@article {pmid41435605,
year = {2025},
author = {Xu, Y and Yang, W and Yang, Z and Pan, Y and Zhu, Y and Shen, B and Chen, J},
title = {Differential and complementary effects of Baizhu and Fuling on spleen deficiency syndrome by regulating microbiota-gut-metabolite axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157690},
doi = {10.1016/j.phymed.2025.157690},
pmid = {41435605},
issn = {1618-095X},
abstract = {BACKGROUND: Atractylodes macrocephala Koidz. (commonly known as Baizhu, BZ) and Poria cocos (Schwan.) Wolf. (referred to as Fuling, FL) are frequently employed in the treatment of spleen deficiency syndrome (SDS) owing to their spleen-tonifying and dampness-eliminating properties. The combination of the two herbs, referred to as the BZ-FL herb pair, exhibited complementary and enhancing effects. Nevertheless, the distinct and complementary mechanisms and effects of BZ and FL individually remain inadequately understood.

PURPOSE: This study aimed to investigate the differential and complementary effects and underlying mechanisms of BZ and FL on SDS.

METHODS: The chemical components in BZ, FL, and the BZ-FL herb pair were qualitatively and quantitatively analyed using UHPLC-Q Exactive HF-X and UPLC-MS technique. SDS model rats were established by a combination of dietary and fatigue-inducing methods and then treated with BZ, FL, and the BZ-FL herb pair. In order to elucidate the effects on gastrointestinal motility, immune function, and water metabolism, the concentrations of gastrointestinal hormones, low-density lipoprotein, high-density lipoprotein, total cholesterol, serum protein levels, and albumin were measured. Additionally, the levels of IL-2, IgA, IL-4, IgG, and IFN-γ in colon tissue were quantified utilizing enzyme-linked immunosorbent assay (ELISA) and biochemical assays. Pathological changes were examined using hematoxylin and eosin staining, while immunofluorescence was used to measure the levels of the intestinal barrier proteins and aquaporins (Aqps) in colonic tissues. The levels of Aqps and cAMP/PKA/CREB signaling pathway were detected in colon and kidney tissues using western blot analysis. Untargeted metabolomics was used to analyze the serum and feces metabolic profile. The 16S rRNA gene high-throughput sequencing was performed to detect the gut microbiota composition in fecal samples.

RESULTS: The quantification of chemical components revealed that BZ significantly enhanced the dissolution of triterpene acids from FL. BZ, FL, and the BZ-FL herb pair effectively mitigated SDS by modulating gastrointestinal hormones, kidney and colon Aqps, and protein expression within the cAMP/PKA/CREB signaling pathway, while also enhancing intestinal barrier integrity. Serum metabolomics analysis demonstrated that BZ influenced bile acid biosynthesis, FL affected the citrate cycle and glycerophospholipid metabolism, and the BZ-FL herb pair impacted all these pathways. Gut microbiota analysis indicated that the efficacy of the BZ-FL herb pair in ameliorating SDS was associated with a preserved gut microbiome, characterized by the relative abundance of microbial taxa such as Escherichia-Shigella, Kurthia, and UCG-005. Fecal metabolomics analysis indicated that the BZ-FL herb pair synergistically enhances and complements each other by influencing metabolites in butanoate, arginine and proline, starch and sucrose, cysteine and methionine, purine, and propanoate metabolism. Moreover, correlation and comprehensive analyses identified a robust association among SDS phenotypes, serum metabolites, fecal metabolites, and microbial genera. In addition, the BZ-FL herb pair and BZ alone exhibited significantly greater regulatory effects on gastrointestinal function-related indicators compared to FL.

CONCLUSIONS: This study presents initial evidence of the differential and complementary effects of BZ and FL, analyzing their chemical compositions and their influence on water-fluid metabolism and the microbiota-gut-metabolites axis in SDS. These findings reflect the rationality and scientific basis of the compatibility theory. The study identified potential mechanisms of the BZ-FL herb pair in treating SDS, providing a reference for future research and clinical applications.},
}

@article {pmid41435506,
year = {2025},
author = {Souto-Silva, MV and Bispo, ECI and de Oliveira, NN and Pogue, R and Zonari, A and Saldanha-Araujo, F and Carvalho, JL},
title = {The cytokine-skin barrier axis in health and disease.},
journal = {Cytokine & growth factor reviews},
volume = {87},
number = {},
pages = {113-123},
doi = {10.1016/j.cytogfr.2025.12.009},
pmid = {41435506},
issn = {1879-0305},
abstract = {The skin barrier functions as both a structural defense and an immunological interface that integrates environmental, microbial, and systemic signals. Its disruption predisposes to cutaneous inflammation and contributes to systemic immune dysregulation. In this review, we provide an integrated analysis of how cytokine signaling regulates skin barrier integrity, highlighting both mechanistic insights and clinical implications across health and disease. We first revisit the architecture of the skin barrier and describe common insults that compromise its function, and the mechanisms by which these activate canonical signalling pathways-NF-κB, MAPK, JAK-STAT, and PI3K/Akt/mTOR-leading to the release of cytokines from keratinocytes and immune cells. Particular attention is given to cytokine families with direct relevance for epidermal physiology: IL-1 and IL-17 in antimicrobial defense and hyperinflammation; IL-20, IL-31, and type 2 cytokines in keratinocyte proliferation, differentiation, and barrier protein suppression; and TNF and interferons in amplifying inflammation and tissue injury. We also discuss how these cytokine networks drive systemic manifestations, linking skin barrier dysfunction to atopic dermatitis (AD), psoriasis, inflammaging, and metabolic disorders. Finally, we review therapeutic approaches that target cytokine signaling or restore barrier integrity, ranging from emollients and microbiome-based strategies to biologics and JAK inhibitors. By systematically reviewing the cytokine-barrier axis, this work highlights how modulation of cytokine signaling represents a promising avenue for clinical and preventive interventions in dermatology and systemic health.},
}

@article {pmid41435214,
year = {2025},
author = {Yoshida-Court, K and Teka, B and Cisneros Napravnik, T and Karpinets, T and El Alam, MB and Firdawoke, E and Chanyalew, Z and Mihret, A and Addissie, A and Gizaw, M and Lan, J and Haymaker, C and Duose, DY and Luthra, R and Colbert, LE and Jhingran, A and Kantelhardt, EJ and Kaufmann, AM and Abebe, T and Klopp, AH},
title = {Linking Microbiome Diversity and Immune Profiles in Ethiopian Patients With Cervical Cancer.},
journal = {JCO global oncology},
volume = {11},
number = {},
pages = {e2500060},
doi = {10.1200/GO-25-00060},
pmid = {41435214},
issn = {2687-8941},
mesh = {Humans ; *Uterine Cervical Neoplasms/immunology/microbiology ; Female ; Ethiopia ; *Microbiota/immunology ; Adult ; Middle Aged ; *Receptors, Antigen, T-Cell/immunology/genetics ; },
abstract = {PURPOSE: This study investigates the interplay between T-cell receptor (TCR) immune characteristics and microbiome profiles to explore the relationship between immune diversity and microbial composition in cervical samples from Ethiopia.

METHODS: Cervical specimens were collected from patients at Tikur Anbessa Specialized Hospital in Addis Ababa, and rural Butajira, south-central Ethiopia. Patient data, including age, human papillomavirus status, pathology, and TCR immune characteristics, were analyzed with a focus on the interactions between TCR profiles and microbiome compositions in malignant samples.

RESULTS: Three distinct TCR profiles were identified: Group 1 (TCR active) exhibited features of active immune engagement, including high diversity, clonal expansion, and repertoire richness. Group 2 (TCR restricted) showed reduced TCR diversity and expansion, suggesting a restricted repertoire. Group 3 (TCR balanced) had moderate diversity and clonal activity. TCR repertoire groups were linked with microbial diversity, with Group 1 (TCR active) showing the highest number of microbes (high operational taxonomic units and microbial diversity). Maximum TCR clonal expansion positivity associated with microbial richness, while Group 3 (TCR balanced) was linked to reduced microbial alpha diversity. Taxonomic analysis revealed specific organisms enriched in TCR repertoire group.

CONCLUSION: Variations in TCR profiles are linked to distinct microbial environments in cervical cancer with greater microbial richness in patients with greater maximum productive frequency. These findings underscore the interplay between TCR diversity, microbiome composition, and malignancy, offering insights into the potential implications for microbiome-targeted therapies and prognostic biomarkers in cervical cancer.},
}

Humans
*Uterine Cervical Neoplasms/immunology/microbiology
Female
Ethiopia
*Microbiota/immunology
Adult
Middle Aged
*Receptors, Antigen, T-Cell/immunology/genetics

@article {pmid41435148,
year = {2025},
author = {Katuwawala, KS and Fernando, WMADB and Bharadwaj, P and Martins, RN},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e098838},
doi = {10.1002/alz70855_098838},
pmid = {41435148},
issn = {1552-5279},
mesh = {Humans ; *MicroRNAs/metabolism ; *Alzheimer Disease/diagnosis/metabolism/genetics ; *Gastrointestinal Microbiome/physiology ; Biomarkers/metabolism ; Feces/chemistry ; Brain/metabolism ; },
abstract = {BACKGROUND: Alzheimer's Disease (AD) is a complex neurodegenerative disorder characterized by cognitive decline and memory loss. Emerging research suggests that gut microbiota play a significant role in AD progression through mechanisms like neuroinflammation and neurotransmitter dysregulation. Fecal microRNAs (miRNAs) have gained attention as non-invasive biomarkers reflecting gut-brain communication, offering potential insights into disease pathogenesis and therapeutic targets. This review examines the significance of fecal miRNA profiles in AD, focusing on their role in early diagnosis, disease monitoring, and potential therapeutic intervention.

METHOD: A systematic literature search was conducted using PubMed, Scopus, Web of Science, and Google Scholar for studies published from 2010 to 2023. Inclusion criteria were based on research articles investigating fecal miRNA expression in AD, miRNAs involved in gut-brain communication, and studies highlighting miRNAs as diagnostic or prognostic biomarkers. Search terms such as "Alzheimer's Disease," "fecal microRNA," "gut microbiome," "biomarkers," and "gut-brain axis" were used. A total of 40 studies, including both clinical and preclinical research, met the inclusion criteria and were reviewed.

RESULT: Key miRNAs such as miR-146a, miR-155, and miR-34a were consistently dysregulated, indicating their involvement in neuroinflammatory pathways and synaptic dysfunction. These miRNAs also influenced amyloid precursor protein (APP) processing and tau phosphorylation, critical factors in AD pathogenesis. Additionally, miR-132 and miR-181c were associated with cognitive decline and AD severity, suggesting their potential as non-invasive biomarkers for disease progression. Preclinical studies also demonstrated that dietary interventions and probiotics could modulate fecal miRNA expression, indicating potential therapeutic strategies targeting the gut microbiome.

CONCLUSION: Fecal miRNA profiles offer valuable insights into the gut-brain axis in Alzheimer's Disease and serve as promising non-invasive biomarkers for early diagnosis and disease monitoring. Altered miRNA expression reflects gut dysbiosis and neuroinflammatory responses, making them potential targets for therapeutic interventions. Future research should focus on validating these findings through large-scale clinical trials and exploring how dietary and probiotic treatments can modify miRNA expression to benefit AD patients. This review emphasizes the need for a multidisciplinary approach to better understand the role of the gut microbiome in neurodegenerative diseases and develop novel strategies for AD management.},
}

Humans
*MicroRNAs/metabolism
*Alzheimer Disease/diagnosis/metabolism/genetics
*Gastrointestinal Microbiome/physiology
Biomarkers/metabolism
Feces/chemistry
Brain/metabolism

@article {pmid41435039,
year = {2025},
author = {Elorriaga, IT and Imatz, E and Ibarlucea, B and Cano, A and Sanmartín, E and Tueros, I and Ayala, U and de Heredia, AG and Zaldua, C and Zugaza, JL and Aleman, IT and Garcia-Sebastian, M and Martínez-Lage, P and Erramuzpe, A},
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e099250},
doi = {10.1002/alz70860_099250},
pmid = {41435039},
issn = {1552-5279},
mesh = {Humans ; Aged ; *Public Health ; Female ; Male ; Aged, 80 and over ; Biomarkers ; Middle Aged ; *Aging ; *Healthy Aging ; },
abstract = {BACKGROUND: The ITTHACA project is a collaborative initiative involving six research institutions from the Basque Country including Universities, Health, Technology and Basic Research Institutions. It builds upon the ongoing CITA GO-ON) CITA Go-On study, ClinicalTrials.gov, NCT04840030) cohort study, which adapts the Finnish FINGER [Ngandu, T., et al. 2015] model to the local context. ITTHACA focuses on enhancing healthy aging by identifying markers, prediction models and sensors for in vivo monitoring that allow the establishment and implementation of combined intervention strategies in the population.

METHOD: This one-year randomized-controlled trial (total n = 250; 125 control and 125 intervention), focused on 60-85-year-old males and females at risk of dementia, adopts a multimodal approach. Biomarker identification includes proteomics and metabolomics in biological fluids (blood) and 16S metagenomics and lipidomics in the gut microbiome (stool), as well as employing a FINGER-like mice model. Biosensor technology under development includes multi-channel bioimpedance spectroscopy for tissue analysis and electrochemical sensors for real-time detection of aging markers in biofluids. Predictive modeling integrates data from these analyses and multiple domains-cognition, cardiovascular health, voice, food texture perception and habits-to generate diagnostic tools that monitor biological aging and inform early interventions. A proof-of-concept study in an older population sample, with special attention to user experience, will evaluate the potential benefits of these findings in improving the quality of life for older adults.

RESULT: Not applicable. The ITTHACA project is ongoing, with outcomes expected to include validated biomarkers, novel biosensors, and predictive models that facilitate early interventions.

CONCLUSION: ITTHACA demonstrates the power of interdisciplinary collaboration in tackling the complex multidomain challenge of aging. By leveraging the expertise of complementary Basque Country Research Centers, this initiative is poised to produce innovative resources for prolonging healthy and autonomous living. The project's outcomes are expected to support new therapeutic strategies and socio-healthcare interventions that address the rising prevalence of aging-related conditions, including cognitive decline.},
}

Humans
Aged
*Public Health
Female
Male
Aged, 80 and over
Biomarkers
Middle Aged
*Aging
*Healthy Aging

@article {pmid41434948,
year = {2025},
author = {Kaiyrlykyzy, A and Zholdasbekova, G and Alzhanova, D and Kozhakhmetov, S and Kushugulova, A and Askarova, S},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e097791},
doi = {10.1002/alz70855_097791},
pmid = {41434948},
issn = {1552-5279},
mesh = {Humans ; Male ; Female ; *Alzheimer Disease/genetics/epidemiology ; Aged ; Kazakhstan/epidemiology ; Polymorphism, Single Nucleotide/genetics ; Gastrointestinal Microbiome ; Cytokines/blood ; Risk Factors ; Cohort Studies ; Middle Aged ; Apolipoproteins E/genetics ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is the leading cause of dementia and a critical social issue. Its multifactorial nature necessitates evaluating risk factors in diverse populations.

METHODS: This study analyzed 181 AD patients and 244 controls in Kazakhstan, comparing clinical, genetic, and microbial traits.

RESULTS: In our cohort, significant dementia-associated variables included smoking, depression, dyslipidemia, insulin resistance, and liver dysfunction. AD patients had higher HDL, bilirubin, AST/ALT ratios, and lower ALT. Genetic analysis identified 13 SNPs linked to AD, notably in APOE, TOMM40, and MED12L genes involved in lipid metabolism, mitochondrial function, and gene transcription. APOE4 increased AD risk 1.9x, with higher prevalence in northern Kazakhstan (Astana). We also found specific alterations in the gut microbiome, specifically, a decreased Firmicutes/Bacteroidetes ratio, a reduced Bifidobacterium, and increased proteobacteria and inflammatory bacteria. The investigation of cytokine profiles demonstrated that pro-inflammatory cytokines such as IFN-γ, IL-6, TNF-β, MCP-1, and IL-17A were significantly elevated in AD patients, along with anti-inflammatory cytokines IL-4 and IL-1RA, suggesting a dysregulated inflammatory response in AD. Additionally, elevated serum adiponectin levels, observed at three times higher than in controls, were strongly correlated with multiple cytokines and specific microbial taxa, such as Actinobacteria and Acidomicrobiia, indicating a potential interplay between gut microbiota, adipose tissue, and neuroinflammation in AD.

CONCLUSION: These findings underscore the importance of considering bio-geographic and environmental factors in AD research. The study's outcomes may aid in further research and the development of personalized approaches for managing and treating AD in distinct geographical regions. Research support: Nazarbayev University Collaborative Research Program Grant [Funder Project Reference: 20122022CRP1602] and the Ministry of Higher Education and Science of the Republic of Kazakhstan Grant [Funder Project Reference: AP14871338].},
}

Humans
Male
Female
*Alzheimer Disease/genetics/epidemiology
Aged
Kazakhstan/epidemiology
Polymorphism, Single Nucleotide/genetics
Gastrointestinal Microbiome
Cytokines/blood
Risk Factors
Cohort Studies
Middle Aged
Apolipoproteins E/genetics

@article {pmid41434766,
year = {2025},
author = {Lwere, K},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e097665},
doi = {10.1002/alz70855_097665},
pmid = {41434766},
issn = {1552-5279},
mesh = {Humans ; *Alzheimer Disease/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Male ; *Cognitive Dysfunction/microbiology ; Female ; Aged ; *Dysbiosis/microbiology ; Uganda ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Feces/microbiology ; Phylogeny ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is the leading cause of global cognitive decline. However, its mechanisms remain poorly understood in sub-Saharan Africa (SSA), where genetic, dietary, and environmental factors differ significantly. Emerging evidence links the gut microbiota to AD through neuroinflammation and gut-brain axis dysfunction. This study investigated phylogenetic and compositional microbiome shifts in AD, Mild Cognitive Impairment (MCI), and healthy controls in Uganda, providing novel insights into microbial dysbiosis and its role in cognitive decline in low-resource settings.

METHOD: In this cross-sectional study, stool samples from 104 participants (AD: 77; MCI: 14; controls: 13) were analyzed using 16S rRNA sequencing (V3-V4 region), with DADA2 generating amplicon sequence variants (ASVs). Beta diversity was assessed using Weighted UniFrac (phylogenetic differences) and Bray-Curtis (compositional differences) metrics. Principal Coordinate Analysis (PCoA) was used to visualize clustering patterns, whereas group differences were assessed using Permutational Multivariate Analysis of Variance (PERMANOVA) at p < 0.05.

RESULT: Beta diversity analysis revealed distinct microbial shifts that were linked to cognitive decline. Weighted UniFrac PCoA showed clear clustering, with Axis 1 (39.46% variation) separating AD patients from controls and Axis 2 (16.28%) capturing within-group variability, particularly in AD. The MCI group occupied an intermediate position, reflecting the microbial gradient associated with cognitive decline. Confidence ellipses highlighted minimal overlap between AD and controls, whereas MCI partially overlapped with both groups, suggesting a transitional profile. Bray-Curtis PCoA confirmed compositional differences, with PC1 (28.66%) separating AD from controls and PC2 (14.44%) capturing MCI dispersion. PERMANOVA confirmed significant group-level differences (Weighted UniFrac: R² = 0.18, p = 0.001; Bray-Curtis: R² = 0.21, p = 0.001), with the strongest divergence between AD and controls (p = 0.001), and significant differences between AD and MCI (p = 0.005).

CONCLUSION: Distinct microbial shifts across AD, MCI, and control groups highlight the role of the gut microbiome in neurodegeneration. The transitional profile of MCI underscores its potential as an early marker of dysbiosis, supporting the development of microbiome-targeted strategies for the early detection and intervention of Alzheimer's disease.},
}

Humans
*Alzheimer Disease/microbiology
Cross-Sectional Studies
*Gastrointestinal Microbiome/genetics
Male
*Cognitive Dysfunction/microbiology
Female
Aged
*Dysbiosis/microbiology
Uganda
RNA, Ribosomal, 16S/genetics
Middle Aged
Feces/microbiology
Phylogeny

@article {pmid41434746,
year = {2025},
author = {Williams, C and Golden, A and Yadav, H and Masternak, MM and , },
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e100453},
doi = {10.1002/alz70860_100453},
pmid = {41434746},
issn = {1552-5279},
mesh = {Humans ; *Public Health ; *Gastrointestinal Microbiome ; *Patient Selection ; },
abstract = {BACKGROUND: Gut microbiota is crucial in nutrient extraction, metabolism, cognition, and immune function. Consequently, the increasing number of microbiome studies aims to link specific bacteria, fungi, and viruses with various cognitive disease outcomes. Unfortunately, clinical studies often exclude many older adults with Alzheimer's Disease and Related Dementia who are homebound or from racially/ethnically diverse populations. The homebound older adult population is estimated to be three times larger than the equally impaired and chronically ill nursing home population. People of color often hesitate to participate in clinical trials due to mistrust, logistical barriers, and lack of awareness. Recruiting a diverse group of patients has been challenging.

METHOD: We review the literature using CINAL, PubMed, Medline, PsycINFO, and Embase to highlight evidence-based strategies for promoting inclusivity among homebound and minority communities in microbiome studies. Additionally, we discussed the inclusion and exclusion criteria necessary for clinical trials.

RESULTS: We identified strategies such as community engagement, culturally appropriate assistance, mobile health units, and strategic partnerships with feedback mechanisms to improve recruitment and retention of underserved populations. We also discussed inclusion and exclusion criteria while highlighting factors that can confound results. While these criteria may complicate trials involving vulnerable populations, they are essential for optimizing outcomes. We must recognize and adequately support these populations while keeping these criteria in mind.

CONCLUSION: This review emphasized recruitment strategies for underrepresented groups in microbiome studies and underscores the importance of inclusion and exclusion criteria to ensure robust study results. Without inclusivity in microbiota clinical trials, we cannot effectively address health inequities or ensure the generalizability of findings. The complexity and long-term nature of these trials suggest that additional support for patients and caregivers may be necessary for participants with cognitive decline. Diverse participation helps uncover variations in disease prevalence, progression, and treatment responses among different populations, leading to more personalized and effective healthcare solutions. It also enhances the overall quality of research by incorporating a wide range of perspectives and experiences.},
}

Humans
*Public Health
*Gastrointestinal Microbiome
*Patient Selection

@article {pmid41434707,
year = {2025},
author = {Dempsey, DA and Agarwal, P and Fernandez, S and Brosch, JR and Quirke, M and Graham-Dotson, Y and Gao, S and Clark, D and Apostolova, LG and Clark, DG and Farlow, MR and Mathew, S and Unverzagt, F and Wang, S and Diaz, E and Schimmel, L and French, R and Blach, C and Kaddurah-Daouk, RF and Saykin, AJ and Risacher, SL and , },
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e105690},
doi = {10.1002/alz70860_105690},
pmid = {41434707},
issn = {1552-5279},
mesh = {Humans ; Male ; Female ; Aged ; *Cognitive Dysfunction/diet therapy ; *Public Health ; Surveys and Questionnaires ; *Diet, Mediterranean ; Middle Aged ; Indiana ; Alzheimer Disease ; Self Report ; Reproducibility of Results ; Aged, 80 and over ; },
abstract = {BACKGROUND: The Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) diet has been associated with cognitive benefits and reduced risk of Alzheimer's disease. Adherence is typically assessed using comprehensive but time-consuming food frequency questionnaires (FFQs). We examined concurrent validity between a brief MIND diet screener and a more extensive FFQ.

METHODS: 94 participants (51 cognitively normal (CN), 31 subjective cognitive decline (SCD), 12 mild cognitive impairment (MCI)) from the Indiana Alzheimer's Disease Research Center (IADRC) who participated in the Alzheimer's Gut Microbiome Project (AGMP) completed both the self-reported 15-item MIND screener and computerized Vioscreen FFQ. For both measures, we used the same cutoff criteria to assign values of 0, 0.5, or 1 corresponding to low, medium, and high intake for the 'healthy' food groups and reverse correspondence for the 'unhealthy' food groups, which were then summed to generate a total MIND diet score (0-15) with higher scores indicating greater adherence. Agreement between the two methods was assessed using Pearson correlation, intraclass correlation coefficient (ICC) for absolute agreement and consistency, and a tertile-based cross-classification. ANOVA was used to test differences in MIND scores between diagnostic groups, adjusting for age, sex, and education.

RESULTS: The mean MIND diet score from the FFQ was 7.49 (range: 2.5-11), and from the screener was 10.05 (range: 5-13.5), with a mean 2.56-point difference showing consistently higher scores on the screener (Figure 1). The screener demonstrated moderate correlation with the FFQ score (r = 0.63, p <0.001, R2=0.40). Absolute agreement was low (ICC=0.34), while consistency was moderate (ICC=0.64) (Figure 2). In cross-classification, 19.15% of individuals were classified into disparate tertiles. A significant difference was observed between CN and MCI groups using both methods, but only the screener-derived score remained marginally significant after adjustments (p = 0.05) (Figure 3).

CONCLUSIONS: The MIND screener shows moderate correlation and consistency with the FFQ, with participants systematically reporting higher scores on the screener, indicating overestimation of their MIND diet score. While the screener does not capture detailed or food item specific dietary variations assessed by the FFQ, it is a valid tool for rapid estimation of MIND diet score and may be useful in research and clinical practice.},
}

Humans
Male
Female
Aged
*Cognitive Dysfunction/diet therapy
*Public Health
Surveys and Questionnaires
*Diet, Mediterranean
Middle Aged
Indiana
Alzheimer Disease
Self Report
Reproducibility of Results
Aged, 80 and over

@article {pmid41434687,
year = {2025},
author = {Hisham, HIH and Lim, SM and Ramasamy, K and Majeed, ABA and Shahar, S},
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e106306},
doi = {10.1002/alz70860_106306},
pmid = {41434687},
issn = {1552-5279},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Public Health ; Aged ; *Cognitive Dysfunction/microbiology/therapy ; *Frailty/microbiology/psychology ; *Dysbiosis/microbiology ; Exercise ; Feces/microbiology ; },
abstract = {BACKGROUND: Cognitive frailty (CF), a condition characterised by the co-occurrence of physical frailty and cognitive impairment, has been linked to dysregulated gut microbiota (i.e., dysbiosis) and increased intestinal permeability. Emerging evidence suggests that the gut microbiome plays a crucial role in maintenance of gut-brain barrier integrity, suppression of neuroinflammation, regulation of neurotransmitter production, and ultimately promotion of psychological health. This study aimed at examining the effects of a 6-month multidomain intervention (i.e., physical exercise, cognitive training, psychosocial training and nutritional guidance) on gut microbiota composition.

METHOD: A total of 27 CF participants (12 control; 15 intervention) were recruited and stool samples were collected for 16S rRNA sequencing. The stool samples were homogenised, and DNA was extracted, followed by PCR amplification, DNA library preparation, and sequencing. Statistical analysis was performed using GraphPad Prism. Normality was assessed using the Shapiro-Wilk Test, and differences between groups were analysed using the Ordinary One-way ANOVA Test. Correlations between genus abundance and psychosocial parameters were evaluated using Pearson's correlation analysis.

RESULT: Microbiota profiling revealed a significant increase of the Blautia genus in the intervention group (IV6, intervention after 6 months) when compared to the control group (C6, control after 6 months) (p = 0.0132), suggesting a positive shift in gut microbial balance following lifestyle modifications. The Blautia genus abundance was negatively correlated with depression (r = -0.4120, p = 0.0022) and loneliness scores (r = -0.3328, p = 0.0184), indicating its potential protective role against psychosocial factors. On the contrary, the Prevotella genera exhibited a positive correlation with depression scores (r = 0.2820, p = 0.04), reinforcing its association with neuroinflammation which disrupts neurotransmitter balance.

CONCLUSION: The present results highlight the positive impact of lifestyle interventions on gut microbial composition and their possible implications for psychosocial health in older adults with CF. The Blautia genus enrichment may serve as a biomarker or therapeutic target for improving psychosocial well-being in CF individuals. This warrants further investigation of the mechanistic pathways linking gut microbiota modifications with psychosocial outcomes.

FUNDING: This study is part of the Transforming Cognitive Frailty to Later-Life Self-sufficiency (AGELESS) project funded by the Ministry of Higher Education, Malaysia under the Long-Term Research Grant Scheme (LRGS/1/2019/UM/01/1/3).},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
*Public Health
Aged
*Cognitive Dysfunction/microbiology/therapy
*Frailty/microbiology/psychology
*Dysbiosis/microbiology
Exercise
Feces/microbiology

@article {pmid41434599,
year = {2025},
author = {Dinesh, D and Morgan, X and Scott, TM and Garelnabi, M and Mangano, KM and Noel, SE and Huttenhower, C and Tucker, KL and Palacios, N},
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e098660},
doi = {10.1002/alz70860_098660},
pmid = {41434599},
issn = {1552-5279},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Aged ; *Public Health ; Puerto Rico/ethnology ; Prospective Studies ; Feces/microbiology/virology ; *Cognition/physiology ; Hispanic or Latino ; Boston ; Cross-Sectional Studies ; Dysbiosis ; *Virome ; Aged, 80 and over ; Middle Aged ; Alzheimer Disease ; White ; },
abstract = {BACKGROUND: Gut bacterial variations and dysbiosis may influence cognitive function via the microbiome-gut-brain-axis. Gut viruses may also, directly or indirectly, impact cognitive function by modulating the gut bacteria. Hispanics/Latinos, who may have unique microbiome characteristics, are at a higher risk of Alzheimer's disease and related dementia. There is a lack of research on the gut microbiome and, especially, the virome in Hispanics/Latinos. Here, we examined variations in the gut bacteriome and virome associated with cognitive function in the Boston Puerto Rican Health Study (BPRHS), a prospective cohort of older Puerto Rican adults residing in the Boston area.

METHOD: This study was conducted in 316 BPRHS participants with fecal metagenomic sequencing and cognitive assessments, summarized as a composite global cognitive score (GCS). Taxonomic profiling of the gut bacteriome was performed using MetaPhlAN 4.0. Gut virome profiles from shotgun sequencing were generated using BAQLaVa 1.0. Cross-sectional associations between bacterial and viral composition and GCS were assessed using alpha (Shannon) and beta (Bray-Curtis) diversity indices. Feature-wise testing was performed using multivariate linear regression (MaAsLin2) to identify bacterial and viral taxa associated with the GCS.

RESULT: Among 316 participants (mean age 68.7 years, 70.9% female), there were no differences in overall bacterial or viral composition, measured by alpha and beta diversity, based on GCS. In feature-wise analyses, adjusted for age, sex, and BMI, among participants with higher GCS (better cognitive function), we observed an enrichment of Faecalibacterium prausnitzii bacterium (β = 0.78, p = 0.01, FDR p = 0.22), and depletion of the phage Carjivirus communis (β = -1.07, p < 0.01, FDR p = 0.09).

CONCLUSION: The observed results suggest an enrichment of F. prausnitzii, a beneficial butyrate producing taxa, among participants with better cognitive function, and enrichment of Carjivirus communis, a Crassvirales dsDNA Bacteroidetes phage, among participants with worse cognitive function. A recent study reported an association between Bacteroidetes phages and amyloid β and Alzheimer's disease pathology. Gut viral variations may modulate gut bacteria, impacting cognitive function. Future work will test interactions of the gut bacteriome, virome and their functional pathways, as related to cognitive function in Puerto Rican adults.},
}

Humans
Female
Male
*Gastrointestinal Microbiome
Aged
*Public Health
Puerto Rico/ethnology
Prospective Studies
Feces/microbiology/virology
*Cognition/physiology
Hispanic or Latino
Boston
Cross-Sectional Studies
Dysbiosis
*Virome
Aged, 80 and over
Middle Aged
Alzheimer Disease
White

@article {pmid41434434,
year = {2025},
author = {de Souza, IC and de Lima, AMDL and Bastiani, M and Borelli, WD and Ebert, ELK and Barth, RA and Senger, JE and Schumacher-Schuh, AF and Moriguchi, EH and Senger, J and Bruscato, NM and Werle, BM and Zanella, L and Netson, LV and Detogni, A and Guerra, RR and Martins, AF and Barboza, JVC and Gaio, EJ and Zimmer, ER},
title = {Developing Topics.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 7},
number = {},
pages = {e108925},
doi = {10.1002/alz70861_108925},
pmid = {41434434},
issn = {1552-5279},
mesh = {Humans ; *Cognitive Dysfunction/microbiology ; Aged ; Male ; *Alzheimer Disease/microbiology ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Saliva/microbiology ; Aged, 80 and over ; *Dysbiosis/microbiology ; *Mouth/microbiology ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is a progressive neurodegenerative disorder that ultimately leads to dementia. Emerging evidence suggests that oral dysbiosis may contribute to AD. The oral microbiota plays a crucial role in maintaining systemic health, and its imbalance has been associated with neurodegeneration. However, beyond the identification of individual taxa, the structure and dynamics of microbial communities-particularly their ecological interactions-remain poorly understood in AD. Here, we investigated abundance association networks of the oral microbiota across the AD continuum.

METHOD: Saliva samples collected from 12 elderly individuals classified as cognitively unimpaired (CU), having mild cognitive impairment (MCI), or having Alzheimer's disease (AD) were sequenced on the Illumina MiSeq™ platform, targeting the V3-V4 regions of the 16S rRNA gene. FASTQ files were processed using the DADA2 pipeline. Amplicon sequence variants (ASVs) were inferred, and taxonomic assignments were performed using the eHOMD 16S rRNA database. ASVs were normalized by rarefaction without replacement. Finally, normalized, centered log-ratio transformed abundance data were used to construct genus-level correlation networks for the CU, MCI, and AD groups.

RESULT: In CU individuals, Eikenella maintained exclusively positive associations with other microbial taxa (Figure 1). However, these interactions were significantly reduced or shifted toward negative relationships in individuals with AD. Notably, one of the most pronounced changes was the weakened association between Eikenella and Lachnospiraceae_G_3 in individuals with AD. Additionally, a positive relationship between Eikenella and Peptostreptococcaceae_XIG_1 observed in CU shifted to a negative relationship in the AD group. These specific microbial associations were not observed in the MCI group.

CONCLUSION: In summary, our results suggest a disruption in microbial synergy, which may reflect or potentially contribute to the underlying pathological mechanisms of AD. Network analysis may provide valuable insights into the dynamic changes within the oral microbiome across different stages of AD, thereby enhancing our understanding of the oral microbiome's role in neurodegenerative processes.},
}

Humans
*Cognitive Dysfunction/microbiology
Aged
Male
*Alzheimer Disease/microbiology
Female
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Saliva/microbiology
Aged, 80 and over
*Dysbiosis/microbiology
*Mouth/microbiology

@article {pmid41434376,
year = {2025},
author = {Blanco, EJ and Gonzalez, R and Perez, G and Piñero, J and Morales, H and Olivieri-Henry, G and Gonzalez, C and Godoy-Vitorino, F and Sepulveda, V},
title = {Developing Topics.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 7},
number = {},
pages = {e108947},
doi = {10.1002/alz70861_108947},
pmid = {41434376},
issn = {1552-5279},
mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Aged ; *Alzheimer Disease/epidemiology/genetics/complications ; *Periodontitis/epidemiology ; Puerto Rico/epidemiology ; Hispanic or Latino ; *Periodontal Diseases/epidemiology ; Aged, 80 and over ; Severity of Illness Index ; White ; },
abstract = {BACKGROUND: Periodontal inflammation has been implicated in Alzheimer's Disease (AD) through systemic inflammatory and neurodegenerative pathways, including microbial dysbiosis and cytokine signaling and microbial infiltration. While the oral microbiome's role in cognitive decline has gained momentumrecently, there is limited research on these associations in Hispanic population, underrepresented in Alzheimer's research and facing disproportionately high burden of both dementia and oral disease.

OBJECTIVE: To evaluate the association between periodontal disease severity and clinical, cognitive, metabolic, and genetic factors in a cohort of Puerto Rican older adults with and without Alzheimer's Disease.

METHODS: We conducted a cross-sectional analysis of 43 community-dwelling participants enrolled in the Association-Gut-Microbiome-AD (IRB: 2290033626) study. Each underwent a full-mouth periodontal examination, including clinical attachment loss (CAL), probing depth (PD), and bleeding on probing (BOP) at six sites per tooth. Periodontal disease severity was classified using CDC-AAP 2012 case definitions: mild, moderate, or severe periodontitis based on interproximal CAL and PDthresholds. Predictor variables included age, BMI, insulin resistance (HOMA-IR), APOE-ε4 status, AD, and cognitive scores (MoCA and CDR). Bivariate analyses and Multinomial logistic regression were used to assess associations.

RESULTS: Eighty-one percent of participants met criteria for periodontitis, including 28% with severe and 49% with moderate disease. Age was the most consistent predictor of worsening periodontal inflammation (p < 0.01). CDR scores were significantly associated with greater severity in both bivariate (p < 0.01) and unadjusted models (CDR mild vs none: OR = 0.13; 95% CI, 0.02-0.86; p = 0.03). Severe periodontitis was more commonly observed in Alzheimer's, showing a higher odds ratio when compared to controls (OR = 2.75; p = 0.44) though not statistically significant. MoCA scores, APOE-ε4 status, BMI, and HOMA-IR were not significantly associated with periodontal severity.

CONCLUSION: Aging and dementia severity (CDR) were the strongest predictors of periodontal inflammation. These findings align with emerging literature linking oral microbial dysbiosis and neuroinflammatory mechanisms in AD. The use of standardized CDC-AAP definitions provided clinical rigor, and the elevated periodontitis prevalence observed in this cohort underscores the need for integrated oral-systemic care strategies in dementia prevention and management, particularly in underrepresented populations such as Puerto Rico.},
}

Humans
Male
Female
Cross-Sectional Studies
Aged
*Alzheimer Disease/epidemiology/genetics/complications
*Periodontitis/epidemiology
Puerto Rico/epidemiology
Hispanic or Latino
*Periodontal Diseases/epidemiology
Aged, 80 and over
Severity of Illness Index
White

@article {pmid41434102,
year = {2025},
author = {Ngouongo, YJW and Muhammad, JA and Bernal, R and Satizabal, CL and Beiser, AS and Ramachandran, VS and Kautz, TF and Seshadri, S and Himali, JJ and Fongang, B},
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e103169},
doi = {10.1002/alz70860_103169},
pmid = {41434102},
issn = {1552-5279},
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Public Health ; *Cognition/physiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Emerging evidence indicates a complex interplay between cardiovascular health, gut microbiome composition, and cognitive function. Life's Essential 8 (LE8), created by the American Heart Association, encompasses crucial cardiovascular health metrics. This study aimed to explore the relationship between LE8 adherence, gut microbiota, and cognition.

METHOD: We used stool samples, LE8 metrics, and cognitive assessment measures from a sample of 781 participants (mean age 54.9 years, 57.1% Female) from the Framingham Heart Study (generation3, New Offspring Spouses, and the Omni2 cohorts) at the 3[rd] examination (2016-2019). Associations between LE8 adherence, gut microbiome diversity, and cognitive performance were evaluated using multivariable linear regression models, adjusting for potential confounders. Mediation analysis was conducted to explore whether specific bacterial taxa mediated the relationship between LE8 adherence and cognitive performance.

RESULT: Participants with greater adherence to LE8 demonstrated significantly increased gut microbial diversity (α-diversity: Chao1, p = 0.0014; Shannon, p = 0.0071) and distinct microbial compositions (β-diversity: PERMANOVA p = 1e-4). Higher adherence to LE8 was related to an increased abundance of genera Barnesiella and Ruminococcus, while reduced abundance of Clostridium was associated with higher LE8 adherence. Greater gut microbial diversity (α-diversity: Chao1, p = 0.0012; Shannon, p = 0.0066), and beneficial genera like Oscillospira correlated with better global cognitive scores (GCS). Taxonomic overlap analyses revealed microbial taxa that simultaneously influence LE8 adherence and cognitive outcomes. Mediation analyses indicated that specific taxa, including Barnesiella and Lentisphaerae, mediated the link between higher LE8 adherence and better cognitive performance. These taxa could be key modulators in the gut-brain axis, connecting cardiovascular and brain health. Conversely, higher Clostridium abundance was associated with poorer cognitive performance.

CONCLUSION: This study highlights the interconnected relationship between cardiovascular health, gut microbiome diversity, and cognitive function. Higher adherence to LE8 was associated with favorable microbial profiles and better cognitive performance, with the gut microbiome serving as a critical mediator. These findings emphasize the importance of integrated lifestyle interventions that address cardiovascular and cognitive health simultaneously. To validate these results and refine therapeutic strategies, future research should prioritize longitudinal studies and randomized controlled trials that explore the causal pathways and clinical applications of these findings.},
}

Humans
Male
Female
*Gastrointestinal Microbiome/physiology
Middle Aged
*Public Health
*Cognition/physiology
Feces/microbiology

@article {pmid41433829,
year = {2025},
author = {Nyame, I and Ngouongo, YJW and Ayele, BA and Djotsa, AN and Jian, X and Fonteh, AN and Seshadri, S and Himali, JJ and Fongang, B and , },
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e096594},
doi = {10.1002/alz70860_096594},
pmid = {41433829},
issn = {1552-5279},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Sleep/physiology ; *Public Health ; Feces/microbiology ; *Cognition/physiology ; Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The American Heart Association has identified eight metrics for improving heart and brain health, including sleep health. Recent studies highlight the strong link between sleep health, gut microbiome, and diseases like Alzheimer's. While sleep deprivation is known to affect gut microbiome and brain health, the specific impact of sleep health on gut microbiome and cognitive disorders remains largely unexplored.

METHOD: We analyzed stool samples and sleep metrics from 781 participants (mean age 54.9, 57.1% female) in the Framingham Heart Study to examine the effect of sleep on gut microbiome composition and cognitive performance. Using the V4 region of the 16S rRNA and Lefse analysis, we identified microbiome profiles related to sleep health. ANOVA assessed the sleep-cognitive performance relationship, while multivariable and differential abundance analyses explored the microbiome's link to cognitive function, controlling for age, sex, and education.

RESULT: Differences in bacterial diversity were observed between low, moderate, and high groups. Lefse analysis showed higher levels of aldenense, bolteae, symbiosium, and lavalense in the low group, while Butyrivibrio, putredinis, and Dorea were less abundant. ANOVA indicated a significant correlation between global cognitive scores and sleep metrics (p = 0.0024). Positive correlations were found between cognitive scores and Pseudobutyrivibrio and Ruminococcus, while negative correlations were observed with Barnesiella and Clostridium. At the species level, xylanivorans and lactaris were positively correlated, whereas boltea, callidus, and intestinihominis were negatively correlated with cognitive scores.

CONCLUSION: Our findings showed that individuals with good sleep scores had higher cognitive performance, while those with lower sleep scores had lower cognitive performance. The results also indicated an association between gut microbiome and sleep metric as well as between gut microbiome and cognitive performance. Finally, our work revealed that the taxa Clostridium and bolteae exhibited association with both sleep metric and cognitive performance. Further studies should be conducted to understand the effects of sleep metric on the relationship between gut microbiome and the risk of developing Alzheimer's Disease and Related Dementias (ADRD).},
}

Humans
Female
Male
*Gastrointestinal Microbiome/physiology
Middle Aged
*Sleep/physiology
*Public Health
Feces/microbiology
*Cognition/physiology
Aged
RNA, Ribosomal, 16S/genetics

@article {pmid41432929,
year = {2025},
author = {Garcia, M and Sadler, NC and Stohel, I and Zhao, S and Krishnamoorthy, S and Farris, Y and Reichart, NJ and Bagwell, CE and Zambare, N and McClure, R},
title = {Community Dynamics Drive Calcium Carbonate Production in an Enriched Consortium of Soil Microbes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02632-y},
pmid = {41432929},
issn = {1432-184X},
abstract = {Recently, there has been a focus on using soil microbes as a means to store carbon in the soil in the form of calcium carbonate, outcomes of which include soil stabilization and biocementation. The molecular processes involved in microbially induced calcium carbonate formation are known, but there is still a significant knowledge gap regarding how community interactions, emergent processes that are distinct from the roles of individual members, may drive the formation of carbonate. To answer these questions, we describe the development and application of a consortium of soil microbes consisting of one species each of the Rhodococcus, Microbacterium, and Curtobacterium genera and two species from the Bacillus genus. We term these five species cultivated together carbon storing consortium A (CSC-A). Growth assays show that only a subset of CSC-A members produces CaCO3 with Rhodococcus producing the most CaCO3 but the complete CSC-A produces significantly higher amounts of CaCO3 compared to the sum total carbonate produced by all member species. The development of CSC-A shows that CaCO3 production may be as much a community process as it is the contribution of individual species, requiring us to move beyond single species analysis to fully understand carbonate formation by microbial communities in nature. CSC-A will allow the scientific community to ask and answer key questions about the molecular interactions surrounding inorganic carbon formation in soil, an important knowledge gap that must be filled if we wish to stabilize soils and harness microbial processes for materials production.},
}

@article {pmid41432837,
year = {2025},
author = {Yu, F and Yan, Y and Chen, L and Song, L and Salama, ES and Su, S},
title = {Salivary microbiome and metabolome profiles associated with dental caries in Tibetan children from high-altitude regions.},
journal = {Odontology},
volume = {},
number = {},
pages = {},
pmid = {41432837},
issn = {1618-1255},
support = {2022LQTD57//Longyuan Youth Innovation and Entrepreneurship Talents/ ; Lzuyxcx-2022-145//Office of English Language Acquisition/ ; 2019-FWZX-03//Lanzhou University Special Research Project of Serving the Economic and Social Development of Gansu Province/ ; },
abstract = {This study investigated, for the first time, the salivary microbiome and metabolome profiles associated with dental caries in Tibetan children of mixed dentition residing in high-altitude areas. Moreover, a diagnostic model for caries was established by exploring the potential cariogenic mechanisms of identified biomarkers. Saliva samples were collected from 28 Tibetan children (aged 10.20 ± 0.67 years in the high caries [HC] group, n = 15; 10.38 ± 0.65 years in the caries-free [H] group, n = 13). Illumina 16S rRNA sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) were employed to analyze microbial composition and metabolic profiles, respectively. Although alpha diversity showed no significant differences among groups, beta diversity analysis revealed distinct microbial and metabolic differences between the HC and H groups. Several bacterial genera exhibited significant variations and were strongly correlated with caries status. Salivary microbial and metabolic compositions differed significantly between Tibetan children with and without caries in high-altitude areas; differential biomarkers may serve as diagnostic or early-warning indicators of dental caries in this unique population. The identified microorganisms and metabolites could be used as non-invasive biomarkers or early warning markers for dental caries detection in Tibetan children in high-altitude areas. Moreover, the further exploration of their pathogenic roles will be helpful for the prevention and discovery of therapeutic drug targets of caries in Tibetan children at high altitude.},
}

@article {pmid41432792,
year = {2025},
author = {Basile, A and Spagoni, L and Visaggio, D and Riggio, FP and Bologna, MA and Mancini, E and Visca, P and Riccieri, A},
title = {The Putative Involvement of Bacterial Symbionts in Cantharidin Biogenesis: An Explorative Study in Meloidae Insects.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02683-1},
pmid = {41432792},
issn = {1432-184X},
abstract = {Insect-microbes holobionts integrate host and microbial functions, with symbionts supporting nutrition, immunity, and defence, while producing metabolites, including beetle-derived compounds with therapeutic potential. Cantharidin is a toxic terpene produced by blister beetles (Coleoptera: Meloidae), endowed with defensive and pharmacological properties. Male insects produce and contain cantharidin in large quantities and transfer it to females upon mating. This study is aimed to gain information about the involvement of insect-associated bacteria in cantharidin biogenesis. To support the possibility that bacteria participate in cantharidin biogenesis, cantharidin antibacterial activity was assessed against six reference strains of representative species of Bacillota and Pseudomonadota from publicly available culture collections. All bacterial strains tolerated concentrations up to 600 µg/ml cantharidin in a standard antibacterial susceptibility test. To identify candidate bacterial lineages, 16S rRNA metataxonomic profiling of the V5-V6 region was performed in males and females from different Meloidae subfamilies and tribes. Analysis of the insect-associated microbiomes of the five cantharidin-producing species (Lydus trimaculatus, Meloe proscarabaeus, Mylabris variabilis, Hycleus polymorphus, Zonitis flava) revealed communities dominated by Pseudomonadota, with secondary contributions from Actinomycetota in Z. flava and M. proscarabaeus and Cyanobacteriota in the other host insects. Although overall community structure and composition did not differ significantly between sexes, a few taxa displayed consistent male-associated patterns, with Staphylococcus, Cutibacterium and one Enterobacteriaceae ASV resulting more abundant in males across all species. The intrinsic bacterial resistance to cantharidin, with both quantitative and qualitative differences in microbiome structure between male and female insects, makes the hypothesis of a putative involvement of bacteria in cantharidin biogenesis still viable.},
}

@article {pmid41432724,
year = {2025},
author = {Zhang, Z and Ye, B and He, J and Xiang, L and Li, S and Zhao, J and Chen, W and Zhang, Q and Zhao, W and Yang, J and Li, Y and Ju, J and Liu, Y and Xia, M},
title = {Microbial metabolites associated with healthy lifestyles in relation to metabolic syndrome and vascular health: a cross-sectional study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143325},
doi = {10.1128/msystems.01433-25},
pmid = {41432724},
issn = {2379-5077},
abstract = {UNLABELLED: Lifestyle behaviors influence the risk of metabolic syndrome (MetS) and affect vascular health. However, the interactions between gut microbiota and lifestyle behaviors in relation to MetS, as well as the specific microbial taxa and metabolites involved, remain unclear. Here, we aimed to investigate the associations among healthy lifestyle behaviors, gut microbiota, and MetS and to explore the potential mediating roles of microbially derived metabolites in these associations. A total of 1,342 participants with complete assessments of the Healthy Lifestyle Score (HLS), MetS, and vascular health were enrolled. Fecal samples were collected and subjected to metagenomic sequencing. Host genetic data were obtained using a high-density genotyping array, and plasma metabolites were quantified by liquid chromatography-mass spectrometry. Using generalized linear models, we found that increased abundances of Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis were associated with higher HLS and a reduced risk of MetS. Eleven microbial metabolic pathways were independently correlated with both HLS and MetS. Furthermore, increased plasma levels of cinnamoylglycine and betaine, driven by enhanced microbial capacity for homolactic fermentation, were identified as potential microbial effectors associated with MetS and vascular health. These findings indicate that the association between HLS and MetS may involve modulation of the gut microbiota and their metabolites and highlight the potential to enhance the beneficial effects of healthy behaviors on MetS and vascular health through microbiota-modifying interventions.

IMPORTANCE: Metabolic syndrome raises the risk of heart disease and diabetes, yet practical levers to prevent it remain limited. We show that everyday healthy habits align with a gut microbial "signature" linked to better vascular health and lower metabolic risk. Using metagenomics, metabolomics, and genetic causal analyses, we identify specific bacteria (Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis) and microbially produced molecules-especially cinnamoylglycine and betaine from enhanced homolactic fermentation-that may mediate these benefits. These findings connect lifestyle, the gut microbiome, and blood metabolites in a single framework, suggesting actionable biomarkers to monitor risk and potential microbiota-targeted strategies (diet and pre/probiotics) to improve cardiometabolic health. By highlighting concrete microbial pathways and metabolites, our work advances the path toward precision prevention and low-cost interventions for metabolic syndrome and vascular disease.},
}

@article {pmid41432650,
year = {2025},
author = {Peter Rimmer, and Zhang, F and Scott, G and , and Hold, GL and Gordon, M and Iqbal, TH and Hansen, R},
title = {The Gut Microbiome at the Onset of Inflammatory Bowel Disease: A Systematic Review and Unified Bioinformatic Synthesis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.09.014},
pmid = {41432650},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Few studies describe gut microbiome signatures in treatment-naïve new-onset inflammatory bowel disease (IBD). We present a novel secondary bioinformatic reanalysis of sequence outputs mapped to the latest microbial taxonomy.

METHODS: MEDLINE and Embase searches were performed for microbiome studies in treatment-naïve IBD. Appraisal was completed with Risk Of Bias In Non-randomized Studies - of Exposures (ROBINS-E). Available 16S ribosomal RNA sequence data sets were downloaded and missing data sets requested. Integrated data were run through a unified QIIME2 bioinformatics pipeline. Multivariable models adjusting for methodologic differences were developed using MaAsLin2.

RESULTS: There were 36 eligible studies; 18 contributed to bioinformatic reanalysis and 24 to supplementary meta-analysis. Samples from 1743 patients were included, comprising 678 from individuals with Crohn's disease (CD), 399 with ulcerative colitis (UC), 130 healthy controls (HCs), and 405 symptomatic controls (SCs); 990 of which were biopsy samples. Alpha diversity was reduced: feces-pediatric UC vs SCs, adult CD and UC vs HCs, and pediatric SCs vs HCs; pediatric biopsy samples-CD vs SCs, CD vs UC, and UC vs SCs. Beta diversity demonstrated clear distinctions between fecal and mucosal biopsy communities, least evident in UC, in addition to community separation by geography. Multivariate modeling revealed depletion of anaerobic and enrichment of aerobic and facultative anaerobic bacteria, alongside enrichment of oral genera across both CD and UC.

CONCLUSIONS: Core microbial perturbations at onset of CD and UC are depletion of anaerobes and enrichment of oxygen-tolerant, orally associated bacteria. As we place greater emphasis on early diagnosis and prediction of IBD risk, this finding may support innovative diagnostic approaches. Microbiome-targeted intervention and alteration of luminal oxygen availability may offer novel therapeutic avenues for new-onset patients and identified high-risk groups.},
}

@article {pmid41432437,
year = {2025},
author = {Bowerman, KL and Lu, Y and McRae, H and Volmer, JG and Zaugg, J and Pope, PB and Hugenholtz, P and Greening, C and Morrison, M and Soo, RM and Evans, PN},
title = {Metagenomic analysis of fecal microbiomes reveals genetic potential for diverse hydrogen management strategies in marsupials.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0160825},
doi = {10.1128/msystems.01608-25},
pmid = {41432437},
issn = {2379-5077},
abstract = {Methane is an end product of plant biomass digestion by gut microbiota, though the amount produced and/or released varies between hosts. On a per-unit-of-feed basis, macropodid marsupials (e.g., kangaroos) have been reported to emit less methane than ruminant livestock, despite a similar diet, although measurements exist for only a subset of macropodid species. Competition for hydrogen within the gut microbiome, particularly through alternative hydrogen sinks to methanogenesis, influences methane production; therefore, characterizing hydrogen management strategies within a host system can provide insights into methane emission profiles. In this study, we analyzed 33 fecal microbiomes of 14 marsupial species (predominantly captive animals) to provide the first systematic characterization of methanogen types and hydrogen-cycling genetic capacity across marsupial gut microbiomes. We recovered 1,394 metagenome-assembled genomes and identified host-associated bacterial signatures that varied significantly between marsupial species. Comparative analysis with fecal microbiomes from high- and low-methane-emitting mammals revealed that marsupials display heterogeneous hydrogen management strategies: some harbor elevated methanogenesis genes (mcrA, methanogen-specific hydrogenases), while others show enrichment of bacterial hydrogen-uptake hydrogenases and alternative electron acceptor pathways (nitrate/nitrite reduction, sulfite reduction). This predicted functional variation occurs both between and within marsupial families and gut types, suggesting that hydrogen management capacity may differ within taxonomic and anatomical classifications. These results demonstrate that marsupial gut microbiomes cannot be treated as a functionally homogenous group regarding methane emissions and highlight the need for species-specific measurements to accurately assess their methanogenic potential and inform ecological models of greenhouse gas production.IMPORTANCEHerbivorous marsupials such as kangaroos and wallabies have been reported to produce significantly lower methane emissions than ruminant livestock despite eating a similar diet, yet the microbial mechanisms underlying this difference remain poorly understood. Here, we conduct a comparative study of fecal microbiomes of 14 marsupial species to provide the first investigation of hydrogen-cycling genetic capacity across these animals. Through comparative analysis with fecal microbiomes of high- and low-methane-producing animals, we identify enrichment of bacterial genes for alternative hydrogen uptake and disposal pathways in some marsupials, supporting competition for hydrogen playing a role in the level of methane production. These data also indicate variation in hydrogen management between marsupials, including within species, suggesting methane emission capacity may vary at the level of the individual.},
}

@article {pmid41432331,
year = {2025},
author = {Tardo, DT and Cortes-Canteli, M and Fuster, V and Sachdev, PS and Kovacic, JC},
title = {The Heart-Brain-Metabolism Axis in Cardiovascular and Neurologic Disease.},
journal = {Journal of the American College of Cardiology},
volume = {86},
number = {25},
pages = {2663-2686},
doi = {10.1016/j.jacc.2025.09.1602},
pmid = {41432331},
issn = {1558-3597},
mesh = {Humans ; *Brain/metabolism/physiopathology ; *Cardiovascular Diseases/metabolism/physiopathology ; *Nervous System Diseases/metabolism/physiopathology ; *Heart/physiopathology ; *Myocardium/metabolism ; },
abstract = {The heart-brain axis has been widely acknowledged in medicine, but arguably it has not been particularly well understood until relatively recent times. For example, we have only recently come to appreciate the profound impact of the HBA on the development of vascular cognitive impairment and dementia (VCID). The complexity of these relationships is further reinforced by appreciating additional autonomic interconnectedness via the gut and metabolic pathways, as well as the spleen and immune pathways, in the form of the heart-brain-metabolism axis. Furthermore, the directionality of these pathways is complex, and all of these elements exert unique effects on the other. This multifaceted system is susceptible to pathologic processes involving multiple organ systems, namely, but not exclusively, the heart, vasculature, brain, autonomic nervous system, gut, and liver, with common clinical outcomes including VCID and cognitive frailty. In this state-of-the-art review, we explore the anatomic and physiologic interconnectedness between the heart, brain, gut, and metabolic systems. A focus has been placed on how relevant pathologic processes affect the cardiovascular and neurologic organ systems, as well as specific aspects of metabolism and the influence of the immune and gastrointestinal systems, all of which can contribute to both nervous system and cardiac dysfunction. Where relevant, we describe how therapeutic efforts should be focused on a preventative approach, with early identification of relevant cardiovascular and neurologic factors, to allow for the timely introduction of therapeutic measures to mitigate the risk of developing disease. Emerging approaches to cognitive risk prediction in cardiovascular disease include clinically accessible tools for older adults, brain imaging biomarkers linking stress-related neural activity to future cardiovascular events, and novel strategies such as gut microbiome modulation. Evidence supports the cognitive safety and potential neuroprotective benefit of statins, and ongoing trials and translational research aim to refine prevention through integrated cardiovascular, neurocognitive, and metabolic interventions.},
}

Humans
*Brain/metabolism/physiopathology
*Cardiovascular Diseases/metabolism/physiopathology
*Nervous System Diseases/metabolism/physiopathology
*Heart/physiopathology
*Myocardium/metabolism

@article {pmid41432253,
year = {2025},
author = {Ricci, F and Hutchinson, T and Leung, PM and Nguyen-Dinh, T and Zeng, J and Jirapanjawat, T and Eate, V and Wong, WW and Cook, PLM and Greening, C},
title = {Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf286},
pmid = {41432253},
issn = {1751-7370},
abstract = {Chemosynthesis, an ancient metabolism that uses chemical compounds for energy and biomass generation, occurs across the ocean. Although chemosynthesis typically plays a subsidiary role to photosynthesis in the euphotic ocean, it is unclear whether it plays a more important role in aphotic habitats within this zone. Here, we compared the composition, function, and activity of microorganisms colonising the sediment of a marine cave at mesophotic depth, across a transect from the entrance to the interior. Microbes thrived throughout this ecosystem, with interior communities having higher diversity than those at the entrance. Analysis of 132 species-level bacterial, archaeal, and eukaryotic metagenome-assembled genomes revealed niche partitioning of habitat generalists distributed along the cave, alongside specialists enriched across the entrance and interior environments. Photosynthetic microbes and photosystem genes declined in the inner cave, concomitant with enrichment of chemosynthetic lineages capable of using inorganic compounds such as ammonium, sulfide, carbon monoxide, and hydrogen. Biogeochemical assays confirmed that the cave communities consume these compounds and fix carbon dioxide through chemosynthesis, with inner communities mediating higher cellular rates. Together, these findings suggest that the persistent darkness and low hydrodynamic disruption in marine cave sediments create conditions for metabolically diverse communities to thrive, sustained by recycling of inorganic compounds, as well as endogenous and lateral organic matter inputs. Thus, chemosynthesis can sustain rich microbial ecosystems even within the traditionally photosynthetically dominated euphotic zone.},
}

@article {pmid41432144,
year = {2025},
author = {Liu, J and Ni, H-B and Yu, M-Y and Qin, S-Y and Elsheikha, HM and Peng, P and Guo, L and Xie, L-H and Liang, H-R and Lei, C-C and Xu, Y and Tang, Y and Yu, H-L and Qin, Y and Liu, J and Sun, H-C and Zhang, X-X and Qiu, B},
title = {Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0144325},
doi = {10.1128/msystems.01443-25},
pmid = {41432144},
issn = {2379-5077},
abstract = {UNLABELLED: Tibetan antelopes, native to high-altitude plateau regions, play an important role in the local ecosystem. Their gut harbors antimicrobial-resistant microbes, including potential pathogens. To explore this, we analyzed 33,925 metagenome-assembled genomes (MAGs), including 7,318 from 68 Tibetan antelopes sequenced in our laboratory. We first profiled the composition of antibiotic resistance genes (ARGs) and then examined their associations with virulence factor genes (VFGs). In total, 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being most prevalent. Two ARGs were located on phage-derived sequences, though their phage taxonomy could not be resolved. ARGs were significantly correlated with VFGs, particularly genes linked to adherence and effector delivery systems. Given potential dissemination risks, we further assessed associations between ARGs and mobile genetic elements (MGEs), finding that insertion elements accounted for the largest number of ARG-MGE links. Comparative analysis with other plateau animals and humans revealed seven ARGs uniquely present in Tibetan antelopes. In summary, this study provides the first comprehensive overview of ARG composition in Tibetan antelope gut microbiomes, establishing a baseline for future hypothesis-driven studies and antimicrobial resistance surveillance in wildlife.

IMPORTANCE: Investigating the drug resistance of Tibetan antelope (Pantholops hodgsonii) gut microbiota serves as a critical biological indicator for assessing the impact of human activities (particularly antibiotic contamination) on the fragile ecosystem of the Qinghai-Tibet Plateau. This study untangles the invasion of antibiotic resistance genes (ARGs) into remote conservation areas, suggesting that Tibetan antelopes may act as potential vectors for ARG dissemination across plateau environments. Such findings not only highlight threats to wildlife health but also provide an ecological warning regarding the pervasive environmental risks posed by the global antimicrobial resistance crisis in natural ecosystems.},
}

@article {pmid41431940,
year = {2026},
author = {Zhang, L and Wang, C and Zhang, X and Li, G and Sheng, Z},
title = {Identification of key gut microbiota and microbial QTL in contributing to the significant differences in body weight between two Chinese local chicken breeds.},
journal = {Animal genetics},
volume = {57},
number = {1},
pages = {e70060},
doi = {10.1111/age.70060},
pmid = {41431940},
issn = {1365-2052},
support = {XM202403//Open Research Fund of Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology/ ; 2021YFD1300100//National Key R&D Program of China/ ; 2021BBA234//Key Research and Develpment Project of Hubei province/ ; HBZY2023B007//the Supporting High Quality Development of Seed Industry Fund Project of Hubei Province/ ; 2023BAA029//Major Program (JD) OF Hubei province/ ; },
mesh = {Animals ; *Chickens/genetics/microbiology/growth & development ; *Gastrointestinal Microbiome/genetics ; *Quantitative Trait Loci ; *Body Weight/genetics ; Genome-Wide Association Study/veterinary ; China ; Phenotype ; Male ; },
abstract = {Previous studies have identified genetic loci that are associated with both feed conversion efficiency and gut microbiota in chickens, suggesting that interactions between the host genome and gut microbiota may influence chicken growth. However, the number of microbial QTL and gut microbiota associated with chicken body weight remains largely unknown. To further explore the impact of host-gut microbiota interactions on chicken body weight and to identify gut microbiota associated with chicken body weight, this study strictly controlled environmental interference and obtained phenotypic, genotypic, and gut microbiota composition data from 100 Langshan and Tibetan chickens (with significant differences in body weight) raised under identical standardized housing conditions. Through genome-wide association studies of chicken body weight, microbiome genome-wide association studies, and Mendelian randomization analysis, we have identified 145 microbial QTL as instrumental variables and screened out seven genera that have a significant causal relationship with chicken body weight, including the genera Blautia and Faecalibacterium. This study identified potential molecular and microbial markers associated with chicken body weight, offering a valuable theoretical framework for enhancing economic efficiency in poultry production.},
}

Animals
*Chickens/genetics/microbiology/growth & development
*Gastrointestinal Microbiome/genetics
*Quantitative Trait Loci
*Body Weight/genetics
Genome-Wide Association Study/veterinary
China
Phenotype
Male

@article {pmid41431830,
year = {2025},
author = {Bakirtas, A and Kiykim, A and Baskin, AK and Anil, H and Bozkurt, HB and Cimen, SS and Demirkale, ZH and Esenboga, S and Ogulur, I and Ardicli, S and Cagdas, D and Kistler, W and Yuksel, H and Akdis, CA},
title = {A Survey on Environmental Protective and Risk Factors and Awareness Related to Epithelial Barrier Integrity, Microbiome and Allergic Diseases.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70190},
pmid = {41431830},
issn = {1398-9995},
}

@article {pmid41431826,
year = {2025},
author = {Quintero, GA and Clay, OK},
title = {How to search for microbiomes: the example of bacteria in gallbladder bile.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/17460913.2025.2601522},
pmid = {41431826},
issn = {1746-0921},
abstract = {Questions surrounding the presence or absence of microbiomes in sites of the human body with at most low bacterial biomass in health are still not fully resolved. We begin with the notion of microbiome as "micro-biome," a community of several species, versus microbiota as simply "living things," and return to the pioneer epoch of biome research, which in one sense could be viewed as beginning already around 1800. Applying the biome notion to bacteria in sites of the human body, we find concordance with more recent attempts to test what is and what is not a (core) microbiome in practice. The biome perspective is then applied to a double question that has been addressed, without a consensus answer so far: (1) does the healthy gallbladder typically have a stable microbiota, and (2) do gallbladder microbiota, in either health or (gallstone) disease, qualify as microbiomes in the sense considered here?},
}

@article {pmid41431748,
year = {2025},
author = {Donnelly, CP and Zi, L and Li, L and Laukens, K and Cuypers, B and Prinsen, E and Okla, MK and Reynaert, S and Verbruggen, E and Asard, H and Beemster, GTS and AbdElgawad, H},
title = {The soil microbiome contributes to the adaptation of grassland plant species to increasingly persistent precipitation regimes by inducing transcriptomic, metabolic, and structural changes.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70788},
pmid = {41431748},
issn = {1469-8137},
support = {GOA: RegimeShift//University of Antwerpen/ ; },
abstract = {Climate change is leading to more persistent precipitation regimes (PRs) featuring prolonged dry and wet periods in Northern Europe. Plants and plant communities can acclimatize, reducing the impact of repeated exposures to extreme PRs. We addressed the hypothesis that PR adaptations by the soil microbiome contribute to the acclimatization of plants. We used soils from grassland mesocosms exposed to a 1-d (1SPR) or a 30-d (30SPR) wet/dry cycle to investigate how soil legacy affects the response of four grassland plant species to subsequent PR events. During the 40-d experiment, 5-d PR (5PR) treatments reduced growth compared with 1-d (1PR) samples, independent of soil legacy. The 30SPR treatment altered soil fungal communities, influencing plant responses, with Plantago and Phleum showing significant stress adaptations when compared with 1SPR. Integrating genome-wide transcriptional, physiological, and biochemical analyses enabled us to propose a mechanistic model showing how soil 30SPR influences four grassland plant species by activating common mechanisms, including redox signaling pathways and stress hormones (jasmonic acid, ethylene, and abscisic acid) under 5PR. These responses lead to cell wall reinforcement through increased lignin and callose, enhancing resilience. Overall, these findings underscore the role of soil legacy in helping grassland plants adapt to potential future PR variations.},
}

@article {pmid41431686,
year = {2025},
author = {Alnek, K and Bärenson, A and Aasmets, O and Janson, H and Talja, I and Laht, B and Vorobjova, T and Kirss, A and Cinek, O and Uibo, R and Tagoma, A and , },
title = {Mother and child stool bacteriomes 1-2 years postpartum: Associations with maternal history of gestational diabetes and child atopic dermatitis.},
journal = {iScience},
volume = {28},
number = {12},
pages = {114087},
pmid = {41431686},
issn = {2589-0042},
abstract = {Gestational diabetes mellitus (GDM) may contribute to the onset of immune-mediated diseases in offspring. This observational study included women belonging to the GDM risk group and aimed to investigate the gut bacteriomes of the mothers with and without recent history of GDM, and those of their children resulting from index pregnancies. Stool and blood samples were collected within one week at 1-2 years postpartum from mother-child pairs. Stool bacteriome 16S rDNA sequencing data were compared with maternal history of GDM, human leukocyte antigen (HLA) haplotypes, metabolic biomarker levels, and children's atopic dermatitis diagnosis, allergen-specific immunoglobulin E (IgE) levels, HLA haplotypes, intestinal fatty acid-binding protein and metabolic biomarker levels, and antibodies to food proteins. The GDM status, atopic dermatitis and IgE positivity were associated with the children's gut bacterial composition. These results indicate that GDM affects children's gut bacteriome composition even 1-2 years after birth.},
}

@article {pmid41431379,
year = {2026},
author = {Al-Btoosh, S and Donnelly, RF and Kelly, SA},
title = {Microbes and medicines: interrelationships between pharmaceuticals and the gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604867},
doi = {10.1080/19490976.2025.2604867},
pmid = {41431379},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; Animals ; Probiotics ; *Bacteria/drug effects/metabolism/classification/genetics ; Fecal Microbiota Transplantation ; Pharmaceutical Preparations/metabolism ; Prebiotics ; Biotransformation ; },
abstract = {The human gut microbiome plays a critical role in modulating pharmacological and toxicological responses to medications. With a gene pool vastly exceeding that of the human host, the gut microbiome acts as a metabolically active organ capable of transforming, inactivating, or accumulating drugs. This review explores the bidirectional interplay between prescription medicines and the gut microbiome, encompassing three key mechanisms: direct biotransformation by microbial enzymes, indirect modulation of host metabolism and signaling pathways, and drug bioaccumulation within microbial cells. Particular attention is given to six major drug classes: immunotherapeutics, chemotherapeutics, antidepressants, statins, hypoglycemics, and antihypertensives. The ways in which individual microbial profiles can influence therapeutic outcomes are also reviewed. We examined how common non-antibiotic pharmaceuticals can significantly alter microbial diversity and promote antimicrobial resistance. Strategies to enhance drug efficacy through microbiome modulation, including probiotics, prebiotics, and fecal microbiota transplantation (FMT), are critically assessed. Experimental models ranging from in vitro batch and chemostat systems to animal and clinical studies are compared in terms of their utility for studying drug‒microbiome interactions. Finally, emerging evidence suggesting the gut microbiota composition may serve as a predictive biomarker for personalized medicine and therapeutic success is highlighted. Understanding and harnessing the complex interrelationships between medicines and microorganisms could offer novel avenues to optimize treatment outcomes and mitigate adverse drug effects.},
}

*Gastrointestinal Microbiome/drug effects
Humans
Animals
Probiotics
*Bacteria/drug effects/metabolism/classification/genetics
Fecal Microbiota Transplantation
Pharmaceutical Preparations/metabolism
Prebiotics
Biotransformation

@article {pmid41431145,
year = {2025},
author = {Porchia, DD and Wang, Y and Zhou, Z and Chen, M and Porges, EC and Cohen, RA and Ghare, S and Barve, S and Cook, RL and Li, Z},
title = {Cannabis use, microbial diversity and Dialister abundance in older adults with HIV: A cross-sectional study.},
journal = {HIV medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/hiv.70180},
pmid = {41431145},
issn = {1468-1293},
support = {R01DA042069/DA/NIDA NIH HHS/United States ; U24AA029959/AA/NIAAA NIH HHS/United States ; },
abstract = {OBJECTIVES: People with HIV frequently experience gastrointestinal symptoms linked to dysbiosis, impaired mucosal barrier integrity and persistent immune activation. Cannabis is widely used for symptom management by people with HIV, but its effects on the gut microbiome are unclear.

METHODS: We conducted a cross-sectional analysis of 63 people with HIV (mean age 59.4 years; 71.4% Black or Hispanic) enrolled in the Marijuana Associated Planning and Long-term Effects study and its microbiome and Alzheimer's substudies, which included participants with and without mild cognitive impairment (MCI). Participants provided faecal samples for 16S rRNA sequencing. Cannabis use was quantified using a validated Timeline Followback. Alpha diversity was estimated using the Shannon index, beta diversity with Bray-Curtis dissimilarity and permutational multivariate analysis of variance (PERMANOVA), and genus-level abundance using the IFAA method. All models were adjusted for age, sex and education.

RESULTS: Higher cannabis consumption showed a statistically significant association with reduced alpha diversity (β = -0.062 per 50-mg Tetrahydrocannabinol (THC) per use-day; 95% confidence interval [CI]: -0.12 to -0.004; p = 0.038). No statistically significant differences in beta diversity were observed between high and low-to-no groups (p = 0.35). At the genus level, Dialister abundance showed a statistically significant dose-dependent association with cannabis use, with a 14.4% reduction in abundance per 50-mg increase in THC per use-day (q = 0.034).

CONCLUSION: Cannabis consumption in older people with HIV, including those with and without MCI, was associated with lower microbial diversity and reduced Dialister abundance, a taxon with dual roles in mucosal integrity and gastrointestinal symptom modulation. Reduced alpha diversity and Dialister depletion are notable given links to impaired mucosal barrier integrity, microbial translocation and systemic immune activation in HIV. These findings suggest cannabis may modify HIV-associated dysbiosis, warranting further longitudinal studies to disentangle symptomatic benefits from long-term impacts on mucosal health and systemic inflammation.},
}

@article {pmid41431112,
year = {2025},
author = {Wang, M and Qin, S and Wu, C and Li, H and Li, H and Yu, J},
title = {Microbiome-Metabolomics Insights into the Brain-Gut Homeostasis of d-gal Induced Aging Mice To Reveal the Antiaging Effects of Lactoferrin and Its Digesta.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11706},
pmid = {41431112},
issn = {1520-5118},
abstract = {Lactoferrin (LF) plays a positive role in attenuating aging. In this study, LF obtained using different processing methods (freeze-dried: F and spray-dried: S) and its gastrointestinal digesta (XF and XS) were supplemented in d-gal-induced mice to explore their antiaging effects. The results showed that LF and its digesta (LFs) effectively ameliorated cognitive decline. Mechanistically, LFs prevented neuronal and synaptic injury by restoring redox balance, inhibiting the activation of microglia and astrocytes, and activating the cAMP-response element binding protein (CREB)/brain-derived neurotrophic factor (BDNF) pathway. Additionally, LFs increased the tight junction proteins and mucin-2, regulated the gut microbiota, particularly enriching bacteria in Firmicutes and restoring the Firmicutes/Bacteroidota ratio to maintain intestinal homeostasis. Meanwhile, LFs altered phospholipids (PLs) and other metabolites involved in glycerophospholipid metabolism such as arachidonic acid. Correlation analysis showed a significant association among metabolites, microbiota, and behaviors. These results indicated that LF and especially its digesta exert antiaging effects through multitarget pathways involving neuronal protection, neuroinflammation suppression, and microbiota-gut-brain axis regulation.},
}

@article {pmid41430778,
year = {2026},
author = {Alula, KM and Nguyen, TT and de Zoeten, EF},
title = {Regulation of intestinal regulatory T cells via stress response pathways in inflammatory bowel disease.},
journal = {Autoimmunity},
volume = {59},
number = {1},
pages = {2602715},
doi = {10.1080/08916934.2025.2602715},
pmid = {41430778},
issn = {1607-842X},
mesh = {Humans ; *Inflammatory Bowel Diseases/immunology/metabolism ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Endoplasmic Reticulum Stress/immunology ; Unfolded Protein Response/immunology ; Animals ; Signal Transduction/immunology ; *Intestinal Mucosa/immunology/metabolism ; Gastrointestinal Microbiome/immunology ; *Intestines/immunology ; },
abstract = {Cell stress, including endoplasmic reticulum (ER) stress, heat shock, and hypoxia, plays a pivotal role in cellular homeostasis and immune regulation, particularly in the intestine. ER stress, a key aspect of cell stress, triggers the unfolded protein response (UPR) to restore balance by managing misfolded proteins or inducing apoptosis if unresolved. The activation of these stress responses has emerged as a critical contributor to intestinal inflammation in conditions like inflammatory bowel disease (IBD). Regulatory T cells (Tregs), vital for maintaining mucosal immune tolerance, are strongly influenced by cellular stress, with the UPR shaping their stability, metabolic programming, and function. Microbial dysbiosis and reduced short-chain fatty acids (SCFAs) disrupt these adaptive pathways, further impairing Treg function. In this review, we explore how UPR signaling shapes Treg metabolism and intestinal inflammation. Identifying gaps in UPR-mediated adaptation and stress thresholds, we thus propose microbiome- and ER-stress-based therapeutic strategies as putative strategies for restoring immune balance in IBD.},
}

Humans
*Inflammatory Bowel Diseases/immunology/metabolism
*T-Lymphocytes, Regulatory/immunology/metabolism
*Endoplasmic Reticulum Stress/immunology
Unfolded Protein Response/immunology
Animals
Signal Transduction/immunology
*Intestinal Mucosa/immunology/metabolism
Gastrointestinal Microbiome/immunology
*Intestines/immunology

@article {pmid41430711,
year = {2025},
author = {Juul, SE and Comstock, BA and Mayock, DE and German, K and Feltner, J and Irvine, J and Lagerquist, E and Heagerty, PJ},
title = {Darbepoetin plus slow-release IntraVenous Iron to decrease transfusions and improve iron status and neurodevelopment in preterm infants (DIVI): study protocol for a randomized, blinded phase II trial.},
journal = {Trials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13063-025-09374-9},
pmid = {41430711},
issn = {1745-6215},
support = {R01HD107003//National Institute of Child Health and Human Development/ ; },
abstract = {BACKGROUND: Infants born preterm are at high risk of anemia, red blood cell transfusions, and iron deficiency, all of which may negatively influence long-term neurodevelopment. To ameliorate these complications of prematurity, we developed a Phase II trial to determine whether treatment with an erythropoietic-stimulating agent, darbepoetin (Darbe), plus a slow-release intravenous (IV) iron preparation (ferumoxytol (FMX) or low-molecular-weight iron dextran (LMW-ID)) might decrease transfusions while maintaining iron sufficiency.

METHODS: This single-center study is a parallel design, prospective, randomized controlled Phase II trial of 120 infants born 24-0/7 to 31-6/7 weeks of gestation cared for in the University of Washington Neonatal Intensive Care Unit. After informed consent, infants less than 72 h of age are randomized to one of five treatment groups: (1) Oral iron (standard care), n = 40, or weekly Darbe 10 µg/kg/dose IV or SQ plus; (2) FMX - 10 mg/kg/dose IV, n = 20; (3) FMX - 20 mg/kg/dose IV, n = 20; (4) LMW-ID - 10 mg/kg/dose IV, n = 20; or (5) LMW-ID - 20 mg/kg/dose IV, n = 20. Infants will be followed to 2-year corrected age with sequential developmental testing. Our primary outcome is ferritin level at 34-36 weeks postmenstrual age. Secondary outcomes include other hematologic assessments, drug safety, evaluation of the gut microbiome, and neurodevelopment to 2 years corrected age.

DISCUSSION: This trial will determine whether darbepoetin plus a slow-release IV iron preparation is safe, which iron preparation and dose best maintain iron sufficiency and decrease or eliminate transfusions, whether IV iron will result in a more diverse, less pathogenic microbiome when compared to oral iron supplementation, and, finally, whether these treatments affect neurodevelopment to 2 years corrected age.

TRIAL REGISTRATION: National Clinical Trial (NCT) NCT05340465. Registered on March 1, 2022.},
}

@article {pmid41430556,
year = {2025},
author = {Luo, Y and Yang, Y},
title = {Network and machine learning integration reveals gut microbiome biomarkers in pediatric IBD.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {797},
pmid = {41430556},
issn = {1471-2180},
}

@article {pmid41430427,
year = {2025},
author = {De Santis, A and Bevilacqua, A and Corbo, MR and Speranza, B and Francavilla, M and Gatta, G and Carucci, F and Sinigaglia, M},
title = {A statistical approach to model soil microbiota versus heavy metals: a case study on soil samples from Foggia, Southern Italy.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-32485-x},
pmid = {41430427},
issn = {2045-2322},
abstract = {Heavy-metal (HM) contamination undermines soil functions and food safety, while risk appraisals often rely on chemical indices that can be unstable in the presence of extremes and only indirectly reflect biological integrity. We present an integrative framework that couples standardized contamination metrics with soil microbiome profiling to deliver stable, interpretable classifications and actionable bioindicators. Twelve peri-urban soils from Southern Italy were analysed for potentially toxic elements, including Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn) and profiled by shotgun metagenomics. We introduce a Standardized Ecological Risk index (SPERI) that preserves the ranking conveyed by conventional composites yet reduces outlier leverage. SPERI strongly agreed with Improved Potential Ecological Risk Index (IPERI) while stabilizing variance (R[2] = 0.896) and improved between-site comparability. Along the contamination gradient, community structure shifted consistently: families such as Pseudomonadaceae, Xanthomonadaceae and Rhodospirillaceae increased with risk, whereas Geodermatophilaceae and Nocardiaceae declined. Simple decision-tree models trained on family-level relative abundances reliably separated SPERI classes and repeatedly selected Zn- and Cd-enriched sites as primary split drivers, aligning microbial signals with chemical risk. By combining open, reproducible analytics with jointly chemical- and microbiome-informed endpoints, this workflow improves the interpretability and transferability of ecological risk assessment and supports targeted remediation and monitoring in contaminated agro-ecosystems.},
}

@article {pmid41430336,
year = {2025},
author = {Bertrand, C and Marmeisse, R and Martin, MC and Binet, F},
title = {Interplay between host and environmental filters drives plant-associated microbiomes in the remote sub-Antarctic Kerguelen Islands.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {154},
pmid = {41430336},
issn = {2524-6372},
abstract = {BACKGROUND: Plants evolve as holobionts, ecological and evolutionary units made up of the host plant and its associated microbiota, which shape plant fitness and adaptive capacity. Isolated ecosystems with low biodiversity and plant cover, such as the fellfields of the remote sub-Antarctic Kerguelen Islands, represent ideal open-air laboratories to disentangle the drivers affecting plant-microbiome interactions. In such pristine environments, endemic plant species and their microbiota have coevolved in isolation possibly since the last ice age. In this study, we investigated the bacterial and fungal communities associated with different soil-plant compartments of two phylogenetically distant endemic plants, the Poaceae Poa kerguelensis and the Brassicaceae Pringlea antiscorbutica, in fellfields with contrasted pedoclimatic conditions.

RESULTS: Using 16S rRNA gene and Internal Transcribed Spacer (ITS) region metabarcoding, we identified a strong soil-plant compartment effect affecting microbial communities, with bacterial and fungal α-diversity higher in bulk and rhizospheric soils and progressively decreasing in roots and above-ground compartments. The microbiota of the different soil-plant compartments studied differ in their recruitment patterns. The bacterial communities of the aerial parts of P. antiscorbutica were less dependent on those of the underground parts compared to those of P. kerguelensis. We also showed that the microbiota of distinct plant species and their different soil-plant compartments respond differently to pedoclimatic variables, with a greater impact of climatic variables over soil ones on aboveground bacterial microbiomes than on belowground microbiomes.

CONCLUSIONS: Our results highlight the dual role of environmental variability and of the identity of the host on the recruitment and diversity of plant microbiomes in the isolated studied ecosystems. As plant holobionts are part of the global biogeochemical ecosystem functioning, our results suggest that plant species-specific microbial recruitment strategies and differential vulnerability to environmental factors should be included in predicting sub-Antarctic ecosystem response to global warming.},
}

@article {pmid41430309,
year = {2025},
author = {Aladejana, OM and Ayorinde, DF},
title = {The intersection between human metapneumovirus and the respiratory microbiome.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-025-02872-x},
pmid = {41430309},
issn = {1743-422X},
abstract = {Human metapneumovirus is one of the viral causes of respiratory illness that can range from mild to life-threatening diseases. In December 2024, there was news about increased cases of human metapneumovirus (HMPV) in China, when 6.2% and 5.4% of positive respiratory illnesses and admissions, respectively, were linked to HMPV, surpassing adenovirus, rhinovirus, and COVID-19. There have been concerns about it becoming another epidemic, and by implication, a pandemic, especially as the world is gradually recovering from COVID-19 and its devastating impacts. Currently, there is no directly acting antiviral drug targeting HMPV, and this has left a gap in its treatment and management, especially in the young, elderly, and immunocompromised, who are prone to having severe manifestations. As the immune system is crucial in fighting and eliminating the infection, modulating the immune system directly or indirectly can treat HMPV. The lung that was initially known to be sterile is now found to house different populations of microorganisms, including bacteriome, virome, and mycobiome. The lung microbiome modulates HMPV infection. The presence of pathobionts like H. influenzae enhances HMPV infection and severity. The detection of the microbiome was made possible by the advent of cutting-edge technologies like next-generation sequencing and bioinformatics tools. The combination of Recombinase Polymerase Assay, CRISPR-Cas12a, and Fluorescence Assay has been used in the rapid detection of HMPV in China. The microbiome plays a crucial role in shaping the immune system. Exploring such can be a way of managing HMPV. Probiotics, prebiotics, and postbiotics are ways in which the microbiota can be manipulated to limit adverse drug reactions. These can be explored in HMPV diagnosis, treatment, and prevention.},
}

@article {pmid41430301,
year = {2025},
author = {Wikki, I and Palmu, J and Kauko, A and Havulinna, A and Jousilahti, P and Lahti, L and Knight, R and Salomaa, V and Niiranen, T},
title = {Prospective association between the gut microbiota and incident pneumonia: a cohort study of 6419 individuals.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-025-03453-w},
pmid = {41430301},
issn = {1465-993X},
support = {330887//Research Council of Finland/ ; 321351, 354447//Research Council of Finland/ ; },
abstract = {BACKGROUND: Previous animal studies have identified the protective capacity of the gut microbiota against respiratory infections. Nevertheless, the prospective association between human gut microbiota and pneumonia risk remains unknown.

OBJECTIVES: To evaluate the links between gut microbiota and incident pneumonia in a representative population sample.

METHODS: We performed shotgun metagenome sequencing on stool samples from 6419 FINRISK 2002 participants. Participants were followed up for incident pneumonia using nationwide health register data. We employed multivariable-adjusted Cox regression models and permutational multivariate analysis of variance (PERMANOVA) to assess the association of gut microbiome alpha diversity, compositional variation (beta diversity), and taxonomic composition with pneumonia risk.

RESULTS: Altogether, 685 patients (10.7%) developed pneumonia during a mean follow-up of 17.8 years. Alpha diversity was not associated with incident pneumonia (hazard ratio [HR] 1.00; 95% confidence interval [CI] 0.93 - 1.08), whereas community composition was (PERMANOVA R[2] = 0.03%; P = 0.02). We observed an inverse association between the relative abundance of butyrate-producing bacteria and incident pneumonia (HR per 1-SD increase 0.91; 95% CI 0.85-0.98). The relative abundance of Bacteroides_F pectinophilus, Eubacterium_G ventriosum, Agathobaculum butyriciproducens, Butyribacter intestini, Eubacterium_I ramulus, CAG-1427 sp000435675, and CAG-603 sp900066105 were inversely associated with pneumonia risk. The relative abundance of Clostridium_AQ innocuum was positively correlated with pneumonia risk.

CONCLUSIONS: The gut microbiota composition, and especially the relative abundance of butyrate-producing bacteria, was associated with lower pneumonia risk in the population. These findings warrant further studies to investigate whether microbiome modulation to increase short chain fatty acid production through diet, prebiotics, or probiotics could reduce pneumonia risk.},
}

@article {pmid41430289,
year = {2025},
author = {Williams, GM and Hoedt, EC and Duncanson, K and Gan, L and Prakoso, E and Talley, NJ and Beck, EJ},
title = {Inverse associations between Mediterranean diet constituents and the gut microbiota in metabolic-associated steatotic liver disease (MASLD): a case-control study.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-025-00939-8},
pmid = {41430289},
issn = {1743-7075},
abstract = {BACKGROUND: Dietary therapy, specifically for weight loss, is currently considered first-line therapy for metabolic-associated steatotic liver disease (MASLD). However, increasing recognition of the role of the gut-liver axis in MASLD highlights potential for microbiota-modulating dietary therapy to improve outcomes. This study aimed to explore dietary variables relevant to gut microbiota in MASLD.

METHODS: Twenty-five adults with MASLD and 25 healthy controls were recruited using a retrospective case-control design and characterised using 3-day dietary intake records, clinical markers, and shotgun metagenomic sequencing.

RESULTS: MASLD participants consumed less dietary fibre (p = < 0.01), very long chain omega-3 fatty acids (p = 0.02), nuts and seeds (p = 0.03), whole grains (p < 0.01) and vegetables (p = 0.04). Participants with MASLD had lower abundance of Alistipes senegalensis (r=-0.01, p = 0.04), Coprococcus eutactus (r=-0.07, p = 0.006), Faecalibacterium (r=-0.02, p < 0.001), and higher abundance of Ruminococcus torques (r = 0.04, p = 0.02), and less expression of functional pathways associated with ethanol production, methionine, folate and branched-chain amino acid metabolism. Bacterial species and functional pathways more abundant in MASLD were positively associated with intake of added sugars and saturated fat, and negatively associated with unsaturated fatty acid and dietary fibre intake.

CONCLUSIONS: Microbiota characteristics differ between individuals with and without MASLD, and this is influenced by dietary intake. Future translation-focused research investigating dietary interventions and the gut-liver-axis in MASLD are warranted.},
}

@article {pmid41430245,
year = {2025},
author = {Kardish, MR and Agans, RT and Barbato, RA and Doherty, SJ and Goodson, MS and Karl, JP and Kokoska, R and Liechty, ZS and McNeal, ND and Racicot, K and Steel, JJ and Sweet, C and Tuck, SM and Leary, DH},
title = {Meeting report of the eight annual Tri-Service Microbiome Consortium Symposium.},
journal = {BMC proceedings},
volume = {20},
number = {Suppl 2},
pages = {2},
pmid = {41430245},
issn = {1753-6561},
abstract = {The Tri-Service Microbiome Consortium (TSMC) was created to foster and enhance cooperation, collaboration, and communication of microbiome research among Department of Defense (DoD) researchers and their collaborators. The 8th Annual TSMC Symposium was held in Colorado Springs, CO on 25-26 September 2024 and featured oral and poster presentations and discussions centered on microbiome-related topics within four broad thematic areas: 1) Surveillance; 2) Health and Performance; 3) Enablers; and 4) Remediation. Collectively this meeting promoted sharing of methods, experiments, and findings across DoD affiliated microbiome research and promoted future and ongoing collaborations. This report summarizes the proceedings of the 8th Annual TSMC Symposium.},
}

@article {pmid41430101,
year = {2025},
author = {Zhou, F and Pan, Y and Zhan, J and Li, X and Yu, S and Tang, L},
title = {Continuous cropping drives assembly process of soil microbial community to alter keystone taxa causing challenges.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04595-z},
pmid = {41430101},
issn = {1471-2180},
support = {2022YFD1901503//National Key Research and Development Program of China/ ; 2022YFD1901503//National Key Research and Development Program of China/ ; 202202AE090025//Major Science and Technology Special Project of Yunnan Province/ ; },
abstract = {BACKGROUND: Healthy soil is crucial for maintaining the sustainability of soil ecosystem services and ensuring food security. The soil microbiome serves as a key indicator of soil health. However, long-term continuous monoculture significantly adversely affects the diversity and functioning of soil microbial communities, posing a serious threat to sustainable agricultural development. Therefore, making it crucial to understand the microbial mechanisms underlying these challenges.

METHODS: In this study, tobacco was subjected to different planting durations: 1 year (CR), 5 years (CC5), 10 years (CC10), and 15 years (CC15). The rhizosphere microbial community assembly process, composition, keystone taxa, and their relationship to continuous cropping challenges were analyzed.

RESULTS: The rhizosphere bacterial community structure of tobacco after 5 years of continuous cropping was significantly separated from other treatments, while no significant separation was observed in the fungal community. Further investigation into the assembly processes of microbial communities under different continuous cropping durations revealed that bacterial community assembly processes exhibited differences, whereas no significant differences were observed in fungal community assembly processes. Specifically, the rhizosphere bacterial community in CC5 was predominantly shaped by deterministic assembly processes, explaining its structural distinctiveness from other treatments. Co-occurrence network analysis revealed that the number of nodes and edges in bacterial-fungal interactions decreased by 22.70% and 79.86%, respectively, in CC5 compared with CR. Differential microbial abundance identified a significant decline in key microbes (Rhodanobacter, Ellin6067, Frankiales, and Setophoma) alongside a marked increase in the abundance of genus Verticillium in CC5 relative to CR. RDA indicated these bacterial genera correlated negatively with pathogen accumulation and disease incidence but postively with yield These relationships potentially constituted the primary driver for exacerbated continuous cropping obstacles in CC5. In CC10, bacterial community assembly was primarily dominated by stochastic processes. Although the number of network nodes and edges increased by 21.96% and 204.73%, respectively, compared to CC5, they remained lower than those in CR. By extending the continuous cropping to 15 years, the bacterial community assembly was shaped by stochastic processes. Compared with CC5, the number of network nodes and edges in CC15 increased by 34.39% and 405.44%, respectively, with beneficial microbes (Rhodanobacter, Ellin6067, Frankiales, and Setophoma) showing remarkable abundance recovery and pathogenic fungi like Verticillium declining, ultimately resulting in microbial community characteristics approximating those observed in the CR.

CONCLUSIONS: The bacterial community in CC5 was driven by deterministic assembly processes, resulting in a distinct structure. The complexity and stability of the co-occurrence network significantly decreased, accompanied by a higher abundance of harmful microbes and a lower abundance of beneficial microbes, which exacerbated the continuous cropping obstacles. In contrast, after 15 years of continuous cropping, the bacterial community assembly shifted to stochastic processes and trans-kingdom co-occurrence network complexity and stability strengthened, beneficial microbes increased, and continuous cropping challenges alleviated.},
}

@article {pmid41430013,
year = {2025},
author = {Wolfgang, A and Temme, N and Tilcher, R and Schumann, M and Berg, G},
title = {Wireworm-Associated Microbial Communities and their Implications on Biological Control.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02672-4},
pmid = {41430013},
issn = {1432-184X},
abstract = {Wireworms (larvae of different click beetles, Elateridae) are significant soil-borne pest species that can cause severe crop losses. They are difficult to control, and biocontrol using entomopathogenic fungi (EPF) display variable field efficacy. To understand microbial interactions and improve biological control, we studied the interplay between insect and soil microbiota in four wireworm species (Agriotes spp.) at temporal and spatial scales. We found that microbiota associated with wireworms are species-specific and primarily soil-derived. Our results further indicate that ectosymbiotic bacterial community composition on wireworm cuticles is relatively stable over time in specimens not deceasing from spontaneous entomopathogen infection. Therefore, successful microbiome homeostasis on cuticles appears to be correlated with long-term survival of wireworms in soil. Interestingly, EPF were prevalent but low-abundant in all wireworm species as well as in soils. Therefore, we analyzed immune priming effects by low-abundant EPF in soil. Mortality was higher in naïve wireworms than in wireworms pre-exposed to EPFs, and molting frequency increased, indicating both developmental adaptations and immune priming as strategies for EPF avoidance in wireworms. This work disentangles the key components of wireworm microbiomes and highlights the importance of microbial interactions for biocontrol. Biocontrol of wireworms could be improved by considering their species-dependency in microbiome homeostasis as well as physiological and behavioral adaptations to soil-borne pathogens. The potential functional synergies between EPF and soil microbes need further exploration.},
}

@article {pmid41429881,
year = {2025},
author = {Hanzely, P and Holm, K and Bjørnholt, JV and Melum, E and Hov, JR and Rasmussen, H},
title = {Efficacy of oral and rectal administration of human faecal microbiota transplant (FMT) in human microbiota-associated mouse models.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-32072-0},
pmid = {41429881},
issn = {2045-2322},
support = {802544/ERC_/European Research Council/International ; },
abstract = {The gut microbiome has gained significant interest due to its association with immune dysregulation, allergies, autoimmune conditions, metabolic disorders, and inflammation-associated malignancies. Understanding underlying mechanisms requires appropriate in vivo models, such as human microbiota-associated mouse models to study the microbiota-host interactions. This study compared the efficacy of oral and rectal administration of human faecal microbiota transplant (FMT) from a single donor in C57BL/6J germ-free mice as these methods are often used interchangeably. Using 16S rRNA sequencing, we quantified colonisation efficacy in luminal and tissue samples from orally- (n = 6) and rectally- (n = 6) colonised mice. We detected 84 genera in the FMT sample, 17 of which were not transferred at all, while additional 7 genera were found exclusively in rectally-colonised mice. A significantly higher proportion of amplicon sequence variants (ASVs) (33% vs. 26%; P < 0.05) and genera (32% vs. 25%; P < 0.05) were absent in orally- compared to rectally-colonised group. Some taxa showed different relative abundances in human vs. mouse samples (e.g. Alistipes and Bacteroides relatively more abundant in mice while Faecalibacterium considerably decreased). Beta diversity analysis revealed greater similarity between FMT and tissue samples irrespective of the administration route, with distinct separation of the tissue and luminal samples. Overall, rectal administration yielded more overlapping genera and ASVs with FMT, highlighting that it could have advantages compared with oral administration for microbiota establishment studies.},
}

@article {pmid41429716,
year = {2025},
author = {Węgrzyn, A and Bloch, S and Węgrzyn, G},
title = {Employing bacteriophages to combat cancer.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {1880},
number = {6},
pages = {189485},
doi = {10.1016/j.bbcan.2025.189485},
pmid = {41429716},
issn = {1879-2561},
mesh = {Humans ; *Neoplasms/therapy/diagnosis/immunology/genetics ; *Bacteriophages/genetics ; Cancer Vaccines/therapeutic use/immunology ; Animals ; *Phage Therapy/methods ; },
abstract = {Bacteriophages are viruses infecting bacterial cells; therefore, their application in cancer research may initially appear counterintuitive. Nevertheless, bacteriophages have been employed in the development of numerous advanced biotechnological tools, which has led to the emergence of multiple approaches utilizing them for improved cancer diagnostics and novel therapeutic strategies. Unlike other recently published reviews in this field, this paper does not emphasize technological principles or focus on specific cancer type. Instead, we provide a broad overview of innovative concepts and highlight recent advances in the use of bacteriophages in anti-cancer research. In particular, we discuss their roles in: (i) early cancer diagnosis and detection of tumorigenic mutations, (ii) elimination of bacteria that promote carcinogenesis and modulation of the microbiome influencing tumor growth, (iii) development of anti-cancer vaccines, (iv) modulation of cancer-related immune responses, (v) targeted delivery of anti-cancer drugs, and (vi) genetic modification of cancer cells through therapeutic DNA delivery.},
}

Humans
*Neoplasms/therapy/diagnosis/immunology/genetics
*Bacteriophages/genetics
Cancer Vaccines/therapeutic use/immunology
Animals
*Phage Therapy/methods

@article {pmid41429281,
year = {2025},
author = {Zhao, Z and Ju, Y and Gao, B and Yu, Y and Ur Rehman, K and Jiménez, N and Gago-Ferrero, P and Subirats, J and Matamoros, V and Wang, D and Li, Q and Zheng, L and Huang, F and Yu, C and Zhang, J and Cai, M},
title = {Functional microbial consortia augmented black soldier fly larvae achieve high efficiency ammonia mitigation during chicken manure bioconversion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133848},
doi = {10.1016/j.biortech.2025.133848},
pmid = {41429281},
issn = {1873-2976},
abstract = {Animal manure management frequently generates substantial ammonia (NH3) emissions, posing serious environmental and health concerns. Black soldier fly larvae (BSFL) bioconversion technology offers a promising solution by converting manure into valuable insect-derived protein and fat, while partially mitigating NH3 release. In this study, a functional microbial consortium (comprising Gordonia sp. AY-3, Lysinibacillus macroides F1, and Lactobacillus plantarum L7) from black soldier fly larvae (BSFL) frass and the larval gut was screened and developed to synergistically enhance BSFL productivity and reduce NH3 emissions. Results showed that optimal performance was achieved at an inoculation ratio of 2:1:1, which significantly reduced NH3 emissions by 37 % and increased larval fresh weight, dry weight, and bioconversion efficiency by 9 %, 9 %, and 12 %, respectively, compared with the control treatment. Functional gene analysis revealed a 37 %-52 % upregulation in nitrification (nxrAB) and denitrification genes (norBC, nosZ, nirK, nirS). Microbiome profiling indicated significant increases in Lactobacillus, Pseudomonas, and Bacteroides populations. Further pilot-scale validation demonstrated a 33 % reduction in environmental NH3 emissions. The daily average NH3 concentration decreased from 55 to 37 mg/m[3], along with a 4 % increase in BSFL fresh weight. Functional gene analyses showed that the consortium enhanced nitrogen assimilation via glutamine synthetase-glutamate synthase (GS-GOGAT) pathways, and upregulated denitrification-related genes. Overall, this BSFL bioconversion combined with microbial augmentation provides an effective strategy for reducing NH3 pollution while enhancing the efficiency of organic waste conversion.},
}

@article {pmid41429263,
year = {2025},
author = {Huang, J and Zhang, Y and Li, Q and Wang, M and Zhou, H and Su, H and Sun, X},
title = {Anti-PD-L1 improves barrier function and reduces CD103[+] DC cell accumulation by regulating gut and lung microbiota and its metabolites to alleviate asthma in juvenile mice.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {100944},
doi = {10.1016/j.bj.2025.100944},
pmid = {41429263},
issn = {2320-2890},
abstract = {BACKGROUND: Programmed death ligand 1 (PD-L1) was found to play an important role in maintaining tolerance and immune balance, and its mechanism of action on asthma still needs to be further clarified. We aim to block P MATERIAL AND METHODS: in a juvenile asthma model, PD-L1 blockers were used to inhibit the expression of PD-L1 in vivo. By evaluating parameters that reflect airway hyperresponsiveness, airway inflammation, tissue damage, intestinal barrier function, and microbiome changes in mice, the impact of PD-L1 blockade on various physiological and immune indicators in asthma models is fully revealed.

RESULTS: PD-L1 blockade reduces leukocyte infiltration in the lungs, including eosinophils, decreased levels of IgE and IgG1, and restored Th1/Th2 imbalance by reducing IL-4, IL-13, and GATA-3 while increasing IFN-γ. In addition, PD-L1 blockade significantly decreased levels of IL-17A/F and increased IL-10. Histological analysis of the lungs showed that PD-L1 blockade attenuated airway inflammatory cell infiltration and mucus hyperproduction. Further testing showed that the intestinal barrier function was improved after PD-L1 blockade. Mechanistic studies revealed that PD-L1 blockade improved microbiota composition in the lungs and gut, increased Lactobacillus, SCFA, and reduced LPS. As well as induced the downregulation of CD103[+] DCs in lung. Correlation analysis showed that airway inflammation is negatively correlated with SCFA and positively correlated with LPS, and barrier function is negatively correlated with LPS.

CONCLUSIONS: PD-L1 blockade alleviated asthmatic airway inflammation by modulating gut and lung microbiota, improving intestinal barrier function, increasing SCFA levels, reducing LPS and CD103[+] DCs activity.},
}

@article {pmid41429213,
year = {2025},
author = {Jopling, E and Metcalfe-Roach, A and Turvey, SE and Mandhane, P and Brett Finlay, B and LeMoult, J and , },
title = {The infant gut microbiome and the intergenerational transmission of psychiatric risk.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106232},
doi = {10.1016/j.bbi.2025.106232},
pmid = {41429213},
issn = {1090-2139},
abstract = {Elevated stress during the prenatal period is associated with increased psychiatric risk among children. However, less is known about the mechanisms through which this intergenerational transmission of risk occurs. The early life microbiome is one candidate mechanism through which maternal stress during the prenatal period could impact offspring mental health, with a growing body of literature highlighting the importance of the early life microbiome in mental health across the lifespan. This study leverages Canada's largest deeply phenotyped birth cohort to elucidate the mechanistic associations between maternal prenatal stress, dynamic changes in the microbiome across the first year of life, and child internalizing symptoms. Analytic sample size with use of full information maximum likelihood methodology was 2,985. Analyses indicated that early diversification of the early life microbiome significantly mediated the relation between higher maternal perceived stress during pregnancy and increased internalizing symptoms among offspring at 5 years of age. Crucially, microbial taxa impacted by early diversification of the microbiome implicated the immune system. This work supports maturational dynamics of the microbiome as one mechanism through which prenatal stress is biologically embedded to impact offspring's later mental health. By linking several burgeoning areas of research, this study lays the groundwork for future multidisciplinary work examining the intergenerational transmission of psychiatric risk through the microbiome.},
}

@article {pmid41429111,
year = {2025},
author = {Santos, LNA and Souza, RBMS and Fernandes, EL and Lima, LS and Silva, HL and Volpe, LM and Oliveira, SG and Félix, AP},
title = {A therapeutic gastrointestinal diet improves nutrient digestibility and modulates fecal microbiota and metabolites in dogs.},
journal = {American journal of veterinary research},
volume = {},
number = {},
pages = {1-10},
doi = {10.2460/ajvr.25.09.0346},
pmid = {41429111},
issn = {1943-5681},
abstract = {OBJECTIVE: To evaluate the effects of a therapeutic gastrointestinal diet on the apparent digestibility coefficients (ADCs), metabolizable energy (ME), and palatability of the diet, fermentative metabolites, and fecal microbiome of dogs.

METHODS: Sixteen 1-year-old healthy Beagles were used. All animals consumed a control diet for healthy adult dogs for 20 days. On day 21, 8 dogs changed to a therapeutic gastrointestinal diet (test diet), and 8 dogs continued receiving the control diet for 35 days. Fresh feces were collected on days 0, 3, 15, and 30 after changing to the test diet for pH, fermentative metabolites, and microbiota analysis. Feces were collected for ADCs and ME analysis of the diets (days 31 through 35). The palatability of the control and test diets was compared at the end of the study.

RESULTS: The test diet presented greater ADCs of nutrients and ME and resulted in lower fecal pH and greater fecal concentrations of ammonia, total biogenic amines, total short-chain fatty acids, and butyrate. β-Diversity analysis revealed distinct fecal microbiome profiles between the diets on days 3, 15, and 30, with a greater abundance of Turicibacter and Faecalibacterium and lower Streptococcus in the test group. Dogs preferred the test to the control diet in the palatability test.

CONCLUSIONS: The test diet presented high ADCs of nutrients, high palatability, and beneficially modulated the fecal microbiome and fermentative metabolites of dogs.

CLINICAL RELEVANCE: Providing a highly digestible and palatable diet with functional ingredients may contribute to the treatment of gastrointestinal disorders of dogs.},
}

@article {pmid41429080,
year = {2025},
author = {Castillo-Ilabaca, C and Jessen, GL and Aranda, M and Fernández, C and Méjanelle, L and Gutiérrez, MH and Pantoja-Gutiérrez, S},
title = {Evidence for priming-enhanced microbial degradation of polycyclic aromatic hydrocarbons in marine sediments.},
journal = {Marine pollution bulletin},
volume = {224},
number = {},
pages = {119163},
doi = {10.1016/j.marpolbul.2025.119163},
pmid = {41429080},
issn = {1879-3363},
abstract = {Priming effect is the enhanced microbial degradation of refractory organic carbon in the presence of labile organic matter. It has been proposed to explain the disappearance of supposedly recalcitrant terrestrial organic matter that reaches the coastal ocean. Here, we experimentally evaluated whether labile organics boosts the degradation of persistent pollutants, phenanthrene and pyrene (polycyclic aromatic hydrocarbons, PAHs). Microcosm incubations were conducted during 11 and 50 days using marine surface sediments from Concepción Bay, a PAH-impacted upwelling ecosystem in central Chile, and the Almirante Montt Gulf, a rather pristine Patagonian Fjord. Addition of yeast extract enhanced the degradation of phenanthrene and pyrene by 14-170 %, while microalgal extract increased the decay rate constant of phenanthrene by 67 %. PAH degradation was accompanied by a pronounced enrichment of hydrocarbonoclastic bacteria, which increased approximately 840-fold (average Log2FC = 9.7) with rather pristine Patagonian sediments but only 12-fold increase (average Log2FC = 3.6) in PAH-impacted Concepción Bay sediments. The broader shift in microbial community structure detected in Patagonian fjords coincides with low ambient PAH contents, as expected in unpopulated areas. Considering the long record and intensity of industrial activity off Concepción Bay and the surrounding area, we suggest that those sediments contain a core microbiome with a toolkit of potential enzymes involved in PAH-degradation pathways capable of processing high inputs of PAHs. This finding may imply that coastal marine sediments store microbial capacity for degradation of contaminants induced by a long history of PAH emissions, and this ability can be further enhanced by exposure to primers.},
}

@article {pmid41428895,
year = {2026},
author = {Vijayan, N and Briseño, J and Simakov, O and Nyholm, SV},
title = {Maintaining microbiota across diverse symbiotic organs in Euprymna scolopes: Insights into shared immune responses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {1},
pages = {e2512903122},
doi = {10.1073/pnas.2512903122},
pmid = {41428895},
issn = {1091-6490},
support = {IOS2247195//NSF (NSF)/ ; 9349 and 12342//Gordon and Betty Moore Foundation (GBMF)/ ; 945026//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; },
mesh = {Animals ; *Symbiosis/immunology ; *Decapodiformes/microbiology/immunology/genetics ; Female ; *Microbiota/immunology ; Aliivibrio fischeri/physiology ; Transcriptome ; Carrier Proteins ; },
abstract = {Many animals have multiple organs or tissues that are colonized by diverse microbiota. The female Hawaiian bobtail squid, Euprymna scolopes, has two organs with distinct symbiotic communities: the accessory nidamental gland (ANG) and the light organ (LO). The ANG hosts a bacterial consortium, whereas the LO has a binary relationship with Vibrio fischeri, housed in extracellular crypt spaces as part of the central core (CC). To understand how the host maintains distinct symbiotic communities, we used transcriptomics to identify immune-related genes that are uniquely and similarly expressed in the ANG and LO-CC compared to organs without a known microbiota. Genes such as peptidoglycan recognition proteins EsPGRP2 and EsPGRP3, cathepsin-Z, alkaline phosphatase, and acidic phospholipase exhibited significant upregulation in the symbiotic organs compared to other tissues like gills, skin, mantle, optic lobe, ovaries, and brain. Moreover, EsPGRP2 displayed distinct localization patterns within the ANG, inversely correlating with bacterial presence, whereas the protein was colocalized with V. fischeri in the LO-CC. Notably, 10 different galaxins (EsGal) were uniquely highly expressed in both the ANG and LO-CC, with EsGal1 messenger RNA predominantly localized to the LO-CC epithelium, while EsGal2 and EsGal3 were primarily found in the epithelia of ANG tubules. Furthermore, antimicrobial assays using partial peptides derived from EsGal1 and EsGal2 showed varying and distinct patterns of inhibitory activity for these peptides. In summary, our findings identify similar immune gene families expressed across functionally distinct symbiotic organs in E. scolopes, suggesting that common immunomodulatory factors may maintain distinct symbiotic niches in the host.},
}

Animals
*Symbiosis/immunology
*Decapodiformes/microbiology/immunology/genetics
Female
*Microbiota/immunology
Aliivibrio fischeri/physiology
Transcriptome
Carrier Proteins

@article {pmid41428865,
year = {2025},
author = {Rutkowski, N and Yang, B and Gray-Gaillard, E and Ruta, A and Mejías, JC and Patatanian, M and Cherry, C and Celik, N and Stivers, KB and Ramanujam, S and Price, NL and Housseau, F and Pardoll, DM and Sears, CL and Elisseeff, JH},
title = {Antibiotic-induced microbiota depletion impairs the proregenerative response to a biological scaffold.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {52},
pages = {e2510841122},
doi = {10.1073/pnas.2510841122},
pmid = {41428865},
issn = {1091-6490},
support = {DGE2139757//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; DGE1746891//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; K99AG081564/GF/NIH HHS/United States ; },
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Gastrointestinal Microbiome/drug effects/immunology ; Mice ; Dysbiosis/immunology/chemically induced ; *Tissue Scaffolds ; Mice, Inbred C57BL ; Male ; Macrophages/immunology ; Female ; Interleukin-4/metabolism ; CD4-Positive T-Lymphocytes/immunology ; },
abstract = {Therapeutic biological scaffolds promote tissue repair primarily through the induction of type 2 immunity. However, systemic immunological factors, including aging, sex, and previous infections, can modulate this response. The gut microbiota is a well-established modulator of immune function across organ systems, yet its influence on type 2-mediated repair remains underexplored. Here, we establish a bidirectional relationship between the gut microbiota and biological scaffold-mediated tissue repair. Utilizing a conventionalized germ-free mouse, we demonstrate that scaffold implantation induces compositional and functional changes in the gut microbiome, particularly affecting amino acid biosynthesis. Additionally, in a model of antibiotic-induced microbiota depletion, we show that dysbiosis disrupts key immune regulators of type 2 immunity, including reductions in eosinophils, proregenerative macrophages, and interleukin-4 (IL-4)-producing CD4[+] T cells. At 6 wk post-scaffold implantation, we observed a significant decrease in myocytes with centrally located nuclei alongside an upregulation in profibrotic gene expression with antibiotic treatment. These findings provide insights into the influence of the gut microbiota on type 2-mediated tissue repair.},
}

Animals
*Anti-Bacterial Agents/pharmacology/adverse effects
*Gastrointestinal Microbiome/drug effects/immunology
Mice
Dysbiosis/immunology/chemically induced
*Tissue Scaffolds
Mice, Inbred C57BL
Male
Macrophages/immunology
Female
Interleukin-4/metabolism
CD4-Positive T-Lymphocytes/immunology

@article {pmid41428827,
year = {2025},
author = {De Sotto, R and Aggarwal, N and Tham, EH and Chang, MW},
title = {Machine Learning in Microbiome Research and Engineering.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00273},
pmid = {41428827},
issn = {2161-5063},
abstract = {Microbiomes, complex communities of microorganisms and their genetic material, hold immense potential for addressing global challenges in diverse sectors, including healthcare, agriculture, and bioproduction. Engineering these intricate ecosystems, however, necessitates a comprehensive understanding of the complex web of microbial interactions. The emergence of machine learning (ML) has revolutionized microbiome research, offering powerful tools to analyze massive data sets, uncover hidden patterns, and predict microbial behavior. ML algorithms have demonstrated remarkable success in identifying and characterizing microbial communities, predicting interactions between organisms and optimizing the design of microbial communities for specific functions. This Perspective examines the transformative applications of ML in the context of microbiome engineering, encompassing both microbiome data analysis and the targeted manipulation of microbial communities. These techniques employ a variety of strategies, including the manipulation of quorum sensing molecules, antimicrobial peptides, growth conditions, the introduction of probiotics, and the utilization of bacteriophages. By integrating ML with experimental approaches, researchers are pushing the boundaries of microbiome engineering, paving the way for novel applications in diverse fields. However, it is important to acknowledge the challenges that ML algorithms face, such as the limited availability of high-quality, large-scale data sets, the inherent complexity of biological systems, and the need for improved integration of experimental and computational methods. This perspective further discusses the future perspectives of the field, highlighting expected developments in data generation, algorithm development, and interdisciplinary collaboration. These advancements hold the key to unlocking the full potential of microbial communities for addressing pressing global challenges.},
}

@article {pmid41428801,
year = {2025},
author = {Sauša, S and Zodāne, A and Kumar, S and Plūme, J and Baranova, J and Kozlova, T and , and Saušs, H and Kloviņš, J and Pīrāgs, V and Mitravinda, KS and Kistkins, S and Brīvība, M},
title = {Rapid and Selective Gut Microbiome Modulation by Polyherbal Formulation in Type 2 Diabetes.},
journal = {Endocrine connections},
volume = {},
number = {},
pages = {},
doi = {10.1530/EC-25-0463},
pmid = {41428801},
issn = {2049-3614},
abstract = {BACKGROUND: Metformin, the first-line treatment for type 2 diabetes, often induces gastrointestinal side effects, affecting treatment adherence. Recent research suggests that the gut microbiome mediates both the efficacy and tolerability of metformin. This study evaluates the effect of a polyherbal formulation, used as an add-on to metformin, on the gut microbiota in patients with type 2 diabetes and metformin intolerance.

METHODS: We report preliminary findings from the first 7-day intervention phase of an ongoing randomized, placebo-controlled, crossover trial (NCT06846138) in 27 adults with type 2 diabetes. Participants received either polyherbal formulations or a placebo alongside metformin for 7 days. Stool samples were collected pre- and post-intervention for shotgun metagenomic sequencing. Microbial diversity, composition, and pathway functions were analyzed using Kraken2, Bracken, and HUMAnN3. Continuous glucose monitoring was used to assess glycemic metrics.

RESULTS: No significant alpha-diversity changes were observed; however, beta-diversity differed significantly between arms (PERMANOVA R2 = 0.04, p = 0.04). In the polyherbal formulation group, 17 species changed post-treatment (FDR < 0.25), with significant increases in six Bifidobacterium spp. (e.g., B. adolescentis, B. ruminantium). In contrast, the placebo group showed no major microbial shifts. Polyherbal formulation also altered 10 microbial pathways (FDR < 0.25). Continuous glucose monitoring revealed no short-term changes in glycemic levels.

CONCLUSION: Short-term polyherbal formulation co-administration significantly modulates gut microbiota, promoting beneficial taxa like Bifidobacterium in metformin-treated type 2 diabetes patients. This supports the potential role of the polyherbal formulation in microbiome-targeted strategies to improve metformin tolerability and effectiveness.},
}

@article {pmid41428602,
year = {2025},
author = {Zhang, Y and Chen, W and Wang, B and Rehman, KU and van Huis, A and Henawy, AR and Cai, M and Zheng, L and Ren, Z and Huang, F and Zhang, J},
title = {Enhancing Salmonella Inhibition in Black Soldier Fly Larvae (Hermetia illucens L.) Conversion by Bioaugmentation With Gut Microbiota.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70242},
doi = {10.1111/1751-7915.70242},
pmid = {41428602},
issn = {1751-7915},
support = {31770136//National Natural Science Foundation of China/ ; 2662022SKYJ006//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY003//Fundamental Research Funds for the Central Universities/ ; 2022hszd013//Major Project of Hubei Hongshan Laboratory/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; },
mesh = {Animals ; Larva/microbiology ; *Gastrointestinal Microbiome ; *Salmonella/growth & development ; Manure/microbiology ; *Diptera/microbiology ; Chickens ; Bacillus ; Metagenomics ; *Antibiosis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Black soldier fly larvae (BSFL) can efficiently convert organic waste into biomass and reduce pathogenic bacteria in organic waste. The microbial composition of the substrate and the gut of BSFL is a pivotal factor in determining the efficacy of BSFL in pathogen elimination. However, there are insufficient data on the gut microbiology of BSFL in relation to pathogen inhibition. To address this gap, we investigated the dynamics of Salmonella during the conversion of chicken manure by BSFL and examined the role of intestinal bacterial communities and core bacteria in reducing Salmonella levels. The results indicate that BSFL treatment can reduce the amount of Salmonella in chicken manure, with the gut microbiome of the BSFL playing a crucial role in this reduction. Combining metagenomic analysis with culturomics methods, we isolated 158 strains from the larval gut, in which seven gut bacteria belonging to the genus Bacillus can promote BSFL to reduce Salmonella. In reinoculation and validation experiments, the combination of BSFL and Bacillus velezensis A2 enhanced the elimination of Salmonella from chicken manure and larvae. This study provides insight into how BSFL can reduce pathogenic bacteria in chicken manure and suggests that pairing BSFL with functional microorganisms can improve the biosafety of organic waste conversion by BSFL.},
}

Animals
Larva/microbiology
*Gastrointestinal Microbiome
*Salmonella/growth & development
Manure/microbiology
*Diptera/microbiology
Chickens
Bacillus
Metagenomics
*Antibiosis
Bacteria/classification/genetics/isolation & purification

@article {pmid41428567,
year = {2025},
author = {Khromova, AM and Timerzyanov, MI and Valeeva, YV and Khaertynova, IM and Endaltseva, KM and Siraeva, ZY},
title = {[The study of the meconial microbiota for the purposes of forensic science and practice].},
journal = {Sudebno-meditsinskaia ekspertiza},
volume = {68},
number = {6},
pages = {47-51},
doi = {10.17116/sudmed20256806147},
pmid = {41428567},
issn = {0039-4521},
mesh = {Humans ; *Meconium/microbiology ; Infant, Newborn ; *Gastrointestinal Microbiome/physiology ; *Forensic Sciences/methods ; Female ; Pregnancy ; *Microbiota ; },
abstract = {UNLABELLED: The issue of the effect of prenatal and perinatal pathological processes on the intestinal microbiome of the fetus and newborn requires increased attention.

OBJECTIVE: To analyze the results of scientific research reflecting the influence of the intestinal microbiome of a newborn on the stages of postembryonic development.

MATERIAL AND METHODS: A search for contemporary scientific studies relevant to the review's objectives was conducted in the scientific citation systems eLibrary (RSCI), Web of Science, PubMed, and Scopus. Thirty-three publications relevant to the review's subject matter were analyzed and included in the list.

RESULTS AND CONCLUSION: The idea of meconium non-sterility due to maternal-fetal transplantental microbial transition has been confirmed. The diagnostic value of detecting violations of the taxonomic composition of the microbiome lies in optimizing disease prevention and treatment strategies.},
}

Humans
*Meconium/microbiology
Infant, Newborn
*Gastrointestinal Microbiome/physiology
*Forensic Sciences/methods
Female
Pregnancy
*Microbiota

@article {pmid41428256,
year = {2025},
author = {Sivarajan, D and Pothayi, V and Devasia, SC and Ramachandran, B},
title = {Impact of dietary composition on behavioural expression and gut microbiome dynamics in zebrafish.},
journal = {Pflugers Archiv : European journal of physiology},
volume = {478},
number = {1},
pages = {13},
pmid = {41428256},
issn = {1432-2013},
support = {CSIR-UGC-JRF-905/2018//University Grants Commission/ ; (ECR/2018/002479)//DST-SERB, India/ ; },
mesh = {Animals ; *Zebrafish/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Behavior, Animal/physiology ; *Diet ; Brain/physiology ; *Animal Feed ; Aggression ; },
abstract = {Diet is a key physiological factor shaping brain function and gut microbiota, which together form the dynamic gut-brain axis. This bidirectional communication system plays a pivotal role in regulating behavioural outcomes. Therefore, it is worth investigating various behavioural aspects and connecting them with gut microbial dynamics shaped by differential dietary composition. Using zebrafish, we examined the effects of monotypic and combined diets of live feed and commercial feed on behavioural outcomes, morphometry, and gut microbiota. After chronic dietary intervention, fish receiving a mixed diet (Artemia, pellet, and spirulina) showed behavioural profile with enhanced exploration, reduced anxiety-like behaviour, and moderate aggression, alongside a balanced gut microbial composition. In contrast, monotypic diets produced distinct effects: Artemia-only fish displayed reduced boldness, heightened anxiety, and pathogenic microbial enrichment, while pellet-only fish showed greater growth but increased aggression. These findings highlight the importance of mixed feeding regimens for maintaining healthy gut-brain-behaviour interactions and support zebrafish as a model for studying diet-microbiota-behaviour relationships.},
}

Animals
*Zebrafish/microbiology/physiology
*Gastrointestinal Microbiome/physiology
*Behavior, Animal/physiology
*Diet
Brain/physiology
*Animal Feed
Aggression

@article {pmid41427854,
year = {2025},
author = {Wang, Y and Yu, J and Gao, L},
title = {Targeting Intratumoral Bacteria for Cancer Nanotherapeutics.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.5c16720},
pmid = {41427854},
issn = {1944-8252},
abstract = {Intratumoral microbiota has emerged as a key modulator of cancer progression and therapeutic response, significantly influencing treatment outcomes. Although conventional microbiome-modulating approaches such as antibiotic administration can enhance cancer treatment efficacy, they frequently lead to inconsistent therapeutic results and disrupt beneficial microbial communities. Nanotechnology, with its capacity for precise interactions at microscopic and molecular scales, offers a promising solution for selectively regulating tumor-associated microbiota and reshaping the tumor microenvironment. This review elucidates current knowledge by conducting a comprehensive analysis of the literature, with a focus on classifying the antibacterial mechanisms of nanotechnology against intratumoral bacteria into physical, chemical, and biological modalities, and further discusses the precision design of nanomaterials, therapeutic outcomes, and antimicrobial mechanisms within each modality. Furthermore, we discuss challenges in precise targeting and safety, examine the translational progress of nanotechnology-based antimicrobial strategies, and propose future directions for research and clinical application.},
}

@article {pmid41427744,
year = {2025},
author = {Burnside, M and Helliwell, E and Treerat, P and Rozendal, T and Merritt, J and Baker, JL and Kreth, J},
title = {Comparative characterization reveals conserved and divergent ecological traits of oral corynebacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297325},
doi = {10.1128/spectrum.02973-25},
pmid = {41427744},
issn = {2165-0497},
abstract = {Corynebacteria are abundant members of the oral microbiome and increasingly recognized as key structural organizers of supragingival biofilms. Despite their prevalence, the ecological roles and phenotypic traits of many oral corynebacterial species remain poorly defined. Here, we isolated and characterized two new strains, Corynebacterium durum JJ2 and Corynebacterium argentoratense MB1, and compared them with previously characterized and published Corynebacterium durum JJ1 and reference strain Corynebacterium matruchotii ATCC 14266. Phenotypic assays revealed that C. durum strains displayed robust aggregation, thick biofilm formation, and extensive extracellular polymeric substance (EPS) networks, whereas C. argentoratense MB1 and C. matruchotii ATCC 14266 formed thinner biofilms with minimal EPS production. All four strains secreted extracellular membrane vesicles capable of inducing chain elongation in Streptococcus sanguinis, underscoring a conserved interspecies signaling function. Genomic analysis demonstrated close relatedness between C. durum and C. matruchotii, while C. argentoratense MB1 was more distantly related, with a reduced genome, fewer metabolic pathways, and the absence of nitrate reductase genes, consistent with its inability to grow under anaerobic conditions. These findings suggest that C. argentoratense MB1 may represent a less specialized or transient inhabitant of the oral cavity, whereas C. durum and C. matruchotii are well adapted to the oral niche. Together, this study expands our understanding of phenotypic diversity, metabolic capacity, and interspecies interactions among selected oral corynebacteria, highlighting their potential importance as biofilm organizers and contributors to oral microbial ecology.IMPORTANCEOral corynebacteria contribute to the structural and ecological stability of supragingival communities. Yet, their species-level functions remain poorly defined. By isolating and characterizing new strains of Corynebacterium durum and Corynebacterium argentoratense, and comparing them with reference strains including Corynebacterium matruchotii, we provide new insight into their phenotypic diversity, metabolic capacity, and ecological roles. Our results demonstrate that C. durum strains form robust biofilms enriched in extracellular polymeric substances, while C. argentoratense produces thinner biofilms and lacks the genomic features required for anaerobic growth, suggesting a less specialized or transient role in the oral cavity. Importantly, we show that extracellular membrane vesicles secreted by all tested strains promote chain elongation in Streptococcus sanguinis, highlighting a conserved mechanism of interspecies communication. These findings advance our understanding of how oral corynebacteria contribute to biofilm organization and microbial homeostasis and position them as critical but understudied players in oral microbial ecology.},
}

@article {pmid41427732,
year = {2025},
author = {O'Brien, CE and Frese, SA and Cernioglo, K and Damian-Medina, K and Mitchell, RD and Casaburi, G and Melnyk, RA and Henrick, BM and Smilowitz, JT},
title = {Randomized, placebo-controlled trial reveals the impact of dose and timing of Bifidobacterium infantis probiotic supplementation on breastfed infants' gut microbiome.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0051825},
doi = {10.1128/msphere.00518-25},
pmid = {41427732},
issn = {2379-5042},
abstract = {UNLABELLED: A dysfunctional gut microbiome has become increasingly common in infants born in high-income countries as Bifidobacterium strains no longer dominate the gut microbiome. Probiotics containing Bifidobacterium infantis have been used in breastfed newborns to successfully restore the gut microbiome; however, no studies to date have demonstrated this effect in older breastfed infants whose gut microbiomes are transitioning toward stability and maturity. This is a 9-week randomized controlled trial wherein 2-4 months old exclusively breastfed infants (n = 40) received 0 CFU/day B. infantis EVC001 (placebo), 4.0 × 10[9] CFU/day B. infantis EVC001 (low), 8.0 × 10[9] CFU/day B. infantis EVC001 (medium), or 1.8 × 10[10] CFU/day B. infantis EVC001 (high) in equal allocation for 28 consecutive days beginning on day 8. Stool samples were collected on study days 7, 10, 14, 21, 28, 35, 42, and 63. Fecal B. infantis levels were significantly higher in all supplement groups compared with placebo on day 28 and day 63. On day 28, fecal B. infantis levels were significantly higher in infants who received any (low, medium, and high) dose compared with baseline. The abundance of fecal Bifidobacteriaceae significantly increased nearly 2-fold in response to B. infantis EVC001 supplementation. No matter the dose, probiotic supplementation with B. infantis in 2- to 4-month-old exclusively breastfed infants resulted in colonization until at least 1 month post-supplementation.

IMPORTANCE: This study found that supplementing exclusively breastfed infants with a probiotic, Bifidobacterium infantis EVC001, between 2 and 4 months of age can successfully restore beneficial bacteria in their gut, even after the newborn period. Although previous research showed this effect in newborns, this is the first study to demonstrate that older infants, whose gut microbiomes are typically more stable, can still benefit. The probiotic was effective at all tested doses, with higher levels of B. infantis and overall Bifidobacteriaceae in infants' stool during and even 1 month after supplementation. This study demonstrates that B. infantis can take hold in the gut and potentially improve gut health in older breastfed babies, offering a promising approach to support infant health in settings where beneficial gut bacteria are often missing.

CLINICAL TRIALS: This study was registered at clinicaltrials.gov as NCT03476447.},
}

@article {pmid41427714,
year = {2025},
author = {Bell, AG and Cable, J and Temperton, B and Tyler, CR},
title = {Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0183825},
doi = {10.1128/spectrum.01838-25},
pmid = {41427714},
issn = {2165-0497},
abstract = {UNLABELLED: Microbiomes on fish mucosal surfaces play crucial roles in nutrient absorption, immune priming, and defense, and disruptions in these microbial communities can lead to adverse health outcomes, including disease. Studying fish microbiomes relies on sequencing microbiota within mucosal-rich samples; however, nucleic acid extraction from these samples is composed predominantly of host DNA, making subsequent bioinformatic processes difficult. Host depletion techniques address this issue by either selectively degrading host DNA before sequencing or retaining bacterial DNA post-extraction. However, their application to fish mucosal samples has been largely unexplored. Here, we assessed the efficacy of various host depletion techniques on fish skin mucosal swabs via either selectively removing CpG-methylated (predominantly eukaryotic) DNA or selectively lysing eukaryotic cells before DNA extraction. Surprisingly, none of the existing methods we assessed effectively reduced host DNA to be practically useful. Furthermore, some methods introduced a bias toward certain bacterial taxa, including the Bacilli class and the Proteobacteria phylum. Our findings illustrate that the currently available host depletion techniques are largely ineffective for reducing host DNA in fish mucosal samples. This poses a major limitation for developing an understanding of the functional composition of fish mucosal microbiomes, as enriching microbiota (and excluding host DNA) is fundamental for cost-effective metagenomic studies and facilitating more accurate analyses of the microbiota metabolome and proteome.

IMPORTANCE: Microbial communities on fish mucosal surfaces are vital for immune function and disease resistance. However, sequencing these communities is hindered by the dominance of host DNA in mucosal samples, which can exceed 99% of total nucleic acids. While host depletion techniques are routinely used in human and mammalian systems to enrich microbial DNA, their efficacy on fish samples remains uncharacterized. In this study, we assessed multiple commercial and published host depletion methods on fish skin microbiomes. None significantly reduced host DNA to levels suitable for high-quality metagenomic sequencing, and some introduced taxonomic bias. We suggest methodological reasons, including differences in fish cell structure and mucus composition compared to mammalian systems, that may explain these shortcomings. Based on our findings, we propose protocol modifications and highlight key areas for improvement. This work identifies critical limitations and offers a foundation for developing optimized host depletion strategies tailored to fish mucosal microbiome research.},
}

@article {pmid41427705,
year = {2025},
author = {Wang, J and Qu, R and Huang, W and Chen, Y and Li, Y and Lin, Q and Wu, Z and Yan, H and Yu, T and Wang, C and Ren, X and Wang, X and Wu, J},
title = {Progressive and concordant alterations in transcriptional and gut microbiota across aortic valve calcification severity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0213725},
doi = {10.1128/spectrum.02137-25},
pmid = {41427705},
issn = {2165-0497},
abstract = {UNLABELLED: Calcific aortic valve disease (CAVD) is a common disorder associated with substantial morbidity and mortality. Although the gut microbiome has complex associations with cardiovascular disease, its variation across the calcification spectrum in CAVD remains poorly defined. We profiled aortic-valve transcriptomes from 31 patients spanning graded calcification and paired these with matched stool microbiome profiles. We identified subtle yet widespread transcriptional changes in mild CAVD (m-CAVD), consistent with a progressive relationship between calcification burden and gene-expression remodeling. At the community level, the gut microbiome in m-CAVD exhibited an intermediate configuration between non- and higher-calcification profiles, suggesting an early shift in the gut ecosystem along the disease continuum. At the genus level, we identified 11 taxa associated with stage; notably, Anaerococcus increased with calcification burden, whereas Rheinheimera declined across stages. These results refine the pathophysiology landscape of CAVD by connecting stage-dependent valvular transcriptional changes with coordinated shifts in the gut microbiome and indicate that early, microbiome-targeted interventions may be promising.

IMPORTANCE: Calcific aortic valve disease is a common valvular heart disease. Due to the difficulty in sampling arterial calcified tissues, research on the interaction between their gene expression and the gut has been limited. In this study, by analyzing the transcriptional profiles of calcified aortic valve tissues from patients with different levels of calcification and the characteristics of their corresponding gut microbiota, we identified consistent features between lesion gene expression and gut microbiota variation. This provides important evidence for the association between the gut microbiota and disease development stages, offering a new perspective for understanding disease progression and early intervention.},
}

@article {pmid41427586,
year = {2026},
author = {Newman, KL and Standke, AK and James, G and Vendrov, KC and Inohara, N and Bergin, IL and Higgins, PDR and Rao, K and Young, VB and Kamada, N},
title = {Miniature bioreactor arrays for modeling functional and structural dysbiosis in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604875},
doi = {10.1080/19490976.2025.2604875},
pmid = {41427586},
issn = {1949-0984},
mesh = {*Dysbiosis/microbiology ; Humans ; *Gastrointestinal Microbiome ; Animals ; Mice ; *Bioreactors/microbiology ; Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology ; Clostridioides difficile/growth & development ; Colitis, Ulcerative/microbiology ; Disease Models, Animal ; Crohn Disease/microbiology ; Female ; Male ; Interleukin-10/genetics/deficiency ; Bacteria/classification/isolation & purification/genetics ; Mice, Inbred C57BL ; },
abstract = {Alterations in the gut microbiota, known as gut dysbiosis, are associated with inflammatory bowel disease (IBD). There is a need for model systems that can recapitulate the IBD gut microbiome to better understand the mechanistic impact of differences in microbiota composition and its functional consequences in a controlled laboratory setting. To this end, we introduced fecal samples from patients with Crohn's disease (CD) and ulcerative colitis (UC), as well as from healthy control subjects, to miniature bioreactor arrays (MBRAs) and analyzed the microbial communities over time. We then performed two functional assessments. First, we evaluated the colitogenic potential of the CD microbiotas in genetically susceptible germ-free IL-10-deficient mice and found that colitogenic capacity was preserved in a bioreactor-cultivated CD microbiota. Second, we tested impaired colonization resistance against Clostridioides difficile in UC microbiotas using the MBRA system and found that UC microbiotas were innately susceptible to C. difficile colonization while healthy microbiotas were resistant, consistent with what is seen clinically. Overall, our results demonstrate that IBD microbiotas perform comparably to healthy donor microbiotas in the MBRA system, successfully recapitulating microbial structure while preserving IBD-specific functional characteristics. These findings establish a foundation for further mechanistic research into the IBD microbiota using MBRAs.},
}

*Dysbiosis/microbiology
Humans
*Gastrointestinal Microbiome
Animals
Mice
*Bioreactors/microbiology
Feces/microbiology
*Inflammatory Bowel Diseases/microbiology
Clostridioides difficile/growth & development
Colitis, Ulcerative/microbiology
Disease Models, Animal
Crohn Disease/microbiology
Female
Male
Interleukin-10/genetics/deficiency
Bacteria/classification/isolation & purification/genetics
Mice, Inbred C57BL

@article {pmid41427415,
year = {2025},
author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS},
title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.09.693354},
pmid = {41427415},
issn = {2692-8205},
abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug resistant Gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii . This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document potential sources of the corresponding resistance genes. This study searched for potential emerging colistin-resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments which all contained eptA genes. We confirmed their ability to confer significant colistin resistance in E. coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter strains, marking them as potential mcr genes or their precursors. This study highlights the goose fecal microbiome as a potential source for colistin resistance in the environment.},
}

@article {pmid41427374,
year = {2025},
author = {Suzuki, E and Deleray, V and Zemlin, J and Kousha, A and Nonoguchi, H and Sun, D and Tsai, CM and Zuffa, S and Kvitne, KE and Dorrestein, PC and Tsunoda, SM and Nizet, V and Liu, GY and Askarian, F},
title = {Effect of Perinatal Ampicillin or Amoxicillin/Clavulanate Exposure on Maternal and Infant Gut Microbiome, Metabolome, and Infant Responses to the 20-valent Pneumococcal Conjugate Vaccine.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.08.692990},
pmid = {41427374},
issn = {2692-8205},
abstract = {Emerging studies suggest that antibiotics can disrupt the gut microbiome and alter vaccine-induced immune responses, but the specific consequences of early-life exposure on neonatal immune development remains poorly understood. Here, we examined how two antibiotics frequently used in perinatal care, broad-spectrum ampicillin (AMP) and the extended-spectrum combination amoxicillin/clavulanate (AMOX/CLAV), administered during gestation and lactation, influence neonatal gut microbiome composition, fecal metabolome profiles, and responses to the 20-valent pneumococcal conjugate vaccine (PCV20). Maternal treatment with AMOX/CLAV, but not AMP, significantly reduced PCV-specific IgG titers at 4-and 6-weeks post-prime immunization compared to untreated controls. Exclusive exposure to AMOX/CLAV also impaired neutrophil-mediated opsonophagocytic killing, indicating diminished antibody functionality. These effects were transient, with immune parameters normalizing by week 8 post-prime immunization. Metabolomic and microbiome profiling revealed that maternal AMP and AMOX/CLAV differentially perturbed specific metabolite classes including bile acids, N -acyl lipids, and indole-derivatives, as well as key commensal taxa including Bacteroidales and Coriobacteriales within the gut microbiota. Together, these findings reveal a previously underappreciated maternal-offspring route of antibiotic influence that transiently disrupts neonatal vaccine responsiveness through microbiome and metabolome alterations. These results highlight maternal antibiotic exposure as a modifiable factor shaping early-life immunity.},
}

@article {pmid41426949,
year = {2025},
author = {Allshouse, T and Amendano, M and Caruso, B and Del Campo, R and Murphy, G and Shaffer, L and Steinberg, E and Sullivan, A and Stowe, E},
title = {The Microbiota of Homemade Tepache Includes Antibiotic-Resistant Microorganisms.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {41426949},
issn = {2578-9430},
abstract = {Tepache is a traditional, homemade Mexican drink made by fermenting pineapple rinds. The natural probiotic bacteria in tepache are said to promote a healthy gut microbiome. This study assessed the microbial community in homemade tepache for diversity, survival in simulated gastric fluid, and antibiotic resistance. Simulated gastric passaging reduced total community numbers but the community density was not strongly impacted by exposure to tetracycline. Metagenomic analysis reveals a community dominated by Bacillus, Meyerozyma and Talaromyces. These results indicate that consuming home fermented beverages may provide helpful probiotic bacteria but could also expose the gut microbiome to antibiotic resistance genes.},
}

@article {pmid41426590,
year = {2025},
author = {Zhang, J and Xu, X and Chen, L and Yang, X and Matsubara, JK and Tian, Y and Liu, J and Jin, X and Chang, H and Xu, M and Zhu, C and Wang, X and Ren, L and Xie, J and Liu, J and Liu, G and Lu, M and Wang, X and Du, L and Ma, Z and Liu, X and Zhao, H and Chen, W and Huo, X and Zheng, G and Xie, C and Xu, C and Zhang, X and Qi, W and Feng, Z},
title = {Circulating microbiome profiling in transjugular intrahepatic portosystemic shunt patients: 16S rRNA vs. shotgun sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1662837},
pmid = {41426590},
issn = {2296-858X},
abstract = {BACKGROUND AND AIM: Current efforts to characterize the circulating microbiome are constrained by the lack of standardized protocols for isolating and sequencing microbial communities in blood. To address this challenge, our study compared 16S rRNA (V3-V4 region) and shotgun metagenomic sequencing for circulating microbiome detection.

MATERIALS AND METHODS: After obtaining ethics committee approval and informed consent, samples were aseptically collected from 10 patients undergoing transjugular intrahepatic portosystemic shunt (TIPS) procedures. Shotgun metagenomic reads were taxonomically classified using the Kraken2-Bracken pipeline. 16S rRNA (V3-V4) data were analyzed through an ASV-based approach, with USEARCH for denoising and VSEARCH for taxonomic annotation. The results from both sequencing methods were then systematically compared.

RESULTS: Shotgun metagenomic sequencing generated 7,024,580,376 raw reads (mean depth: 234,152,679.2 reads/sample), while 16S rRNA sequencing produced 6,612,678 raw reads (mean depth: 220,422.6 reads/sample). 16S rRNA amplicon sequencing captured a broader range of microbial signals. Although the taxonomic profiles from both sequencing methods showed limited overlap, the core microbiota common to both were still identified. These conserved core microbial communities exhibited stable α- and β-diversity indices across separate vascular compartments.

CONCLUSION: In our study, 16S rRNA amplicon sequencing captured more diverse microbial signals than shotgun metagenomics. A stable microbial community structure was observed across vascular compartments, suggesting a homogeneous microbial composition throughout the circulatory system.},
}

@article {pmid41426531,
year = {2025},
author = {Jijón, G and Hough, C and Gedris, D and Frandsen, PB and Chaston, JM},
title = {Gut microbiome composition of Trichoptera larvae across functional feeding groups: a case study from the Provo River, Utah, USA.},
journal = {ZooKeys},
volume = {1263},
number = {},
pages = {165-177},
pmid = {41426531},
issn = {1313-2989},
abstract = {Diet is known to be a major factor in the gut microbiome of many groups of insects. Larvae from the insect order Trichoptera have varied feeding behaviors, encompassing all functional feeding groups, making them an excellent group for studying the links between diet and gut microbe community variation. However, no previous study has examined these links in caddisflies. Here, we characterize the gut microbiome composition of four caddisfly genera belonging to four different functional feeding groups over two sampling periods using 16S metabarcoding. We found that the sampling date had the strongest influence on gut microbiome variation. Host functional feeding groups and phylogeny also influenced gut community composition; however, improved sampling is necessary to confirm this relationship. Our preliminary results point to interesting differences among larvae from different feeding groups and suggest future areas for research, including performing species-level identification of the caddisfly larvae, using more taxa within and between functional feeding groups, using temporal and larval stage-matched replicates, assessing the degree of microbiome residency in caddisfly guts, and performing deeper sequencing.},
}

@article {pmid41426377,
year = {2025},
author = {Li, Z and Zhang, Y and Luo, X and Wang, Y and Peng, L and Zou, L},
title = {Dynamic relationships between bilirubin concentrations and the gut microbiota in the neonatal period: A pilot prospective cohort study.},
journal = {Pediatric investigation},
volume = {9},
number = {4},
pages = {347-360},
pmid = {41426377},
issn = {2574-2272},
abstract = {IMPORTANCE: Understanding the dynamic interplay between gut microbiota development and bilirubin metabolism may provide new insights into the pathophysiology of neonatal jaundice. Identifying microbial taxa associated with bilirubin fluctuations could help inform early prediction and microbiota-targeted interventions for hyperbilirubinemia.

OBJECTIVE: To investigate the correlation between dynamic changes in the gut microbiota and bilirubin concentrations during the neonatal period.

METHODS: Bilirubin concentrations were monitored daily throughout the neonatal period. Fecal samples were collected from neonates on days 1, 3, 7, 14, 21, and 28 after birth. The composition of the gut microbiome was assessed by 16S rRNA gene amplicon sequencing of the fecal samples. Within-subject, same-day associations between transcutaneous bilirubin (TcB) and genus-level abundance were quantified using a repeated-measures correlation.

RESULTS: Thirty neonates were included in the final analysis. Among the top-30 genera, six exhibited false discovery rate significant, same-day within-subject associations with TcB under the repeated-measures correlation framework (|rrm| ≥0.30). Changes in the abundances of the genera Streptococcus (r rm = +0.416, 95% confidence interval [CI] 0.272-0.543, P = 2.084 × 10[-7]; P-adj = 3.126 × 10[-6]) and Rothia (r rm = +0.340, 95% CI 0.187-0.476; P = 3.134 × 10[-5]; P-adj = 1.567 × 10[-4]) were positively correlated with bilirubin concentrations throughout the neonatal period. In complementary cross-sectional analyses centered on meconium, additional genus-bilirubin correlations were identified for TcB measured on postnatal days 3-7 and for the neonatal TcB peak, with multiplicity controlled separately for each endpoint.

INTERPRETATION: A correlation was found between dynamic changes in the gut microbiome and bilirubin concentrations during the neonatal period. The identified genera might be potential markers or targets for intervention for neonatal jaundice.},
}

@article {pmid41426333,
year = {2025},
author = {Turgeman, I and Henick, BS and Mezquita, L},
title = {Editorial: Nature and nurture in early onset lung cancer.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1750797},
pmid = {41426333},
issn = {2234-943X},
}

@article {pmid41426250,
year = {2025},
author = {Dai, YK and Li, DY and Cong, LL and Liao, Y and Wang, XC and Fan, JW and Chen, WJ and Fan, CH and Ma, T and Wu, YJ},
title = {Mechanism of Chronic Atrophic Gastritis: A 20-Year Bibliometric Analyses.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {17457-17475},
pmid = {41426250},
issn = {1178-7031},
abstract = {BACKGROUND AND PURPOSE: Chronic atrophic gastritis (CAG), affecting approximately 20-30% in high-risk populations, contributes to significant morbidity and mortality due to its progression to gastric cancer. Despite two decades of research into its pathogenesis, the vast body of literature has not yet been systematically mapped. A comprehensive bibliometric analysis mapping the field's evolution, collaborative networks, and knowledge gaps remains lacking. Therefore, we conduct a 20-year bibliometric analysis (2005-2024) of research on the mechanism of CAG to identify seminal works, emerging themes, evaluate global collaboration networks, and highlight translational challenges and opportunities.

PATIENTS AND METHODS: Data were retrieved from the Web of Science Core Collection (WoSCC) spanning from January 1, 2005, to December 31, 2024. Bibliometric analysis was performed using CiteSpace and VOSviewer to analyze publication trends, influential authors and institutions, keyword clusters, and citation bursts.

RESULTS: A total of 954 papers were identified, with China leading in publication output (41.51%), followed by the USA (15.20%). The USA demonstrated high centrality in international collaboration. Key journals included WORLD J GASTROENTERO and GASTROENTEROLOGY. Prolific authors such as Liu Yuetao and co-cited authors like CORREA P were identified. Keyword analysis revealed "Helicobacter pylori" as the most prominent term, with clusters focusing on traditional Chinese medicine, macrophage biology, and gastric intestinal metaplasia.

CONCLUSION: The study highlights the significant research output and collaboration in CAG, emphasizing the importance of interdisciplinary approaches and international partnerships. Future research should focus on integrating traditional knowledge with modern mechanistic studies and addressing emerging themes such as microbiome dysbiosis and precision medicine.},
}

@article {pmid41426219,
year = {2025},
author = {Jeong, JY and Park, SH and Kim, M and Kang, HK and Park, NG},
title = {Comparative gut microbiota, growth performances, and cytokine indices in broiler chickens with or without litter.},
journal = {Journal of animal science and technology},
volume = {67},
number = {6},
pages = {1328-1342},
pmid = {41426219},
issn = {2055-0391},
abstract = {Developmental patterns of the gut microbiota are important for improving chicken health and productivity. However, the influence of litter and litter microbes on cecal microbiota is still unclear. This study aimed to identify broiler cecal microbiota at different ages according to litter usage in cage (without litter) and conventional (with litter) conditions. The cecal contents of the broilers from each group were collected from 1-5 wk. The development and function of the gut microbiota were evaluated using 16S rRNA gene sequencing. The final body weight of the chickens was higher in the cage group than that in the conventional group. In particularly, α-diversity was higher at 3 wk than that at 1 wk. The phyla Firmicutes predominated at 3 wk. In contrast, the abundance of Bacteroidetes and fibrinolytic bacteria increased significantly at 1 and 2 wk compared to that at 3 and 5 wk. Corynebacterium was the most abundant genus in the conventional group after 3 wk. In conclusion, the cecal microbiota are influenced by environmental factors, such as cage, which improves the chicken gut environment.},
}

@article {pmid41425942,
year = {2025},
author = {Li, Z and Peng, X and Wang, Q and Guo, L and Liu, S and Xu, L},
title = {Host sweet preference modulates the salivary microbiome and its divergent associations with plaque-associated and non-plaque-related oral diseases.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1732083},
pmid = {41425942},
issn = {1664-302X},
abstract = {BACKGROUND: Microorganisms play a critical role in the progression of oral diseases. However, it remains unclear whether the frequency of sweet consumption influences the salivary microbiota in both plaque-associated and non-plaque-related oral diseases.

METHODS: Based on salivary microbiome analysis, unstimulated saliva samples were collected from university students aged 17-20, including healthy controls (HC), dental caries (DC), and dental fluorosis (DF) groups, under different sweet consumption frequencies. Microbiota potentially critical in disease development were identified.

RESULTS: No significant differences in α- and β-diversity were observed among the three groups. However, distinct microbial structures at the genus and species levels were evident under different sweet consumption conditions. Under high sweet consumption, the caries group exhibited enrichment of microbiota closely associated with sugar metabolism and acid production (e.g., Streptococcus, Rothia), while Ralstonia was significantly enriched in the caries group, suggesting its potential role in high-sweet-induced caries development. Under low sweet consumption, the healthy control group showed enrichment of taxa such as Stenotrophomonas, potentially linked to ecological stability, whereas the dental fluorosis group demonstrated significant enrichment of Fastidiosipila, reflecting specific fluoride-induced selective pressure on the microbiome. This study indicates that although sweet consumption frequency did not significantly alter overall microbial diversity, it reshaped the oral microbiota structure in a disease-specific context. The caries group was more prone to developing a cariogenic microbial profile under high-sugar conditions, while the fluorosis group exhibited unique ecological adaptive characteristics.},
}

@article {pmid41425940,
year = {2025},
author = {Zheng, B and Wang, L and Sun, S and Yuan, X and Liang, Q},
title = {The molecular interplay between the gut microbiome and circadian rhythms: an integrated review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1712516},
pmid = {41425940},
issn = {1664-302X},
abstract = {This integrated review synthesizes current evidence on the molecular interplay between the gut microbiome and circadian rhythms, emphasizing a sophisticated bidirectional communication system crucial for maintaining metabolic, immune, and neurological homeostasis. The host circadian clock orchestrates microbial composition and function through rhythmic changes in feeding-fasting cycles, hormone secretion, immune responses, and bile acid metabolism. In return, microbial metabolites, including short-chain fatty acids such as butyrate, secondary bile acids like lithocholic acid, and tryptophan derivatives, act as timing cues that influence core clock gene expression via epigenetic mechanisms, receptor-mediated signaling (GPR41/43, FXR), and neuroendocrine pathways. Disruption of this finely tuned dialogue, known as chronodisruption, often driven by modern lifestyles, predisposes individuals to a range of pathologies, including metabolic syndrome, inflammatory bowel disease (IBD), neurodegenerative disorders, and cancer. The review also evaluates promising chronotherapeutic interventions such as time-restricted eating (TRE), targeted probiotic use, and chronopharmacology, which aim to resynchronize host-microbe rhythms and restore physiological balance. Elucidating these mechanisms provides a foundational framework for developing personalized health strategies that target the gut-clock axis.},
}

@article {pmid41425933,
year = {2025},
author = {Zhai, C and Sun, W and Li, Y and Han, H and Zhang, Y and Ma, B},
title = {Pre-release environmental acclimation enhances wild adaptability of endangered Kaluga sturgeon (Huso dauricus): insights from digestive, immune, and gut-microbiome perspectives.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1720688},
pmid = {41425933},
issn = {1664-302X},
abstract = {INTRODUCTION: Pre-release environmental acclimation is an effective strategy for improving post-stocking survival and restoring wild genetic resources in hatchery-reared juveniles. However, environmental acclimation protocols for the endangered Kaluga sturgeon (Huso dauricus) are currently non-existent.

METHODS: Here, cultured H. dauricus were transferred to a tributary of the Songhua River in autumn and exposed to an in-situ environmental acclimation protocol for 30 days. Subsequently, a hatchery control (HK) and seven environmental acclimation groups-HC1 (day 2), HC2 (day 5), HC3 (day 10), HC4 (day 15), HC5 (day 20), HC6 (day 25) and HC7 (day 30)-were monitored for feeding rate, digestive and immune enzyme activities, immune-gene expression, and gut microbiota change.

RESULTS: During the initial phase of wild conditioning, feeding rate remained negligible until HC2 group, then increased to 66%, 88.89% and 100% in groups HC4, HC5 and HC6, respectively. Meanwhile, digestive enzyme activities stabilized between groups HC4 and HC5, and immune enzyme activities in the wild-conditioned sturgeon were markedly higher than those of the control group. In addition, compared with the control group, the pro-inflammatory cytokine Interleukin-6 (IL-6) was significantly up-regulated, whereas the anti-inflammatory genes Interleukin-10 (IL-10) and Transforming growth factor-beta (TGF-β) were significantly down-regulated in HC4 group (P < 0.05). At the phylum level, the dominant microbiota shifted from Pseudomonadota to Bacillota by day 20 (HC5 group) and thereafter remained stable.

DISCUSSION: This study provides a theoretical framework for characterizing the physiological and biochemical responses of H. dauricus during environmental acclimation and provides a scientific basis for conserving its wild genetic resources.},
}

@article {pmid41425932,
year = {2025},
author = {Quijia-Pillajo, J and Chapin, LJ and Owen, JS and Altland, JE and Jones, ML},
title = {Fertilization influences the substrate, rhizosphere, and endosphere bacteriome of Petunia × hybrida.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1719754},
pmid = {41425932},
issn = {1664-302X},
abstract = {INTRODUCTION: In controlled environment agriculture (CEA), soil is replaced with soilless substrates that have poorly understood microbiome dynamics. We investigated the rhizosphere and endosphere bacteriome of Petunia × hybrida 'Picobella Blue' (Picobella) and 'Wave Purple' (Wave) grown in a soilless substrate (80% sphagnum peat and 20% perlite) under three fertilization rates (25, 100, and 200 mg·L[-1] N).

METHODS: Plant growth was assessed with the TraitFinder phenotyping platform, shoot dry weight, and nutrient analysis. Bacteriomes were profiled by 16S rRNA amplicon sequencing from unplanted substrate, bulk substrate, rhizosphere, and endosphere samples.

RESULTS: Both cultivars grew largest and healthiest at 200 mg·L[-1] N. Picobella fertilized with 100 and 200 mg·L[-1] N were equally green, whereas Wave was greenest at 200 mg·L[-1] N. Distinct bacteriomes were observed across unplanted substrate, rhizosphere, and endosphere. In unplanted substrate, fertilizer rate shaped bacterial community composition but not alpha diversity. In the rhizosphere, pH changes driven by fertilization strongly influenced bacterial community structure and reduced diversity. Endosphere and rhizosphere communities were further shaped by cultivar and fertilization rate.

DISCUSSION: These findings highlight nutrient management as a key driver of bacteriome dynamics across the substrate-plant continuum, underscoring the complex interactions between fertilization, plant genotype, and microbial communities in soilless culture.},
}

@article {pmid41425929,
year = {2025},
author = {Li, P and Yu, J and Li, T and Gong, X and Li, L and Cui, Y and He, J and Li, B and Wu, S and Guan, Q and Zhang, Z and Dai, X and Li, Z},
title = {The metabolite ILA of Akkermansia muciniphila improves AP-related intestinal injury by targeting and inhibiting CASP3 activity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1669383},
pmid = {41425929},
issn = {1664-302X},
abstract = {OBJECTIVE: Acute Pancreatitis (AP) is a common acute abdominal disease in clinical practice. The gut microbiome is recognized as a key regulator in the development of acute pancreatitis. Akkermansia muciniphila (AKK) is recognized as a functional probiotic strain and has a beneficial effect on the progression of many diseases. However, the role of the AKK in the development of AP remains unclear. Here, we evaluated the potential contribution of AKK to AP.

DESIGN: Relative abundance of gut microbial AKK in AP was evaluated. A rat model of acute pancreatitis was established by retrograde pancreatic duct infusion of sodium taurocholate. Non-targeted and targeted metabolomics analysis were used for metabolites analysis.

RESULTS: We first found that the relative abundance of gut microbial AKK in AP patients was significantly reduced compared with that in healthy subjects. Live AKK supplementation, as well as supplementation with its culture supernatant, remarkably alleviates AP-related intestinal injury in AP rat models. Metabolomics studies found that the live AKK was able to generate Indole-3-lactic acid (ILA). ILA exerted a protective effect against AP-related intestinal injury, and significantly reduce inflammatory cell activation and pro-inflammatory factor overproduction. The mechanistic study revealed that ILA inhibits the apoptosis of intestinal epithelial cells by suppressing the activity of CASP3, and improves the role of intestinal barrier dysfunction in the AP model.

CONCLUSION: We revealed that ILA, derived from live AKK, may act as a novel endogenous agonist for CASP3. ILA may serve as a new potential treatment method for intestinal injury in AP after successfully translating its efficacy into clinical practice.},
}

@article {pmid41425928,
year = {2025},
author = {Rodríguez-Moreno, A and Martín-Blázquez, S and de Heredia, UL and Soto, Á and Lázaro, E},
title = {Impact of simulated microgravity in short-term evolution of an RNA bacteriophage.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1680651},
pmid = {41425928},
issn = {1664-302X},
abstract = {INTRODUCTION: Microgravity is a critical environmental factor in space that can alter microbial physiology and virus-host interactions. Understanding these effects is essential for planetary protection and crew health during long-term missions. Bacteriophage Qβ, an RNA virus infecting Escherichia coli F+ strains, provides a relevant model due to its potential presence in the human gut microbiome and its well-characterized evolutionary dynamics.

METHODS: We simulated microgravity using a custom-built 3D-clinostat and compared Qβ infections in semisolid medium under standard gravity and simulated microgravity. Twelve evolutionary lines were propagated for ten serial transfers under four experimental conditions combining bacterial growth and infection environments. Viral titers were quantified by plaque assay, and consensus sequences were determined by Sanger sequencing.

RESULTS: Initial infections under simulated microgravity yielded significantly lower viral titers than those in standard gravity, likely due to hindered phage diffusion and delayed infection initiation. After ten transfers, mutation C2011A (amino acid substitution T222N in the A1 virus protein) was fixed in all lines evolved under simulated microgravity but remained absent or polymorphic in standard gravity lines. Under simulated microgravity, the mutation increased virus titers and promoted faster initiation of infections in semisolid medium. However, those effects were not appreciable in normal gravity.

DISCUSSION: Our findings highlight the adaptability of Qβ and the potential impact of microgravity on phage-host interactions, offering insights into virus evolution in extraterrestrial conditions and its implications for space missions and planetary protection.},
}

@article {pmid41425927,
year = {2025},
author = {Qin, R and Li, C and Yuan, X and Chen, Y},
title = {Microbiome-targeted Alzheimer's interventions via gut-brain axis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1729708},
pmid = {41425927},
issn = {1664-302X},
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder with limited treatment options, underscoring the need for novel therapeutic targets. The gut-brain axis has emerged as a critical bidirectional communication system, with growing evidence establishing gut dysbiosis as a causal factor in AD pathogenesis. This dysbiosis, characterized by a reduction in beneficial microbes and an increase in pro-inflammatory taxa, compromises intestinal and blood-brain barrier integrity, promoting systemic inflammation and the translocation of neurotoxic agents like lipopolysaccharide (LPS). Consequently, the balance of key microbial metabolites is disrupted, reducing neuroprotective short-chain fatty acids (SCFAs) and indoles while elevating inflammatory mediators, which collectively exacerbate neuroinflammation, amyloid-β (Aβ) deposition, and tau pathology. This review evaluates promising interventions, including probiotics, anti-inflammatory diets, exercise, and phytochemicals that can restore microbial balance, enhance barrier function, and improve cognitive outcomes in preclinical and early clinical studies. However, clinical translation is hindered by an overreliance on animal models, short-term studies, and insufficient mechanistic insight. Future research must prioritize large-scale human trials, multi-omics integration to elucidate signaling pathways, and personalized approaches that account for host genetics and baseline microbiome composition to fully harness the therapeutic potential of the gut-brain axis for AD.},
}

@article {pmid41425925,
year = {2025},
author = {Sukchawalit, R and Goryluk-Salmonowicz, A and Hobman, JL and Popowska, M},
title = {Editorial: Impacts of metal and xenobiotic-induced stress on antibiotic resistance in microbial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1745065},
doi = {10.3389/fmicb.2025.1745065},
pmid = {41425925},
issn = {1664-302X},
}

@article {pmid41425919,
year = {2025},
author = {Kasani, PH and Yun, CH and Cho, KH and Jeong, SJ},
title = {Neonatal gut microbiota stratification and identification of SCFA-associated microbial subgroups using unsupervised clustering and machine learning classification.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1668451},
pmid = {41425919},
issn = {1664-302X},
abstract = {BACKGROUND: The neonatal gut microbiome plays a critical role in infant health through the production of short-chain fatty acids (SCFAs). However, the organization of SCFAs-producing microbial communities in neonates remains poorly characterized. This study applied unsupervised clustering and machine learning to classify microbial subgroups associated with SCFAs production, providing insight into their composition and metabolic potential.

METHODS: This study recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples within five days postpartum. Microbial diversity was analyzed by 16S rRNA gene sequencing (V3-V4 region) at the genus level, and SCFAs were quantified from the same samples. To identify functionally distinct microbial subgroups, K-Means, Agglomerative, Spectral, and Gaussian Mixture Model clustering were applied. Clustering validity was assessed using Silhouette Score, Calinski-Harabasz Index, Davies-Bouldin Index, and Prediction Strength Validation, with t-distributed Stochastic Neighbor Embedding (t-SNE) visualization to evaluate cluster separation. SCFAs distributions across clusters were compared, while random forest and logistic regression models were used to classify SCFAs-associated microbial clusters through Receiver Operating Characteristic curves (ROC).

RESULTS: The clustering analysis identified distinct microbial subgroups linked to SCFAs production, with Agglomerative clustering outperforming K-Means in capturing functionally relevant structures. Cluster 1 had higher SCFAs levels, enriched in Bacteroides, Prevotella, and Enterococcus, while Cluster 2 exhibited lower SCFAs concentrations with a more heterogeneous composition. The introduction of a third cluster in multi-class analysis revealed an intermediate metabolic profile, suggesting a continuum in microbial metabolic function. Classification analysis confirmed random forest model superiority, achieving ROC score of 91.05% (Agglomerative) and 87.74% (K-Means) in binary classification, and 92.98% (Agglomerative) and 89.84% (K-Means) in multi-class classification, demonstrating RF's strong predictive ability for SCFAs-based clusters.

CONCLUSION: Unsupervised clustering combined with classification analysis effectively predict SCFAs-associated subgroups and paving the way for future research on longitudinal tracking and functional genomic integration in early-life metabolic health.},
}

@article {pmid41425837,
year = {2025},
author = {Oladele, P and Johnson, TA},
title = {Trehalose and maltodextrin preserve microbial community structure in freeze-dried fecal samples for fecal microbiota transplantation.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf204},
pmid = {41425837},
issn = {2730-6151},
abstract = {Fecal microbiota transplantation (FMT) is a promising approach for restoring gut microbial balance in both humans and animals. However, the logistical limitations of transplanting fresh fecal samples have increased interest in freeze-dried (lyophilized) fecal material as a transplant inoculum. While lyophilization facilitates storage, it can compromise bacterial viability, which is essential for FMT effectiveness. Lyoprotectants are often used to protect bacterial cultures during freeze-drying, but their effect on complex microbial communities remains unclear, as they may preferentially preserve some taxa over others. This study investigated the impact of four lyoprotectants-mannitol, maltodextrin, trehalose, and a maltodextrin-trehalose mixture-on bacterial viability and community structure in pig fecal samples post-lyophilization. Propidium monoazide (PMA) treatment combined with 16S rRNA sequencing (PMAseq) was used to differentiate viable from non-viable bacteria. In the total community (without PMA), microbial profiles appeared similar across treatment groups. However, when focusing on the viable community (PMA-treated), lyoprotectant choice significantly influenced the post-lyophilization community composition. Gram-negative bacterial viability was especially sensitive to lyophilization. Trehalose and maltodextrin preserved bacterial viability and community structure more effectively than mannitol. Mannitol-treated samples had reduced viable bacterial cells and altered community composition, while trehalose and maltodextrin better maintained diversity and structure of the viable (PMA-treated) communities. Taken together, lyoprotectants have differential effects on microbial composition during lyophilization. Among those tested, trehalose and maltodextrin best preserved both viability and community structure, making them promising candidates for FMT applications. Future research should explore optimizing lyoprotectant formulations to enhance microbiome stability and functional outcomes.},
}

@article {pmid41425836,
year = {2025},
author = {Yin, X and Ang, LP and Zhu, RL and Azarbad, H and Ni, HH and Chai, ML and Liu, C and Kong, F and Liu, LJ and Liu, SL and Ma, Y and Zhou, HD and Luo, ZS and He, XK and Ye, LX and Li, H and Shu, L},
title = {Host-specific and environmental core bacteria differentially shape the stability and function of the Sphagnum phyllosphere.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf221},
pmid = {41425836},
issn = {2730-6151},
abstract = {Sphagnum mosses maintain peatland ecosystem stability through intimate associations with their microbiomes. As the foundational component of these communities, the core microbiome enables ecosystems to resist, absorb, and recover from environmental changes, yet the roles and processes of Sphagnum core members remain poorly understood, particularly in subtropical ecosystems. Here, we identified different components of core microbiomes and found that host-specific and environmental core microbiomes differentially shape the stability and function of Sphagnum phyllosphere bacteria by examining vertical stratification within a litter-Sphagnum-soil system in a subtropical mountain forest. Sphagnum harbors a microbial community that is significantly distinct from its surrounding environment (i.e. litter and soil), with community assembly primarily driven by deterministic processes, whereas litter and soil communities are more strongly shaped by stochastic processes. Sphagnum host-specific core taxa, enriched in carbon- and nitrogen-cycling lineages (i.e. Ca. Eremiobacterota), stabilized microbial composition, whereas environmental core taxa enhanced interaction strength and network robustness, and these groups responded differently to environmental filters (e.g. pH and elevation). Our framework highlights that core microbiomes are not functionally homogeneous, but instead reflect contrasting strategies that collectively shape ecosystem stability.},
}

@article {pmid41425703,
year = {2025},
author = {Feng, Y and Yang, H and Liang, G and Chen, J and Li, T and Wang, Y and Chang, J and Li, Y and Yang, M and Zhou, X and Wang, Z and Ge, C},
title = {Immune Checkpoint Inhibitors Combined with Oncolytic Virotherapy: Synergy, Heterogeneity, and Safety in Cancer Treatment.},
journal = {Oncology research},
volume = {33},
number = {12},
pages = {3801-3836},
pmid = {41425703},
issn = {1555-3906},
mesh = {Humans ; *Oncolytic Virotherapy/methods/adverse effects ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology ; *Neoplasms/therapy/immunology ; Combined Modality Therapy ; Tumor Microenvironment/immunology/drug effects ; Oncolytic Viruses/immunology ; Immunotherapy/methods ; Animals ; },
abstract = {Immune checkpoint inhibitor (ICI) has limited efficacy in the treatment of immune "cold" tumors. Due to insufficient T cell infiltration and heterogeneous programmed death ligand 1 (PD-L1) expression, the ORR is only 5%-8% compared with 30%-40% of "hot" tumors. This article reviews the synergistic mechanism, clinical efficacy and optimization strategy of oncolytic virus (OVs) combined with ICIs in the treatment of refractory malignant tumors. Systematic analysis of mechanistic interactions across tumor types and clinical trial data demonstrates that OVs transform the immunosuppressive microenvironment by inducing immunogenic cell death and activating innate immunity. Concurrently, ICIs enhance adaptive immunity by reversing T-cell exhaustion and expanding T-cell diversity. Clinical trials in melanoma, head and neck cancer and breast cancer showed superior efficacy. The Objective Response Rate (ORR) of combination therapy was 39%-62%, while the ORR of ICI monotherapy was 18%. Treatment heterogeneity is mainly attributed to virus-related factors, including targeting specificity and replication efficiency, tumor characteristics, such as antigen presenting ability and mutation load, and host immune status, including pre-existing antiviral antibodies and microbiome composition. This combined approach represents a paradigm shift in cancer immunotherapy, which effectively transforms immune "cold" tumors into "hot" tumors through the continuous activation of innate and adaptive immune responses. In the future, it is expected to improve the therapeutic effect of treatment-resistant malignant tumors through the integration of immune regulatory molecules, accurate biomarkers to guide the treatment scheme and triple combination strategy by a new generation of engineering viruses.},
}

Humans
*Oncolytic Virotherapy/methods/adverse effects
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology
*Neoplasms/therapy/immunology
Combined Modality Therapy
Tumor Microenvironment/immunology/drug effects
Oncolytic Viruses/immunology
Immunotherapy/methods
Animals

@article {pmid41425618,
year = {2025},
author = {Fuller-Shavel, N and Davies, EJ and Peleg Hasson, S},
title = {Nutritional strategies in supporting immune checkpoint inhibitor, PI3K inhibitor, and tyrosine kinase inhibitor cancer therapies.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1670598},
pmid = {41425618},
issn = {2296-861X},
abstract = {Nutritional status of patients undergoing cancer treatment has been associated with cancer therapy and survival outcomes across multiple therapy types. Targeted therapies, including immune checkpoint inhibitors (ICIs), phosphatidylinositol 3-kinase (PI3K) inhibitors and EGFR-tyrosine kinase inhibitors (TKIs), are both influenced by and themselves influence the patients' nutritional and metabolic status. Precision nutrition approaches that address specific aspects of targeted therapies, from minimizing toxicities and treatment resistance to potential therapeutic synergies, offer an important avenue to optimize clinical outcomes for patients receiving targeted oncological treatments as a part of an overall precision integrative oncology approach. Optimizing ICI treatment may necessitate gastrointestinal microbiome modulation and managing systemic inflammation with a variety of dietary approaches under study, including the Mediterranean diet, increasing fiber and fermented food intake, fasting and fasting mimicking diet and the ketogenic diet. Supplementation approaches using live biotherapeutics alongside ICIs predominate over prebiotic, postbiotic and synbiotic studies, which require further attention and investment, alongside human research on mycotherapy and fucoidan-based combinations. Optimizing PI3K treatment tolerance requires close attention to monitoring and managing glycemic control through nutrition, lifestyle and pharmacological intervention as necessary, and in supporting patients with EGFR-TKIs both nutritional prehabilitation and close attention to managing gastrointestinal toxicities is paramount. Rational individualized approaches based on detailed and dynamic clinical assessment of patient-, cancer- and treatment-related factors, using validated prognostic scores and biomarkers, are needed to maximize the potential of precision nutrition now and in future trials in this arena.},
}

@article {pmid41425608,
year = {2025},
author = {Yaghoubi Khanghahi, M and AbdElgawad, H and Curci, M and Garrigues, R and Korany, SM and Alsherif, EA and Verbruggen, E and Spagnuolo, M and Addesso, R and Sofo, A and Beemster, GTS and Crecchio, C},
title = {Transcriptomic, biochemical, and microbiome assessments into drought and salinity tolerance in durum wheat mediated by plant growth-promoting bacteria.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {31},
number = {12},
pages = {2121-2143},
pmid = {41425608},
issn = {0971-5894},
abstract = {UNLABELLED: This study investigates the efficacy of plant growth-promoting bacteria (PGPB) in improving stress tolerance in plants by analyzing the molecular and biochemical bases in durum wheat grain. An experiment was conducted where soil and seeds were inoculated with PGPB, under drought and salinity stress. 16 S rRNA sequencing indicated no change in grain bacterial communities in response to biofertilizers and stress. However, a genome-wide analysis identified 153 up-regulated and 33 down-regulated plant genes in response to PGPB, predominantly enriched in stress-related biological processes. These genes specifically encode for proteins involved in metabolite interconversion enzyme, chaperone, protein modifying enzyme, and transporters, which are functionally related groups assisting protein folding in the cell under stress conditions. Moreover, pathway analysis confirmed related changes at the metabolite and enzyme activity levels. In this regard, PGPB-treated plants exhibited heightened activity of both enzymatic and non-enzymatic (e.g., thioredoxins, peroxiredoxins, etc.) antioxidants under stress, showcasing significant enhancements ranging from + 27% to + 283% and + 36% to + 266%, respectively. Further elucidation of biochemical pathways revealed alterations in the activation of non-antioxidant enzymes in PGPB-treated plants, exemplified by increased activities of glutamate synthase (40-44%) and decreased activities of protein-tyrosine-phosphatase (29-31%) under both stresses, as well as elevated activities of anthocyanidin reductase (91%) and lipoxygenases (18%) specifically under drought. Overall, the present research highlighted the potential of beneficial bacteria in improving plant stress tolerance, especially under drought, through shifting transcriptome expression of plant genes and employing multiple protective strategies which can complement each other.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-025-01686-z.},
}

@article {pmid41425546,
year = {2025},
author = {Müller, L and Di Benedetto, S},
title = {Immunosenescence and inflammaging: Mechanisms and modulation through diet and lifestyle.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1708280},
pmid = {41425546},
issn = {1664-3224},
mesh = {Humans ; *Immunosenescence ; *Inflammation/immunology/metabolism ; *Life Style ; *Diet ; Animals ; Gastrointestinal Microbiome/immunology ; *Aging/immunology ; },
abstract = {Aging is associated with profound alterations in the immune system, characterized by immunosenescence and inflammaging, which together compromise host defense, promote chronic low-grade inflammation, and contribute to the development of age-related diseases. Immunosenescence involves thymic involution, hematopoietic stem cell skewing, accumulation of senescent immune cells, and impaired adaptive and innate responses. Inflammaging arises from persistent activation of innate immune pathways, senescence-associated secretory phenotype (SASP) signaling, metabolic dysregulation, and age-related alterations in the gut microbiome. These processes are interconnected through feedback loops and network-level interactions among immune, metabolic, and microbial systems, creating a self-perpetuating cycle of immune dysfunction and systemic inflammation. Emerging evidence indicates that immunosenescence and inflammaging can be modulated through integrative strategies that combine nutrition, microbiome modulation, and lifestyle interventions to sustain immune resilience across the lifespan. Nutrient-specific strategies, including polyphenols, omega-3 fatty acids, and micronutrients, regulate oxidative stress, cytokine signaling, and immune cell metabolism. Holistic dietary patterns such as the Mediterranean diet, caloric restriction, and microbiome-supportive diets enhance gut barrier integrity, modulate systemic inflammation, and improve adaptive immunity. Lifestyle factors, including regular physical activity, adequate sleep, and stress reduction, further support immune resilience. Personalized nutrition and lifestyle strategies, guided by immunobiological profiling, enable tailored approaches to mitigate immune aging. Collectively, these insights highlight a multidimensional framework for understanding and modulating immunosenescence and inflammaging. Integrating dietary, lifestyle, and pharmacological strategies offers a promising path toward enhancing immune function, reducing chronic inflammation, and promoting healthy longevity.},
}

Humans
*Immunosenescence
*Inflammation/immunology/metabolism
*Life Style
*Diet
Animals
Gastrointestinal Microbiome/immunology
*Aging/immunology

@article {pmid41425113,
year = {2025},
author = {Wang, D and Zhang, J and Wang, B and Gao, J and Zhang, G},
title = {Current Trends and Future Insights on Rosacea Treatment: A Bibliometric Analysis.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {18},
number = {},
pages = {3397-3412},
pmid = {41425113},
issn = {1178-7015},
abstract = {BACKGROUND: Rosacea involves immune, neurovascular, and microbial factors, but its complex mechanisms are poorly understood, hindering effective treatment development. This study aims to examine research trends and significant contributions in the treatment of rosacea.

METHODS: Publications related to rosacea treatment were retrieved from the Web of Science Core Collection (WoSCC). Bibliometric analysis and visualization were performed using VOSviewer, CiteSpace, and the R package "bibliometrix".

RESULTS: By June 7, 2024, 1389 English-language publications published between 1970 and 2024 were identified for analysis. The leading research countries were the United States (446 articles) and China (149 articles), with the Central South University (95 articles) being the most productive institution. Key journals included Journal of the American Academy of Dermatology (impact factor = 12.8) and the British Journal of Dermatology (impact factor = 11). James Q. Del Rosso was identified as a major contributor (h-index = 20). Keywords cluster analysis revealed five prominent themes: 1) pharmacological treatment and clinical trials, 2) epidemiology and associated risk factors, 3) pathophysiology and pathogenesis, 4) skin barrier function and related dermatoses, and 5) laser and physical therapies. Representative terms of emerging trends include "pathogenesis", "pathophysiology", and "standard classification", suggesting increasing focus on immune dysregulation, neurovascular mechanisms, and microbiome-related pathways. These insights indicate that future rosacea treatment research may shift toward targeted, mechanism-based therapeutic strategies.

CONCLUSION: This study underscores the dynamic landscape of research in rosacea treatment, synthesizes current areas of emphasis, and forecasts future trends. Future developments in rosacea research may concentrate on integrating precision medicine approaches by linking molecularly defined pathogenic mechanisms with standardized classification systems, thereby facilitating targeted and multidisciplinary treatment strategies.},
}

@article {pmid41424975,
year = {2025},
author = {Ma, L and Wang, H and Jin, Q and Sun, Z and Yu, S and Zhang, Y},
title = {The Gut-Liver Axis: Molecular Mechanisms and Therapeutic Targeting in Liver Disease.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {7531-7546},
pmid = {41424975},
issn = {1178-7074},
abstract = {The gut microbiota, often termed the "second genome", demonstrates profound therapeutic potential through its intricate biological network connecting multiple distal organs. Although microbial diversity is strongly correlated with intestinal health, its systemic implications on overall physiological homeostasis remain incompletely understood. This review synthesizes the latest evidence from clinical trials, randomized controlled trials (RCTs), systematic reviews, and meta-analyses to elucidate the biological pathways and therapeutic applications of the gut-liver axis. Through comprehensive schematic illustrations, we delineate the molecular mechanisms underlying bidirectional gut-liver communication, including microbial metabolite signaling, immune modulation networks, and enterohepatic circulation dynamics. Although interventional studies have confirmed the beneficial physiological effects of microbial modulation, current mechanistic insights are predominantly derived from animal models with limited clinical translation. While large-scale cohort studies with long-term follow-up data remain imperative, the existing evidence strongly supports the clinical value of microbiome-targeted strategies for treating hepatic diseases and related complications. These findings establish a critical theoretical framework for the development of next-generation microbial therapeutics targeting the gut-liver axis. The novelty of this review lies in its systematic classification of gut microbiota and their metabolites in the pathogenesis and treatment of various liver diseases, its detailed elaboration on signaling pathways, and its dedicated focus on the role of Traditional Chinese Medicine (TCM) in modulating the gut-liver axis.},
}

@article {pmid41424906,
year = {2025},
author = {Goswami, A and Ghosh, S and Bandyopadhyay, A and Saha, RG and Sengupta, P and Bhuniya, U and Mandal, P},
title = {Comparative Analysis of Vaginal Microbiome Associated with Oncogenic HPV Infection Among Different Ethnic Groups of Women of the Eastern Region of India.},
journal = {Indian journal of microbiology},
volume = {65},
number = {4},
pages = {1877-1890},
pmid = {41424906},
issn = {0046-8991},
abstract = {The study aimed to identify the influence of vaginal bacterial composition on HPV infection among tribal women of the eastern region of India compared to non-tribal women of the same region. For this study, 13 tribal women and 12 non-tribal women were recruited. DNA was isolated from vaginal swab samples, and subsequently, 16S rRNA gene analysis was performed. We identified two distinct clusters of samples based on taxonomic profiling and bacterial diversity. One cluster belonged to HPV negative samples and the other to HPV16/18 positive samples. The abundance of three bacterial species was significantly lower (p value < 0.05) among oncogenic HPV positive samples (mean abundance = 4.33, 0, and 0, respectively) compared to HPV negative samples (mean abundance = 29.71, 45.73, and 19.01, respectively) irrespective of their ethnicities, such as Lactobacillus amylolyticus, Bacillus coagulans, and Costridium sensu stricto. HPV16/18 positive samples also represent the differential microbiome composition between the two ethnic groups of women. Ethnicity specific variations in human vaginal microbiome composition might be recommended for geographically tailored microbiome-based therapeutic strategies.},
}

@article {pmid41424898,
year = {2025},
author = {Chattopadhyay, P and Biswas, I and Banerjee, G},
title = {Analysing the Metagenomic Dynamics of Soil Microbiota Affected by Tea Pruning and Skiffing Methods in Tea Plantations of Dibrugarh, Assam, India.},
journal = {Indian journal of microbiology},
volume = {65},
number = {4},
pages = {2015-2020},
pmid = {41424898},
issn = {0046-8991},
abstract = {Beginning with the centralization of young tea (Yt) to encourage low branch growth, subsequent light pruning (LP) and deep skiffing (DS) techniques are employed to promote branch spread, ensuring an ideal leaf area index and manageable plucking height. This study investigates the effects of LP and DS compared to Yt on soil biota, a previously unexplored topic. Soil samples from Yt, LP, and DS sites within the Rajgarh Tea Estate in Assam, India, were analyzed for standard parameters and metagenomic DNA using Illumina sequencing. While all samples exhibited a clay loam texture with minimal parameter variation, significant variations in soil phyla abundance were observed. Acidobacteria dominated across all samples, but linear discriminant analysis revealed distinct phyla compositions. At the genus level, Geobacter, Verticiella, and Glaciihabitans were most abundant in S11, S7, and S9 samples, respectively. However, the relative abundance of phyla in the soil samples from Yt, LP, and DS sites varies significantly. But the difference in bacterial community at genus level resolution was not significant at p value 0.05 level. These findings indicate that pruning and skiffing primarily impact on the relative abundance of soil phyla, not microbial diversity. Understanding the soil microbiota in relation to tea cultivation practices through metagenomics can pave the way for developing new microbial consortia for an integrated crop management system in tea cultivation.},
}

@article {pmid41424782,
year = {2025},
author = {Xu, M and Yu, Y and Li, L and Zhao, K and Lai, J and Wei, L and Ge, L},
title = {Rhein ameliorates inflammation, gut dysbiosis, and renal injury in obesity-related glomerulopathy mice.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1654062},
pmid = {41424782},
issn = {1663-9812},
abstract = {OBJECTIVE: Obesity-related glomerulopathy (ORG) lacks targeted therapies. Rhein, a bioactive anthraquinone from Rhei Radix et Rhizoma, was evaluated for its effects on inflammation, renal function, and gut microbiota in high-fat diet-induced ORG mice.

METHODS: C57BL/6J mice were fed a 60% fat diet for 12 weeks to establish ORG, followed by 300 mg/kg/day rhein free intake for 12 weeks. Serum cytokines (IL-6, TNF-α), renal histopathology, and 16S rRNA microbiome sequencing were analyzed.

RESULTS: Rhein significantly reduced body weight (P < 0.001), serum triglycerides (P < 0.01), and proteinuria (P < 0.001), while improving glomerular lesions. It also markedly lowered serum levels of IL-6, TNF-α, and creatinine. 16S rRNA sequencing revealed that rhein restored gut microbiota diversity (e.g., Chao1 index increased from 303.58 to 425.78) and reversed the Firmicutes/Bacteroidetes imbalance (76.86%-62.15%). Analysis of similarities (ANOSIM) further confirmed a significant difference in microbial community structure between the Rhein and Model groups (R = 0.926, p = 0.008).

CONCLUSION: Rhein mitigates ORG progression is associated with anti-inflammatory, lipid-lowering, and microbiota-modulating mechanisms, offering a novel therapeutic strategy.},
}

@article {pmid41424704,
year = {2025},
author = {Araújo, JPM and Przelomska, NAS and Smith, RJ and Drechsler-Santos, ER and Alves-Silva, G and Martins-Cunha, K and Hosoya, T and Luangsa-Ard, JJ and Perrigo, A and Repullés, M and Matos-Maraví, P and Woods, R and Pérez-Escobar, OA and Antonelli, A},
title = {A new species of Purpureocillium (Ophiocordycipitaceae) fungus parasitizing trapdoor spiders in Brazil's Atlantic Forest and its associated microbiome revealed through in situ "taxogenomics".},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e168534},
pmid = {41424704},
issn = {2210-6340},
abstract = {Our planet is inhabited by an estimated 2.5 million species of fungi, of which fewer than 10% have been scientifically described. Some of the most understudied yet remarkable fungal species are those capable of parasitizing arthropods, notably insects and spiders. Here, we explore the hidden diversity of a spider-attacking (araneopathogenic) fungus and its associated microbiome in one of the world's most biodiverse yet threatened biomes, the Atlantic Forest. We apply a field-based "taxogenomic" approach, comprising the integration of classical fungal taxonomy and genomic characterization of a sample's endogenous, associated, and incidental DNA. The data we produced in the field reveal a new species of Purpureocillium fungus belonging to the P. atypicola group, parasitizing trapdoor spiders, and provide a snapshot of its associated bacterial and fungal microbiota. Molecular, morphological, and ecological data support P. atypicola as a complex of cryptic species infecting a variety of ecologically distinct spider species globally. We call for consolidated efforts to accelerate and facilitate the publication of both new species and the characterization of the genomic composition of their associated taxa.},
}

@article {pmid41424695,
year = {2025},
author = {Wang, X and Yue, R and Wen, J and Wu, H and Zhou, X and Chen, Y and Luo, L and Lin, S and Ai, Q and He, Y and Zhao, W},
title = {Alanyl-Glutamine Attenuates Soybean Meal-Induced Intestinal Dysfunction and Growth Retardation in Largemouth Bass (Micropterus salmoides).},
journal = {Aquaculture nutrition},
volume = {2025},
number = {},
pages = {7842137},
pmid = {41424695},
issn = {1365-2095},
abstract = {This study investigated the mitigating effects of alanyl-glutamine (AG) on soybean-meal-induced enteritis (SBMIE) in largemouth bass (Micropterus salmoides). Three experimental diets were prepared: a fishmeal (FM) diet as a positive control, a 50% soybean meal (SBM) replacement FM protein (SBM50) diet as a negative control, and the SBM50 diet supplemented with 1% AG (SBM50 + 1% AG). Fish (initial weight: 10.20 ± 0.20 g) were distributed into three groups in triplicate (25 fish per tank) and fed for 8 weeks. Results demonstrated that the SBM50 + 1% AG group exhibited markedly higher final body weight, weight gain rate, and specific growth rate compared to the SBM50 (p < 0.05). The SBM50 + 1% AG group markedly elevated serum levels of free glycine, lysine, and total essential amino acids compared to the FM group (p < 0.05). In addition, the SBM50 + 1% AG group markedly increased the intestinal plica height (PH) and goblet cell numbers compared to the SBM50 group (p < 0.05). Pathological alterations, including villous atrophy, nuclear pyknosis, mitochondrial matrix dissolution, and inner membrane disruption, were shown in the SBM50 group, all of which were ameliorated by AG supplementation. In addition, the addition of AG significantly reduced Caspase3 activity compared to the FM group (p < 0.05). Microbiome analysis revealed dietary AG significantly increased α-diversity and the proliferation of potentially beneficial taxa (Bacteroidota, Bacteroides, and Prevotella) (p < 0.05). Transcriptomics showed dietary AG upregulated intestinal barrier-related pathways (including focal adhesion, cell adhesion molecules, and adherens junction), along with tight junction gene expression (zo-1, claudin-3, and filamin-B). In conclusion, high dietary SBM inclusion impairs growth performance and induces intestinal inflammation in largemouth bass. Dietary AG effectively mitigates SBMIE by remodeling the intestinal microbiota, enhancing intestinal barrier integrity, and modulating immune responses.},
}

@article {pmid41424621,
year = {2025},
author = {Shangguan, Y and Zhu, J and Ye, J and Korpelainen, H and Li, C},
title = {Selenium phytofortification: enhanced stress resistance and nutraceutical enrichment in horticultural crops.},
journal = {Horticulture research},
volume = {12},
number = {12},
pages = {uhaf236},
pmid = {41424621},
issn = {2662-6810},
abstract = {As a bridge between human health and plant nutrition, Selenium (Se) phytofortification represents a promising strategy for achieving a safe and effective dietary Se supplementation. Due to chemical similarities, Se absorption, transformation, and storage in crops primarily follow the sulfur metabolic pathway. Se enhances horticultural crop resilience against abiotic and biotic stresses by: (i) boosting antioxidant capacity, (ii) inducing hormonal cascades, (iii) promoting the accumulation of key metabolites (e.g. amino acids, flavonoids), (iv) strengthening cellular functions, and (v) harnessing plant-microbiome interactions. In horticultural crops, most Se exists in organic forms, such as selenoamino acids, selenoproteins, selenium-polysaccharides, and selenium-polyphenols, which contribute to unique quality traits. Additionally, Se regulates the synthesis of core nutrients, including amino acids, flavonoids, phenolic compounds, soluble sugars, mineral elements, alkaloids, and volatile compounds. It also extends postharvest shelf life by delaying senescence and deterioration. Current phytofortification strategies focus on enhancing bioavailable Se in edible parts through agronomic interventions and plant breeding. Artificial Se fertilization is the most common agronomic approach, classified by the application method (soil fertilization, foliar spraying, hydroponic supplementation, and seed soaking) and fertilizer type (inorganic, organic, nano-Se, and biosynthesized fertilizers). Optimizing plant species, fertilization methods, dosage, timing, and elemental synergies maximize phytofortification efficiency.},
}

@article {pmid41424618,
year = {2025},
author = {Pandey, SN and Goyal, K and Rana, M and Menon, SV and Ray, S and Ali, H and Kumbhar, PS and Disouza, J and Singh, SK and Gupta, G and Wong, LS and Kumarasamy, V and Subramaniyan, V},
title = {Microbiome-derived bile acids as endogenous regenerative mediators in liver repair.},
journal = {Regenerative therapy},
volume = {30},
number = {},
pages = {681-690},
pmid = {41424618},
issn = {2352-3204},
abstract = {The liver's extraordinary capacity for self-repair is often compromised by chronic injury, fibrosis, or extensive resection, creating an urgent need for innovative regenerative therapies to restore liver function. Emerging evidence suggests that microbiome-derived bile acid metabolites are potent endogenous mediators of hepatic regeneration. Beyond their canonical role in lipid emulsification, these chemically diverse molecules engage nuclear and membrane receptors, most notably the farnesoid X receptor (FXR) and Takeda G protein-coupled receptor 5 (TGR5), to stimulate hepatocyte proliferation, modulate inflammatory responses, and reactivate quiescent progenitor cells. In this review, we integrate mechanistic insights from partial hepatectomy, germ-free, and antibiotic-treated animal models with early clinical observations to illuminate how primary and secondary bile acids orchestrate cell cycle progression, cytokine balance, and extracellular matrix remodeling. We then examined the therapeutic landscape, from synthetic FXR/TGR5 agonists to live-biotherapeutic approaches, genetically modified probiotic strains, and fecal microbiota transplantation. We highlight the preliminary indicators of efficacy and challenges in manufacturing consistency, safety profiling, and regulatory classification. We address the interindividual variability in microbiome composition, potential biomarkers such as serum FGF19, imaging-based measures of functional liver mass, and considerations for optimal trial design. This is the first comprehensive review to frame microbiome-driven bile acids as direct modulators of liver regeneration and chart a coherent translational development pathway. By integrating stem cell biology, hepatology, microbiology, and bioengineering perspectives, we demonstrate the underexplored therapeutic potential of these approaches to transform the future of hepatic repair.},
}

@article {pmid41424605,
year = {2025},
author = {Kay, E and Kazi, M and Burton, J and Parvathy, SN},
title = {Therapeutic properties of plant-derived prebiotics in melanoma.},
journal = {Exploration of targeted anti-tumor therapy},
volume = {6},
number = {},
pages = {1002354},
pmid = {41424605},
issn = {2692-3114},
abstract = {Immune checkpoint inhibitor (ICI) therapy has revolutionized metastatic melanoma treatment, yet only a subset of patients respond effectively, and the treatment can induce a variety of immune-related adverse events (irAEs), including colitis. The gut microbiome plays a critical role in determining patient responses to immunotherapy, prompting exploration of gut-modifying strategies such as prebiotics, probiotics, and fecal microbiota transplantation (FMT) to overcome both primary and acquired resistance and improve treatment outcomes. Prebiotics, defined as dietary substrates that selectively support the growth and/or activity of beneficial gut microorganisms, represent a feasible and safe strategy for microbiome reshaping. Plant-derived prebiotics like castalagin, inulin, fructooligosaccharides, galactooligosaccharides, mushroom extract, kale extract, and konjac glucomannan offer unique advantages over synthetic or animal-derived alternatives due to their natural fiber content alongside their ability to enhance gut microbial diversity. Prebiotics are known to achieve health benefits by selectively stimulating beneficial gut bacteria, producing short-chain fatty acids (SCFAs) that modulate the host immune system, suppressing pathogenic microbes, enhancing mucin production, and modulating systemic and gut-associated immune responses. SCFAs generated through prebiotic fermentation influence host innate and adaptive immunity and regulate metabolic activity via inhibition of histone deacetylases (HDACs), influencing mTOR/MAPK signaling and cytokine production. They also act as ligands for G-protein-coupled receptors (GPCRs), altering intracellular calcium and cAMP to modulate immune cell gene expression. However, the specific mechanisms by which individual prebiotics interact with host genetics, beneficial gut bacteria, and their metabolites are not very well understood. This is crucial to optimize their therapeutic potential in cancer immunotherapy. This review synthesizes current evidence on plant-derived prebiotics, highlighting the impact of beneficial gut bacteria and their metabolites. Given their established safety for human consumption, prebiotics represent a promising, low-risk option to improve gut microbiome composition and potentially enhance immunotherapy and clinical outcomes in cancer.},
}

@article {pmid41424562,
year = {2025},
author = {Andargie, YE and Lee, G and Kim, MJ and Fentie, EG and Jeong, M and Tagele, SB and Lim, K and Azizoglu, U and Shin, JH},
title = {Soil microbial load modulation improves plant-microbe interactions and bioinoculant efficacy in pathogen-stressed soils.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1712997},
pmid = {41424562},
issn = {1664-462X},
abstract = {Plants establish a close association with a community of microbes naturally living in the soil, known as resident soil microbiome, which typically maintains a dynamic equilibrium that confers resilience against biotic and abiotic perturbations. However, this microbiome can also reduce the success of adding new helpful microbes (bioinoculants) by reducing their functional integration with the host plant. Although bioinoculants often perform well under controlled conditions, their efficacy in pathogenic soils is frequently compromised even after repeated applications. While several factors influencing inoculation success have been examined, the impact of soil microbial load, its dynamics, and associated transcriptomic consequences remain largely overlooked. To address this gap, we induced dysbiosis in the resident soil microbiome using moist heat treatment (MHT) thereby generating a gradient in microbial load. We then assessed the phenotypic and transcriptomic responses of Cucumis sativus L., for bioinoculants alongside relative and quantitative rhizosphere microbiome profiling. MHT reduced resident soil bacterial abundance by 96.4% ± 0.9%, with 78% recovery observed after planting. This recolonization promoted plant growth and overall health by restructuring the rhizosphere microbiome and activating plant-microbe interaction pathways such as sugar metabolism, nitrogen metabolism, and aromatic compound degradation. In contrast, moist heat untreated (native) rhizosphere, with a microbial load threefold higher, resisted restructuring, favoring metabolic pathways that preserve microbial stability, such as cell wall and signal molecule biosynthesis, at the expense of plant health. Transcriptomic analyses revealed that, in moist heat treated (dysbiotic) soil conditions, bioagent inoculation triggered induced systemic resistance in cucumber, characterized by downregulation of PAL and POX gene families together with SAMDC, and upregulation of auxin-regulatory and calcium uniporter genes. This response reflected a reallocation of metabolic energy from defense to growth, while maintaining active signaling for beneficial colonization and pathogen perception via modulation of calcium influx. Our findings highlight microbial load modulation as a key strategy to facilitate rhizosphere remodeling, enhance bioinoculant efficacy, and promote plant transcriptomic responses.},
}

@article {pmid41424555,
year = {2025},
author = {Qiao, J and Shen, L and Liu, J and Sun, J and Dai, Z and Hu, J and Du, C and Yang, J and Li, J and Zhao, J and Chen, X},
title = {Graphene oxide promotes soybean growth by reshaping the rhizosphere microbiome and enhancing soil fertility.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1683882},
pmid = {41424555},
issn = {1664-462X},
abstract = {Soybean (Glycine max L.) one of the world's most important crops that is prized for its high protein and lipid content. As a prominent member of the carbon nanomaterial family, graphene oxide (GO) exhibits remarkable fertilizer adsorption and slow-release capabilities owing to its high specific surface area and abundant oxygen-containing functional groups, demonstrating broad application prospects in agricultural production. However, its potential role in regulating soybean growth and modulating the rhizosphere microbiome remains poorly understood. To elucidate the mechanism by which GO modulates soybean growth, we investigated eight cultivars (SN24, CD5, 7534, 15GI-16, ZH75, G135, L2012-7, and CD13) with a 30 mg/L GO treatment. The results demonstrate that GO application significantly enhanced key agronomic traits, increasing plant height by 7.17-51.05%, stem diameter by 12.39-63.34%, and the number of root nodules by 33.33-328.57%, along with increase in root biomass. Rhizosphere microbiome analysis revealed that GO restructured microbial communities in L2012-7 and significantly increased bacterial and fungal abundance or diversity based on operational taxonomic unit (OTU) levels (p < 0.05). Taxonomic profiling identified GO-enriched beneficial genera (Sinorhizobium, Sphingomonas and Trichoderma), with LEfSe and Random Forest analyses confirming that Sinorhizobium is a keystone taxon. Mechanistically, Sinorhizobium fredii (Sf01) was successfully isolated and identified from soybean rhizosphere soil, which was shown to promote soybean growth. Treatment with 5, 30, and 50 mg/L GO promoted the colony growth of S. fredii (Sf01) by 40.2%, 42.9%, and 55.5%, respectively, whereas 100 mg/L GO inhibited its growth compared to the control. Furthermore, soil nutrient analysis demonstrated that GO significantly enhanced the contents of soil organic matter, total nitrogen, available potassium, available phosphorus, ammonium nitrogen, and humic acid in soybean rhizosphere soil. Our experimental results demonstrate that GO reshapes the soybean rhizosphere microbial community, which in turn enriches keystone beneficial microbes S. fredii (Sf01) and enhances soil fertility retention capacity. This cascade of effects collectively promotes soybean plant growth, offering a nano-enabled strategy to reduce reliance on synthetic fertilizers.},
}

@article {pmid41424302,
year = {2026},
author = {Meng, X and Hao, R and Liu, K and Zhang, P and An, C and Zhang, Y and Li, H and Wu, B and Li, M and Yu, X and Tong, X},
title = {The trilateral nexus of autoimmune thyroiditis: integrating immunological triggers, endocrine disruption, and gut microbiome alterations for treatment strategies.},
journal = {Autoimmunity},
volume = {59},
number = {1},
pages = {2601015},
doi = {10.1080/08916934.2025.2601015},
pmid = {41424302},
issn = {1607-842X},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Thyroiditis, Autoimmune/immunology/therapy/metabolism/etiology/microbiology ; Dysbiosis/immunology ; Animals ; Thyroid Hormones/metabolism ; Thyroid Gland/immunology/metabolism ; Autoantibodies/immunology ; },
abstract = {The pathogenesis of autoimmune thyroiditis (AIT) is intricately linked to immune dysregulation, endocrine imbalance, and gut microbiota dysbiosis. The immune system drives autoimmune attacks against thyroid tissue through Th1/Th2 cell imbalance, Treg dysfunction, and excessive release of proinflammatory cytokines. Thyroid hormone regulation primarily occurs via the hypothalamic-pituitary-thyroid (HPT) axis. Elevated levels of TPOAb and TgAb in AIT patients can lead to hypothyroidism by affecting the HPT feedback loop. Thyroid hormone regulation of immune cell metabolism and differentiation, in turn, affects immune homeostasis, forming a bidirectional regulatory network. Recent studies further reveal that the gut microbiota influences systemic immune tolerance by regulating intestinal barrier integrity and metabolites (e.g. short-chain fatty acids and secondary bile acids). Abnormal abundance of specific genera (e.g. Bacteroides and Prevotella) can promote the production of thyroid autoantibodies (TPOAb/TgAb), and increased intestinal permeability caused by microbiota dysbiosis may facilitate cross-reactivity between microbial antigens and thyroid antigens. Furthermore, the gut microbiota indirectly regulates thyroid function through the HPT axis. This review aims to summarize the current knowledge regarding the specific molecular mechanisms of gut microbiota-immune-endocrine interactions in AIT, offer important references for researching the treatment directions of AIT.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Thyroiditis, Autoimmune/immunology/therapy/metabolism/etiology/microbiology
Dysbiosis/immunology
Animals
Thyroid Hormones/metabolism
Thyroid Gland/immunology/metabolism
Autoantibodies/immunology