile at ICU admission. Overall, 90 patients were enrolled. The three variables of location before ICU admission (adjusted odds ratio [aOR], 3.54; 95% CI, 1.21-10.3 for ICU transfer vs. emergency department [ED]; aOR, 6.09; 95% CI, 1.89-19.6 for hospital ward vs. ED), prior culture-proven infection within 1 year (aOR, 2.46; 95% CI, 1.02-5.96), and VRE status on ICU admission (aOR, 4.18; 95% CI, 1.44-12.1 for positive vs. negative swab) were sufficient to describe a quasi-linear trend in alpha diversity at ICU admission.

CONCLUSIONS: Baseline gut microbiome Shannon alpha diversity at ICU admission could be described with three readily ascertained clinical variables. Our model shows promise as a preliminary framework of factors that collectively best predict baseline alpha diversity at ICU admission and warrants validation in larger independent cohorts.},
}

Humans
*Intensive Care Units/statistics & numerical data/organization & administration
Female
Retrospective Studies
*Gastrointestinal Microbiome/physiology
*Sepsis/microbiology/drug therapy
Male
Middle Aged
Aged
Anti-Bacterial Agents/therapeutic use
Vancomycin-Resistant Enterococci/isolation & purification

@article {pmid42497072,
year = {2026},
author = {Wang, C and Bi, L and Wang, Y},
title = {Bidirectional Modulation of the Tumor Immune Microenvironment by Gut Microbiota-Derived Indoles: Mechanisms and Therapeutic Potential.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {14},
pages = {e72048},
doi = {10.1096/fj.202601162R},
pmid = {42497072},
issn = {1530-6860},
support = {82474230//The National Natural Science Foundation of China/ ; Qian Ke He XKBF (2025)027//Special Funds for High-level Creative Talents Cultivation in Guizhou Province/ ; 2021KJ03-12//Shanghai Frontier Research Base of Disease and Syndrome Biology of Inflammatory Cancer Trans-formation/ ; HQL2025OPA016//Open Foundation of Chinese Medicine Guangdong Laboratory/ ; },
mesh = {Humans ; *Indoles/metabolism ; *Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Neoplasms/immunology/therapy ; },
abstract = {The tumor immune microenvironment (TIME) plays a decisive role in cancer progression and therapeutic response. Emerging evidence highlights gut microbiota-derived indole metabolites, produced from dietary tryptophan, as key regulators of tumor immunity. These metabolites function through complex metabolic networks and exert dual immunomodulatory effects: they can enhance antitumor immunity by promoting CD8[+] T cell stemness, increasing tumor immunogenicity, and relieving immunosuppression, while also suppressing immunity by inducing regulatory T cells (Tregs), M2 macrophage polarization, and anti-inflammatory cytokine production. This review systematically summarizes the biosynthetic pathways and microbial sources of major indole compounds, and discusses their context-dependent roles in shaping the TIME via aryl hydrocarbon receptor (AhR)-dependent and -independent mechanisms. Unlike previous reviews that often extrapolate findings from non-tumor inflammation models to cancer without adequate contextualization, we critically evaluate evidence from both tumor and non-tumor models, with explicit distinction between direct tumor-relevant findings and speculative insights for the tumor immune microenvironment (TIME). Special attention is given to the therapeutic potential of indoles as adjuvants to immune checkpoint blockade and their promise in precision immuno-oncology. By integrating microbiology, immunology, and metabolomics, we aim to provide a theoretical foundation for developing indole-based strategies to overcome immunotherapy resistance and improve clinical outcomes.},
}

Humans
*Indoles/metabolism
*Tumor Microenvironment/immunology
*Gastrointestinal Microbiome/immunology
Animals
*Neoplasms/immunology/therapy

@article {pmid42497111,
year = {2026},
author = {Dubey, I and Yadav, M and Kushwaha, S},
title = {Irisin-treated microbiota restore blood-testis barrier integrity and spermatogenesis in chronically stressed rats.},
journal = {Tissue barriers},
volume = {},
number = {},
pages = {2700679},
doi = {10.1080/21688370.2026.2700679},
pmid = {42497111},
issn = {2168-8370},
abstract = {Chronic psychological stress impairs male fertility by disrupting spermatogenesis and the blood-testis barrier (BTB), which is essential for testicular function. Irisin, a myokine/adipokine involved in metabolic regulation, protects against testicular dysfunction and may beneficially modulate gut microbiota, highlighting its potential in the gut-testis axis. This study investigated the effect of fecal microbiota transplantation (FMT) from irisin-treated rats in restoring BTB integrity in a chronic unpredictable stress (CUS) rat model. Male Sprague-Dawley rats were randomized into four groups: Control, CUS, CUS + Control-FMT, and CUS + Irisin-FMT. CUS-exposed rats received FMT (5 mL, intra-rectally, on alternate days for 2 weeks) from donors treated with either irisin (100 ng/kg, subcutaneously, 4 weeks) or vehicle. The CUS + Irisin-FMT group showed marked improvements in sperm quality, and hormonal profiles, including testosterone, LH, FSH, and irisin. Irisin-FMT increased crypt length, goblet cells, and histological scores, and improved the testicular histological structure and Johnsen's index. These effects were accompanied by upregulation of BTB proteins, E- and N-cadherin, spermatogonia markers, suppression of inflammatory markers (NF-κB, IL-1β, IL-6), and activation of integrin-FAK/Akt/mTOR signaling. Microbiota analysis revealed an increase in beneficial genera, including Lactobacillus and Blautia, as well as the restoration of key families and phyla. Dysbiosis promotes systemic inflammation by altering butyrate and acetate, impairing BTB integrity and testicular function via immune activation, oxidative stress, and endocrine disruption. Irisin-FMT mitigates stress-induced testicular dysfunction by modulating gut microbiota and activating protective signaling pathways, highlighting a novel microbiome-based strategy for male infertility.},
}

@article {pmid42497250,
year = {2026},
author = {Zhou, Z and Yang, Y and Zhou, F and Liang, K and Gong, T and Zhou, X and Li, J and Luo, J and Li, J and Yang, J},
title = {Energy-assisted CRISPR cleavage and probiotic vesicle signaling platform: Microbiome reprogramming for homeostasis.},
journal = {Science advances},
volume = {12},
number = {30},
pages = {eaef1760},
doi = {10.1126/sciadv.aef1760},
pmid = {42497250},
issn = {2375-2548},
mesh = {*Probiotics ; *Homeostasis ; *Microbiota/genetics ; *Streptococcus mutans/genetics/metabolism ; Adenosine Triphosphate/metabolism ; *CRISPR-Cas Systems ; Quorum Sensing ; *Extracellular Vesicles/metabolism ; Humans ; Signal Transduction ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Animals ; },
abstract = {Pathogenic infections drive microbial dysbiosis and persistent inflammation, posing therapeutic challenges due to difficulties in precise pathogen eradication and microbiome restoration. Although CRISPR-based therapeutics enable pathogen-specific antibacterial targeting, their effectiveness in treating pathogenic infections is constrained by difficulties in navigating complex microbial ecosystems, penetrating pathogenic barriers, sustaining energy-intensive intracellular cleavage, and, critically, restoring microbial balance after pathogen clearance. Here, we engineer a probiotic vesicle-synergized CRISPR platform by encapsulating gtfB-targeting CRISPR plasmids within hybrid extracellular vesicles from probiotics and pathogenic Streptococcus mutans. The pathogen-derived vesicle component enables targeted uptake by S. mutans, facilitating intracellular cleavage of the virulence gene gtfB. Vesicle-carried endogenous adenosine triphosphate (ATP) boosts CRISPR activity, amplifying targeted DNA cleavage for potent and selective pathogen elimination. Probiotic-derived vesicle components further remodel quorum-sensing networks and immunity, restoring microbial homeostasis. This probiotic vesicle-based strategy integrates ATP-enhanced CRISPR cleavage with microbiome and immune modulation, offering a next-generation therapeutic paradigm for microbiome-associated diseases.},
}

*Probiotics
*Homeostasis
*Microbiota/genetics
*Streptococcus mutans/genetics/metabolism
Adenosine Triphosphate/metabolism
*CRISPR-Cas Systems
Quorum Sensing
*Extracellular Vesicles/metabolism
Humans
Signal Transduction
*Clustered Regularly Interspaced Short Palindromic Repeats
Animals

@article {pmid42497358,
year = {2026},
author = {Vibert, J and Stojanov, M and Da Silva, T and Baud, D and Pluchino, N},
title = {Microbiome and chronic pelvic pain in women: a mini-review.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/deag110},
pmid = {42497358},
issn = {1460-2350},
abstract = {Chronic pelvic pain (CPP) is a prevalent, disabling syndrome encompassing overlapping disorders such as endometriosis/adenomyosis, bladder pain syndrome/interstitial cystitis, irritable bowel syndrome, vulvodynia, and myofascial pain syndrome. Despite distinct clinical phenotypes, these conditions converge on shared biological axes-immune dysregulation, endocrine imbalance, and central sensitization-that sustain chronic pain. Increasing evidence implicates the human microbiome as a potential upstream regulator of these pathways. Dysbiosis across the gut, vaginal, urinary, and endometrial microbial ecosystems may promote local and systemic inflammation, compromise epithelial barrier integrity, alter estrogen recirculation through the estrobolome, and engage aberrant neuroimmune signalling along gut-brain and hypothalamic-pituitary-ovarian circuits. Recent multi-site profiling suggests that microbial alterations often co-occur across pelvic compartments but remain anatomically distinct, with shifts in anaerobic taxa and paired cervicovaginal immune signatures supporting microbiome-immune interactions in CPP pathophysiology. This narrative review synthesizes observational, multi-omics, and mechanistic evidence linking microbial dysbiosis to CPP, highlights microbial metabolites as key functional mediators, and evaluates causal data from experimental models. Finally, it discusses translational opportunities and limitations, including microbiome-targeted interventions (dietary modulation, probiotics/psychobiotics, postbiotics, and microbiota transfer approaches) and the need for harmonized, longitudinal and biomarker-embedded trials to enable mechanism-based stratification and rational therapeutic development.},
}

@article {pmid42497521,
year = {2026},
author = {Su, S and Ren, L and Wang, S and Zhang, Z and Yang, K and Zhou, D and Wang, M and Xi, X and Zhong, W},
title = {Targeting cystathionine-β-synthase (CBS)-mediated cell stemness and gut microbiome homeostasis: mechanism and clinical study of combined resveratrol-curcumin treatment for ulcerative colitis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {159},
number = {},
pages = {158625},
doi = {10.1016/j.phymed.2026.158625},
pmid = {42497521},
issn = {1618-095X},
abstract = {BACKGROUND: Durable mucosal healing is the primary therapeutic goal in ulcerative colitis (UC). Intestinal epithelial stemness and microbiota homeostasis drive this healing process. Cystathionine-β-synthase (CBS) is a key enzyme in endogenous sulfur metabolism. Sulfur metabolism is essential for mitochondrial energy production and mucosal integrity. However, the precise role of CBS in UC pathogenesis remains unclear. Single plant-derived polyphenols, such as resveratrol or curcumin, show limited clinical efficacy due to low bioavailability. The combined effect of these botanical agents on CBS-mediated gut homeostasis requires further investigation.

PURPOSE: This study aimed to define the molecular function of CBS in colitis and to evaluate the therapeutic mechanism and clinical translational potential of a combined plant-derived resveratrol-curcumin treatment for UC.

STUDY DESIGN: A comprehensive bench-to-bedside translational approach was employed. The study integrated human clinical sample analysis, in vivo animal experiments using transgenic models, in silico molecular docking, and a pilot clinical trial.

METHODS: CBS expression was quantified in colonic biopsies from UC patients and healthy controls. Dextran sulfate sodium (DSS) was used to induce colitis in wild-type (WT) and CBS knockout (Cbs[-/-]) mice. Clinical phenotypes, mucosal protein expression, microbiota composition, and short-chain fatty acid (SCFA) profiles were systematically assessed. Molecular docking evaluated the binding affinity between the CBS protein and the resveratrol-curcumin combination. The in vivo efficacy of this combination was tested in both WT and Cbs[-/-] mice. Finally, a pilot clinical trial assessed the combination therapy alongside mesalamine in UC patients.

RESULTS: Colonic CBS expression was downregulated in both UC patients and colitis mice. CBS deficiency worsened DSS-induced clinical damage. It disrupted intestinal barrier homeostasis and severely impaired SCFA production. Molecular docking demonstrated strong binding affinity between the resveratrol-curcumin combination and the CBS protein. In vivo, this combined treatment effectively alleviated colitis symptoms. It reduced pro-inflammatory cytokines, upregulated mucosal proteins via CBS activation, and restored microbiota structure. Notably, these mucosal protective effects were completely abolished in Cbs[-/-] mice, confirming CBS as the essential target for this combined protective effect. In the pilot trial, the addition of resveratrol and curcumin to mesalamine improved clinical outcomes in UC patients.

CONCLUSION: CBS acts as a crucial endogenous protector in the colon. It maintains epithelial stemness and microbiota metabolic homeostasis. The plant-derived resveratrol-curcumin combination specifically targets and restores CBS expression, promoting epithelial regeneration and microbiota remodeling. These findings highlight host-microbiome interactions in UC pathogenesis and offer a novel, targeted polyphenol strategy to achieve mucosal healing.},
}

@article {pmid42497625,
year = {2026},
author = {Jamshed, H and Arslan, J and Iqbal, MP and Siddiqi, HS and Gilani, AU},
title = {Beyond the gut-dietary fiber mediated interorgan crosstalk and systemic health: Mechanistic insights and human evidence.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {151},
number = {},
pages = {113345},
doi = {10.1016/j.nut.2026.113345},
pmid = {42497625},
issn = {1873-1244},
abstract = {Dietary fibers (DFs) are increasingly recognized as key modulators of systemic physiology, exerting effects beyond the gastrointestinal tract through coordinated interorgan communication. Advances in nutrition and microbiome research indicate that physicochemical properties of DFs, including structure, viscosity, fermentability, and molecular weight, shape their metabolic and immunological functions. By serving as substrates for microbial fermentation, DFs promote the production of short‑chain fatty acids and other bioactive metabolites that influence epithelial integrity, immune regulation, bile‑acid signaling, and host metabolic pathways across multiple gut-organ axes. Human studies consistently demonstrate that higher fiber intake is associated with reduced cardiovascular risk, improved hepatic lipid metabolism in non‑alcoholic fatty liver disease, lower gut‑derived uremic toxins in chronic kidney disease, enhanced pulmonary outcomes in inflammatory airway diseases, and potential benefits for mood, cognition, and sleep via neuroimmune pathways. Despite these well-established effects, global intake remains below recommended levels (25-38 g/day), contributing to a measurable burden of noncommunicable diseases, including an estimated ∼453,000 deaths attributable to low fiber intake worldwide. This review provides a focused synthesis of DF-mediated interorgan crosstalk by integrating mechanistic insights with human evidence across major gut-organ axes, with particular emphasis on the role of fiber characteristics in shaping clinical outcomes. Collectively, the evidence positions DFs as a low‑risk, scalable, and mechanism‑guided intervention for improving systemic health. Addressing the global "fiber gap" represents a promising strategy for reducing chronic disease risk through precision nutrition approaches. However, the current evidence remains heterogeneous, with several extraintestinal outcomes supported mainly by observational studies and a limited number of long-term randomized trials.},
}

@article {pmid42497724,
year = {2026},
author = {Jiang, G and Yin, Y and Tian, L and Lu, JN and Cai, X and Deng, T and Cao, Y and Wang, S and Tang, YT and Morel, JL and Qiu, R and Ruan, Z and Chao, Y},
title = {Keystone and potentiator taxa in hyperaccumulator rhizospheres: A new perspective for microbiome-assisted phytoremediation.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143053},
doi = {10.1016/j.jhazmat.2026.143053},
pmid = {42497724},
issn = {1873-3336},
abstract = {Soil heavy-metal contamination threatens agroecosystem functioning, and hyperaccumulators, together with their rhizosphere microbiomes, offer promise for the phytoremediation of contaminated soils. Most rhizosphere microbiome studies have emphasized keystone taxa, but abundant and stable non-keystone members may also contribute to community functioning. Here, we examined the rhizosphere microbiome of the Ni hyperaccumulator Odontarrhena chalcidica using a combination of amplicon and metagenomic sequencing. Keystone taxa were identified as taxa supported by multiple ecological inference approaches, whereas potentiator taxa were defined as abundant and stable taxa that were not identified as keystones. We then compared their taxonomic composition, functional potential, and model-predicted metabolic interactions. Keystone and potentiator taxa were taxonomically distinct. Potentiator taxa showed broader functional potential than keystone taxa, suggesting that these stable non-keystone members may contribute functions that are overlooked by keystone-focused analyses alone. Genome-scale metabolic modeling further predicted greater metabolite exchange in mixed keystone-potentiator assemblages than in single-role assemblages, with model-predicted metabolic support directed mainly from potentiator taxa to keystone taxa. These findings indicate that abundant and stable non-keystone taxa can complement keystone taxa in the rhizosphere microbiome of a Ni hyperaccumulator. More broadly, this study provides an analytical strategy for identifying candidate microbial combinations that may support microbiome-assisted phytoremediation of metal-contaminated soils.},
}

@article {pmid40930304,
year = {2026},
author = {Nguyen, L and Feuerstadt, P and Allegretti, JR and Axelrad, J},
title = {Fecal Microbiota-Based Therapies Compared to Fecal Microbiota Transplantation for Preventing Recurrent C difficile Infection.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {24},
number = {8},
pages = {2305-2307},
pmid = {40930304},
issn = {1542-7714},
support = {K23 DK124570/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Clostridium Infections/prevention & control/therapy ; Clostridioides difficile ; Female ; Male ; Anti-Bacterial Agents/therapeutic use ; *Secondary Prevention/methods ; Treatment Outcome ; Feces/microbiology ; Recurrence ; Gastrointestinal Microbiome ; },
abstract = {Fecal microbiota-based therapies are safe and effective in preventing recurrent Clostridioides difficile infection (rCDI) after standard of care (SOC) antibiotic treatment with either vancomycin or fidaxomicin.[1,2] Prior studies of United States Food and Drug Administration (FDA)-unapproved, full-spectrum fecal microbiota transplant (FMT) following SOC antibiotic therapy have been shown to prevent rCDI through restoration of the gut microbiota by infusion of healthy donor stool. In November of 2022 and April of 2023, the FDA approved fecal microbiota, live-jslm (RBL), and fecal microbiota spores, live-brpk (VOS), to prevent rCDI by targeting dysbiosis and restoring the gut microbiome following SOC antibiotic therapy in those at greatest risk for future recurrence.[3,4] The efficacy of these novel microbiota-based live biotherapeutics in a real-world cohort and compared with conventional FMT remains unknown. Thus, we aimed to analyze the efficacy and safety of RBL and VOS in a real-world multicenter patient population and compare this with FDA-unapproved FMT.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Clostridium Infections/prevention & control/therapy
Clostridioides difficile
Female
Male
Anti-Bacterial Agents/therapeutic use
*Secondary Prevention/methods
Treatment Outcome
Feces/microbiology
Recurrence
Gastrointestinal Microbiome

@article {pmid42485357,
year = {2026},
author = {Hu, K and Jin, L and Feng, Z and Yu, Q and Si, X and Ding, L and Han, Y and Zhu, M and Shi, C and Zeng, X and Wang, K and Wei, J and Lv, Y and Kong, D and Qin, L and Yu, L and Wang, L and Zhang, M and Qian, P and Hu, Y and Wang, D and Huang, H},
title = {The Gut Microbiome Drives Endogenous T Cell Activation Following CAR-T Cell Therapy.},
journal = {Cancer immunology research},
volume = {},
number = {},
pages = {},
doi = {10.1158/2326-6066.CIR-25-1230},
pmid = {42485357},
issn = {2326-6074},
abstract = {Chimeric antigen receptor (CAR)-T cell therapy has become a promising clinical approach against hematological malignancies, but patients receiving CAR-T cell therapy still presented inconsistent clinical outcomes and are complicated by incomplete tumor eradication. The gut microbiome has shown strong correlation with the therapeutic outcomes of CAR-T cell therapy. However, the underlying mechanism of how gut microbiota affect CAR-T cell therapeutic potency remained undetermined. In this study, we established a syngeneic CD19+ murine lymphoma model which allows for the evaluation of both endogenous immune cells and gut microbiota following CD19-CD28ζ CAR-T therapy. Using single-cell transcriptomic analyses, we report that CAR-T cell infusion led to the activation of peripheral and gut-infiltrating endogenous CD8+ T cells towards an effector-like phenotype. In parallel, 16S RNA sequencing revealed substantial alterations of gut microbiota post-infusion. The composition of gut bacteria was associated with the activation status of endogenous CD8+ T cells and responsiveness to CAR-T therapy. More specifically, we identified gut bacteria strains Turicibacter and Parvibactor as critical determinants towards effective CAR-T treatment. Supplementation of these species of gut bacteria during CAR-T cell therapy led to superior antitumor efficacy. Furthermore, both strains facilitated CAR-T therapy-induced activation of endogenous CD8+ T cells, enhancing their capability to express activation-associated surface markers as well as tumor-lysis potency. In summary, our results demonstrate that gut microbiome plays an essential role in endogenous immune activation after CAR-T therapy and provide specific targets for therapeutic interventions.},
}

@article {pmid42485436,
year = {2026},
author = {Rouanne, M and Chen, N and Mariuzza, DL and Yang, Z and Li, F and de Los Santos-Alexis, K and Savage, TM and Vincent, RL and Mendelsohn, CL and Danino, T and Arpaia, N},
title = {Tumor-specific antibodies elicited by engineered bacteria promote bladder cancer immunotherapy in preclinical mouse models.},
journal = {Science translational medicine},
volume = {18},
number = {859},
pages = {eadv7600},
doi = {10.1126/scitranslmed.adv7600},
pmid = {42485436},
issn = {1946-6242},
mesh = {Animals ; *Immunotherapy ; *Urinary Bladder Neoplasms/immunology/therapy ; Humans ; Disease Models, Animal ; *Escherichia coli/metabolism/genetics ; Mice ; Cell Line, Tumor ; *Antibodies, Neoplasm/immunology ; Female ; Chemokine CXCL13/metabolism ; Mice, Inbred C57BL ; },
abstract = {The intratumoral microbiome has recently emerged as a potential hallmark of cancer, with implications for response or resistance to therapy. Bacteria can either promote or inhibit cancer growth. However, intratumoral bacteria can also be engineered using synthetic biology to remodel the tumor microenvironment. Here, we engineered the probiotic bacterium Escherichia coli Nissle 1917 (EcN) to express the human chemokine CXCL13 (C-X-C motif chemokine ligand 13), a critical component of germinal center (GC) formation. Antibody affinity maturation and class switching are fundamental aspects of adaptive immune response. Both occur primarily in the GCs of secondary lymphoid organs for defense against pathogens. Immune checkpoint blockade (ICB) efficacy is primarily driven by T cells; however, recent studies in mice and humans have shown that humoral immune responses act as critical partners for ICB-mediated antitumor activity. Using orthotopic models of bladder cancer, intravesically delivered engineered CXCL13-expressing EcN colonized bladder tumors and elicited GC responses in bladder tumor-draining lymph nodes after intravesical delivery. When combined with programmed cell death protein 1 (PD-1) blockade, engineered EcN improved antitumor activity in two aggressive, fast-growing, and immunologically cold orthotopic mouse models of bladder cancer. Mechanistically, this antitumor effect was dependent on the presence of CD8[+] T cells and CD4[+] T follicular helper cells; combination therapy increased tumor-specific antibody responses and promoted long-term survival and protective immunity upon tumor rechallenge. Thus, we demonstrate that synthetically engineered CXCL13-expressing EcN can enhance the efficacy of PD-1 checkpoint blockade immunotherapy by amplifying tumor-specific humoral immunity.},
}

Animals
*Immunotherapy
*Urinary Bladder Neoplasms/immunology/therapy
Humans
Disease Models, Animal
*Escherichia coli/metabolism/genetics
Mice
Cell Line, Tumor
*Antibodies, Neoplasm/immunology
Female
Chemokine CXCL13/metabolism
Mice, Inbred C57BL

@article {pmid42485503,
year = {2026},
author = {Khanamani Falahatipour, S and Soltani, M},
title = {Targeting the Gut-Brain Axis: Pharmacological Modulation of the Microbiome for Neurological and Behavioural Disorders in Companion Animals.},
journal = {Veterinary medicine and science},
volume = {12},
number = {4},
pages = {e71105},
doi = {10.1002/vms3.71105},
pmid = {42485503},
issn = {2053-1095},
mesh = {Animals ; Dogs ; Cats ; *Gastrointestinal Microbiome/drug effects ; *Cat Diseases/microbiology/drug therapy ; *Dog Diseases/microbiology/drug therapy ; *Nervous System Diseases/veterinary/drug therapy/microbiology ; *Mental Disorders/drug therapy/microbiology ; *Pets ; *Brain ; Prebiotics ; },
abstract = {BACKGROUND: The gut-brain axis (GBA) represents a paradigm shift in veterinary neuropharmacology, offering novel approaches for managing neurological and behavioural disorders in companion animals.

OBJECTIVES: This review synthesizes current evidence on the bidirectional communication between the gut microbiome and the central nervous system, examining the neural, endocrine, immune, and metabolic pathways that facilitate this dialogue. We explore the unique aspects of canine and feline microbiomes and their implications for species-specific drug development and critically evaluate emerging pharmacological strategies, including psychobiotics, prebiotics, synbiotics and faecal microbiota transplantation (FMT), highlighting their clinical applications in conditions ranging from anxiety and aggression to cognitive dysfunction and epilepsy.

METHODS: This narrative review followed established guidelines for evidence synthesis in veterinary medicine. A comprehensive literature search was performed using PubMed, Google Scholar and Scopus databases covering publications from January 2011 to March 2026.

RESULTS: While promising results have been demonstrated with specific strains, such as Bifidobacterium longum BL999 and Lactiplantibacillus plantarum PS128, significant challenges remain. These include methodological limitations in microbiome research, the predominance of correlative over causal evidence and the need for standardized diagnostic tools.

CONCLUSIONS: Future directions must prioritize large-scale longitudinal studies, robust clinical trials and advanced multi-omics approaches to establish causal mechanisms and develop personalized, microbiome-targeted therapies. Realizing this potential requires a shift from correlative data to causal mechanisms, from a one-size-fits-all approach to species-specific therapeutics and from rodent models to rigorous trials in dogs and cats.},
}

Animals
Dogs
Cats
*Gastrointestinal Microbiome/drug effects
*Cat Diseases/microbiology/drug therapy
*Dog Diseases/microbiology/drug therapy
*Nervous System Diseases/veterinary/drug therapy/microbiology
*Mental Disorders/drug therapy/microbiology
*Pets
*Brain
Prebiotics

@article {pmid42485555,
year = {2026},
author = {Wang, P and Liu, M and Zhao, C and Lu, Q and Gao, S and Guo, L and Li, Y and Wan, J and Yuan, L and Yi, F and Cai, C and Liu, J and McClung, CR and Zhang, X and Liu, X and Xu, X and Cai, Y and Xie, Q},
title = {Circadian Clock Gates Verticillium dahliae Defence in Cotton by Modulating JAZs Expression.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
pmid = {42485555},
issn = {1467-7652},
support = {2022YFD1200303//National Key Research and Development Program of China/ ; 2021YFA1300402//National Key Research and Development Program of China/ ; 234200510023//Zhongyuan Science and Technology Innovation Leadership Talent Project/ ; 32170259//National Natural Science Foundation of China/ ; 32170275//National Natural Science Foundation of China/ ; U1904202//National Natural Science Foundation of China/ ; 32100250//National Natural Science Foundation of China/ ; 32370084//National Natural Science Foundation of China/ ; 32522005//National Natural Science Foundation of China/ ; U25A20661//National Natural Science Foundation of China/ ; 262300421262//National Science Foundation of Henan Province/ ; },
abstract = {The circadian clock plays critical roles in orchestrating temporal regulation of diverse physiological processes. However, its role in mediating root-associated immunity against soil-borne pathogens in crops remains poorly understood. Here, we show that cotton circadian clock gates nighttime resistance to vascular fungal pathogen Verticillium dahliae by shaping rhizosphere microbiome composition and activating jasmonic acid (JA)-dependent immune signalling. Pathogen infection, in turn, accelerates clock pace and perturbs nighttime microbial community structure. We identify GhLUX, an evening complex component, as a key regulator of this defence program. GhLUX enhances immunity by repressing GhJAZ expression, thereby amplifying JA signalling at night. Overexpression of GhLUX in field trials confers enhanced resistance to V. dahliae while simultaneously improving cotton fibre yield and quality. These findings uncover a mechanistic link between the circadian clock, rhizosphere microbiota and root immunity in cotton and suggest that circadian regulators can be harnessed to optimize both disease resistance and agronomic performance.},
}

@article {pmid42485562,
year = {2026},
author = {Dalal, R and Barot, J and Binsuwaidan, R and Alshammari, N and Adnan, M and Patel, M and Patel, K},
title = {Substrate-Driven Microbiome Assembly in Water Hyacinth Vermicompost: Combined 16S rRNA and Shotgun Metagenomics for Sustainable Agriculture.},
journal = {Journal of basic microbiology},
volume = {66},
number = {7},
pages = {e70185},
pmid = {42485562},
issn = {1521-4028},
support = {PNURSP2026R304//Princess Nourah bint Abdulrahman University/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Eichhornia/microbiology ; Metagenomics ; Biomass ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Animals ; *Soil Microbiology ; Archaea/classification/genetics/isolation & purification/metabolism ; Composting ; Agriculture ; Fungi/classification/genetics/isolation & purification/metabolism ; Shotgun Sequencing ; Phylogeny ; },
abstract = {Substrate composition is a primary determinant of microbial succession and functional dynamics in vermicomposting systems. However, comparative insights into how biomass pre-treatment influences microbial architecture and how different sequencing approaches capture these changes remain limited. In this study, evaluation was carried out on microbial community structure and metabolic potential in vermicompost derived from three forms of Eichhornia crassipes (water hyacinth) biomass, burnt biomass (BB), composted biomass (CB) and dry biomass (DB) using both 16S rRNA gene amplicon sequencing and shotgun metagenomics. All treatments were dominated by bacterial communities (> 97%), with Proteobacteria (Pseudomonadota), Firmicutes (Bacillota), Actinobacteria and Bacteroidota representing core phyla across substrates. However, metagenomics revealed broader domain-level coverage, detecting Archaea and Fungi that were underrepresented in 16S datasets. Substrate-specific signatures were evident such as, composted biomass exhibited enrichment of lignin degradation and carbon cycling pathways; dry biomass showed methanogenesis, fermentation and phosphate solubilization signatures; and burnt biomass was associated with nitrogen fixation and sulphur metabolism. Shannon diversity was highest in composted biomass (H' = 5.21), reflecting enhanced niche diversification during substrate maturation. Comparative analysis demonstrated that 16S rRNA sequencing effectively captured dominant bacterial structure, whereas shotgun metagenomics provided superior taxonomic resolution and direct functional inference, particularly for low-abundance and non-bacterial taxa. Notably, functional differentiation among treatments was more pronounced than broad taxonomic shifts, indicating that biomass pre-treatment exerts stronger influence on ecological function than on core community composition. These findings demonstrate that integrating taxonomic and functional metagenomics enables substrate-specific optimization of vermicompost formulations and provides a framework for designing microbiome-informed strategies for sustainable agriculture and invasive biomass valorization.},
}

RNA, Ribosomal, 16S/genetics
*Eichhornia/microbiology
Metagenomics
Biomass
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
Animals
*Soil Microbiology
Archaea/classification/genetics/isolation & purification/metabolism
Composting
Agriculture
Fungi/classification/genetics/isolation & purification/metabolism
Shotgun Sequencing
Phylogeny

@article {pmid42485614,
year = {2026},
author = {Zhang, J and Xu, W and Xing, J and Sun, Y and Huang, S and Su, X},
title = {CAM-Net: a context-aware network for identifying reliable microbial relations via optimal consortium.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {4},
pages = {},
pmid = {42485614},
issn = {1477-4054},
support = {2025Z154//Innovation Yongjiang 2035 Key R&D Program/ ; 25-3-1-11-zyyd-jch//Qingdao Natural Science Foundation/ ; 32572519//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; Algorithms ; *Computational Biology/methods ; *Microbial Interactions ; },
abstract = {Microbes exist within complex community contexts, particularly for key functional species whose stable colonization critically depends on specific ecological partners. However, conventional microbial correlation analyses predominantly rely on isolated pairwise metrics (e.g. Spearman, SparCC, and FlashWeave), which ignore community-level dependencies. This limitation leads to spurious associations in large-scale datasets and obscures the true structure of microbial interactions. Here, we introduce CAM-Net, a context-aware framework that identifies a target microbe's optimal consortium, a fully connected network subset that accurately predicts its abundance. By constructing networks via multi-hop information propagation, CAM-Net effectively filters false positives from indirect associations and captures complex, context-dependent patterns that are inaccessible to traditional pairwise approaches. We evaluated CAM-Net on over 25 000 human gut microbiome samples using Akkermansia muciniphila and Lactobacillus acidophilus as representatives of indigenous and transient colonizers. CAM-Net identified a coherent and reproducible consortium for A. muciniphila, but only weak association structures for L. acidophilus, consistent with their ecological behaviors. In contrast, pairwise methods produced spurious associations for both species. Notably, despite substantial geographic heterogeneity, Alistipes shahii consistently emerged as a conserved core member of the A. muciniphila consortium, demonstrating the advantage of context-aware modeling. The source code is available at https://github.com/qdu-bioinfo/CAM-Net.},
}

Humans
*Microbiota
Algorithms
*Computational Biology/methods
*Microbial Interactions

@article {pmid42485917,
year = {2026},
author = {Lyte, JM and Proszkowiec-Weglarz, M},
title = {Importance of methods selected for microbiome studies: State of the science and challenges.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107417},
doi = {10.1016/j.psj.2026.107417},
pmid = {42485917},
issn = {1525-3171},
abstract = {The microbiota has impact on virtually every aspect of poultry production, including performance, health, and food safety. It is therefore not surprising that considerable promise exists for the application of microbiota science in addressing current and future challenges faced across the poultry industry. Yet, methodological variation among poultry microbiota studies has had negative impact on reproducibility of findings, thereby slowing the application of effective microbiota-based solutions in a production setting. The experimental workflow in microbiota research involves many steps, ranging from sample collection to bioinformatic processing. Likewise, at each experimental stage there exists a vast methodological toolbox available to poultry microbiota researchers. As the technical decisions made at each experimental stage have demonstrable impact on each downstream step, outcomes in microbiota research are largely dependent on the methodologies employed. In order to improve translatability and reproducibility between different methodological pipelines, it is essential that a best practice framework be adopted in poultry science regarding microbiota research. The present review seeks to briefly encapsulate our symposium on microbiome methodology in poultry research. This symposium discussed the need for a robust set of evidence-based guidelines that streamline microbiota research in poultry. Attention was given to each major stage of a typical poultry microbiota study, including sample collection, storage, extraction, library preparation, sequencing, bioinformatic and data analyses, as well as data reporting and repositories. The use of positive and negative controls, improved reporting of raw data, and other tangible aspects that improve consistency and reproducibility across poultry microbiota study designs were highlighted. Ultimately, it was the goal of this symposium not to advocate a single methodology, but instead to demonstrate the need for robust practices at each experimental stage that enable cross-study comparisons of findings in poultry microbiota research.},
}

@article {pmid42485926,
year = {2026},
author = {de Bruijn, DGJ and Gusinac, A and Ederveen, THA and Le, ND and Kulkarni, P and Meijer, RI and Janssen, MCH and Zweers, HEE},
title = {Gut microbiota alterations in individuals with mitochondrial disease caused by the m.3243A >G mutation.},
journal = {Molecular genetics and metabolism},
volume = {149},
number = {1-2},
pages = {110208},
doi = {10.1016/j.ymgme.2026.110208},
pmid = {42485926},
issn = {1096-7206},
abstract = {People with mitochondrial disease (MD) associated with the m.3243 A > G mutation often experience gastrointestinal complaints and dysmotility, suggesting dysbiosis of the gut microbiome. A common phenotype of the m.3243 A > G mutation is Maternally Inherited Diabetes and Deafness (MIDD). Previous studies have shown that other forms of diabetes are associated with an altered gut microbiome. Therefore, our study aimed to investigate the gut microbiota of people with MD caused by the m.3243 A > G mutation compared to healthy controls (Lifelines®) and people with type 1 diabetes (T1D). Fecal samples of 30 people with the m.3243 A > G mutation were used for shotgun metagenomic sequencing. The MD group was compared with 60 healthy controls and 60 people with T1D from different datasets, and were matched for age, sex, and BMI. We found that the Bray-Curtis β-diversity of the gut microbiota differed significantly between MD compared to healthy controls and T1D, while there was a non-significant reduction in Shannon α-diversity in the MD group. The gut microbiota of the MD group was characterized by reduced Faecalibacterium prausnitzii, and increased Escherichia coli, Ruminococcus gnavus, and Ruminococcus torques levels compared to healthy controls and T1D. This pattern aligns with microbial signatures reported in inflammatory bowel disease, which is associated with mitochondrial dysfunction in intestinal epithelial cells. Overall, our explorative study suggest that people with the m.3243 A > G mutation exhibit a dysbiotic gut microbiota, which may pave the way for future research aimed at developing new therapies, dietary adjustments and their potentials to improve quality of life.},
}

@article {pmid42485957,
year = {2026},
author = {Zannini, E and Nyhan, L and Gobbetti, M and Di Cagno, R and Arendt, EK},
title = {The food microbiome: an evolutionary architect, a modern healer, and a future shield.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103555},
doi = {10.1016/j.copbio.2026.103555},
pmid = {42485957},
issn = {1879-0429},
abstract = {The food microbiome, comprising microorganisms present in foods and fermentation, links diet, environment, and host physiology. This review examines its evolutionary, contemporary, and future nutritional relevance, including emerging applications of artificial intelligence (AI). In early human diets, fermentation likely improved food safety and nutrient accessibility, although its contribution to encephalization remains unproven. In modern populations, fermented foods and microbial metabolites shape the composition of the gut microbiome and modulate host metabolic, immune, and neuroactive functions. Rising atmospheric CO2 is projected to reduce protein and micronutrient concentrations in staple crops, increasing interest in microbial fermentation as a strategy to enhance nutrient availability. Integration of AI with multi-omics enables functional characterisation of fermentation ecosystems and supports the development of targeted, personalised nutritional strategies, although translational and mechanistic challenges remain unresolved.},
}

@article {pmid42485963,
year = {2026},
author = {Fu, Y and Chen, M and Zhang, X and Yu, G and Jiang, P and Liu, J and You, S},
title = {Multi-omics analysis of the rhizosphere effects and molecular mechanisms of Ageratum conyzoides linn. at different stages of Cd, Pb, and Zn co-stress.},
journal = {Journal of environmental management},
volume = {414},
number = {},
pages = {130461},
doi = {10.1016/j.jenvman.2026.130461},
pmid = {42485963},
issn = {1095-8630},
abstract = {Ageratum conyzoides Linn. is a promising candidate for multi-metal remediation. This study examined the rhizosphere microecology and molecular regulation of A. conyzoides under Cd, Pb, and Zn co-stress after 21 and 50 days of exposure. The ethanol-extracted fraction was found to be the predominant form of Cd, Pb, and Zn in the roots, whereas the NaCl-, HCl-, and HAc-extracted fractions prevailed in the shoots. Heavy metals were mainly distributed in the cell wall and soluble fractions. Metabolome and microbiome analyses revealed dynamic changes in rhizosphere exudate metabolic profiles and bacterial community composition in the rhizosphere soil after 21 and 50 days of exposure to stress. After 21 days of stress, increased exudation of oxalic acid, L-valine, and L-glutamate was correlated with the enrichment of Clostridium_sensu_stricto_12 and norank_p_FCPU426. After 50 days of stress, significantly increased exudation of jasmonic acid, gibberellin A24, and 4-hydroxynonenal was correlated with the enrichment of Bauldia, Candidatus_Udaeobacter, and norank_f_Anaerolineaceae. Transcriptome analysis revealed that prolonged stress upregulated the expression of SEC61A2, Uggt, Ggt7, gss, and PRX1 in A. conyzoides leaves; the differentially expressed genes were found to be significantly enriched in the protein processing in the endoplasmic reticulum pathway and glutathione metabolic pathway. Overall, these findings provide a theoretical foundation for optimizing phytoremediation using A. conyzoides.},
}

@article {pmid42485992,
year = {2026},
author = {Vallini, F and Salvucci, B and Biava, M and Carradori, S and Poce, G and Tammaro, C},
title = {Targeting Fusobacterium nucleatum in cancer therapy: A new frontier in solid tumor treatment.},
journal = {European journal of medicinal chemistry},
volume = {318},
number = {},
pages = {119170},
doi = {10.1016/j.ejmech.2026.119170},
pmid = {42485992},
issn = {1768-3254},
abstract = {Recently, the tumor-infiltrating microbiome (TIM) has gained increasing attention due to its pivotal role in carcinogenesis, tumor progression, resistance to chemotherapy, and immune evasion. Although the composition of these microbial communities is not yet fully elucidated, emerging studies have demonstrated that certain bacteria exert pro-tumoral effects, either through enzymatic activities or by modulating the host immune response. Among them, Fusobacterium nucleatum (Fn) represents one of the most pathogenic residents of several solid tumors, making it a novel and promising target in the fight against cancer. In detail, Fn promotes oncogenic signaling, epithelial-mesenchymal transition, inflammatory responses, and autophagy-mediated drug resistance, thereby contributing to poor clinical outcomes. This review explores different strategies to selectively target Fn, aiming to reduce its pro-tumoral behavior, spanning from drug repurposing, synthetic small molecules, natural products, and antimicrobial peptides to advanced nanoformulations, vaccine-based platforms, and sequence-specific interventions, such as antisense oligomers and microbiota-modulating strategies. A focused section covers stimuli-responsive and biomimetic nanoplatforms potentially capable of eradicating Fn and restoring chemosensitivity, while sparing the commensal gut microbiota. Collectively, these findings support the feasibility of targeting the TIM in combination with canonical anticancer regimens. Although further refinements and additional investigations are needed, targeting Fn represents a novel paradigm shift in the management of bacterially colonized solid tumors.},
}

@article {pmid42486137,
year = {2026},
author = {Davido, B and Loubet, P and Saleh-Mghir, A and Leroux, P and Rottman, M and Corcione, S and , },
title = {mRNA vaccines for multidrug-resistant bacteria: promise, challenges, and microbiome-informed strategies.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101467},
doi = {10.1016/j.lanmic.2026.101467},
pmid = {42486137},
issn = {2666-5247},
abstract = {Antimicrobial resistance (AMR) has made multidrug-resistant organisms (MDROs), particularly ESKAPE-E pathogens (including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp, and Escherichia coli), a major threat to modern medicine. Although novel antibiotics, antimicrobial stewardship, and infection prevention remain essential, such interventions are unlikely to offset projected AMR trends on their own. Vaccines can help to mitigate AMR by preventing infections and reducing antibiotic exposure. WHO estimates that vaccines targeting 23 pathogens (excluding Neisseria gonorrhoea) could reduce global antibiotic need by 22%, equivalent to 2·5 billion defined daily doses annually. In the mRNA era, modular vaccine platforms enable rapid design of protein antigens and multivalent constructs, with emerging preclinical proof of concept against selected bacterial pathogens. In this Personal View, we argue that mRNA vaccines should be considered enabling platforms for selected protein-based MDRO targets rather than universal solutions for antibacterial vaccine development. We propose a microbiome-informed framework that distinguishes systemic protection from mucosal decolonisation and aligns antigen selection, delivery route, and trial endpoints with colonisation dynamics, microbiome resilience, and AMR reduction goals.},
}

@article {pmid42486172,
year = {2026},
author = {Hanifeh, M and Huhtinen, M and Ganz, HH and Heilmann, RM and Huang, W and Spillmann, T and Suchodolski, JS},
title = {Clinical trial reveals limited clinical and microbiome effects following oral fecal microbiota transplantation in dogs with chronic enteropathy responsive to tylosin.},
journal = {Journal of the American Veterinary Medical Association},
volume = {},
number = {},
pages = {1-11},
doi = {10.2460/javma.26.03.0178},
pmid = {42486172},
issn = {1943-569X},
abstract = {OBJECTIVE: To evaluate clinical response and fecal biomarkers in dogs with tylosin-responsive enteropathy (TRE) treated with oral fecal microbiota transplantation (FMT).

METHODS: In this prospective, randomized, double-blind, placebo-controlled trial (conducted between August 1, 2020, and December 31, 2022), 14 client-owned dogs with confirmed tylosin-responsive enteropathy entered the treatment phase. Dogs received oral FMT (n = 7) or placebo (7) for 4 weeks; 1 placebo-treated dog was excluded (pyometra), leaving 7 FMT-treated and 6 placebo-treated dogs for analysis. Canine Chronic Enteropathy Clinical Activity Index, fecal consistency, and fecal biomarkers (dysbiosis index, core bacteria, bile acids, short-chain fatty acids, lactate, and calprotectin) were assessed at pretreatment and posttreatment visits. Intestinal permeability was evaluated with serum iohexol. Analyses were limited to pre- and posttreatment comparisons.

RESULTS: Relapse occurred in 2 of 7 FMT-treated dogs (28.6%) and 3 of 6 placebo-treated dogs (50.0%). The dysbiosis index decreased over time in both groups, with no treatment effect. Faecalibacterium spp increased, with higher posttreatment values in the FMT group, whereas Turicibacter spp increased in both groups. Peptacetobacter hiranonis increased over time without between-group differences. Bile acid conversion was observed in a subset of dogs without group differences. Other biomarkers showed no consistent treatment-specific effects.

CONCLUSIONS: Oral FMT was associated with variable microbiome changes and inconsistent clinical response, with no clear treatment-specific effects compared with placebo. These findings support further evaluation of optimized microbiome-based therapies in larger studies.

CLINICAL RELEVANCE: Oral FMT may serve as an adjunctive strategy for microbiome modulation in dogs with chronic enteropathy; however, clinical benefits were inconsistent and optimized protocols may be required.},
}