@article {pmid41508594,
year = {2026},
author = {Zhao, W and Zhang, Y and Ma, H and Sun, P and Zhang, Y},
title = {Characterization of the follicular fluid microbiome in endometriosis patients undergoing in vitro fertilization.},
journal = {Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology},
volume = {42},
number = {1},
pages = {2612148},
doi = {10.1080/09513590.2025.2612148},
pmid = {41508594},
issn = {1473-0766},
mesh = {Humans ; Female ; *Follicular Fluid/microbiology ; *Endometriosis/microbiology/complications ; *Fertilization in Vitro ; Adult ; *Microbiota/genetics ; Pregnancy ; *Infertility, Female/microbiology/therapy/etiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Pregnancy Rate ; },
abstract = {BACKGROUND: Endometriosis (EMs) is a common gynecological disorder associated with infertility. EMs patients often require assisted reproductive technology (ART) but exhibit lower success rates. This study aimed to characterize the follicular fluid microbiome in EMs patients undergoing in vitro fertilization (IVF) and provide insights into mechanisms underlying lower pregnancy rates.

METHODS: Follicular fluid samples were collected from EMs patients and control subjectsundergoing IVF. Microbial DNA was subjected to 16S rRNA gene sequencing. Bioinformatic analyses, including alpha and beta diversity analysis, microbial composition profiling and biomarker identification, were performed.

RESULTS: The follicular fluid microbiome in EMs patients exhibited altered alpha and beta diversity compared to controls. Distinct microbial compositions were observed at various taxonomic levels. Differentially abundant taxa were identified as potential biomarkers for EMs. Microbial profiles were associated with clinical parameters such as oocyte quality and fertilization rates. Models based on microbial profiles were constructed to elucidate the relationship between EMs and IVF outcomes. Functional predictions suggested alterations in metabolic pathways in the follicular fluid microbiome of EMs patients.

CONCLUSIONS: This study revealed significant alterations in the follicular fluid microbiome of EMs patients, providing a basis for further research into the role of the microbiome in EMs-related infertility.},
}

Humans
Female
*Follicular Fluid/microbiology
*Endometriosis/microbiology/complications
*Fertilization in Vitro
Adult
*Microbiota/genetics
Pregnancy
*Infertility, Female/microbiology/therapy/etiology
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Pregnancy Rate

@article {pmid41508551,
year = {2026},
author = {Winn, M and Karra, P and Benson, R and Pauleck, S and Chaiyakunapruk, N and Khaing, W and Veettil, SK and McFarland, MM and Casucci, T and Xu, Y and Hu-Lieskovan, S and Litchman, M and Playdon, M and Hardikar, S},
title = {Metabolic Syndrome and Obesity-related cancer Risk and Survival: An Umbrella Review of Systematic Reviews With Meta-analysis of Observational Studies.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70073},
doi = {10.1111/obr.70073},
pmid = {41508551},
issn = {1467-789X},
support = {NCIF30CA278348/CA/NCI NIH HHS/United States ; NCIK07CA222060/CA/NCI NIH HHS/United States ; NCIR00CA218694/CA/NCI NIH HHS/United States ; NCIK00CA2644000/CA/NCI NIH HHS/United States ; NCIF99CA264400/CA/NCI NIH HHS/United States ; T32DK091317/DK/NIDDK NIH HHS/United States ; },
abstract = {INTRODUCTION: Metabolic syndrome (MetS) may be associated with obesity-related cancer (ORC) owing to shared risk factors like physical inactivity, insulin resistance, gut microbiome dysfunction, and inflammation. We conducted an umbrella review of systematic reviews with meta-analysis to synthesize the evidence on the association between MetS and ORC risk and survival.

METHODS: Searches in five databases (Medline, Embase, CINAHL, Cochrane Library, and Scopus) retrieved 2524 systematic reviews with meta-analyses (SRMAs), which underwent title and abstract screening (2524), full-text review (41), and data extraction for included SRMAs (21). Summary effects and 95% confidence intervals were re-estimated using random-effects models. Methodological quality, certainty of evidence, and publication bias were assessed using the AMSTAR 2, modified Ioannidis criteria, and Egger's test, respectively.

RESULTS: A total of 25 associations between MetS and ORC risk and five between MetS and survival were evaluated. Overall, 10 associations evaluating MetS and ORC risk were highly suggestive (four) or suggestive (six), while the rest were classified as weak (seven) or nonsignificant (eight). One association was suggestive for MetS and ORC survival, while the rest were classified as weak (three) or nonsignificant (one). The Egger's and excess significance tests were significant for 8(32%) associations between MetS and ORC risk and 3(60%) associations between MetS and ORC survival.

CONCLUSION: This umbrella review suggests metabolic syndrome increases the risk of several obesity-related cancers and worsens colorectal cancer survival. Despite study variability, consistent associations across diverse populations highlight the urgency of prevention and management strategies targeting metabolic dysfunction to reduce cancer burden. Summary In this umbrella review, highly suggestive and suggestive evidence supports associations between MetS and the risk and survival of several obesity-related cancers. However, a better understanding of the relationship between metabolic syndrome and obesity-related cancers is still needed to provide appropriate clinical care, design optimal interventions, and prevent subsequent increases in the risks of cancer, morbidity, and mortality.},
}

@article {pmid41508485,
year = {2026},
author = {Wang, X and Qiu, M and Shao, Y and Tu, Z and Liu, J},
title = {Mechanism of high-fat diet exacerbating α-lactalbumin-induced allergic responses: Microbiome and metabolomic insights.},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {118064},
doi = {10.1016/j.foodres.2025.118064},
pmid = {41508485},
issn = {1873-7145},
mesh = {Animals ; *Lactalbumin/immunology/adverse effects ; *Diet, High-Fat/adverse effects ; *Metabolomics ; Mice ; *Food Hypersensitivity/microbiology/metabolism/immunology/etiology ; *Gastrointestinal Microbiome ; Immunoglobulin E/blood ; Male ; Mice, Inbred C57BL ; Histidine/metabolism ; Staphylococcus ; Cytokines/metabolism ; Immunoglobulin G/blood ; *Microbiota ; },
abstract = {High-fat diet (HFD) is a key contributor in exacerbating food allergy, but there is little in-depth research on the mechanisms by which HFD affects allergic responses induced by α-lactalbumin (ALA). The mechanism of HFD exacerbating ALA-induced allergic responses (H-ALA) was studied via microbiome and metabolomics. HFD induced alterations in body weight and temperature in ALA-sensitized mice, while exacerbating allergic responses by increasing ALA-specific IgG/IgE levels and disrupting Th1/Th2 cytokine balance. In H-ALA, 16S rRNA gene sequencing revealed that Staphylococcus and Bilophila were the dominant genera, and untargeted metabolomics demonstrated an upregulation of histidine accompanied by reduced indole-3-acetic acid. Correlation analysis and subsequent mechanistic validation suggested that HFD might exacerbate ALA-induced allergic responses through promoting the expansion of Staphylococcus and elevating histidine levels. These findings will provide a theoretical foundation for the prevention and intervention of HFD-exacerbated food allergy.},
}

Animals
*Lactalbumin/immunology/adverse effects
*Diet, High-Fat/adverse effects
*Metabolomics
Mice
*Food Hypersensitivity/microbiology/metabolism/immunology/etiology
*Gastrointestinal Microbiome
Immunoglobulin E/blood
Male
Mice, Inbred C57BL
Histidine/metabolism
Staphylococcus
Cytokines/metabolism
Immunoglobulin G/blood
*Microbiota

@article {pmid41507958,
year = {2026},
author = {Ramadan, YN and Alatawi, MN and Albalawi, AS and Hetta, HF},
title = {Bacterial contributions to cancer development: mechanisms, dysbiosis, and cross-cancer associations.},
journal = {Infectious agents and cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13027-025-00722-7},
pmid = {41507958},
issn = {1750-9378},
}

@article {pmid41507781,
year = {2026},
author = {Vlasblom, AA and Patel, S and Lawlor, PG and Claesson, MJ and Crespo-Piazuelo, D and Eckenberger, J and Huseyin, CE and Elend, C and Wagenaar, JA and Zomer, AL and Duim, B},
title = {Targeted isolation of bacteria with potential to competitively exclude Staphylococcus aureus in the upper respiratory tract of pigs.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04613-0},
pmid = {41507781},
issn = {1471-2180},
support = {50-52900-98-043//JPIAMR (JPIAMR-2017-1-B/ ; },
abstract = {BACKGROUND: Considering global antimicrobial resistance (AMR) prevalence, alternative or complementary strategies to antimicrobial use, are of interest. Livestock- associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is of particular interest as despite significant AMU reduction, LA-MRSA prevalence in pig husbandry has not decreased. To develop such strategy, we performed targeted isolation of bacterial species with potential antagonism against LA-MRSA in pig farms.

RESULTS: Duplicate piglet nasal swabs from three European countries (Germany, Ireland and The Netherlands) were taken longitudinally from birth up to 10 weeks, one for amplicon sequencing and qPCR, and the other was cryopreserved for culturing. We identified potential probiotic species by anticorrelation analysis of bacterial abundance from amplicon sequencing data with quantitative S. aureus estimates from qPCR data from the samples. A literature-screen was performed on the species identified, to determine their probiotic potential. Following this, 1302 isolates were grown from selected cryopreserved swabs and identified using MALDI-TOF and additional 16S rRNA gene sequencing to isolate the anticorrelating species. Ninety-five isolates of interest were screened for absence of tetracycline resistance and hemolytic activity and whole genome sequencing was conducted to verify their taxonomy and to assess their AMR and virulence gene profile. Additional phenotypic antimicrobial resistance testing selected three different Lactococcus lactis strains. During an in vitro challenge using spent medium, all three strains demonstrated inhibition against two S. aureus strains.

CONCLUSIONS: Our study, using an anticorrelation based targeted approach, identified three L. lactis strains with weak negative correlation with S. aureus, suitable for in vivo safety and efficacy testing in pigs. These L. lactis strains may have the ability to be used safely to reduce LA-MRSA carriage in the nasal passages of pigs but further in vivo testing is necessary to confirm this potential.},
}

@article {pmid41507780,
year = {2026},
author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L},
title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04664-3},
pmid = {41507780},
issn = {1471-2180},
support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; },
abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.

STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.

RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.

CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.},
}

@article {pmid41507771,
year = {2026},
author = {Agorsor, IDK and Khadka, P and Danna, CH},
title = {The Arabidopsis UMAMIT30 transporter contributes to amino acid root exudation.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07930-8},
pmid = {41507771},
issn = {1471-2229},
support = {SG00409//University of Virginia 4-VA grant/ ; IOS-1943120//National Science Foundation CAREER Award/ ; },
abstract = {BACKGROUND: Root exudation is an important trait that enables plants to shape their interactions with soil-borne organisms. Amino acids present in root exudates play important roles in bacterial chemotaxis, bacterial metabolism, and root colonization, contributing to plant nutrition and health. Notwithstanding the importance of amino acids in shaping the rhizosphere microbiome, the identities of the plant amino acid transporters that mediate their root exudation have remained elusive.

RESULTS: Here, we report that the Arabidopsis UMAMIT30 transporter, robustly expressed in root and shoot tissues, significantly contributes to amino acid root exudation. umamit30 loss-of-function mutants were compromised for amino acid root exudation as shown by the low concentration of amino acids, particularly glutamine, recovered from root exudates compared to wild-type plants. Amino acid quantification, as well as uptake and secretion assessments using radiolabelled glutamine, revealed that the shoots of umamit30 accumulate amino acids and have a reduced capacity to secrete glutamine, impacting root exudation.

CONCLUSIONS: Our results identify UMAMIT30 as a broadly specific amino acid exporter strongly expressed in Arabidopsis vasculature. Loss-of-function mutants displayed reduced amino acid levels in root exudates, with significant drops in glutamine and asparagine among others, yet exhibited no detectable growth defects under our growth conditions. UMAMIT30 disruption led to elevated shoot amino acid content and reduced glutamine efflux from shoots, suggesting a role in phloem uploading as an upstream step necessary for root exudation. Despite decreased levels of root-exuded amino acids, the plant growth-promotion conferred by the soil-borne beneficial bacterium Pseudomonas simiae WCS417r remained unmodified in umamit30 mutants.},
}

@article {pmid41507594,
year = {2026},
author = {Gandham, A and Prokopidis, K and Glavas, C and Scott, D and Lorentzon, M},
title = {Impact of probiotic, prebiotic, and synbiotic supplementation on the gut microbiome in older adults with sarcopenia, obesity, and sarcopenic obesity.},
journal = {Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA},
volume = {},
number = {},
pages = {},
pmid = {41507594},
issn = {1433-2965},
abstract = {Gut microbiome plays an important role in several metabolic, immune, and inflammatory pathways; however, there is limited evidence for its role in body composition and musculoskeletal health. Sarcopenia, defined as a loss of skeletal muscle mass and function, and obesity, can co-exist in a condition known as sarcopenic obesity. This condition is highly prevalent among older adults, hence increasing the risk of negative health implications such as metabolic dysfunction, chronic inflammation, reduced physical performance, and poor quality of life. These age-related conditions are closely associated with alterations to the gut microbiome, including microbial profiles and a reduction in beneficial metabolites such as short-chain fatty acids (SCFAs). Probiotic, prebiotic, and synbiotic interventions are therefore emerging as promising strategies to improve the gut microbiome by enhancing microbial diversity and restoring microbial communities. This review utilizes current evidence on the impact of these interventions on gut microbiota composition, inflammatory and metabolic biomarkers, body composition, and functional outcomes in older adults with sarcopenia, obesity, and sarcopenic obesity. Probiotics, containing live beneficial microorganisms, have shown potential in enhancing SCFA production, reducing inflammation, and improving insulin sensitivity. Prebiotics are non-digestible fibers that selectively activate the growth of beneficial gut bacteria, further supporting gut health by proliferating the growth of SCFA-producing bacteria. Synbiotics, a combination of probiotics and prebiotics, provide a synergistic approach to gut health, accounting for the microbial composition and functional capability. Recent studies have demonstrated that probiotics, prebiotics, and synbiotics may reduce inflammation and improve muscle mass and strength among older adults with sarcopenia, obesity, and sarcopenic obesity. These interventions have the potential in mitigating obesity-related metabolic dysfunction and inflammation, particularly in individuals with sarcopenic obesity. Although, preclinical studies in mice exhibit beneficial effects, clinical studies in older adults remain limited, with heterogeneity of study design, intervention types, and outcome measures. This review highlights the need for robust, well-designed clinical trials to understand the mechanistic and molecular pathways through which probiotic, prebiotic, and synbiotic supplementation may modulate the gut microbiome and improve musculoskeletal health among older adults. These interventions may provide innovative, non-invasive therapeutic strategies for managing sarcopenia, obesity, and sarcopenic obesity, ultimately contributing to healthier aging and improved quality of life of older adults. This review also underscores the potential of microbiome-targeted interventions for aging populations, highlighting the need for further research.},
}

@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41507585},
issn = {2058-5276},
support = {BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}

@article {pmid41507362,
year = {2026},
author = {Elettrico, L and Piacenti, G and Levra Levron, C and Ansai, O and Croce, A and Duval, C and Proserpio, V and Donati, G},
title = {Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.},
journal = {Cell death and differentiation},
volume = {},
number = {},
pages = {},
pmid = {41507362},
issn = {1476-5403},
support = {IG2023 - Id.21640//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; postdoc fellowship//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; MFAG 2023 - Id.29203//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; postdoc fellowship//Fondazione Umberto Veronesi (Umberto Veronesi Foundation)/ ; },
abstract = {Skin homeostasis depends on interactions between epithelial cells and the microbiome mediated by molecular and biochemical factors. Perturbations of this interplay are linked to inflammatory disorders, including wound healing and cancer. While research has mainly illuminated shifts in microbial community composition, novel computational approaches are starting to reveal the host-microbe functional interactome in the cutaneous ecosystem. In this review, we specifically focus on known molecular and metabolic mechanisms linking skin epithelial cells and microorganisms in health and disease. Additionally, we summarise computational tools available to investigate these interactions integrating omics data. Furthermore, we present potential applications of this functional crosstalk to advance therapies targeting skin pathologies. Finally, we propose a comparative interactomics approach to envision the existence of ecological memories in the skin ecosystem, in parallel with the one described in the gut, hypothesising a link between epithelial and microbial memories in barrier tissues.},
}

@article {pmid41507168,
year = {2026},
author = {Lan, J and Wang, J and Huang, S and Li, C and Deng, Z and Hao, Z and Ma, Y},
title = {Neuropeptide SP protects against colitis and linked anxiety-like behavior through the putative roles of gut microbiota and metabolite inositol.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {295},
pmid = {41507168},
issn = {2041-1723},
support = {31772686//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Microglia/metabolism/drug effects ; *Colitis/chemically induced/metabolism/microbiology/prevention & control ; Mice ; *Inositol/metabolism ; Male ; *Anxiety/metabolism ; NF-kappa B/metabolism ; Mice, Inbred C57BL ; *Substance P/pharmacology/metabolism ; Dextran Sulfate ; Hippocampus/metabolism/drug effects/pathology ; Astrocytes/metabolism/drug effects ; Disease Models, Animal ; Signal Transduction ; },
abstract = {The gut-brain axis links gut inflammation to psychiatric symptoms in inflammatory bowel disease (IBD), but the underlying mechanisms remain unclear. We demonstrate that neuropeptide substance P (SP) alleviated intestinal injury and behavioral disorders induced by dextran sodium sulfate in mice. SP mitigated hippocampal neuroinflammation and inhibited microglial activation and astrocyte loss. Furthermore, SP improved gut microbiome dysregulation, and its protective effects depended on the putative roles of microbiota. Notably, through modulating microbiota, SP dampened the NF-κB pathway in microglia, and increased GABAergic/Ca[2+] signaling within astrocytes. SP elevated the microbiota-derived metabolite inositol. Supplementing inositol mimicked SP's benefits and activated GABAergic signaling, while the inositol inhibitor reversed SP's neuroprotective impacts, highlighting inositol's indispensable role. Collectively, SP exerts beneficial effects via microbiota's putative roles and inositol, involving the suppression of microglial NF-κB pathway while enhancing astrocytic GABAergic/Ca[2+] signaling. Our findings underscore SP's potential as a therapeutic intervention for these disorders in IBD.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
Microglia/metabolism/drug effects
*Colitis/chemically induced/metabolism/microbiology/prevention & control
Mice
*Inositol/metabolism
Male
*Anxiety/metabolism
NF-kappa B/metabolism
Mice, Inbred C57BL
*Substance P/pharmacology/metabolism
Dextran Sulfate
Hippocampus/metabolism/drug effects/pathology
Astrocytes/metabolism/drug effects
Disease Models, Animal
Signal Transduction

@article {pmid41506609,
year = {2026},
author = {Wang, W and Zhang, K and Liu, Z and Liu, X and Wang, X},
title = {Effects of Polyethylene Microplastics and Cadmium Co-contamination on the Soybean-Soil System:Integrated Metabolic and rhizosphere Microbial Mechanisms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127643},
doi = {10.1016/j.envpol.2026.127643},
pmid = {41506609},
issn = {1873-6424},
abstract = {The coexistence of microplastics (MPs) and heavy metals in agricultural soils presents complex and poorly understood ecological risks. While previous studies have examined the individual effects of these pollutants, the interactive mechanisms governing their combined impact on plant-soil systems, particularly through integrated metabolic and microbial pathways remain unclear. This study investigated the effects of polyethylene microplastics (PE-MPs) and cadmium (Cd) co-exposure on soybean-soil systems. Under moderate Cd exposure (20 mg/kg), specific PE-MPs concentrations (1% and 5%) enhanced Cd accumulation in soybean roots, whereas this trend reversed under high Cd levels (50 mg/kg). Co-exposure maintained stable shoot growth through activation of stress-response pathways (β-alanine, porphyrin, and pantothenate metabolism). Rhizosphere microbiome analysis revealed that 5% and 10% PE-MPs reduced the abundance of Sphingomonas and Bradyrhizobium in Cd-contaminated soil and suppressed nitrogen-cycling functionality. Integrated metabolite-microbe network analysis identified malonyldaidzin as a potential mediator linking soybean leaf metabolism with rhizobacterial interactions, associated with root Cd accumulation. These findings demonstrate that PE-MPs fundamentally alter Cd behavior through tripartite plant-metabolite-microbe interactions, thereby highlighting the need to incorporate MPs effects into ecological risk assessments of heavy metal contamination in agricultural ecosystems.},
}

@article {pmid41506211,
year = {2026},
author = {Zhao, N and Zhang, Z and Ding, H and Guillemot, T and Wang, D and Wang, H},
title = {Electron transfer versatility of a Geobacter sp. links PAH degradation with multi-electron acceptor respiration, including crystalline magnetite.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {141052},
doi = {10.1016/j.jhazmat.2026.141052},
pmid = {41506211},
issn = {1873-3336},
abstract = {Anaerobic degradation of polycyclic aromatic hydrocarbons (PAHs) is often constrained by the availability and accessibility of terminal electron acceptors in anoxic, metal-rich environments. Here we characterize a Geobacter sp. (strain GeoA) that couples phenanthrene oxidation to respiration with nitrate, Mn(IV), Fe(III)-citrate, sulfate, Cr(VI), and crystalline magnetite. Phenanthrene removal (initial 280 μM) proceeded fastest with Mn(IV) and nitrate (about 96 % within 5-7 d), followed by Fe(III)-citrate (about 95 % in 20 d), sulfate (about 95 % in 24 d), and Cr(VI) (about 61 % in 56 d, concomitant with complete reduction of 2.1 mM Cr(VI)). While previous studies mainly focused on amorphous or poorly crystalline Fe(III) minerals, the role of highly crystalline magnetite as an active electron sink has remained unclear. In this study, GeoA reduced ∼35 % of supplied magnetite (20 mM Fe(III) basis) and exhibited an acetate:Fe(III) stoichiometry (∼1:8) consistent with dissimilatory reduction. XPS and AQDS enhancement assays, together with upregulation of pilA and the flavin exporter yeeO, indicate that both direct and shuttle-facilitated extracellular electron transfer contribute to crystalline iron oxide reduction. Metabolite profiling with [13]C-bicarbonate labelling, together with genomic evidence, supports a carboxylation-initiated route for anaerobic phenanthrene activation. An analysis of Earth Microbiome Project datasets shows Geobacter predominance among dissimilatory iron-reducing genera in soils and sediments, consistent with ecological adaptation to solid-phase electron acceptors. These findings expand the known respiratory flexibility and bio-remediation potential of PAH-degrading bacteria and provide the first mechanistic evidence of PAH oxidation coupled to magnetite reduction by a single pure strain, highlighting crystalline magnetite as a relevant electron sink in PAH-metal co-contaminated anoxic environments.},
}

@article {pmid41505994,
year = {2026},
author = {Zhao, S and Xu, H and Liu, R and Wang, J and Zhi, B and Fu, X and Cao, X and Ma, X and Shao, Z},
title = {Biodegradation and disintegration of expanded polystyrene by sphaeromatid isopods Sphaeroma via their gut bacteria.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119207},
doi = {10.1016/j.marpolbul.2025.119207},
pmid = {41505994},
issn = {1879-3363},
abstract = {Wood-boring isopods have been documented inhabiting the plastic floats of expanded polystyrene (EPS), which is extensively utilized in mariculture as buoyant material. However, little is known about their role in the plastic fragmentation and degradation. This report confirmed that globally distributed Sphaeroma gnawed and ingested EPS foam, and digested it via their gut microbiome. After 7 days of exposure, each Sphaeroma consumed 4.4 ± 0.2 mg EPS, ingested 50 microbeads and egested 2.5 ± 0.7 × 10[3] microplastics. Analyses using μFTIR, GPC, and GC-MS revealed polystyrene (PS) degradation in the gut of Sphaeroma. High throughput 16S rRNA sequencing revealed that Exiguobacterium spp. and Brevibacterium spp. were associated with PS diets in the gut microbiome of Sphaeroma, suggesting their potential key role in vivo. Further characterizations of PS weight loss, changes in chemical and thermal properties, and identification of metabolic intermediates confirmed that PS can be degraded by five gut bacteria from the above two genera. Antibiotic bioassay confirmed that gut microbes are essential for the EPS depolymerization in Sphaeroma by. All these results demonstrate that the gut microbiome contributes to EPS digestion in the host. Together, these results found marine isopods in coastal negatively influenced the environmental fats of the plastic fate, by fragmenting plastics and generating microplastics, via their PS-degrading gut microbiota.},
}

@article {pmid41505190,
year = {2026},
author = {McGarrity-Yoder, M and Cope, EK and Wayment, HA and Rodriguez-Pla, A and Crane, TE},
title = {Biopsychosocial Determinants, Diet Quality, Gastrointestinal Health, and Disease Activity in Adults With Rheumatoid Arthritis: Cross-Sectional Descriptive Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e79889},
doi = {10.2196/79889},
pmid = {41505190},
issn = {1929-0748},
mesh = {Humans ; Cross-Sectional Studies ; *Arthritis, Rheumatoid/psychology/physiopathology ; Adult ; Female ; Male ; Arizona ; *Diet ; Middle Aged ; *Gastrointestinal Tract/physiopathology ; Aged ; Surveys and Questionnaires ; },
abstract = {BACKGROUND: Rheumatoid arthritis (RA) causes pain, fatigue, joint deformity, disability, and an increased risk for serious sequelae, often despite treatment, in 1.3 million Americans. RA is affected by numerous biopsychosocial determinants, which greatly complicate treatment, including altered efficacy.

OBJECTIVE: The purpose of this study is to examine associations between individual biopsychosocial determinants, diet quality, gastrointestinal (GI) health, and disease activity in adults with RA.

METHODS: This cross-sectional, descriptive study has been approved by the Northern Arizona University Internal Review Board (# 2111208-12). We will include 96 adults with RA recruited from across Arizona using social media and community events (through the Arthritis Foundation) and various primary care and rheumatology practices in Flagstaff and the greater Phoenix metro area. Individual biopsychosocial factors will be measured with a demographic survey and direct measures. The Arizona Food Frequency Questionnaire will measure dietary intake for the past 6 months, and Healthy Eating Index-2020 scores will be calculated from these data. The Automated Self-Administered 24-hour diet recall will measure recent dietary intake. Fecal analyses for gut microbiome diversity and composition and fecal calprotectin will measure current GI health. Disease activity will be measured by the Health Assessment Questionnaire-Disability Index and pain scale, Disease Activity Score of 28 Joints, and hematology results (C-reactive protein and erythrocyte sedimentation rate). In addition to descriptive statistics, hierarchical linear regression will examine hypothesized associations between diet quality, GI health, and disease activity. We hypothesize that individual biopsychosocial determinants will be associated with diet quality, which will be indirectly associated with disease activity through gut microbiome diversity and level of GI inflammation in adults with RA.

RESULTS: This study was funded in February 2024. As of December 19, 2025, a total of 80 individuals have been recruited. Data analysis has not yet commenced at the time of manuscript submission. Study results are expected to be published in fall 2026.

CONCLUSIONS: RA is a complicated disease that impacts millions. Few individuals reach sustained remission, even while following provider recommendations. A better understanding of the various factors that impact this complicated disease has the potential to support changes in research and care that will improve the lives of people with RA. The knowledge gained in this study will provide a foundation to inform future interventional research targeting diet quality to support GI health and decrease RA disease activity. Further, the details of this research plan provide methodological resources for other RA researchers, and research results have the potential to improve communication between rheumatology providers and patients.

PRR1-10.2196/79889.},
}

Humans
Cross-Sectional Studies
*Arthritis, Rheumatoid/psychology/physiopathology
Adult
Female
Male
Arizona
*Diet
Middle Aged
*Gastrointestinal Tract/physiopathology
Aged
Surveys and Questionnaires

@article {pmid41505077,
year = {2026},
author = {Ghaemi, M and Ghaemi, A and Tavakkoli, H and Mashhadinejad, M and Kheradmand, D},
title = {The MOF-Microbiome Axis: a New Paradigm for Precision Nanomedicine.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41505077},
issn = {1867-1314},
abstract = {The gut microbiome is crucial for human health, and its imbalance, known as dysbiosis, is associated with diseases such as inflammatory bowel disease, metabolic disorders, and neurological disorders. Traditional treatments, such as probiotics and fecal microbiota transplants, often lack precision, making the emerging field of nanomedicine a promising alternative. This review introduces the "MOF-Microbiome Axis," which explores the interactions between metal-organic frameworks (MOFs), versatile, porous materials, and the gut microbiome. It focuses on designing gastrointestinal-targeted MOFs that are biocompatible and responsive to stimuli. We discuss how MOFs can serve as scaffolds, controlled-release vehicles, and metabolite scavengers, highlighting their therapeutic applications in targeted antimicrobial therapy, enhanced probiotic delivery, and immunomodulation. The review also addresses important challenges in biosafety, scalable production, and personalized treatment, suggesting future directions such as bio-hybrid systems and precision microbiome editing. Overall, the MOF-Microbiome Axis offers a new perspective on microbiome engineering and advanced therapeutic approaches.},
}

@article {pmid41504923,
year = {2026},
author = {Yousefi, F and Salehi, B and Ghorbani, N and Yaghmayee, S and Eslami, M},
title = {Integrative analysis of placental metabolic reprogramming and microbiome alterations in gestational diabetes mellitus (GDM).},
journal = {Acta diabetologica},
volume = {},
number = {},
pages = {},
pmid = {41504923},
issn = {1432-5233},
}

@article {pmid41504672,
year = {2026},
author = {Somboonna, N and Rujirawan, P and Wongsaroj, L and Promvaranon, T and Rerknimitr, P},
title = {Nail Fold Microbiome Alterations in Patients Treated With Epidermal Growth Factor Receptor Inhibitors.},
journal = {Experimental dermatology},
volume = {35},
number = {1},
pages = {e70201},
doi = {10.1111/exd.70201},
pmid = {41504672},
issn = {1600-0625},
support = {RA61/079//The Ratchadapiseksomphot Endowment Fund, Faculty of Medicine, Chulalongkorn University/ ; },
}

@article {pmid41504597,
year = {2026},
author = {Larner, W and Thölke da Silva Grego, N and Panfilio, KA},
title = {Intraspecific microbiome dynamics across the life cycle of the milkweed bug Oncopeltus fasciatus.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
doi = {10.1099/mgen.0.001583},
pmid = {41504597},
issn = {2057-5858},
mesh = {Animals ; *Heteroptera/microbiology/growth & development ; RNA, Ribosomal, 16S/genetics ; Female ; *Microbiota/genetics ; Life Cycle Stages ; *Bacteria/genetics/classification/isolation & purification ; Male ; *Hemiptera/microbiology ; Phylogeny ; },
abstract = {The microbiome is an important part of the complete nutritional and genomic profile of insects. The species-rich insect order Hemiptera (aphids, cicadas and true bugs) is highly diverse for mode of microbiome acquisition, with the conundrum that species in the seed-feeding subfamily Lygaeinae have lost obvious anatomy for housing bacteria, either in bacteriocytes or midgut crypts. Here, we characterize the microbiome of the milkweed bug Oncopeltus fasciatus as a tractable lygaeinid, using 16S rRNA gene sequencing. We assess how bacterial taxa vary between the sexes and across life history stages in a controlled environment, focusing on maternal-to-embryo transmission and distinguishing egg-stage constituents that are superficial or internal (transovarially transmitted). Among a core microbiome of 28 genera, the egg stage shows the greatest diversity, with a particular expansion of the family Comamonadaceae. We also analyse inter-individual variability in nymphs and adults and validate structured, stage-specific detection of seed material. Comparative analysis identifies Rhizobium as a notable microbiome constituent in seed-feeding Hemiptera, which we had previously shown to lack nitrogen metabolism components in the genome. Overall, we provide a nuanced assessment of bacterial abundance dynamics between individuals and across the life cycle and discuss the implications for acquisition and potential relevance as nutritional endosymbionts. This will underpin comparative investigations in seed-feeding bugs and future work in O. fasciatus on tissue-specific and diet-specific microbiome profiles, including in natural populations.},
}

Animals
*Heteroptera/microbiology/growth & development
RNA, Ribosomal, 16S/genetics
Female
*Microbiota/genetics
Life Cycle Stages
*Bacteria/genetics/classification/isolation & purification
Male
*Hemiptera/microbiology
Phylogeny

@article {pmid41504479,
year = {2026},
author = {Vompe, AD and Hamidizade, M and López, MM and O'Connor, E and Kaur, L and Hockett, KL and Bull, CT},
title = {Translational microbiomes in agriculture: microbial communities as tools to effect host and system health for improved crop production.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0170425},
doi = {10.1128/aem.01704-25},
pmid = {41504479},
issn = {1098-5336},
abstract = {The boom of microbiome research in agriculture over the past several decades allows scientists, growers, policymakers, and businesses to collaborate on a unique opportunity-deploying microbiomes and microbiome attributes for the improvement of crop production. The idea of translational microbiomes is well established in the medical field; however, this framework is relatively new to agriculture. In this review, we discuss a series of methodologies grounded in microbiome science to enhance crop health. These include diagnostic approaches (pathogen and toxin detection and the monitoring of stress-related community ecology patterns) and intervention strategies (synthetic communities, microbiome-aware crop management practices, passaging microbiomes, and exploiting the vertical and lateral transmission of microbiomes to seeds). Developing and implementing these approaches remain challenging due, in part, to a shortage of long-term in situ studies demonstrating the robustness and effectiveness of translational microbiome efforts against the background of heterogeneity and ecological complexity of agricultural systems. Moreover, the cost and availability of 'omics methods central to microbiome analysis, disparate standards for microbiome product development, and limited longstanding relationships with stakeholders have slowed down the application of microbiome-based solutions. However, the increasing cost-effectiveness of microbiome approaches in crop management makes translational microbiomes likely assets in the movement toward precision agriculture. This "personalized treatment" for plants holds promise for improved food security and environmental sustainability, by reducing commonplace synthetic amendments and promoting native microbial biodiversity.},
}

@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0305125},
doi = {10.1128/spectrum.03051-25},
pmid = {41504449},
issn = {2165-0497},
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}

@article {pmid41504323,
year = {2026},
author = {Lanzara, R and Conti, C and Zito, L and Anaclerio, F and Affaitati, GP and Giamberardino, MA and Stuppia, L and Porcelli, P},
title = {Gut Microbiota and Psychological Distress in Fibromyalgia: A Systematic Review.},
journal = {Biopsychosocial science and medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/PSY.0000000000001463},
pmid = {41504323},
issn = {2998-8756},
abstract = {OBJECTIVE: This systematic review aimed to summarize the recent evidence of the relationship between gut microbiota and psychological distress in patients with fibromyalgia (FM).

METHODS: According to PRISMA guidelines, we conducted a systematic search of the literature on PubMed, Scopus, EBSCO, WOS, and Cochrane. The records were selected using multiple combinations of relevant search terms involving microbiota, psychological distress, and FM. Articles in English with human participants were reviewed.

RESULTS: The initial search identified 135 records, excluding duplicates, of which 10 research reports met the predefined inclusion criteria and were analyzed. Most studies (n=7) were case-control, two were randomized controlled trials, and one was observational. Most studies found an imbalance in the gut microbial communities of FM patients and a significant difference between FM patients and HC in microbiome composition/diversity or gut permeability. Intestinal dysbiosis and gut permeability were also associated with high psychological distress (emotional, cognitive, and somatic symptoms).

CONCLUSION: Alterations in the gut microbiota of FM patients seem to support the hypothesis that gut-brain axis regulation is impaired in stress-related pain conditions. Although the results are promising, further studies are needed to clarify the role of the microbiota-gut-brain axis in the pathophysiological mechanisms underlying FM.},
}

@article {pmid41504275,
year = {2026},
author = {Xu, C and Antonacci, S and Marques, FZ},
title = {The maternal microbiome influence on pregnancy success: breeding comparison of germ-free and conventionalized mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2609405},
doi = {10.1080/19490976.2025.2609405},
pmid = {41504275},
issn = {1949-0984},
mesh = {Female ; Animals ; Pregnancy ; Mice ; *Germ-Free Life ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation & purification/metabolism ; Male ; Diet ; Fertility ; Breeding ; },
abstract = {Germ-free (GF) animals, which are entirely devoid of all microorganisms, are one of the most powerful tools for studying the role of the microbiome in a phenotype, moving the microbiome field from association to causation. They allow the introduction of specific microbes or microbial communities to interrogate the causality of microbiomes in protecting against or contributing to a phenotype. Here, we report critical and underappreciated challenges in using GF models to investigate the intergenerational effects of maternal diet and microbiota on offspring health. Using 57 GF and littermate conventionalized GF dams, we observed unexpectedly high maternal (odds ratio 11.5, p < 0.0001) and offspring (odds ratio 4.12, p < 0.0001) mortality in GF animals. Remarkably, GF dams had an extremely low pregnancy and parturition (pmicrobiome < 0.0001) and a high incidence of cecal torsion (18.2%) compared to the conventionalized group, underscoring the indispensable role of the maternal microbiome in reproductive success and early development. Notably, even conventionalized GF mothers on high-fiber diets exhibited poor fertility, suggesting that microbial colonization timing and maternal microbial capacity to metabolize fiber are crucial. These findings not only reveal significant limitations in GF breeding protocols but also indicate that the maternal microbiota might influence offspring health far earlier than previously recognized, with implications for the developmental origins of health and disease research.},
}

Female
Animals
Pregnancy
Mice
*Germ-Free Life
*Gastrointestinal Microbiome
Mice, Inbred C57BL
Bacteria/classification/genetics/isolation & purification/metabolism
Male
Diet
Fertility
Breeding

@article {pmid41504254,
year = {2026},
author = {Lin, P},
title = {The importance of the microbiome in uveitis.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICU.0000000000001197},
pmid = {41504254},
issn = {1531-7021},
abstract = {PURPOSE OF REVIEW: The purpose of this review was to summarize the literature on preclinical and clinical studies demonstrating the impact of the intestinal microbiome in noninfectious uveitis.

RECENT FINDINGS: Preclinical studies using the experimental autoimmune uveitis (EAU) model have shown commensals such as Desulfovibrio and Prevotella, as well as Ruminococcaceae, associated with uveitis, which overlap with some clinical studies in uveitis patients. Interventions that target the microbiome that can be developed for the treatment of uveitis include antibiotics, fecal metabolites or metabolite agonists that are protective in uveitis, probiotics, dietary interventions, or fecal microbial transplant.

SUMMARY: There is significant data supporting the importance of the intestinal microbiome in noninfectious uveitis through enrichment or depletion of certain gut bacteria as well as their metabolites. Targeting the intestinal microbiome or their metabolites might be a viable option for the treatment of noninfectious uveitis.},
}

@article {pmid41504167,
year = {2026},
author = {Zhou, Q and Gao, X and Wu, Q and Zeng, W and Cao, W and Zhou, T and Cui, X and Chen, J and Gao, D and Zhao, H},
title = {Cross-Kingdom Synthetic Microbiota Suppresses Wheat Fusarium Crown Rot by Remodeling the Rhizosphere Microbiome and Metabolome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11786},
pmid = {41504167},
issn = {1520-5118},
abstract = {Fusarium crown rot (FCR) of wheat lacks sustainable control. We assembled a cross-kingdom synthetic microbial community (SMC) of Trichoderma harzianum T19 and five Bacillus strains and tested it in nonsterile soil challenged with Fusarium pseudograminearum. The SMC treatment significantly suppressed FCR, reducing the disease severity index by approximately 70%. Wheat growth and yield were simultaneously enhanced. In the rhizosphere, SMC improved soil health by elevating soil organic matter and nitrogen levels by over 50%, while mitigating pathogen-induced nutrient imbalances and boosting nutrient-cycling enzyme activities. Amplicon sequencing revealed that SMC suppressed pathogenic Fusarium in the rhizosphere and enriched beneficial microbes, including antagonistic fungi (Trichoderma, Chaetomium) and plant growth-promoting bacteria (Pseudomonas, Paenibacillus). Co-occurrence network analysis showed that SMC treatment restructured the rhizosphere microbial network with higher connectivity, stability, and a prevalence of positive cooperative interactions under F. pseudograminearum stress. Defense-related metabolites, such as epi-jasmonic acid, allantoin, Nβ-acetyltryptamine, and dihydrodaidzein, accumulated to higher levels with SMC. These findings demonstrate that the cross-kingdom SMC modulates soil nutrients, microbial community structure, and rhizosphere metabolites to synergistically promote wheat growth and enhance resistance to FCR.},
}

@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).

METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.

RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.

CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Hyperuricemia/microbiology
Male
Female
*Overweight/microbiology
Middle Aged
Cross-Sectional Studies
Feces/microbiology
Adult
Metagenomics
Metagenome

@article {pmid41503894,
year = {2026},
author = {Kim, HS},
title = {Do Akkermansia mutants underlie to the global metabolic disease epidemic?.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2612582},
doi = {10.1080/19490976.2025.2612582},
pmid = {41503894},
issn = {1949-0984},
mesh = {Humans ; *Metabolic Diseases/epidemiology/microbiology ; *Mutation ; Anti-Bacterial Agents/pharmacology/adverse effects ; *Akkermansia/genetics/drug effects ; Gastrointestinal Microbiome/drug effects ; Epidemics ; },
abstract = {Antibiotic-induced mutations in Akkermansia muciniphila promote bacterial survival while compromising beneficial host interactions, revealing a potential new link between antibiotic-driven microbiome disruption and metabolic disease. The widespread presence of these mutants suggests that they may contribute to the increasing prevalence of metabolic disorders. If validated in diverse global human cohort studies, these mutants could serve as biomarkers of disease susceptibility and as targets for therapeutic intervention.},
}

Humans
*Metabolic Diseases/epidemiology/microbiology
*Mutation
Anti-Bacterial Agents/pharmacology/adverse effects
*Akkermansia/genetics/drug effects
Gastrointestinal Microbiome/drug effects
Epidemics

@article {pmid41503829,
year = {2026},
author = {Zhang, H and Wang, Y and Ning, B and Wang, Y and Sun, T and Xu, J},
title = {The gut microbiota-obesity axis in the pathogenesis and prognosis of breast cancer.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2611203},
doi = {10.1080/07853890.2025.2611203},
pmid = {41503829},
issn = {1365-2060},
mesh = {Humans ; *Obesity/complications/microbiology/immunology ; *Breast Neoplasms/microbiology/immunology/pathology/therapy ; *Gastrointestinal Microbiome/physiology/immunology ; Female ; *Dysbiosis/microbiology/complications/immunology ; Prognosis ; Probiotics/therapeutic use ; },
abstract = {BACKGROUND: Breast cancer (BC) remains a major global health concern, accounting for 11.7% of all cancer cases and ranking as the second leading cause of female cancer-related deaths worldwide. Increasing evidence highlights the interplay between gut microbiota (GM) dysbiosis and obesity-associated metabolic dysfunction in BC progression. This review aims to elucidate the role of GM in obese patients with BC.

METHODS: A systematic literature search was conducted in PubMed and Web of Science databases for publications from July 2015 to January 2025. Search terms combined BC, GM, obesity, dysbiosis, immunity, and microbiome. Article selection prioritized studies investigating microbial alterations in BC patients, mechanistic links between obesity and cancer progression, and GM-targeted interventions. Both original studies and authoritative reviews were included, supplemented by manual reference screening.

DISCUSSION: Obesity may trigger systemic inflammation, altered adipokine secretion, and disrupted steroid hormone metabolism via gut-derived β-glucuronidase activity, thereby exacerbating BC occurrence and recurrence. GM dysbiosis-driven metabolites such as branched-chain amino acids (BCAAs) and short-chain fatty acids (SCFAs) can activate oncogenic signaling pathways and immunosuppressive myeloid-derived suppressor cells (MDSCs), fostering tumor immune evasion. Conversely, dietary interventions, probiotics, and fecal microbiota transplantation (FMT) can alleviate dysbiosis, strengthen gut barriers, and restore anti-tumor immunity, improving chemotherapy response and reducing recurrence. However, challenges persist in deciphering BC subtype-related microbial signatures and optimizing microbiota-targeted therapies.

CONCLUSION: Future longitudinal studies are needed to clarify causal relationships, validate microbial biomarkers, and translate preclinical findings into clinical applications. Addressing the gut-breast axis may offer transformative potential for precision oncology in obesity-driven BC.},
}

Humans
*Obesity/complications/microbiology/immunology
*Breast Neoplasms/microbiology/immunology/pathology/therapy
*Gastrointestinal Microbiome/physiology/immunology
Female
*Dysbiosis/microbiology/complications/immunology
Prognosis
Probiotics/therapeutic use

@article {pmid41503825,
year = {2026},
author = {Kang, K and Kim, JY and Yim, JJ and Kim, D},
title = {Gut-lung axis and microbiome alterations in mycobacterial infections: from pathogenesis to therapeutic potential.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2612428},
doi = {10.1080/19490976.2025.2612428},
pmid = {41503825},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/therapy ; *Lung/microbiology/immunology ; Animals ; Probiotics ; Fecal Microbiota Transplantation ; *Mycobacterium Infections/microbiology/therapy ; },
abstract = {Mycobacterial lung diseases, including tuberculosis (TB) and nontuberculous mycobacterial pulmonary disease (NTM-PD), are increasingly recognized as disorders influenced not only by host immunity but also by microbiota. Emerging evidence identifies the gut-lung axis (GLA) as a key bidirectional communication network linking intestinal and pulmonary homeostasis. Mycobacterial infection itself induces airway and gut dysbiosis through immune and metabolic disturbances, which is further exacerbated by prolonged antibiotic therapy. Dysbiosis within either site reciprocally affects the other via GLA, leading to reduced microbial diversity, impaired epithelial integrity, and systemic inflammation. These alterations disrupt metabolite-mediated immunoregulation and attenuate IL-22-driven epithelial defense, thereby weakening bacterial clearance and promoting chronic inflammation. Distinct microbial features, such as the depletion of beneficial SCFA-producing taxa and enrichment of pro-inflammatory anaerobes, are observed in both TB and NTM-PD. Moreover, therapy-induced microbiome remodeling influences treatment response and disease relapse. Restoring microbial balance through probiotics, prebiotics, postbiotics, dietary modulation, or fecal microbiota transplantation offers a promising adjunctive strategy. This review integrates current evidence linking microbiome dysbiosis to mycobacterial pathogenesis and highlights microbiome-targeted interventions as an emerging therapeutic frontier in pulmonary mycobacterial diseases.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/therapy
*Lung/microbiology/immunology
Animals
Probiotics
Fecal Microbiota Transplantation
*Mycobacterium Infections/microbiology/therapy

@article {pmid41503704,
year = {2026},
author = {De Palma, G and Costanzini, A and Mohan, V and Sidani, S and Saqib, Z and Pigrau, M and Lu, J and Causada Calo, N and Pinto-Sanchez, I and Verdu, EF and Marcon, M and Barbara, G and Stanghellini, V and De Giorgio, R and Collins, SM and Bercik, P},
title = {The role of gut microbiota in chronic intestinal pseudo-obstruction: exploring fecal microbiota transplantation as a treatment option.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2610597},
doi = {10.1080/19490976.2025.2610597},
pmid = {41503704},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; *Intestinal Pseudo-Obstruction/therapy/microbiology ; *Gastrointestinal Microbiome ; Animals ; Humans ; Mice ; Male ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Chronic Disease/therapy ; Aged ; Feces/microbiology ; Disease Models, Animal ; Italy ; },
abstract = {Chronic intestinal pseudo-obstruction (CIPO) is characterized by bowel dilation and obstructive symptoms without any structural blockage. Although the microbiota is known to affect gastrointestinal function, its role in CIPO is poorly understood. We aimed to characterize the CIPO microbiota, investigate its role in disease expression and explore the therapeutic role of fecal microbiota transplantation (FMT). CIPO patients (n = 14) and healthy controls (HC, n = 12) were recruited from Italy and Canada. Microbiota profiles and functions were assessed by 16S rRNA sequencing and PICRUSt. Germ-free NIH Swiss mice were colonized with HC and CIPO microbiota, their intestinal transit and bowel distension were assessed by videofluoroscopy and computed tomography (CT), and the expression of host genes by NanoString®. The CIPO microbiota exhibited reduced microbial diversity with dominance of Proteobacteria and altered metabolic function. Mice with CIPO microbiota developed marked bowel distension and slow intestinal transit associated with altered expression of multiple genes related to immunity, the intestinal barrier and neuromuscular function. FMT from a HC improved the microbiota profile, intestinal transit and bowel distension in both CIPO mice and a selected CIPO patient, in whom a marked clinical improvement was sustained for 8 y. Thus, our findings support the use of microbiota-directed therapies to induce clinical improvement in CIPO patients.},
}

*Fecal Microbiota Transplantation
*Intestinal Pseudo-Obstruction/therapy/microbiology
*Gastrointestinal Microbiome
Animals
Humans
Mice
Male
Female
Middle Aged
Adult
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Chronic Disease/therapy
Aged
Feces/microbiology
Disease Models, Animal
Italy

@article {pmid41503689,
year = {2026},
author = {Broedlow, CA and McGaugh, A and Glynn, TR and Cherenack, EM and Miller, C and Alcaide, ML and Bauermeister, JA and Grov, C and Parisi, R and Martinez, D and Carrico, AW and Klatt, NR and Manuzak, JA},
title = {Douching Is Associated With Dysregulated Rectal Mucosal Immunity in Sexual Minority Men.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf577},
pmid = {41503689},
issn = {1537-6613},
support = {//AIDS Healthcare Foundation/ ; //IDSA GERM/ ; P30AI073961//University of Miami Center for AIDS Research/ ; T32AI007433//University of Miami Center for AIDS Research/ ; K23DA060719//University of Miami Center for AIDS Research/ ; L60DA059128//University of Miami Center for AIDS Research/ ; 1F32AI162229//University of Miami Center for AIDS Research/ ; },
abstract = {BACKGROUND: Receptive condomless anal sex (CAS) associates with elevated rectal inflammation and mucosal injury, increasing HIV acquisition risk. Although douching may amplify rectal inflammation and alter microbial communities, this has not been well characterized in sexual minority men (SMM).

METHODS: Ninety-two SMM (median age, 34.6 years) who were HIV negative and reported receptive CAS provided rectal swabs during sexually transmitted infection (STI) clinic visits. Associations among rectal douching, rectal cytokine/chemokine levels, and microbial communities, evaluated via immunoassay and 16S rRNA gene sequencing, respectively, were assessed.

RESULTS: When compared with nondouching SMM (n = 27), SMM who douched (n = 64) reported more receptive CAS partners and displayed elevations in rectal cytokine/chemokines linked to immune activation and inflammation. Lower microbial richness, evenness, and Shannon diversity in SMM who reported douching were observed. Significant associations were identified between microbial alpha diversity metrics and rectal chemokine/cytokine levels. Finally, significant correlations were observed between rectal cytokine/chemokine levels and individual microbial genera.

CONCLUSIONS: Among SMM engaging in receptive CAS, douching may identify those with amplified biobehavioral HIV and STI risk. Elucidating the mechanisms whereby douching dysregulates rectal immune function and alters rectal microbial communities could yield targets for biomedical approaches to optimize HIV/STI prevention in SMM during receptive CAS.},
}

@article {pmid41503622,
year = {2026},
author = {Briard, M and Guillon, B and Venot, E and Grauso, M and Bruneau, A and Rossignol, MN and Fenaille, F and Castelli, F and Thomas, M and Lezmi, G and Leite-de-Moraes, M and Adel-Patient, K and Saint-Criq, V},
title = {Datasets of 16S rRNA gene amplicon sequences, metabolites, and soluble immune components in bronchoalveolar lavage samples from severe asthmatic and age-matched control children.},
journal = {Data in brief},
volume = {64},
number = {},
pages = {112359},
pmid = {41503622},
issn = {2352-3409},
abstract = {Severe asthma (SA) is a heterogeneous condition characterized by multiple phenotypes, each characterized by different endotypes. Understanding the mechanisms occurring in the lungs of children with SA can help in understanding pathogenesis and in providing the most effective therapeutic strategies. This article describes microbiota, metabolites, and soluble immune components assessed in bronchoalveolar lavage (BAL) fluids from children with severe asthma (n = 20) and age-matched disease controls (n = 10). The article includes: (i) the protocol used to process BAL samples for 16S rRNA gene amplicon sequencing, metabolomic profiling and immune components assays; (ii) the bioinformatics steps applied to 16S rRNA and metabolomics dataset; (iii) an overview of the raw 16S rRNA gene amplicon sequencing data, presented as ASV and affiliation tables, raw data from untargeted metabolomics and the abundances of each of the eighty eight metabolites annotated with the highest confidence level, and concentrations of seventy three cytokines and of total IgG, IgA and IgE. Each dataset is available in the INRAE data repository (https://entrepot.recherche.data.gouv.fr/dataverse/inrae) with respective DOI: MICROBIOTA: 10.57745/LL3TFW, METABOLITES: 10.57745/1L8VRI, IMMUNE COMPONENTS: 10.57745/JOOGRQ These datasets provide valuable resources for further investigating the molecular mechanisms underlying severe asthma in children and its trajectories. They also offer the potential to identify a local signature of severe asthma through complementary multi-omics analyses and to discover local biomarkers associated with asthma endotypes. Datasets can also be reused to compare with other cohorts (children or adults) or to serve as reference datasets for other pulmonary diseases.},
}

@article {pmid41503571,
year = {2026},
author = {Bajaj, JS and Fagan, A and Sterling, RK and Sikaroodi, M and Gallagher, ML and Lee, H and Matherly, SC and Bartels, A and Mousel, T and Davis, BC and Puri, P and Fuchs, M and Thacker, LR and McGinley, JP and Khoruts, A and Gillevet, PM},
title = {The multi-omic basis for hepatic encephalopathy recurrence: Analysis of the THEMATIC trial.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {1},
pages = {101634},
pmid = {41503571},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: The THEMATIC trial demonstrated that fecal microbiota transplantation (FMT) reduces recurrence of hepatic encephalopathy (HE) in patients already receiving lactulose and rifaximin. The aim of this analysis was to identify multi-omic predictors of HE recurrence among THEMATIC trial participants.

METHODS: The THEMATIC trial enrolled patients with cirrhosis and HE who received oral or enema FMT vs. placebo (1-3 administrations) and were followed for 6 months. Outcomes included safety and HE recurrence. Serum, urine, and stool samples were collected at baseline and post-FMT for all participants. Stool metagenomics, serum and urine metabolomics, inflammatory cytokines, and clinical data were analyzed. Differences between patients with and without HE recurrence were assessed using pathway, random forest, and latent factor analyses.

RESULTS: HE recurred in 10 of 60 patients (17%), with significantly higher recurrence in the placebo vs. the FMT groups (40% vs. 8%; p = 0.005). Due to the low recurrence rate in the FMT arms, all patients with recurrence were combined and compared with those without recurrence. Stool metagenomics showed that the abundance of short-chain fatty acid (SCFA) producers (Faecalibacterium, Eubacterium, Bacteroides, Blautia spp.) was lower, while that of GABA-producing taxa (Lactobacillus, Bifidobacterium spp.) was higher, in patients with recurrence. Urine and serum metabolomes separated HE recurrence groups on PLS-DA, with serum butyrate and isobutyrate being most significantly associated (p = 0.008). Pathway analyses revealed upregulation of GABA and neurotransmitter pathways in patients with HE recurrence. Random forest and latent factor analysis indicated that SCFA producers and secondary bile acids were protective, whereas IL-6, GABA producers, nicotine metabolites, and primary bile acids were associated with HE recurrence.

CONCLUSIONS: Secondary analysis of the THEMATIC randomized controlled trial indicates that HE recurrence in patients on lactulose and rifaximin is associated with distinct microbiome and metabolomic profiles, particularly involving SCFAs, GABA metabolism, bile acids, and IL-6.

IMPACT AND IMPLICATIONS: Fecal microbiota transplantation (FMT) reduced hepatic encephalopathy (HE) recurrence in patients receiving lactulose and rifaximin in the THEMATIC trial, but the multi-omic mechanisms underlying this effect were unclear. In this secondary analysis, we found that HE recurrence - regardless of FMT or placebo assignment - was associated with distinct multi-omic signatures, including reduced short-chain fatty acid-producing and increased pathobiont taxa, lower urinary and serum short-chain fatty acids, secondary bile acids, and acetaminophen derivatives, and higher GABA-related and nicotine metabolites, along with elevated IL-6 levels. Notably, patients with greater donor microbiota engraftment had lower rates of HE recurrence. These findings suggest that HE recurrence after FMT reflects a multifactorial process involving alterations in gut metagenomics, systemic metabolomics, inflammation, and donor engraftment.

TRIAL REGISTRATION: www.clinicaltrials.gov: NCT03796598.},
}

@article {pmid41503489,
year = {2026},
author = {Goddard, TR and Carlson-Jones, JA and Morton, J and Ooi, CY and Tai, A and Warner, MS and Wong, J and Evans, IE and Hopkins, E and Iredell, JR and Jersmann, HP and Whiteson, KL and Bouras, G and Doane, MP and Falk, NW and Green, R and Grigson, SR and Mallawaarachchi, V and Martin, B and Roach, MJ and Ryan, FJ and Tarasenko, A and Papudeshi, B and Drigo, B and Giles, SK and Harker, CM and Hesse, RD and Hodgson, RJ and Hussnain, A and Hutton, A and Inglis, LK and Keneally, C and Kerr, EN and Liddicoat, C and Peddle, SD and Watson, CD and Yang, Q and Decewicz, P and Speck, PG and Mitchell, JG and Dinsdale, EA and Edwards, RA},
title = {Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.28.25342520},
pmid = {41503489},
abstract = {Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the model's universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.},
}

@article {pmid41503459,
year = {2026},
author = {Steuart, R and Atkinson, SN and Hoffman, LR and Hung, L and Ding, X and Salzman, N and Russell, CJ},
title = {Longitudinal dynamics of respiratory microbiome composition in infants after tracheostomy placement.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.29.25342834},
pmid = {41503459},
abstract = {Abnormal respiratory microbiomes are reported in children with artificial airways, yet the timing and persistence of these disruptions have not been defined in infants following new tracheostomy placement. We conducted a prospective longitudinal study to characterize airway microbiome dynamics following new tracheostomy placement during early life, a critical period for microbiome development. Fifteen hospitalized infants <=12 months contributed 84 tracheal aspirate samples collected from day 1 through 3 to 4 months post-procedure. 16S rRNA sequencing revealed immediate and sustained community shifts. Staphylococcus abundance increased after tracheostomy, peaking at 40 days (mean 27%) before declining, with a more pronounced bloom in infants without home mechanical ventilation (HMV). Alpha diversity decreased significantly in the first 30 days (p<0.05) and returned to baseline by 61 to 90 days. Beta diversity analysis demonstrated marked compositional changes immediately post-tracheostomy and ongoing divergence through 3 to 4 months. Time since tracheostomy and clinical factors (gestational age, HMV, neurologic impairment) were significantly associated with microbiome structure (p=0.001). These findings provide novel evidence that tracheostomy induces rapid and prolonged airway microbiome disruption in infants, highlighting a previously uncharacterized window of vulnerability with implications for respiratory health and individualized care.},
}

@article {pmid41503395,
year = {2026},
author = {Oosthuysen, H and Coetzer, K and Madisha, MT and Coetzer, WG},
title = {An Analysis of Vegetation and Microbiome Recovery in Abandoned Agricultural Fields.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72865},
pmid = {41503395},
issn = {2045-7758},
abstract = {Biodiversity is a key indicator of an ecosystem's resilience to disturbances, but farming practices like monocultures can be disruptive. Assessing the biodiversity levels in abandoned fields can help to reveal recovery patterns and inform strategies to conserve biodiversity in agricultural landscapes. The main aim of this study was to assess the pace of natural recovery for a chronosequence of formerly planted fields in a grassland habitat in the Eastern Cape, South Africa. The plant communities were evaluated using species counts, while the bacterial communities were assessed through high-throughput sequencing (HTS) of the 16S rRNA gene. The alpha diversity indices indicated that the diversity levels within the old fields have started to resemble natural conditions for both the plant and microbial communities. Furthermore, the NMDS analyses identified clear variations in bacterial and plant community compositions among differently aged successional groups and the natural habitats. This study provides evidence that biodiversity levels within crop fields can recover from agricultural disturbances. However, considering the significant changes in climate and rainfall patterns in the study area, it remains unclear whether the community structures of the crop fields will reach native conditions in the coming decades, if at all.},
}

@article {pmid41503377,
year = {2026},
author = {Bonato, A and Parisi, C and Cascetta, P and Reni, A and Meyer, ML and Riudavets, M and Planchard, D and Besse, B and Remon, J and Facchinetti, F and Belluomini, L and Derosa, L and Barlesi, F},
title = {Gut Dysbiosis as a Potential Guide for Immunotherapy (Dis)Continuation After 2 Years in NSCLC: A Brief Report.},
journal = {JTO clinical and research reports},
volume = {7},
number = {1},
pages = {100928},
pmid = {41503377},
issn = {2666-3643},
abstract = {BACKGROUND: Although most phase III pivotal trials have set the duration of immune checkpoint blockers (ICB) for advanced NSCLC at 2 years, the criteria for safely discontinuing ICB remain undefined. Growing evidence links ICB efficacy to gut microbiota, positioning gut microbial taxonomic profiling as a promising biomarker to guide treatment decisions. We performed a retrospective analysis exploring clinical outcomes and the utility of multiomic decision-making tools in patients with NSCLC at Gustave Roussy who completed 24 months of ICB-based therapy without disease progression (PD).

METHODS: Patients receiving ICB between July 2016 and January 2023 were identified from the ONCOBIOTICS (NCT04567446) and STING (NCT04932525) study datasets. We selected those who reached 24 months of treatment without disease progression. Clinical characteristics and multiomic assessments, including gut microbiota profiling (TOPOSCORE by whole-genome sequencing), positron emission tomography-18-fluorodeoxyglucose imaging, and circulating tumor DNA, collected at 24 months, were analyzed. Key outcomes included overall survival (OS), progression-free survival (PFS), and PFS rates at 24 months after the completion of 2 years of ICB, stratified by molecular, metabolic, and microbial signatures.

RESULTS: Out of 123 patients treated for at least 18 months, 35 completed 24 months, with 31 eligible for the analysis. Of these, 68% continued ICB, whereas 32% discontinued therapy at the physician's decision. Clinical characteristics were similar across groups. After a median follow-up of 59.1 months, OS and PFS did not differ significantly between those who discontinued and those who continued treatment (OS p = 0.9012). Among all multiomic tools, gut microbiota composition exhibited a trend (though not statistically significant) association with PFS rates at 24 months after the completion of 2 years of ICB. Patients with a favorable microbiota profile had a higher rate of sustained response at 24 months compared with those with dysbiotic signatures (81% versus 44%, respectively, p = 0.0870).

CONCLUSIONS: Discontinuing ICB after 24 months did not negatively impact OS in our real-world cohort. Although limited by the small sample size, these findings support the potential of gut microbiota profiling as a promising tool to guide ICB duration. Integrating a translational multiomic algorithm, in particular microbial signals, may help personalize treatment strategies and safely shorten immunotherapy courses.},
}

@article {pmid41503356,
year = {2025},
author = {Alobaidi, S},
title = {The gut-kidney axis in chronic kidney disease: mechanisms, microbial metabolites, and microbiome-targeted therapeutics.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1675458},
pmid = {41503356},
issn = {2296-858X},
abstract = {Chronic kidney disease (CKD) remains a major global health issue, affecting millions and presenting persistent diagnostic and therapeutic challenges. Conventional biomarkers such as serum creatinine and estimated glomerular filtration rate have well-recognized limitations, underscoring the need for novel diagnostic tools and interventions. Emerging evidence highlights the gut-kidney axis as a central contributor to CKD pathogenesis, shaped by microbial dysbiosis and altered metabolite production. Harmful metabolites such as indoxyl sulfate, p-cresyl sulfate, and trimethylamine-N-oxide promote inflammation, endothelial dysfunction, and fibrosis, while loss of protective short-chain fatty acids impairs barrier integrity and immune regulation. This review integrates mechanistic, translational, clinical, and therapeutic perspectives, offering a comprehensive and distinctive synthesis of current knowledge. We emphasize both harmful and protective microbial metabolites, incorporate the often-overlooked oral-gut-kidney axis, and highlight advances in multi-omics and computational approaches for biomarker discovery. Microbiome-targeted interventions-including dietary strategies, prebiotics, probiotics, synbiotics, oral adsorbents, and fecal microbiota transplantation-are critically evaluated with respect to efficacy, safety, and translational readiness. By bridging basic science, clinical evidence, and therapeutic implications, this review provides a forward-looking framework for integrating microbiome insights into CKD diagnosis and management. Our synthesis complements existing literature while highlighting unmet needs, thereby informing future research priorities and guiding the development of clinically relevant microbiome-based strategies.},
}

@article {pmid41502987,
year = {2026},
author = {Mohan, R and Johnson, SD and Dean, PN and Acharya, A and Byrareddy, SN},
title = {Methods to characterize the vaginal microbiome in a rhesus macaque model of simian human immunodeficiency virus (SHIV) transmission uncover epithelium-associated enrichment of Prevotella.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100526},
pmid = {41502987},
issn = {2666-5174},
abstract = {The vaginal microbiome plays a crucial role in maintaining mucosal integrity and mitigating pathogen transmission, yet its comprehensive characterization remains challenging due to limited sampling and analysis methods. In this study, we aimed to characterize bacterial and fungal taxa diversities in the vaginal microbiomes of Simian Human Immunodeficiency (SHIV)-infected rhesus macaques, as well as their metabolic activities, using three sampling methods. The cervicovaginal lavage (CVL), vaginal swab, and vaginal mucosal tissue methods offer novel insights into microbial diversity and their potential impacts on HIV transmission. Using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, we assessed bacterial and fungal community composition and abundances, respectively, across all sampling methods. PICRUSt2 was used for functional predictions, and a modified glycosidase assay to further characterize glycan-degrading enzymatic activity in CVL samples. Our findings reveal that tissue samples were uniquely enriched for microbial taxa such as Prevotella spp. and Helicobacter spp., showing notable abundance differences compared to CVL and swab samples. Tissue samples exhibited higher alpha diversity and distinct metabolic prediction profiles, particularly elevated sialidase activity. While fewer differences were found in fungal microbiome composition and diversity, marked correlations were observed between bacterial and fungal taxa, emphasizing complex interkingdom interactions. These results highlight the significance of sampling methods in microbial ecology studies, which should be carefully considered due to their potential influence on pathogen transmission risk.},
}

@article {pmid41502951,
year = {2025},
author = {Oliveira, RA and McSpadden, E and Pandey, B and Lee, K and Yousef, M and Chen, RY and Triebold, C and Haro, F and Aksianiuk, V and Patel, R and Shriram, K and Ramanujam, R and Kuehn, S and Raman, AS},
title = {Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.02.28.582635},
pmid = {41502951},
issn = {2692-8205},
abstract = {Engineering functional microbiomes is challenging due to complex interactions between bacteria and their environments [1-6] . Using a set of 848 gut commensal strains and clearance of multi-drug resistant Klebsiella pneumoniae (Kp -MH258) as a target function, we engineered a functional 15-member synthetic microbiome-SynCom15-through a statistical approach agnostic to strain phenotype, mechanism of action, bacterial interactions, or composition of natural microbiomes. Our approach involved designing, building, and testing 96 metagenomically diverse consortia, learning a generative model using community strain presence/absence as input, and distilling model constraints through statistical inference. SynCom15 cleared Kp -MH258 across in vitro , ex vivo , and in vivo environments, matching the efficacy of a fecal microbiome transplant in a clinically relevant murine model of infection. The mechanism of suppression by SynCom15 was related to fatty acid production coupled with environmental acidification. SynCom15 also suppressed other pathogens- Clostridioides difficile , Escherichia coli , and other K. pneumoniae strains-but through different mechanisms. Sensitivity analysis revealed models trained on strain presence/absence captured the statistical structure of pathogen suppression, illustrating that community representation was key to our approach succeeding. Our framework, 'Constraint Distillation', could be a general and efficient strategy for building emergent complex systems, offering a path towards synthetic ecology more broadly.},
}

@article {pmid41502883,
year = {2025},
author = {Zhang, C and Lin, G and Lu, X and Yu, X},
title = {Exploring the role of the gut microbiome in pediatric gastrointestinal and neurological health.},
journal = {Translational pediatrics},
volume = {14},
number = {12},
pages = {3449-3472},
pmid = {41502883},
issn = {2224-4344},
abstract = {The gut microbiome, a complex ecosystem of microorganisms that inhabit the gastrointestinal (GI) tract, is now understood to be a central regulator of pediatric health and development. This review discusses its centrality in GI and neurological outcomes, with a particular focus on the devastating effects of malnutrition. It also discusses how microbial homeostasis (dysbiosis), especially that induced by protein-energy and micronutrient deficiencies, interferes with nutrient absorption, enhances intestinal inflammation, and alters gut-brain communication. Dysbiosis is mechanistically connected to the pathogenesis and severity of other pediatric disorders, such as inflammatory bowel disease (IBD), autism spectrum disorder (ASD), and attention-deficit/hyperactivity disorder (ADHD). The most important pathways of gut dysbiosis-related disease mechanisms. include the altered production of microbial metabolites such as short-chain fatty acids (SCFAs), impaired gut barrier integrity ("leaky gut"), and disrupted immune and neuroendocrine signaling. To address these issues, this article outlines potential therapeutic solutions that seek to restore microbial balance. Targeted probiotic and prebiotic supplementation, dietary interventions, and the emerging field of precision nutrition, which enables interventions to be tailored based on a child's individual microbiome and genetic makeup, are also mentioned as possible ways to improve the GI and neurological health of malnourished children. Learning how these interactions between the gut microbiome, nutrition, and the gut-brain axis (GBA). Work could revolutionize the development of new treatments for preventing and treating pediatric diseases caused by microbial imbalances.},
}

@article {pmid41502856,
year = {2025},
author = {Sherwani, SK and Kahsen, JJ and Wu, LYA and Green, SJ},
title = {Novel short primers for next-generation 16S rRNA gene amplicon sequencing.},
journal = {Journal of biomolecular techniques : JBT},
volume = {36},
number = {4},
pages = {5-18},
pmid = {41502856},
issn = {1943-4731},
mesh = {*RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *DNA Primers/genetics ; Sequence Analysis, DNA/methods ; Feces/microbiology ; },
abstract = {Primers for 16S rRNA gene amplification are generally degenerate to account for mismatches between primers and templates, but primer lengths are typically not adjusted. However, prior research has shown that primers are most sensitive to mismatches at the 3' end, and 3' mismatches can limit the ability of primers to amplify target genes from complex microbial communities. We present here a novel approach to primer design by creating staggered and truncated (both the 5' and 3' ends) versions of commonly used microbial 16S ribosomal RNA (rRNA) primers while maintaining consistent melting temperatures. Genomic DNA extracted from complex microbial communities (skin, feces, wastewater, soil) was profiled using deep sequencing of 16S rRNA gene amplicons generated with standard and truncated primers. Sequence data were compared using standard bioinformatics pipelines evaluating alpha and beta diversity. Despite using primers as short as 10 bases, observed microbial communities generated with truncated primer pools were highly similar to those generated with standard primer pools. In analyses of skin, truncated amplicons had significantly increased relative abundance of Cutibacterium which contain 3' mismatches with standard primers. Further analysis revealed a single nucleotide position in a common 16S rRNA gene primer that enriched microorganisms from the domain Archaea with truncated primers. These results demonstrate the viability of using short primers for amplicon NGS, indicating the availability of greater primer design flexibility for future studies.},
}

*RNA, Ribosomal, 16S/genetics
*High-Throughput Nucleotide Sequencing/methods
*DNA Primers/genetics
Sequence Analysis, DNA/methods
Feces/microbiology

@article {pmid41502473,
year = {2026},
author = {Joyce, J and K, PV and K, J and K, RE},
title = {Application of AI for the functional elucidation of rice associated microbial community for the improved productivity.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {63},
pmid = {41502473},
issn = {2190-572X},
abstract = {UNLABELLED: Rice microbiome plays a critical role in the growth, health, stress tolerance, nutrient uptake, root development, and productivity of its host. In this study, advanced machine learning algorithms were applied to analyze the genomic data from 1365 rice-associated bacteria sourced from Bacterial and Viral Bioinformatics Resource Center (BV-BRC) database. After filtering, the genomic data of 280 organisms were selected and annotated to identify their respective genes. These were further categorized into ortholog groups, and based on the presence and absence of the ortholog groups, the organisms were clustered into eight groups. Genes encoding amino acid transport, inorganic ion transport and metabolism were the most common Clusters of Orthologous Genes (COG) categories observed across the various clusters while cellular process, biological regulation, and response to stimuli were the most common gene ontology terms. However, the presence of a large proportion of genes having unknown functions suggests the distribution of novel genes which could facilitate the functions including the plant colonization. Further to this, machine learning models were used to classify the organisms as either beneficial or pathogenic. Here, Support Vector Machine based analysis showed the highest accuracy (92.98%) when compared to the Logistic Regression (90.16%) and Random Forest (57.80%). From the analysis, ABC-type transporters such as ABC-type oligopeptide transport system were more abundantly distributed in beneficial bacteria. On the other hand, transposase such as Transposase InsA were observed to be common among pathogenic strains. From the results obtained, the presence of genes responsible for the nutrient transport and metabolic versatility was found to be significant for the beneficial bacteria, while the genetic variability was remarkable for the pathogens. The information generated in this study hence highlights the power of AI for predicting the beneficial interactions between the rice and its microbiome, and thereby offer its applications in enhancing the crop resilience and productivity for the sustainable agricultural practices.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04665-z.},
}

@article {pmid41502470,
year = {2026},
author = {Shukla, A and Yadav, M and Malik, MZ and Aditya, AK and Kumar, A and Tandon, R and Shalimar, and Ray, AK},
title = {Soil influences on rural versus urban human gut microbiota and implications on cardio-metabolic health: a comparative pilot study.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {62},
pmid = {41502470},
issn = {2190-572X},
abstract = {UNLABELLED: Humans are exposed to surrounding soil environment and this exposure has reduced with growing urbanisation. Limited evidence exists on how rural and urban soils shape human gut microbiome and related functions. Here, we performed metagenomic analysis, functional prediction, gene ontology using QIIME2, PICRUSt, and DAVID by taking human stool and soil samples (n = 20) from rural and urban settings to characterise gut microbiota and their resemblance to their respective soil microbiota and its functional implications. Our findings demonstrated that soil environment affects gut microbial diversity and abundance of its immediate human inhabitants in both groups and observed shared microbial and functional properties in rural- and urban-guts characteristic of their respective soil microbiota. In rural-group, phylum Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, class Actinobacteria were major overlapping features, while in the urban-counterpart phylum Proteobacteria, Firmicutes, class Gammaproteobacteria were observed. We also demonstrated implication of this differential composition on human health in both settings, and observed enrichment of cytokines like IL-12, IFN-ϒ, and oxidative phosphorylation pathway in rural group vital to metabolic homeostasis. While enrichment of response to toxic substances, methane metabolism, and potentially low levels of alanine in the urban counterpart, linked to impaired immune response and metabolism, suggests urban group may be prone to the cardio-metabolic disease risk. These observations were consistent with other findings emphasising rural groups have healthy sets of microbiome compared to their urban counterpart. In conclusion, our findings unveil the significance of soil microbiota in evolution and shaping of human gut microbiota, thereby potentially beneficial to human health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04675-x.},
}

@article {pmid41502453,
year = {2026},
author = {Xie, H and Hu, X and Wang, S and Liu, H and He, Z and Ji, H and Lv, K and Zhu, T and Wang, J},
title = {Unraveling the differences in meat flavor of duck and its regulatory mechanisms based on microbiomics, metabolomics, and flavoromics sequencing.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101281},
pmid = {41502453},
issn = {2665-9271},
abstract = {Consumers increasingly demand high-quality duck meat flavor, with reports showing notable flavor variations among different duck breeds. This study aims to clarify the flavor differences between Jinling white duck (JL), Cherry Valley duck (CV), and Liancheng white duck (LC), as well as to elucidate the regulatory mechanisms. Electronic-nose results revealed distinct flavor differences among LC, CV, and JL. The analysis showed that the JL vs. CV group contains 330 differential VOCs and 119 differential water-soluble compounds, while the JL vs. LC group has 112 differential VOCs and 74 differential water-soluble compounds. Metabolomic analysis of the pectoral muscle revealed 74 differential precursors compounds in the JL vs. CV comparison, and 147 in JL vs. LC comparison. Multi-omics analysis suggested that Anaerotruncus and Lautropia may negatively regulate the deposition of flavor precursor LPE O-14:1 in pectoral muscle, influencing 3-methyl-pentadecane and cholic acid levels, thereby affecting the duck meat flavor. These findings demonstrate that JL exhibits distinct flavor characteristics compared to LC and CV, providing valuable insights for meat quality improvement in the poultry industry.},
}

@article {pmid41502447,
year = {2025},
author = {van Bentum, S and O'Banion, BS and Gates, AD and Van Pelt, HA and Bakker, PAHM and Pieterse, CMJ and Lebeis, SL and Berendsen, RL},
title = {Microbiome responses to natural Fusarium infection in field-grown soybean plants.},
journal = {Plant and soil},
volume = {516},
number = {2},
pages = {1347-1363},
pmid = {41502447},
issn = {0032-079X},
abstract = {AIMS: The rhizosphere microbiome influences plant health, for example, by mediating plant-pathogen interactions. Plants can recruit protective microbes in response to disease, but the consistency of this process in field conditions is unclear. We aimed to identify candidate beneficial microbes enriched during pathogen infection across multiple fields, offering potential to support crop resilience against disease.

METHODS: DNA amplicon sequencing was employed to examine the rhizosphere microbiome of field-grown soybean (Glycine max L.) naturally infected with root pathogens across three commercial fields in Kentucky, USA. Symptomatic and asymptomatic plants were sampled to assess disease-associated shifts in the bacterial and fungal rhizosphere microbiome.

RESULTS: We identified a diverse Fusarium community, with one Fusarium solani amplicon sequence variant (ASV) consistently enriched in diseased plants, identifying it as the likely pathogen. While microbial communities differed between diseased and healthy plants, these shifts were largely field-specific. Several fungal ASVs with known biocontrol potential (Clonostachys rosea, Penicillium, and Trichoderma) were enriched in healthy plants, implying a role in disease suppression. A Sphingomonas ASV, representing a genus previously linked to plant protection, was more abundant in diseased plant rhizospheres in two fields, suggesting pathogen-triggered recruitment. Conversely, Macrophomina phaseolina, a generalist root pathogen, was enriched in the rhizosphere of diseased plants in all fields, indicating possible co-infection with F. solani.

CONCLUSIONS: These findings reveal complex pathogen-associated patterns in the rhizosphere microbiome of field-grown plants and emphasize the need for field-specific microbiome research to inform sustainable disease management strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07798-5.},
}

@article {pmid41502197,
year = {2025},
author = {Hasan, I},
title = {Short-Chain Fatty Acids in the Gut-Brain-Liver Axis: Implications for Hepatic Encephalopathy.},
journal = {Acta medica Indonesiana},
volume = {57},
number = {4},
pages = {433-435},
pmid = {41502197},
issn = {2338-2732},
mesh = {Humans ; *Hepatic Encephalopathy/metabolism/etiology/epidemiology/microbiology ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; *Liver Cirrhosis/complications ; Indonesia/epidemiology ; *Liver/metabolism ; *Brain/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; },
abstract = {Hepatic encephalopathy (HE) is one of the serious complications of liver cirrhosis, characterized by a broad spectrum of neuropsychiatric symptoms, ranging from subtle cognitive impairment to coma, due to brain dysfunction associated with acute or chronic liver failure and/or portosystemic shunting. Globally, the prevalence of hepatic encephalopathy (HE) is reported to range from 20% to 80% in patients with liver cirrhosis, depending on whether the assessment includes minimal (MHE) or overt (OHE) forms. In Indonesia, determining the true prevalence of HE is challenging due to diagnostic difficulties, with estimates ranging from 30% to 84%. At Cipto Mangunkusumo General Hospital, the prevalence of HE in 2009 was 63.2%. In recent years, evidence has highlighted the role of the gut microbiota in the pathogenesis of hepatic encephalopathy (HE), a concept now widely referred to as the "gut-liver-brain axis." Short-chain fatty acids (SCFAs) are gut microbial-derived metabolites that provide numerous health benefits. SCFA has been demonstrated to impact gut barrier function, immunomodulation, and glucose homeostasis. In this issue, Ferdianto et al. conducted a cross-sectional observational study comparing the amount and composition of fecal SCFA in cirrhotic patients with and without HE. The study revealed no significant difference in SFA levels between HE and non-HE groups; however, the HE groups demonstrated higher levels of total SCFA, acetate, and butyrate compared to the non-HE groups. While this study contributes valuable early evidence from an Indonesian cohort, several important limitations should be acknowledged. First, the diagnostic approach for covert or minimal HE requires clarification. The authors did not explicitly state the neuropsychological tools and specific criteria used. Clear definitions are essential, as minimal and covert HE is susceptible to the choice of diagnostic method and can substantially influence group classification. Second, although SCFAs represent key microbial metabolites, the study did not explore the underlying microbiome composition. Without bacterial taxonomy or species-level data, it remains difficult to determine whether differences in SCFA levels truly reflect gut dysbiosis or altered microbial diversity. SCFA concentrations may be influenced by multiple factors, and therefore, inclusion of metagenomic or sequencing data would strengthen the mechanistic interpretation and allow linking specific bacterial taxa with cognitive impairment. Future studies that include larger and more heterogeneous cohorts, alongside integrated analyses of microbiome composition and validated neurocognitive testing, will be crucial to validate the role of SCFAs in HE development.},
}

Humans
*Hepatic Encephalopathy/metabolism/etiology/epidemiology/microbiology
*Gastrointestinal Microbiome
*Fatty Acids, Volatile/metabolism
*Liver Cirrhosis/complications
Indonesia/epidemiology
*Liver/metabolism
*Brain/metabolism
Cross-Sectional Studies
Feces/chemistry

@article {pmid41502172,
year = {2026},
author = {Ushijima, B and Beurmann-Grant, S and Ruiz-Toquica, J and Gongaware, CK and Jefferson, T and Weber, WC and Videau, P and Häse, CC},
title = {The Coral Host Microbiome Modulates the Virulence of the Bacterial Pathogen Vibrio coralliilyticus.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70224},
pmid = {41502172},
issn = {1462-2920},
support = {//University of North Carolina Wilmington/ ; //Oregon State University/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Vibrio/pathogenicity/genetics ; Virulence ; *Microbiota ; Quorum Sensing/genetics ; Coral Reefs ; Pseudoalteromonas/pathogenicity ; Host-Pathogen Interactions ; },
abstract = {Coral disease outbreaks pose a major threat to reef ecosystems, often leading to widespread mortality and declines in coral cover. A key factor predicted in disease susceptibility is the coral microbiome, which is thought to protect corals from pathogens like Vibrio coralliilyticus. However, this protective function has not been empirically demonstrated with live coral, nor is it well understood how these microbiome-pathogen interactions contribute to the observed variation in virulence among different V. coralliilyticus strains. This study investigated the role of the Hawaiian rice coral (Montipora capitata) microbiome in susceptibility to infection by endemic and non-endemic strains of V. coralliilyticus. Laboratory infection experiments revealed that antibiotic-induced dysbiosis generally increased host susceptibility, though infection rates varied between strains. Notably, the type of M. capitata colour morph did not influence infection outcomes, and induced dysbiosis did not affect susceptibility to another pathogen, Pseudoalteromonas piratica. Additionally, the quorum sensing genes vcpR and aphA were examined for their roles in V. coralliilyticus pathogenicity in relation to the host microbiome. These findings underscore the protective function of the coral microbiome and highlight the complexity of host-pathogen interactions, contributing to a deeper understanding of coral disease dynamics and informing future mitigation strategies.},
}

*Anthozoa/microbiology
Animals
*Vibrio/pathogenicity/genetics
Virulence
*Microbiota
Quorum Sensing/genetics
Coral Reefs
Pseudoalteromonas/pathogenicity
Host-Pathogen Interactions

@article {pmid41501907,
year = {2026},
author = {Ben Fredj, S and Kechiche, H and Chouchen, A and Akkari, I and Ghammam, R and Zammit, N and Douss, N and Skhiri, A and Maoua, M and Maatoug, J and Harrabi, I and Maalel, OE},
title = {Probiotic intake and mental health in healthy working adults: a systematic review and meta-analysis of randomized controlled trials.},
journal = {BMC psychology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40359-025-03885-5},
pmid = {41501907},
issn = {2050-7283},
abstract = {BACKGROUND: Workers face significant mental health challenges from stress, anxiety, and depression, impacting individuals, organizations, and society. Emerging research indicates a link between the gut microbiome and mental well-being, suggesting probiotics as a potential support. This study objectively evaluated probiotic supplementation's effects on depression, anxiety, stress, sleep, and related biological markers in this population.

METHODS: We conducted a systematic review and meta-analysis following PRISMA 2020 guidelines. EMBASE, Cochrane Library, and PubMed were searched for randomized controlled trials assessing probiotic supplementation on a range of psychological outcomes. The primary outcomes were perceived symptoms of depression, anxiety, stress, and sleep quality. The secondary outcomes were physiological markers of mental health, such as cortisol and C-reactive protein levels, in working populations. Eligible studies included healthy employed adults (≥ 18 years), without psychiatric, neurodegenerative, genetic, infectious, or endocrine disorders, including pregnancy.

RESULTS: Twelve studies involving 3,350 participants were incorporated. Probiotic consumption had a modest yet statistically significant positive effect on subclinical psychological outcomes, including symptoms of depression, anxiety, and stress, in healthy working adults (standardised mean difference (SMD) = -0.21, 95% CI [-0.34, -0.09], p = 0.001). These findings were maintained despite moderate statistical heterogeneity that was likely due to variations in probiotic strains, dosages, and duration of supplementation used. Moreover, the probiotic interventions were associated with a statistically significant reduction in cortisol levels, a key biomarker of physiological stress (SMD = -0.26, 95% confidence interval [CI] [-0.45, -0.08], p = 0.005). Conversely, no statistically significant effects were observed for probiotic supplementation on the C-reactive protein levels, a marker of systemic inflammation. However, due to the lack of available evidence, it was impossible to draw firm conclusions about the effects of probiotics on sleep quality and biomarkers of oxidative stress.

CONCLUSION: This systematic review and meta-analysis provide preliminary evidence suggesting that probiotic supplementation may hold promise as an approach to improve mental well-being within working populations. However, further high-quality randomised controlled trials targeting this population are needed to determine the optimal probiotic strains, dosages, and treatment durations for addressing specific mental health outcomes.

TRIAL REGISTRATION: PROSPERO number CRD42024510170.},
}

@article {pmid41501865,
year = {2026},
author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H},
title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02300-w},
pmid = {41501865},
issn = {2049-2618},
support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; },
abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.

RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.

CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.},
}

@article {pmid41501528,
year = {2026},
author = {Huang, Z and Liu, Y and Wu, Y and Zhang, F and Yu, L and Gao, S and Wen, W and Wang, G and Su, R and Xia, P and Zhou, Q and Bie, Y and Hu, P and Burgermeister, E and Lan, P and Wu, X and Zhang, H and Zhang, F and El-Omar, EM and Zuo, T},
title = {Gut mucosal mycobiome profiling in Crohn's disease uncovers an AMP-mediated anti-inflammatory effect of Cladosporium sphaerospermum.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {41501528},
issn = {2522-5812},
support = {82172323//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100134//National Natural Science Foundation of China (National Science Foundation of China)/ ; 823B2010//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32372334//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82304144//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Crohn's disease (CD) is a subtype of inflammatory bowel disease that most commonly affects the terminal ileum and is associated with abnormal gut microbiome composition. However, the fungi of the small bowel mucosa and their metabolic functions, particularly protective ones, remain largely unexplored. We enrolled patients with CD and healthy individuals from three independent cohorts and conducted multi-omics profiling of the ileal mucosal mycobiome and bacteriome, along with the faecal mycobiome, bacteriome and metabolome. We show that compared to a healthy mucosa, the fungus Cladosporium sphaerospermum is remarkably depleted in the mucosa of patients with CD, yet remains unchanged in faeces. Subsequent causality studies reveal that C. sphaerospermum occupies the intestinal crypt niche and counteracts intestinal inflammation partly by adenosine 5'-monophosphate (AMP) production, as demonstrated in mice, in vitro and in fungal cultures. Mechanistically, C. sphaerospermum upregulates epithelial cell junctions and the Wnt signalling pathway. Our study unveils a mucosa-associated beneficial fungus, suggesting potential novel microbial intervention strategies for CD.},
}

@article {pmid41500802,
year = {2026},
author = {Lee, CH and Bui, TPN and Petitfils, C and Jian, C and Wong, GC and Puel, A and Le Roy, T and Bellais, S and Ben Abdallah, B and Nehlich, M and Leicht, T and Jia, M and Hoyles, L and Federici, M and Fernández-Real, JM and Burcelin, R and Dumas, ME and Delzenne, NM and Clavel, T and Boeren, S and Troise, AD and Scaloni, A and Muccioli, GG and De Vos, WM and Van Hul, M and Cani, PD},
title = {Novel myo-inositol to butyrate fermentation pathway in the prevalent human gut species Dysosmobacter welbionis, a bacterium associated with improved metabolic and liver health.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336617},
pmid = {41500802},
issn = {1468-3288},
abstract = {BACKGROUND: Dysosmobacter welbionis is a recently discovered butyrate producer whose presence in stool correlates with improved metabolic health. Whether its abundance is reduced in individuals with metabolic dysfunction-associated steatotic liver disease (MASLD) remains unknown. Mechanistic insight into its butyrate production from myo-inositol, a dietary compound from fruits, beans, grains and nuts with metabolic benefits, is also limited.

OBJECTIVE: To assess population-level distribution, relative abundance and strain diversity of D. welbionis in humans, and to elucidate its metabolic capacity to ferment myo-inositol into butyrate.

DESIGN: We analysed several human cohorts for associations with liver health and evaluated D. welbionis J115[T] supplementation in a diet-induced steatosis mouse model. An antibody-guided anaerobic cell-sorting strategy enabled isolation of distinct strains. We combined [13]C-labelled inositol isotopes with NMR, mass spectrometry, genomics and proteomics.

RESULTS: We found that D. welbionis and two related species (D. hominis and D. segnis) are prevalent gut bacteria in the human gut. D. welbionis abundance was reduced in MASLD across two cohorts and inversely correlated with fibrosis score in a third cohort. Treatment with D. welbionis J115[T] improved glycaemia and hepatic steatosis in high-fat diet fed mice. We identified a non-canonical myo-inositol-to-butyrate fermentation pathway. 19 human strains were isolated, comparative genomics of 23 strains revealed an open pangenome (about 2100 core genes) including the full myo-inositol fermentation pathway.

CONCLUSION: D. welbionis possesses a unique, conserved route to convert dietary myo-inositol into butyrate, distinguishing it from other commensals and supporting its potential as a next-generation probiotic for metabolic and liver health.},
}

@article {pmid41500696,
year = {2025},
author = {Huang, Y and Yang, X and Zhang, S},
title = {[Multi-target mechanism and clinical transformation of hyperbaric oxygen therapy in the treatment of hypoxic-ischemic brain injury after cardiopulmonary resuscitation].},
journal = {Zhonghua wei zhong bing ji jiu yi xue},
volume = {37},
number = {12},
pages = {1170-1175},
doi = {10.3760/cma.j.cn121430-20250605-00317},
pmid = {41500696},
issn = {2095-4352},
mesh = {Humans ; *Hyperbaric Oxygenation ; *Cardiopulmonary Resuscitation/adverse effects ; *Hypoxia-Ischemia, Brain/therapy/etiology ; Heart Arrest/therapy ; Oxidative Stress ; Apoptosis ; Blood-Brain Barrier ; },
abstract = {Cardiopulmonary resuscitation (CPR) is a critical life-saving intervention for patients who have suffered cardiac arrest (CA), which helps the organism of CA patients to rapidly restore respiratory and circulatory functions. However, the survival rate of patients after CPR is extremely low. Globally, sudden cardiac arrest causes over 3 million deaths annually, and the survival rate after CPR is less than 8%. Hypoxic ischemic brain injury (HIBI) is the primary cause of death in 68% of these cases. Hyperbaric oxygen therapy (HBOT) enhances the dissolution of oxygen in plasma, increases the arterial blood oxygen partial pressure in the body, and improves tissue hypoxia. It is widely used in conditions of cerebral ischemia and hypoxia (such as stroke, CA, etc), but its role in HIBI following CPR has not been fully studied. Therefore, this article systematically reviews the multi-target mechanisms of HBOT in the treatment of HIBI, including the inhibition of cell apoptosis and necrosis, improvement of oxidative stress, reduction of neuroinflammation, and enhancement of blood-brain barrier permeability and collateral circulation. It also discusses emerging treatment strategies such as HBOT combined with gut microbiome modulation and active abdominal compression-decompression CPR (AACD-CPR), exploring their potential as new therapeutic targets for HIBI post-CPR, with the aim of identifying more promising clinical translation paths to improve neurological functional prognosis and quality of life after CPR.},
}

Humans
*Hyperbaric Oxygenation
*Cardiopulmonary Resuscitation/adverse effects
*Hypoxia-Ischemia, Brain/therapy/etiology
Heart Arrest/therapy
Oxidative Stress
Apoptosis
Blood-Brain Barrier

@article {pmid41500417,
year = {2026},
author = {Derrick, A and Zheng, Y and Fred, B and Boateng, AG and Wang, H and Mrope, P and Azupio, S and Zhang, S},
title = {Effects of short-term exposure to ferrous sulfate on bioaccumulation, oxidative stress biomarkers, immunity, and intestinal microbiota in Litopenaeus vannamei.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {302},
number = {},
pages = {110450},
doi = {10.1016/j.cbpc.2026.110450},
pmid = {41500417},
issn = {1532-0456},
abstract = {The accumulation of heavy metals in aquatic environments poses critical threats to aquaculture, with iron (Fe) being one of the most prevalent contaminants from industrial and agricultural effluents. This study evaluated the acute toxicity and mechanistic impacts of ferrous sulfate (FeSO4) on the Pacific white shrimp (Litopenaeus vannamei). Acute toxicity tests established the 96-h median lethal concentration (LC50) of Fe at 2.52 mg/L, determined across exposure intervals of 0, 24, 48, 72, and 96-h at nominal concentrations ranging from 0.2, 1.0, 5.0, 25.0, 125.0, and 625.0 mg/L. No mortality occurred in control shrimp, whereas mortality increased progressively with both concentration and duration of FeSO4 exposure. FeSO4 exposure caused significant Fe accumulation in hepatopancreas and muscle, accompanied by elevated reactive oxygen species and malondialdehyde, and suppression of key antioxidant and immune enzymes; superoxide dismutase (SOD), catalase (CAT), and lysozyme (LZM). Transcriptional analysis revealed strong upregulation of stress proteins (HSP70, HSP90, GSH-Px), apoptotic regulators (caspase-3, p53), and immune effectors (metallothionein), whereas ferritin expression decreased, indicating disruption of Fe homeostasis. Microbiota sequencing demonstrated pronounced dysbiosis: control shrimp maintained balanced commensal taxa, while Fe-exposed groups were enriched in stress-tolerant and opportunistic genera such as Shewanella and Vibrio. Functional prediction (Tax4Fun) indicated that Fe exposure enhanced xenobiotic biodegradation, immune diseases, and cell-death-related pathways, while functions associated with energy, amino-acid and carbohydrate metabolism, and nervous system were comparatively downregulated. Collectively, FeSO4 exposure impaired antioxidant defences, triggered apoptosis, and induced intestinal dysbiosis, with implications for aquaculture health management and environmental risk assessment.},
}

@article {pmid41500324,
year = {2026},
author = {Stiernborg, M and Yang, LL and Skott, E and Giacobini, M and Melas, PA and Debelius, JW and Lavebratt, C},
title = {Altered gut microbiome function in ADHD: More Prevotella, less vitamin B12 biosynthesis, and beneficial modulation by synbiotic treatment.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106259},
doi = {10.1016/j.bbi.2026.106259},
pmid = {41500324},
issn = {1090-2139},
abstract = {The effect of psychostimulant medication in ADHD on the gut microbiome remains unknown. Oral Synbiotic 2000, comprising multiple lactic acid bacteria and dietary fibers, reduces psychiatric symptoms and plasma immune markers in ADHD, but its impact on the gut microbiome is unexplored. This study aimed to (i) study the fecal bacterial microbiome, focusing on species and bacterial gene modules, in ADHD patients and neurotypical controls, and (ii) examine microbiome changes attributable to Synbiotic 2000. Fecal samples were collected from 147 participants at baseline, and 106 completers at follow-up from a randomized placebo-controlled trial of Synbiotic 2000 conducted in children and adults with ADHD. At baseline, adult samples were compared to those of 52 adult controls, and patients on psychostimulants were compared to those not on psychostimulants in adults and children separately. The fecal microbiome was sequenced using shallow shotgun sequencing and analyzed for diversity and differential abundance using machine learning. Plasma short-chain fatty acids (SCFAs) and serum vitamin B12 levels were measured. At baseline, adult ADHD patients had significantly different abundances of four species compared to controls. In children, those on psychostimulants exhibited a higher abundance of species from the genus Prevotella, alongside a lower abundance of the vitamin B12-synthesis module, M00122, than those not on such medication. The lower M00122 abundance was associated with a looser stool consistency, implicating a shorter colonic transit time. Synbiotic 2000 did not affect taxonomic or functional α-diversity in adults or children. However, looser baseline stool consistency was linked to greater increases in evenness in the Synbiotic group over time. There was a significant Synbiotic-specific effect on taxonomic and functional β-diversity, not only the increased abundance of the Synbiotic 2000 species. Plasma levels of formic acid and propionic acid increased towards control levels in the Synbiotic group. In conclusion, distinct species were differently abundant in adults with ADHD compared to controls. The implications of the lower abundance of the vitamin B12-synthesis module, in children on psychostimulant medication, for the gut ecosystem and host intestine remain to be elucidated. Synbiotic 2000 influenced the taxonomy and functionality of the fecal microbiome and increased plasma SCFA levels towards normal. Further research is warranted to explore the clinical implications of microbiome modulation in the treatment of ADHD.},
}

@article {pmid41202214,
year = {2026},
author = {Feng, Z and Ronholm, J},
title = {Examining the competitive exclusion and pathogenic potential of Pseudomonadota isolated from healthy chickens.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-11},
doi = {10.1139/cjm-2025-0179},
pmid = {41202214},
issn = {1480-3275},
mesh = {Animals ; *Chickens/microbiology ; Probiotics ; Genome, Bacterial ; Phylogeny ; Poultry Diseases/microbiology ; Gastrointestinal Microbiome ; Intestines/microbiology ; },
abstract = {The chicken intestine presents a complex environment for microbial survival due to high interbacterial competition, high bile salt concentrations, a low pH, and microaerophilic conditions. While most probiotics contain members of the Bacillota phylum, members of the Pseudomonadota phylum are known to be more important in competitive exclusion-which may be an important consideration in the formulation of future probiotics. Little is known about commensal Pseudomonadota in healthy chickens, or what benefits members of this phylum may offer the host; most studies on Pseudomonadota focus on aspects of opportunistic pathogenesis and dysbiosis. In this study, we use an in silico approach to evaluate the pathogenic potential, competition strategies, and potential host benefits of Pseudomonadota isolates from healthy chickens. We analyzed the draft genomes of 29 representative isolates of Pseudomonadota using Bagle4, AntiSMash, SeCreT6, KEGG mapper, and Virsorter2 to identify key interbacterial competition strategies including secondary metabolite biosynthesis, secretion systems, quorum sensing, and prophages. Our results revealed that each isolate exhibits distinct interbacterial competitive strategies, often independent of their taxonomic affiliation. Including Pseudomonadota in future poultry probiotics may be critical to improving colonization resistance in industrially raised poultry.},
}

Animals
*Chickens/microbiology
Probiotics
Genome, Bacterial
Phylogeny
Poultry Diseases/microbiology
Gastrointestinal Microbiome
Intestines/microbiology

@article {pmid41500299,
year = {2026},
author = {Zhang, W and Gu, L and Yan, W and Zhao, D and Liu, J},
title = {Acetochlor and sulfamethoxazole co-selection alter soil microbial nitrogen metabolism and resistome in agroecosystem.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123688},
doi = {10.1016/j.envres.2026.123688},
pmid = {41500299},
issn = {1096-0953},
abstract = {Agricultural soils increasingly face co-contamination by herbicides and antibiotics, yet the ecological impacts of such multipollutant exposure remain poorly understood. This study employed a soil-plant microcosm combined with metagenomic sequencing to investigate the co-selective effects of acetochlor (ACE) and sulfamethoxazole (SMX) on soil microbiomes and antibiotic resistance genes (ARGs). The results showed that SMX functioned as the dominant ecological filter, significantly reducing microbial diversity and restructuring community composition via suppressing Pseudomonadota while enriching Acidobacteriota. Co-exposure further decreased diversity and shifted nitrogen metabolic pathways: SMX inhibited denitrification and nitrogen fixation, whereas co-combination synergistically enhanced the potential of nitrous oxide emission. Critically, herbicide-antibiotic co-exposure drove the emergence of clinically relevant ARGs (e.g., CMY-80, MCR-2.5) and enhanced their dissemination by increasing network complexity among host microorganisms. Moreover, ACE acted as an 'antibiotic adjuvant', accelerating resistance evolution through stress-induced physiological responses and mobility activation. ACE dose-dependent responses revealed the dual ecological role of agrochemicals: signaling molecules at low concentrations (2.5 mg/kg) and stressors at elevated levels (5.0 mg/kg). Genomic analysis further showed a higher chromosomal than plasmid-borne ARG abundance, reflecting a dynamic equilibrium between persistent and mobile resistance under fluctuating environmental pressures. These findings underscore the necessity of incorporating multipollutant scenarios into risk assessment, as single-contaminant evaluations underestimate the ecological and public health risks in agricultural ecosystems.},
}

@article {pmid41500160,
year = {2026},
author = {Shahid, MAH and Jha, R and Mishra, B},
title = {Changes in the gut microbiome, metabolic pathways, and intestinal gene expression during the peak, mid, and decline egg production phases in laying hens.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106372},
doi = {10.1016/j.psj.2026.106372},
pmid = {41500160},
issn = {1525-3171},
abstract = {The decline in egg production due to aging poses a significant challenge for the egg industry. This study investigated the cecal microbiota, predicted metabolic pathways, and ileal gene expression to clarify how gut health, nutrient availability, and physiological status influence egg production in laying hens across different ages. Cecal digesta and ileal tissues were collected from Hy-Line-W36 laying hens at peak-production (37-weeks of age), mid-decline (67-weeks of age), and decline-phase (87-weeks of age) (n = 15/ group). DNA from cecal digesta (8/group) was used for 16S rRNA gene sequencing with the Illumina and QIIME2 platforms to refine the raw reads. Ileal tissues were used for RNA extraction, and gene expression was quantified through qPCR. R, PICRUSt2, and STAMP were used for statistical analysis. Despite similar richness, hens in the mid-decline and decline-phases of egg production exhibited reduced microbial diversity. At peak production, the microbiome was dominated by carbohydrate-fermenting genera such as Prevotella, Megasphaera, and Anaerotignum; mid-decline hens acquired more Limosilactobacillus and butyrate-producing Acutalibacteraceae, while the decline-phase hens were enriched with maintenance-oriented taxa, including Peptostreptococcaceae. Functional predictions mirrored these shifts, where peak-production hens' profiles favored glycolysis, nucleotide synthesis, and rapid acetyl-CoA turnover; mid-decline hens showed enhanced amino acid biosynthesis, iron scavenging, and SCFA production; and decline-phase hens emphasized nucleotide/cofactor repair and stress-response pathways while central-carbon routes declined. Additionally, age-related changes in enzymatic functions suggested reduced metabolic efficiency. In decline-phase, the expression of ileal antioxidant (SOD1, SOD2, GPX1) and tight-junction genes (CLDN1, OCLN) significantly decreased. The higher expression of Gadd45b at the decline-phase suggests cellular damage and leakage at the ileum. Moreover, decline-phase hens exhibited decreased levels of TLR4 and NF-κB, along with higher levels of IL-4 and IL-12, indicating a compromised immune response. Additionally, reduced expression of solute carrier transporter SLC1A1, SLC5A1 (amino acid and peptide), SLC7A6 (L-lysine, L-arginine), SLC19A2 (Thiamin), and FATP4 (Fatty acid) during the decline-phase, indicating insufficient energy availability for the hens, ultimately leading to a decrease in egg production. These findings reveal age-related changes in gut microbiota, nutrient transport, and immunity, contributing to decreased egg production in hens. This information could be pivotal for developing dietary and management strategies to enhance flock health and productivity.},
}

@article {pmid41500036,
year = {2026},
author = {Wanli, J and Xingyue, S and Xinning, L and Yashuo, Z and Xiaojing, Q and Cheng, H and Yan, H},
title = {Banxia Xiexin Decoction modulates short-chain fatty acid metabolism and mitigates ulcerative colitis by reshaping the intestinal microbiota.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {271},
number = {},
pages = {117332},
doi = {10.1016/j.jpba.2025.117332},
pmid = {41500036},
issn = {1873-264X},
abstract = {Ulcerative colitis (UC) is a chronic inflammatory disorder that significantly impacts the quality of life for patients. Dysbiosis of gut microbiota and changes in short-chain fatty acid (SCFA) metabolism play a role in both the initiation and progression of UC. Banxia Xiexin Decoction (BXD), a formula in traditional Chinese medicine, has shown therapeutic effects; however, its underlying mechanism remains unclear. A rat model of colitis induced by dextran sulfate sodium (DSS) was created, and various doses of BXD were administered. The principal components of BXD were analyzed through high-pressure liquid chromatography (HPLC). In order to clarify the mechanisms, 16S rRNA sequencing, serum metabolomics, targeted profiling of SCFAs via gas chromatography-mass spectrometry (GC-MS), and assessments of enzyme activity were conducted. BXD exerted protective effects against DSS-induced UC, as indicated by attenuated histological damage and reduced expression of pro-inflammatory cytokines. Untargeted metabolomics revealed that BXD modulated multiple metabolic pathways, enhancing SCFA-related processes, such as propanoate and butanoate metabolism. GC-MS revealed that BXD could increase the level of acetate, propionate, butyrate, isobutyrate, valerate, isovalerate and hexanoate. Microbiome sequencing indicated that BXD increased the abundance of beneficial taxa (e.g. Firmicutes, Bacteroidetes), while reducing pro-inflammatory genera. Altogether, BXD restored the microbial balance and promoted anti-inflammatory metabolite production. Our results demonstrated that BXD ameliorated UC by reprogramming gut microbial composition and enhancing SCFA biosynthesis, thereby suppressing intestinal inflammation. The potential of BXD as a therapy aimed at the microbiota for UC is emphasized in these studies, which also offer mechanistic insights using multi-omics approaches.},
}

@article {pmid41499990,
year = {2026},
author = {Chen, C and Wang, C and Li, H and Wang, T and Jiao, X},
title = {Sweet poison for the eyes: High-Fructose diets as drivers of metabolic disruption and ocular diseases - Insights and therapeutic horizons.},
journal = {Experimental eye research},
volume = {264},
number = {},
pages = {110852},
doi = {10.1016/j.exer.2026.110852},
pmid = {41499990},
issn = {1096-0007},
abstract = {Excess consumption of added sugars, commonly delivered through sucrose and high-fructose corn syrup, has increased in parallel with obesity, metabolic syndrome, and type 2 diabetes. These systemic metabolic disturbances are consistently associated with a range of ocular conditions. However, whether high-fructose intake exerts independent and fructose-specific effects on ocular tissues remains uncertain, because most human evidence is indirect, often mediated through metabolic syndrome phenotypes, and frequently confounded by mixed dietary exposures and total energy intake. This review synthesizes mechanistic pathways that are plausibly enriched by fructose biology, including hepatic fructose metabolism with ATP depletion and uric acid generation, oxidative and inflammatory signaling, altered lipid handling, and gut barrier and microbiome perturbations. We evaluate how these systemic changes may intersect with ocular surface homeostasis, retinal neurovascular integrity, intraocular pressure regulation, and choroidal and macular vulnerability. Across dry eye disease, diabetic retinopathy, glaucoma-related outcomes, age-related macular degeneration and choroidal neovascular responses, and cataract, we distinguish fructose-specific exposure studies from metabolic syndrome only and mixed diet reports, and we emphasize limitations related to exposure definition, replication, and translation to humans. Overall, current evidence supports the view that excess fructose may amplify ocular susceptibility in metabolically stressed states, but direct causal links in humans remain preliminary. We conclude by outlining methodological priorities and testable study designs needed to clarify fructose-specific contributions to ocular disease risk. Some experimental findings, particularly those related to ocular-surface responses, originate from single research groups and require independent replication, underscoring that current evidence remains preliminary and hypothesis-generating.},
}

@article {pmid41499871,
year = {2026},
author = {Rasta, M and Lashkaryan, NS and Shi, X and Taleshi, MS and Vayghan, AH and Ahmadi, A and Kakakhel, MA and Zahid, A and Jarf, MP and Manke, J and Liu, L and Wu, Y},
title = {Flow-dependent modulation of microplastic toxicity in grass carp: Insights from multi-level biological endpoints and machine learning.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {141020},
doi = {10.1016/j.jhazmat.2025.141020},
pmid = {41499871},
issn = {1873-3336},
abstract = {Microplastics (MPs) are emerging contaminants in freshwater systems, yet how hydrodynamic conditions modulate their biological effects remains unclear. This study investigated the accumulation, histopathology, immune response, and gut microbiota disruption in Ctenopharyngodon idella exposed to 5 µm polystyrene MPs (1000 µg/L; ∼ 1.46 × 10[7] particles/L) under static conditions and water velocities of 1, 3, and 5 Body Lengths per second (BL/s), representing low, medium, and high flow. Water velocity alone caused notable tissue damage, including gill lesions and intestinal alterations, and significantly upregulated immune response genes, with the strongest responses observed at high flow. MPs accumulated in both gill and intestinal tissues, with highest concentration observed under high velocity flow. Combined exposure (MPs + flow) induced more severe effects, including gill necrosis, lamellar fusion, intestinal mucosal degeneration, inflammatory infiltration, and further immune gene upregulation, with IL-6 and TNF-α demonstrating the most substantial effect sizes (Cohen's d > 5). Gut microbiome evaluations indicated trends towards reduced alpha diversity and an elevation in pathogenic taxa in different groups, specifically with increased abundance of Aeromonas and Vibrio under the influence of combined stressors. Mediation analysis suggested a possible role for tissue damage in dysbiosis development, although wide confidence intervals precluded definitive conclusions. These initial findings indicate that hydrodynamic conditions alone can impact fish physiology and microbiota, and that flow can exacerbate MPs accumulation and toxicity through multiple biological pathways, emphasizing the imperative for extensive research efforts to confirm these relationships within aquatic ecological systems.},
}

@article {pmid41499519,
year = {2026},
author = {Ocampo Morales, BN and Hernández Montes, A and Estrada, K and Valadez Moctezuma, E},
title = {Physicochemical and microbiome changes in queso Crema de Chiapas during ripening.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0323038},
doi = {10.1371/journal.pone.0323038},
pmid = {41499519},
issn = {1932-6203},
mesh = {*Microbiota ; *Cheese/microbiology/analysis ; Bacteria/genetics/classification/isolation & purification ; Food Microbiology ; },
abstract = {The dynamic changes in the physicochemical, microbiological, and metagenomic profiles of Crema de Chiapas cheese were evaluated across three ripening stages (2, 29, and 58 days). Although the main physicochemical properties -including fat content- remained remarkably stable, salt and protein levels showed noticeable variation throughout ripening. Protein content had the strongest influence on sample differentiation across ripening stages in unsupervised multivariate models, enabling the clustering of microbial diversity according to maturation time. A clear shift in microbial diversity was detected, marked by a reduction in bacterial genera and a concurrent decline in fungal and yeast populations as ripening advanced. The predominant bacterial genera throughout ripening were Streptococcus, Lactobacillus, and Lactococcus. While Streptococcus and Lactobacillus increased over time, Lactococcus exhibited the opposite trend. Metagenomic analysis revealed a decrease in Candida etchellsii and a concomitant increase in Candida tropicalis as ripening progressed. Quantitative PCR (qPCR) confirmed the presence of C. etchellsii at T1 (Ct = 7.22) and C. tropicalis at T3 (Ct = 9.84). The presence of three additional bacterial genera-Chryseobacterium, Aeromonas, and Enterobacter-identified by next-generation sequencing (NGS), was also assessed by qPCR. Chryseobacterium was detected at T2 (Ct = 3.26), whereas Aeromonas and Enterobacter were absent across all stages. Collectively, these findings suggest that potentially pathogenic microorganisms were not present at biologically relevant levels.},
}

*Microbiota
*Cheese/microbiology/analysis
Bacteria/genetics/classification/isolation & purification
Food Microbiology

@article {pmid41499160,
year = {2026},
author = {Hai, Q and Li, D and Huang, T and Dang, X and Xu, J and Ma, Z and Zhou, Z},
title = {The Honeybee Gut Microbiome: A Novel Multidimensional Model of Antimicrobial Resistance Transmission and Immune Homeostasis from Environmental Interactions to Health Regulation.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag001},
pmid = {41499160},
issn = {1574-6976},
abstract = {The honeybee gut microbiome has emerged as a model system in microbial ecology, valued for its structural stability and host specificity, and has garnered significant attention for elucidating universal principles of host-microbe interactions. This review advocates for the honeybee as a multidisciplinary model organism, highlighting the unique role of its gut microbiota in maintaining colony immune homeostasis, driving host co-evolution, unraveling the transmission mechanisms of antibiotic resistance genes (ARGs), and enhancing host adaptability to environmental stressors. By integrating multidimensional factors, including environmental gradients and apicultural practices, we construct an "Environment-Microbiota-Host Health" interaction framework to transcend the limitations of single-factor analyses. This framework provides a novel paradigm for the ecological containment of antimicrobial resistance, the conservation of pollinator resources, and microbiome-based engineering interventions. The review underscores the unique value of the honeybee model in unraveling social insect-microbe coevolution and resistance transmission dynamics, while also prospecting its application potential in developing novel antimicrobial peptides, designing probiotic formulations, and monitoring environmental resistance.},
}

@article {pmid41499051,
year = {2026},
author = {Maulvi, FA and Desai, DT and Vyas, BA and Shah, DO and Willcox, MD},
title = {Fasting as a Multisystem Health Modulator: A Narrative Review of Metabolic, Cardiovascular, Immune, Neurocognitive, and Psychospiritual Effects.},
journal = {Current nutrition reports},
volume = {15},
number = {1},
pages = {4},
pmid = {41499051},
issn = {2161-3311},
mesh = {Humans ; *Fasting/physiology/psychology ; Gastrointestinal Microbiome/physiology ; *Cognition/physiology ; Immune System/physiology ; Energy Metabolism ; Cardiovascular System/metabolism ; Circadian Rhythm ; Cardiovascular Diseases/prevention & control ; },
abstract = {BACKGROUND: Fasting, practiced in clinical, cultural, and faith-based contexts, has emerged as a non-pharmacological strategy capable of modulating multiple physiological systems. Contemporary evidence suggests that diverse fasting patterns (intermittent and time-restricted fasting, Ramadan fasting, alternate-day and periodic fasting, dry fasting, and fasting-mimicking diets) converge on shared metabolic-circadian-immune pathways and can be conceptualized within an integrated resilience framework.

AIM: This narrative review synthesizes current experimental and human data on fasting as a multisystem health modulator, linking metabolic, cardiovascular, immune, gut-liver-microbiome, neurocognitive, endocrine, and psychospiritual effects to common regulatory axes, particularly the Metabolic-Circadian-Immune (MCI) and Energy-Information-Resilience (EIR) models.

RESULTS: Across fasting modalities, activation of energy-sensing pathways (AMPK-SIRT1-mTOR), metabolic switching to lipolysis and ketogenesis, enhanced autophagy/mitophagy, and improved insulin sensitivity have been shown to support the management of obesity, type 2 diabetes, dyslipidemia, hypertension, and non-alcoholic fatty liver disease. Fasting also modulates immune and inflammatory tone, reshapes the gut microbiome, and may benefit autoimmune conditions such as rheumatoid arthritis and multiple sclerosis. Cardiovascular, endocrine, and neurocognitive domains show improvements in blood pressure, lipid profiles, neurotrophic signaling, mood, and cognitive resilience, while structured religious fasting (e.g., Ramadan) can additionally reinforce psychological discipline and spiritual well-being. At the same time, responses are heterogeneous, and prolonged or intensive regimens may pose risks in vulnerable populations.

CONCLUSION: Fasting can be viewed as a low-cost, multidimensional "biopsychospiritual" health intervention acting through interconnected metabolic, circadian, immune, and neurobehavioral pathways. By integrating traditional and religious fasting practices with contemporary mechanistic and clinical data, this review highlights shared energy- and immune-regulatory axes and underscores the potential of fasting within integrative, preventive, and personalized care. Standardized protocols, long-term outcomes, and multimodal trials combining immunophenotyping, microbiome/metabolomic profiling, and neuroimaging remain priorities for future research.},
}

Humans
*Fasting/physiology/psychology
Gastrointestinal Microbiome/physiology
*Cognition/physiology
Immune System/physiology
Energy Metabolism
Cardiovascular System/metabolism
Circadian Rhythm
Cardiovascular Diseases/prevention & control

@article {pmid41498979,
year = {2026},
author = {Tischer, J and Dietze, N and Marx, K and Trawinski, H and Lübbert, C},
title = {[New antimicrobial substances to combat increasing resistance].},
journal = {Innere Medizin (Heidelberg, Germany)},
volume = {},
number = {},
pages = {},
pmid = {41498979},
issn = {2731-7099},
abstract = {Increasing antimicrobial resistance (AMR) is one of the greatest threats to global health. In 2021, 4.71 million deaths worldwide were closely associated with AMR, and 1.14 million deaths could be directly attributed to infections caused by multidrug-resistant organisms (MDROs), particularly multidrug-resistant Gram-negative bacteria (MDRGN). Enterobacterales (e.g., Escherichia coli and Klebsiella spp.) resistant to third-generation cephalosporins and carbapenems, multidrug-resistant Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii (CRAB) have been identified by the World Health Organization as the most problematic pathogens. In addition to new diagnostic methods for the rapid identification of AMR, several new antibiotics have been approved in the last 10 years, expanding the treatment options, particularly for MDRGN infections. Pharmaceutical strategies have so far focused primarily on modifying already known classes of antibiotics with the aim of circumventing class-specific resistance mechanisms and reducing resistance rates. In addition to cefiderocol, the first siderophore cephalosporin, new combinations of β‑lactam antibiotics and β‑lactamase inhibitors (BLIs) such as ceftolozan/tazobactam, ceftazidime/avibactam, cefepime/enmetazobactam, imipenem/cilastatin/relebactam, and meropenem/vaborbactam, as well as the monobactam/BLI combination aztreonam/avibactam, have been approved and successfully implemented in clinical care. In addition, there is the synthetic tetracycline antibiotic eravacycline, which has a broad spectrum of activity against Gram-positive, Gram-negative (particularly clinically relevant Enterobacterales), anaerobic, and multidrug-resistant bacteria, and the new glycopeptide antibiotic dalbavancin, which is effective against Gram-positive bacteria. Since a change in legislation in 2021, the Joint Federal Committee (Gemeinsamer Bundesausschuss, G‑BA) in Germany has been authorized to classify newly approved antibiotics as reserve antibiotics. This classification allows for an exception to the regular additional benefit assessment as part of the early benefit assessment. The pipeline of antibiotics in development with novel targets and chemical structures-which had almost completely dried up-has been re-filled with new candidates for clinical trials. Some of these agents have already been tested with promising results in smaller phase 1/2 studies. In addition, monoclonal antibodies, antimicrobial peptides, small molecules, microbiome-modifying biotherapeutics, and bacteriophages, all enabling targeted and personalized treatment, are currently being investigated in studies.},
}

@article {pmid41498910,
year = {2026},
author = {Li, Y and Shen, X and Wang, D and Sun, K},
title = {The gut microbiome in colorectal cancer: mechanisms of carcinogenesis and emerging microbiota-targeted therapies.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-025-04367-1},
pmid = {41498910},
issn = {2730-6011},
}

@article {pmid41498848,
year = {2026},
author = {Protachevicz, AP and Boldt, ABW and Pileggi, M},
title = {The microbiota-epigenome axis in healthy longevity: roles of microbial and gerobiotic metabolites - a narrative exploratory review.},
journal = {Biogerontology},
volume = {27},
number = {1},
pages = {34},
pmid = {41498848},
issn = {1573-6768},
support = {process 8888.7.884402/2023-00.//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; process 307602/2025-7.//CNPq Productivity Fellowship/ ; },
mesh = {Humans ; *Longevity/genetics/physiology ; *Gastrointestinal Microbiome/physiology ; *Epigenesis, Genetic ; *Healthy Aging/genetics ; Animals ; *Aging ; },
abstract = {Aging is a dysbiotic and pro-inflammatory process that increases susceptibility to multiple chronic comorbidities. Centenarians and supercentenarians offer a unique biological model for elucidating the molecular determinants of healthy aging and exceptional longevity, as they display distinctive epigenetic signatures and a gut microbiome configuration that diverges from both younger and typically aging individuals, although substantial interindividual variability exists. The gut microbiota constitutes a strategic hub of microorganisms and bioactive metabolites with probiotic and postbiotic potential that modulate host epigenetic circuits through precursors and substrates for epigenetic "writer" and "eraser" enzymes, thereby shaping the aging trajectory. In this review, we examine the interactions between the microbiota and its metabolites, including short-chain fatty acids, lipopolysaccharides, trimethylamine N-oxide (TMAO), p-cresol, and secondary bile acids, and their roles in epigenetic modulation associated with healthy aging. We highlight (i) the attenuation of classical pro-inflammatory pathways through downregulation of NF-κB/COX-2, modulation of the Th17/Treg balance, and also the lower systemic LPS levels of centenarians, which are associated with enhanced SIRT1 activity (↑LPS/↓SIRT1); (ii) the reprogramming of energy metabolism via activation of SIRT1/AMPK and SIRT1/p-53, modulation of mTOR, and attenuation of the IGF-1/insulin axis; (iii) the strengthening of the intestinal barrier through upregulation of tight junction proteins such as ZO-1, occludin, and claudins, resulting in reduced permeability and zonulin levels; and (iv) the optimization of antioxidant defenses. Collectively, these findings suggest translational potential for microbiota-derived metabolites in gerobiotic strategies, although clinical evidence remains limited.},
}

Humans
*Longevity/genetics/physiology
*Gastrointestinal Microbiome/physiology
*Epigenesis, Genetic
*Healthy Aging/genetics
Animals
*Aging

@article {pmid41498557,
year = {2026},
author = {Zhao, Y and Gao, K and Shang, Y and Cheng, S and Ren, Q and Guo, F and Wang, Y},
title = {Clostridium butyricum RH2 ameliorates diarrhea in juvenile mice under continuous antibiotic exposure by modulating gut microbiota and metabolome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0197625},
doi = {10.1128/spectrum.01976-25},
pmid = {41498557},
issn = {2165-0497},
abstract = {Antibiotic-associated diarrhea (AAD) is a self-limiting disorder triggered by antibiotic therapy in pediatric populations. Although multiple probiotics are clinically employed for AAD management, the therapeutic efficacy of Clostridium butyricum (C. butyricum) in pediatric AAD and its underlying mechanisms remain poorly characterized. This study aimed to establish a juvenile mice model of AAD and investigate the therapeutic potential of oral C. butyricum administration in juvenile mice subjected to continuous antibiotics exposure. We systematically assessed pathological changes in colonic tissue, colitis severity, intestinal epithelial barrier integrity, fecal metabolomic profiles, and gut microbiota diversity. Our analysis demonstrates that C. butyricum ameliorates intestinal inflammation, enhances barrier function by modulating the gut microbiota and its metabolites, and significantly alleviates diarrhea symptoms in juvenile AAD mice. Collectively, these findings indicate that the therapeutic benefits of C. butyricum are closely linked to its ability to tolerate continuous antibiotic exposure, providing a scientific rationale for its co-administration with antibiotics.IMPORTANCEClostridium butyricum demonstrates significant therapeutic potential for pediatric antibiotic-associated diarrhea (AAD) by dual modulation of gut microbiota and host physiology. This study reveals its capacity to alleviate intestinal inflammation, restore barrier integrity via upregulation of tight junction proteins and mucins, and rebalance gut microbiota linked to key anti-inflammatory metabolites-even under ongoing antibiotic exposure. These findings position C. butyricum as a targeted probiotic therapy for AAD, offering mechanistic insights to advance microbiome-driven interventions for antibiotic-induced diarrhea in children.},
}

@article {pmid41498552,
year = {2026},
author = {Schussman, MK and Feng, S and Schmoldt, A and Bootsma, MJ and Dennis, K and Janssen, KH and McLellan, SL},
title = {Environmental reservoirs account for high levels of carbapenem resistance genes in wastewater.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173725},
doi = {10.1128/spectrum.01737-25},
pmid = {41498552},
issn = {2165-0497},
abstract = {UNLABELLED: Wastewater surveillance has moved to the forefront as a practical and informative public health tool for assessing viral and bacterial pathogens in the human population; however, the usefulness for tracking antimicrobial-resistance genes (ARGs) of clinical concern is not straightforward given the large reservoir of free-living bacteria within sewer systems. In this study, we examined six high-priority carbapenem resistance gene targets and common host organisms in wastewater collected from two treatment plants. Polymerase chain reaction (PCR)-based assays demonstrated an extremely high abundance of blaKPC, blaOXA-24/40, and blaOXA-48 with mean concentrations as high as 3.55E+06 copy number (cn)/L for blaKPC. In addition, blaVIM and blaIMP were detectable in ~99% of samples at lower levels of ~1.5E+05 cn/L and 1.0E+04 cn/L, respectively. The target blaNDM was readily detected but quantifiable in only 49% of samples with levels of ~1.0E+03 cn/L. Each PCR target showed one to two dominant sequence types that matched exactly to reported clinical strains, indicating that high levels could not be attributed to non-specific amplification. Select ARG targets showed moderate-to-weak correlations to human fecal markers and Klebsiella pneumoniae or Escherichia coli, whereas blaOXA-24/40 most closely correlated to Acinetobacter baumannii. The two treatment plants showed different dynamics, suggesting that the inherent characteristics of the individual conveyance systems influence concentrations. Culture on selective media revealed an abundance of Aeromonas in addition to sporadic Enterobacteriaceae carrying blaKPC. Understanding the ecological dynamics of bacteria harboring ARGs will be important for understanding reservoirs and interpreting wastewater surveillance data.

IMPORTANCE: Wastewater surveillance for carbapenem-resistant bacteria has been proposed as a potentially valuable tool for assessing the human burden, but their distribution in environmental reservoirs is not well understood. Untreated sewage contains a high density of resident organisms mixed with human inputs, which are transported through the complex environment of sewer conveyance systems. In addition to resident microbial community members, organisms seeded into the system from the human microbiome have the potential to grow. This work shows that environmental bacteria may be a significant source of carbapenem resistance genes collected from sewer systems, making wastewater surveillance data difficult to interpret or use for public health actions. More knowledge is needed to unravel the ecology of these systems and identify targets for surveillance that are meaningful to clinicians. This work sheds light on the complex dynamics and confounding factors for antimicrobial-resistance gene wastewater surveillance, which will improve the interpretation of wastewater surveillance data.},
}

@article {pmid41498506,
year = {2025},
author = {He, L and He, Z and Zhang, Y and Wu, F and Liu, H and Liu, XG and Zheng, DX and Shao, RQ and Hu, L and Jiang, QS},
title = {Divergent Oral Microbiome after Rinsing with of H2O2, Chlorhexidine and Essential Oil Mouthrinses: a Proof of Principle Study.},
journal = {The Chinese journal of dental research},
volume = {28},
number = {4},
pages = {297-305},
doi = {10.3290/j.cjdr.b6745473},
pmid = {41498506},
issn = {1867-5646},
mesh = {Humans ; *Mouthwashes/pharmacology ; *Chlorhexidine/pharmacology ; *Oils, Volatile/pharmacology ; *Hydrogen Peroxide/pharmacology ; *Microbiota/drug effects ; Male ; Adult ; Female ; Saliva/microbiology ; *Mouth/microbiology ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Anti-Infective Agents, Local/pharmacology ; },
abstract = {OBJECTIVE: To compare the effects on the oral microbiome after rinsing with hydrogen peroxide (H2O2), chlorhexidine and essential oil mouthrinses and identify formulations that suppress pathogenic bacteria while preserving beneficial species and maintaining oral microbial bal-ance.

METHODS: Twelve healthy volunteers were randomly assigned to three groups: H2O2, chlorhexi-dine and essential oil mouthrinse. Saliva samples were collected at three time points: before and 5 minutes and 1 hour after rinsing with mouthrinse. Microbiome composition was analysed using 16S rRNA gene sequencing.

RESULTS: Alpha and beta diversity showed no statistically significant differences among time points. The genus-level microbiome composition remained relatively stable in the H2O2 and essential oil groups but changed significantly in the chlorhexidine group. In the H2O2 group, Neisseria decreased significantly, while Actinomyces increased. In the chlorhexidine group, Porphyromonas, Veillonella, Streptococcus, Neisseria and Gemella decreased significantly. In the essential oil group, Leptotrichia decreased, and Haemophilus increased significantly.

CONCLUSION: Essential oil mouthrinse and chlorhexidine exhibit stronger bacteriostatic effects against oral pathogens than H2O2. However, chlorhexidine may disrupt microbial equilibrium, whereas essential oil mouthrinse more effectively preserves a stable oral microbiome. Thus, es-sential oil mouthrinse could serve as a viable alternative to chlorhexidine for oral microbiome management, though its long-term efficacy requires further investigation.},
}

Humans
*Mouthwashes/pharmacology
*Chlorhexidine/pharmacology
*Oils, Volatile/pharmacology
*Hydrogen Peroxide/pharmacology
*Microbiota/drug effects
Male
Adult
Female
Saliva/microbiology
*Mouth/microbiology
Young Adult
RNA, Ribosomal, 16S/genetics
Anti-Infective Agents, Local/pharmacology

@article {pmid41498123,
year = {2026},
author = {Ladewig, L and Kinfu, BM and Fokt, H and Bethge, H and Tufail, MA and Baines, JF and Schmitz, RA},
title = {Exploring Bacteroidota strains from human stool and animal feces: phenotyping and functional diversity.},
journal = {microLife},
volume = {7},
number = {},
pages = {uqaf039},
pmid = {41498123},
issn = {2633-6693},
abstract = {Bacteroidota, a diverse phylum of bacteria, includes classes whose members are increasingly recognized for their significant contributions to host health, particularly through their antimicrobial properties. This study investigates the functional diversity of 42 new Bacteroidia and Sphingobacteriia strains enriched and identified from diverse hosts, including mouse ceca and human stool samples. Using 16S rRNA gene sequencing, we phylogenetically characterized the strains of the genera Bacteroides, Phocaeicola, and Sphingobacterium and assessed their functional properties related to potential beneficial functions. The strains were evaluated concerning their ability to inhibit biofilm formation of the World Health Organization-declared clinically significant pathogens, including Gram-positive Staphylococcus aureus and Staphylococcus epidermidis, Gram-negative Klebsiella oxytoca and Pseudomonas aeruginosa, and the eukaryotic yeast Candida albicans. Additionally, we investigated bile salt hydrolase and quorum-quenching (QQ) activities of the strains, as these functions contribute to microbial community interactions and host-microbe dynamics. Our findings demonstrate that all examined Bacteroidota strains consistently exhibit a capacity to inhibit biofilm formation but to different extents. Furthermore, 14 strains showed QQ activity, and 39 bile salt hydrolase activity, indicating functional diversity among the isolates. High biofilm inhibition as well as QQ activity against both autoinducers, AHL and AI-2, were predominantly observed in Bacteroides caecimuris and Bacteroides muris. These traits suggest that such strains may play important roles in shaping microbial communities and interfering with pathogens and their communication. Overall, this study provides valuable insights into strain-specific functions that could support future microbiome-based strategies for pathogen control and host health modulation.},
}

@article {pmid41497693,
year = {2025},
author = {Rusman, RD and Akil, F and Parewangi, ML and Daud, NA and Bachtiar, R and Kusuma, SH and Rifai, A},
title = {Gut microbiota and metabolic-associated steatosis liver disease: Unveiling mechanisms and opportunities for therapeutic intervention.},
journal = {World journal of experimental medicine},
volume = {15},
number = {4},
pages = {107316},
pmid = {41497693},
issn = {2220-315X},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) has become a leading cause of chronic liver disease, closely linked with metabolic syndrome. Recent evidence spotlights the gut-liver axis as a major player in MASLD pathogenesis. Dysbiosis of gut microbiota alters the intestinal barrier and enhances endotoxemia, hepatic inflammation, insulin resistance and fibrosis. Microbial metabolites including short-chain fatty acids, bile acids and ethanol impact host metabolism and immunity, and their dysregulation contributes to disease progression. This review summarises the mechanistic associations between dysbiosis and MASLD involving altered microbial composition, leaky gut, toll-like receptor signalling and immune dysregulation. It also reviews microbially targeted therapeutic strategies, such as probiotics, prebiotics, synbiotics, faecal microbiota transplantation, diet changes, and postbiotic metabolites. Although these interventions may have clinical potential, the heterogeneity of outcomes highlights the interindividual nature of the microbiome and warrant personalized interventions. Developments in multi-omics and precision medicine provide possibilities to discover microbial biomarkers and customize therapeutic approach. Resolving methodological heterogeneity and providing a clear definition of MASLD-related dysbiosis are key for translating microbiome science into the clinic. In conclusion, modulation of gut microbiota is an emerging strategy for the adjunctive treatment of MASLD alongside lifestyle and pharmacologic therapies.},
}

@article {pmid41497648,
year = {2025},
author = {Trepka, KR and Van Blarigan, EL and Kyaw, TS and Olson, CA and Partipilo, G and Ortega, EF and Noecker, C and Upadhyay, V and Zhang, C and Gempis, D and Steiding, P and Stanfield, D and Venook, AP and Atreya, CE and Kidder, WA and Turnbaugh, PJ},
title = {Shifts in the human gut microbiome during cancer chemotherapy are diet-dependent.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41497648},
issn = {2692-8205},
abstract = {Numerous studies have implicated both dietary intake and the human gut microbiome in colorectal cancer (CRC) treatment outcomes. However, little is known about how patients adjust their dietary intake during cancer chemotherapy or if these dietary changes contribute to treatment-associated alterations in the gut microbiome. We performed paired longitudinal diet and microbiome analysis during CRC treatment with oral fluoropyrimidines (NCT04054908) and validated key associations using cell culture assays. Diet quality significantly decreased during chemotherapy. Carbohydrate and refined grain intake increased, accompanied by decreased consumption of fats, nuts and seeds, and fat-soluble micronutrients. Multiple individual dietary components were strongly linked to the gut microbiome. Decreases in theobromine intake correlated with decreases in overall microbial diversity and more gastrointestinal toxicities. Diet shifts partly explained changes in bacterial abundance during chemotherapy, including more severe depletion of Faecalibacterium prausnitzii in patients with decreased vitamin K1 intake. Changes in diet were correlated with multiple bacterial gene families involved in micronutrient metabolism and drug sensitivity. Increased copper intake was linked to decreased Fusobacterium nucleatum in patients and inhibited F. nucleatum in cell assays. Together, these data suggest that chemotherapy-related decreases in diet quality and micronutrient intake contribute to changes in gut bacterial diversity, taxonomic composition, and gene abundance. Our approach may generalize to other cancer therapies and emphasizes the need for collecting more robust dietary data in clinical microbiome studies.},
}

@article {pmid41497646,
year = {2025},
author = {Anyaso-Samuel, SC and Li, S and Herrera-Ossa, G and Vogtmann, E and Wang, X and Hua, X and Qin, F and Zhao, W and Rahman, M and Yang, X and Brown, K and Zhu, B and Moore, S and Abnet, C and Zhang, T and Landi, MT and Yu, K and Albert, P and Shi, J},
title = {Identifying High-Dimensional Genomic Factors Modulating Biological Networks Across Multi-Omics Data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.18.695273},
pmid = {41497646},
issn = {2692-8205},
abstract = {Biological traits such as genes, metabolites, and microbial taxa interact within complex networks, yet how genomic factors shape these interactions remains poorly understood. Here, we introduce GFBioNet, a computationally efficient method for identifying factors that modulate direct associations between biological traits within network models. Our two-stage strategy first estimates a baseline network using Gaussian graphical models and then tests whether genomic factors modulate specific network edges (trait-trait relationships), enabling scalable analysis of high-dimensional multi-omics data while explicitly controlling the false discovery rate (FDR). Simulations demonstrate reliable FDR control and high statistical power across a broad range of settings. Applied to multiple datasets, GFBioNet reveals host genetic variants influencing oral microbiome relationships, gut microbial taxa modulating metabolite networks in colorectal cancer, and somatic mutations and copy-number alterations reshaping gene expression networks in lung adenocarcinoma. By expanding network analysis to evaluate modifiers of trait-trait relationships, GFBioNet offers a versatile tool for uncovering the genomic architecture of biological networks across multi-omics studies.},
}

@article {pmid41497638,
year = {2025},
author = {Liou, CS and Louwies, T and Iakiviak, M and Rajniak, J and Murugkar, PP and Higginbottom, SK and Weakley, A and Meng, X and Htet, P and Cabrera, AV and Jasper, M and Dimas, A and Schulman, EA and Fischbach, MA and Kashyap, PC and Sattely, ES},
title = {Gut microbiota gate host exposure to cholinesterase inhibitors from dietary Solanums.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.20.584512},
pmid = {41497638},
issn = {2692-8205},
abstract = {Dietary plants are molecularly rich but the fates of these compounds post-ingestion and their implications for human health are largely unknown. Here, we systematically characterized the major chemical contributions of widely consumed Solanum species (nightshades) to the human metabolome. Using untargeted metabolomics, we found that a series of steroidal alkaloids resulting from glycoalkaloids tomatine, solanine, and chaconine are dominant diet-derived compounds in systemic circulation following ingestion of tomato and potato. By comparing serum and tissue metabolomes of colonized and microbiome-depleted mice, we determined that the gut microbiota modifies these compounds extensively, altering their absorption and gating host exposure. By screening the metabolic products in human urine and stool samples, we established that steroidal glycoalkaloid metabolism varies inter-individually in a population. Furthermore, using a collection of representative human commensal type strains, we found that a limited set of strains is responsible for steroidal glycoalkaloid metabolism, with the chemical output of a community determined by its strain-level composition. These findings enabled the rational design of complex synthetic microbial communities that controlled host exposure to steroidal alkaloid metabolites in vivo . Importantly, microbial metabolism of Solanum metabolites alters their acetylcholinesterase inhibition in vitro and gut motility in vivo . Our study provides insights into the molecular mechanisms of a diet-microbiome interactions and the effects of dietary metabolites on host physiology.},
}

@article {pmid41497462,
year = {2025},
author = {Dunisławska, A and Bełdowska, A and Yatsenko, O and Biesek, J and Siwek, M},
title = {Molecular response in the pectoral muscles and livers of broiler chickens to mitochondrial stimulation by in ovo administration of prebiotics.},
journal = {Journal of veterinary research},
volume = {69},
number = {4},
pages = {639-646},
pmid = {41497462},
issn = {2450-7393},
abstract = {INTRODUCTION: Mitochondria are the primary sites for adenosine triphosphate production through oxidative phosphorylation, thus supporting the high metabolic demands of avian physiology. By administering prebiotics in ovo, the aim was to analyse how an early host-supporting strategy can modulate mitochondrial activity and affect the physicochemical composition of the pectoral muscles of chickens.

MATERIAL AND METHODS: Three hundred incubated Ross 308 broiler eggs were injected: 60 with 0.2 mL of 0.2 mmol/L physiological saline (control group), and 60 each with 0.5 mg of xylotriose (XOS3 group), xylotetraose (XOS4 group), mannotriose (MOS3 group) or mannotetraose (MOS4 group) carried in 0.2 mL of physiological saline. On day 42 after hatching, the liver and pectoral muscle were collected from eight individuals from each group after sacrifice, and the muscle was evaluated physicochemically. Relative mitochondrial DNA (mtDNA) copy numbers were analysed in a real-time quantitative PCR (qPCR). Gene expression was determined by a reverse-transcription qPCR (RT-qPCR) for a mitochondrial gene panel.

RESULTS: The experimental factor was not shown to affect pectoral muscle weight. Water loss was significantly greater in the XOS4 group's muscles. The overall mtDNA copy number was stable in both tissues. The XOS3 and MOS4 groups' gene expression was significantly changed in pectoral muscle. Contrastingly, the XOS4 and MOS3 groups' gene expression was more altered in the liver. Statistically significantly different expression was detected of the CS, EPX, CYCS, TFAM and NRF1 genes in pectoral muscles and of all tested genes in livers.

CONCLUSION: The potential of in ovo prebiotic administration is indicated as a strategic approach to optimise mitochondrial function, ultimately contributing to better growth rates and enhanced health in broiler chickens.},
}

@article {pmid41497397,
year = {2025},
author = {Miyauchi, E and Yamaoka, M and Kamimura, I and Mizuta, M and Takenaka, M and Akiyama, U and Kawasumi, M and Sasaki, N and Ohno, H and Ando, S and Yamasaki, S and Nishida, A and Mogi, K and Nagasawa, M and Kikusui, T},
title = {Dog ownership during adolescence alters the microbiota and improves mental health.},
journal = {iScience},
volume = {28},
number = {12},
pages = {113948},
pmid = {41497397},
issn = {2589-0042},
abstract = {Adolescents who own dogs have higher well-being than those who do not; however, it is unclear what the underlying mechanism explains how dog ownership affects adolescents' well-being. As dog ownership influences the composition of the microbiota in the home environment, we examined the microbiome of dog-owning adolescents and analyzed associations with mental health and behavior in the teenage cohort participants (n = 345). Our findings reveal that dog-owning adolescents showed fewer problems with psychological scores, and some commensals were correlated with adolescents' psychological scores. Mice treated with the microbiota of dog-owning adolescents showed a higher social approach to a trapped cagemate. An association analysis was conducted between the adolescents' psychological scores and the mouse behavior with the abundance of each amplicon sequence variant (ASV) of the microbiome, and we found that ASVs belonging to Streptococcus were correlated with the social approach in ex-germ-free mice and mental scores in adolescents. These results suggest that microbiota may be partly involved in improving the well-being of adolescents living with dogs.},
}

@article {pmid41497367,
year = {2025},
author = {Aftab, G and Arab, P and Faranoush, P},
title = {A Comparative Study on the Impact of FIV and FeLV Infection on the Ocular Microbiota in Persian Cats: Insights From Co-Infection and Single Infections.},
journal = {Veterinary medicine international},
volume = {2025},
number = {},
pages = {8146795},
pmid = {41497367},
issn = {2090-8113},
abstract = {BACKGROUND: The ocular microbiome of cats infected with feline immunodeficiency virus (FIV) or feline leukemia virus (FeLV) might differ from that of healthy cats. This study aimed to examine and compare the conjunctival bacterial and fungal flora in these groups.

METHODS: Bacterial and fungal cultures were conducted from the conjunctiva of 80 Persian cats, categorized into four groups: normal, FIV-infected, FeLV-infected, and co-infected with both FIV and FeLV. PCR assays confirmed the presence of FIV, FeLV, Chlamydia, and Mycoplasma. The microbiological analysis was compared across the different.

RESULTS: The conjunctival bacterial flora of normal cats was predominantly Gram-positive, with Staphylococcus species as the most common isolates. Escherichia coli was absent in the normal group but present in all infected groups, with the highest prevalence in the co-infected group (17.5%). Co-infection with FIV and FeLV led to a distinct microbiota with Streptococcus agalactiae, Corynebacterium renale, Fusarium, and Aspergillus brasiliensis exclusively found in this group.

CONCLUSIONS: The co-infection of FIV and FeLV significantly alters the conjunctival microbiome, promoting the colonization of specific opportunistic pathogens. These findings may influence the clinical management of cats with these viral infections, especially in combination, and may create a more favorable environment for the growth of certain bacteria and fungi in the conjunctiva.},
}

@article {pmid41497166,
year = {2026},
author = {Mehmood, MS and Danaf, N},
title = {Bacteroides fragilis toxin in colorectal tumors activates STAT3 and drives microsatellite instability.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {957-958},
pmid = {41497166},
issn = {2049-0801},
abstract = {Colorectal cancer (CRC) remains a global malignancy with over 1.9 million new cases annually. Emerging evidence implicates enterotoxigenic Bacteroides fragilis (ETBF) and its toxin (BFT) in activating STAT3 and promoting microsatellite instability (MSI), a novel microbial oncogenic axis. In analyses of more than 1200 CRC tumors, B. fragilis abundance correlated with a 2.14-fold higher MSI-high frequency and increased CpG island methylator phenotype. Mechanistically, BFT triggers E-cadherin cleavage, β-catenin activation, and IL-6/IL-17 up-regulation, fostering inflammation, oxidative stress, and mismatch-repair suppression. Animal models demonstrate a more than 60% rise in tumor burden following ETBF colonization, while human studies show B. fragilis present in about 80% of CRC tissues versus 50% of controls. These findings establish BFT-induced STAT3 signaling as a driver of genomic instability and tumor evolution. Targeting this pathway offers new prospects for biomarker development and precision therapy in colorectal cancer.},
}

@article {pmid41497144,
year = {2026},
author = {Mehmood, MS and Qasim, Z and Rauf, S and Danaf, N},
title = {Intratumoral Fusobacterium nucleatum metabolizes chemotherapy before it reaches cancer cells.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {939-940},
pmid = {41497144},
issn = {2049-0801},
abstract = {Fusobacterium nucleatum (Fn) has emerged as a crucial microbial determinant of chemotherapeutic failure in colorectal cancer. Detected in nearly 50% of all colorectal tumors, its presence is consistently associated with poorer prognosis and higher recurrence rates. Recent translational studies demonstrate that Fn metabolically interferes with cytotoxic drugs such as 5-fluorouracil and oxaliplatin, reducing active drug availability by up to 45%. This bacterium expresses nitroreductases and oxidoreductases capable of enzymatic inactivation, while its dense biofilms further hinder drug diffusion within the tumor microenvironment. Experimental depletion of Fn restores intratumoral drug levels and enhances tumor regression by approximately 60%, underscoring its direct role in metabolic resistance. Clinically, Fn-positive patients show diminished chemotherapy response and heightened inflammatory profiles. These findings collectively highlight that intratumoral microbiota, particularly Fn, can metabolize or neutralize chemotherapeutics before they reach cancer cells, an overlooked mechanism that challenges current cancer treatment paradigms.},
}

@article {pmid41497134,
year = {2026},
author = {Mehmood, MS and Abid, M and Hajj, F},
title = {Engineered Lactobacillus expressing tumor-killing cytokines: a novel biotherapeutic.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {1040-1041},
pmid = {41497134},
issn = {2049-0801},
abstract = {Cancer accounts for over 10 million deaths annually, with solid tumors responsible for nearly 90% of cases worldwide. Systemic cytokine administration remains limited by severe toxicity, high-dose interleukin-2 (IL-2) therapy induces grade 3-4 adverse effects in >60% of patients, and treatment-related mortality is around 4%. In this context, engineered Lactobacillus strains designed to express tumor-killing cytokines such as IL-12, IL-15, and TRAIL represent a novel biotherapeutic strategy that combines microbial safety with precision immune activation. Experimental evidence shows that Lactobacillus plantarum secreting IL-12 reduces colorectal tumor volume by 65%, L. casei expressing TRAIL decreases pancreatic tumor mass by 40%, and L. reuteri producing IL-15 enhances CD8+ T-cell infiltration by 45% and improves survival by 30% in murine models. These data illustrate that cytokine-expressing probiotics can replicate the efficacy of systemic cytokine therapy while avoiding dose-limiting toxicity. Integrating synthetic biology tools such as inducible promoters and biosafety kill switches further refines control and containment, making this a viable candidate for translational development. The convergence of immunotherapy and microbiome engineering thus establishes engineered Lactobacillus as a novel, locally acting, and low-toxicity antitumor biotherapeutic with the potential to reshape next-generation cancer treatment.},
}

@article {pmid41353192,
year = {2025},
author = {Hamann, LK and Washburn, RL and Makii, M and Brown, E and Hampton, M and Schlabritz-Lutsevich, N and Ventolini, G and Rumbaugh, KP and Tipton, C and Redman, WK},
title = {Microbial load and composition of intrauterine device string correlates with symptomatic removals in parous women.},
journal = {Contraception and reproductive medicine},
volume = {11},
number = {1},
pages = {5},
pmid = {41353192},
issn = {2055-7426},
abstract = {BACKGROUND: A contraceptive intrauterine device (IUD) is a US Food and Drug Administration (FDA) approved method of contraception that is effective and generally well tolerated by patients. However, reports show that IUDs might be associated with inflammation, leading to symptoms like abnormal bleeding and pelvic pain. Pelvic inflammation potentially could be linked to IUD pathogenic biofilm colonization. However, the role of non-pathological microbial communities in this context is not well understood. The aim of the present observational study was to describe the microbiome of the IUD string located in the vagina and cervix in patients with and without IUD related complications.

METHODS: Patients being seen for the removal of their IUD were identified for this study and were grouped according to removal for ‘asymptomatic’ or ‘symptomatic’ reasons. Asymptomatic removals included IUD expiration and desire to conceive while symptomatic removals stemmed from patient complaints, including abnormal bleeding, pelvic pain, and vaginitis. The IUD strings were sent for microbiome profiling by 16S ribosomal ribonucleic acid (rRNA) gene sequencing to characterize bacterial composition and universal 16S quantitative polymerase chain reaction (qPCR) to estimate bacterial bioburden. Microbial composition was compared to determine if symptomatic IUD removal was associated with altered bacterial load, diversity, or composition, with an emphasis on Lactobacillus and non-Lactobacillus abundance.

RESULTS: Asymptomatic removals (group A, n = 8) had higher parity (p = 0.012) while relative abundance of Lactobacilli did not differ between groups (p = 0.57). Group A demonstrated a higher abundance of Lactobacillus reuteri compared to symptomatic removals (group S, n = 5), which showed increased overall bacterial load (p = 0.011) and a greater relative abundance of non-Lactobacillus species (p = 0.054), including potentially pathogenic genera such as Fusobacterium and Haemophilus.

CONCLUSIONS: This study revealed differences in bacterial populations associated with symptomatic IUD removal with a higher overall bacterial burden and abundance of non-Lactobacillus genera. Though the current study is not powered to make conclusions on whether different types of IUDs have differential microbiota or how IUD type relates to complications, these results suggest that the microbiome may contribute. Future research should investigate bacterial composition through the duration of IUD use as well as the variation of the bacterial composition on the different components of the IUD device and explore the potential of targeted intervention with probiotics or antibiotics to prevent or reduce complications associated with IUD contraception.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40834-025-00413-z.},
}

@article {pmid41497123,
year = {2026},
author = {Mehmood, MS and Hajj, F},
title = {Noninvasive early detection of colorectal cancer through gut microbiome-derived biomarkers.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {997-998},
pmid = {41497123},
issn = {2049-0801},
abstract = {Colorectal cancer (CRC) remains a major global burden, with 1.9 million new cases and 935000 deaths reported in 2024. Despite available screening tools, nearly 45% of cases are still diagnosed at advanced stages, where the 5-year survival rate falls below 14%, compared to >90% in early detection. The limitations of colonoscopy its invasiveness, cost, and poor compliance (<40% globally) demand innovative, noninvasive diagnostic solutions. Gut microbiome profiling has recently emerged as a transformative approach, with specific bacterial signatures such as Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus anaerobius showing AUC values between 0.85 and 0.93 for early CRC identification. Integrating metagenomic and metabolomic data enhances diagnostic accuracy to 89% sensitivity and 91% specificity. Moreover, altered microbial metabolites including decreased short-chain fatty acids and elevated secondary bile acids correlate with a 2.3- to 3.1-fold higher risk of carcinogenesis. Novel CRISPR-Cas13a-based assays further allow sub-attomolar detection of microbial RNA transcripts, underscoring a new frontier in microbiome-driven cancer diagnostics. Collectively, gut microbiome-derived biomarkers represent a noninvasive, mechanistically grounded, and highly sensitive platform for early CRC detection with significant translational potential.},
}

@article {pmid41497081,
year = {2026},
author = {Mazandarani, M and Lashkarbolouk, N and Ejtahed, HS and Qorbani, M},
title = {Effect of probiotics and synbiotics on antimicrobial resistance in frequent infections: a systematic review of clinical trials.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {698-717},
pmid = {41497081},
issn = {2049-0801},
abstract = {BACKGROUND: Antibiotic resistance and recurrent infections, driven by increased antibiotic use, represent a global health problem. This study aims to evaluate the effect of probiotics and synbiotics consumption on antibiotic resistance in common infections.

METHODS: A systematic search was performed on international electronic databases (PubMed/Medline, Scopus, and Web of Science) using predefined keywords to identify relevant clinical trials published prior to 1 March 2025. Study quality was assessed, and the PRISMA 2020 guideline was followed.

RESULTS: In our systematic review, 47 studies were included. Twenty studies reported positive effects on antibiotic resistance, eradication rates, and recurrence, particularly in gastrointestinal infections. In contrast, 10 studies reported no effect, and 2 indicated a negative effect of these interventions on infection recurrence and antibiotic resistance. In three studies focusing on children, probiotics significantly lowered the risk of urinary tract infection (UTI) recurrence and antibiotic resistance. However, an adult study found that probiotics had minimal effect on UTI recurrence. Four studies examined the effect of probiotics on respiratory infections in both children and adults, showing improvements in antibiotic resistance outcomes. Three studies involving preterm infants found that probiotics could modify their gut microbiome composition, with two studies confirming this effect.

CONCLUSION: Our study indicates that incorporating probiotics and synbiotics into common infection therapy could improve antibiotic resistance, eradicate rates, minimize side effects, and boost treatment compliance. However, concerns remain regarding the potential transfer of antibiotic resistance genes via probiotics.},
}

@article {pmid41497069,
year = {2026},
author = {Mehmood, MS and Danaf, N},
title = {Microbial metabolites regulating PD-L1 and checkpoint pathways: translational implications.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {953-954},
doi = {10.1097/MS9.0000000000004267},
pmid = {41497069},
issn = {2049-0801},
abstract = {Recent advances in microbiome research reveal that microbial metabolites directly regulate programmed death ligand-1 (PD-L1) expression and influence checkpoint immunotherapy outcomes. Multi-cohort analyses of over 1300 patients show that elevated short-chain fatty acids, indole derivatives, and secondary bile acids modulate PD-L1 and T-cell activity through histone deacetylase inhibition, STAT3 phosphorylation, and aryl hydrocarbon receptor signaling. High fecal butyrate correlates with a 2.4-fold higher response rate and 6.3-month improvement in progression-free survival during PD-1 blockade. Conversely, dysbiosis-associated metabolites, including lipopolysaccharide and succinate, induce PD-L1 hyperexpression and immune resistance. Metabolomic profiling now achieves AUCs of 0.82-0.89 in predicting immunotherapy response, outperforming tumor mutational burden and PD-L1 IHC. These findings establish microbial metabolites as active immunoregulatory mediators, offering new translational strategies for microbiome-informed immunotherapy personalization and biomarker integration in oncology.},
}

@article {pmid41497008,
year = {2026},
author = {Mehmood, MS and Masood, M and Danaf, N},
title = {Engineered food-borne probiotics delivering checkpoint-inhibitor modulators.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {27-28},
pmid = {41497008},
issn = {2049-0801},
abstract = {Engineered food-borne probiotics represent an emerging food-oncomicrobiology strategy that unites synthetic biology, nutrition, and cancer immunotherapy. Preclinical models demonstrate potent antitumor effects: Lactococcus lactis secreting soluble CD80-reduced tumor growth by 64%; Escherichia coli Nissle 1917 producing PD-L1 nanobodies achieved complete regression in 50% of treated mice with a two-fold rise in CD8[+]IFNγ[+]TNFα[+] T-cell infiltration; and Lactobacillus plantarum delivering IL-2 enhanced NK-cell activity 2.5-fold and extended survival by 30%. Clinical meta-analyses reveal that gut-microbiome diversity increases checkpoint-inhibitor response by 40% and median progression-free survival by 12 months. A phase I trial in Non-Small Cell Lung Cancer (NSCLC) showed reduced immune-related colitis (from 14% to 6%) and higher response rates (36% vs 21%) with probiotic co-therapy. Remaining challenges in colonization and biosafety, together with advances in controllable genetic circuits, make edible biologics a promising, low-toxicity immunotherapeutic platform.},
}

@article {pmid41496990,
year = {2026},
author = {Saif, P and Tausif, M and Fatima, M and Imtiaz, A and Hassan, M},
title = {CRISPR-targeted microbiome modulation in rare Henoch-Schonlein purpura IgA nephropathy-gastritis: insights into the gut-kidney axis.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {1090-1091},
pmid = {41496990},
issn = {2049-0801},
}

@article {pmid41496973,
year = {2026},
author = {Mehmood, MS and Abid, M and Danaf, N},
title = {Microbiome-selective DNA Pol IIIC inhibitors in oncology infection management.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {1070-1071},
pmid = {41496973},
issn = {2049-0801},
abstract = {Oncology patients experience high rates of bacterial infection due to chemotherapy-associated mucosal injury and immunosuppression, with up to 60% developing infectious complications and 20-30% of hematopoietic transplant recipients requiring hospitalization. Broad-spectrum antibiotics, although essential, frequently induce gut microbiome dysbiosis, which is associated with recurrent infection and reduced immune checkpoint inhibitor (ICI) effectiveness. Meta-analyses indicate that antibiotic exposure near ICI initiation leads to a 30-50% decrease in overall survival and a 25-40% reduction in progression-free survival. DNA polymerase IIIC inhibitor antibiotics, including ibezapolstat, have demonstrated 88-96% clinical cure rates in Clostridioides difficile infection while preserving gut microbial diversity and limiting expansion of antimicrobial-resistant organisms. Recent conference data suggest these microbiome-sparing effects may be class-wide. This targeted antimicrobial mechanism offers a potential strategy to maintain immune function, reduce recurrent infection, and support anticancer treatment response in immunocompromised patients.},
}

@article {pmid41496941,
year = {2026},
author = {Mehmood, MS and Iqbal, I and Hajj, F},
title = {CRISPR-Cas13a diagnostics for circulating microbial transcripts in pancreatic cancer.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {1038-1039},
pmid = {41496941},
issn = {2049-0801},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is the seventh leading cause of global cancer deaths, with a 5-year survival rate below 11% and over 80% of cases diagnosed at advanced, unresectable stages. Current biomarkers such as CA19-9 show suboptimal diagnostic accuracy (sensitivity 65-75%; specificity 70-80%), necessitating more precise and minimally invasive diagnostic tools. Recent advances in CRISPR-Cas13a technology, an RNA-guided, RNA-targeting system with attomolar sensitivity and >95% diagnostic accuracy, enable rapid detection of circulating RNA molecules. Concurrently, microbial transcriptomic studies have revealed distinct bacterial RNA fragments in plasma of PDAC patients, including Fusobacterium and Enterobacter small RNAs, detected in up to 68% of advanced and 41% of early-stage cases. Integrating Cas13a platforms with microbial RNA biomarkers could revolutionize liquid biopsy diagnostics by providing a fast (<30 min), low-cost ( }

@article {pmid41496931,
year = {2026},
author = {Mehmood, MS and Danaf, N},
title = {Helicobacter pylori persists in pancreatic ductal adenocarcinoma despite eradication therapy.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {955-956},
pmid = {41496931},
issn = {2049-0801},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with global 5-year survival below 12%. Recent molecular analyses have revealed that Helicobacter pylori may persist within the pancreatic ductal microenvironment despite successful gastric eradication. In a 2024 multicenter study, H. pylori DNA was detected in 41.6% of PDAC tissues, including patients with documented eradication. Metagenomic sequencing identified H. pylori 16S rRNA reads comprising up to 2.5% of total microbial DNA, supporting selective intrapancreatic survival. Mechanistically, CagA/VacA-mediated STAT3 and NF-κB activation drives cytokine release, oxidative stress, and mismatch repair suppression, enhancing oncogenic inflammation and genomic instability. Chronic colonization increased pancreatic intraepithelial neoplasia by more than 60% in murine models, underscoring its pathogenic potential. These findings suggest that H. pylori persistence represents a novel microbial co-factor in PDAC, warranting further exploration as a diagnostic biomarker and therapeutic target.},
}

@article {pmid41496502,
year = {2026},
author = {Majzoub, ME and Santiago, FS and Raich, SS and Sirigeri, P and Simovic, I and Tedla, N and Kaakoush, NO},
title = {Immunoglobulin A protease from Sutterella wadsworthensis modifies outcome of infection with Campylobacter jejuni and is associated with microbiome diversity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611543},
doi = {10.1080/19490976.2025.2611543},
pmid = {41496502},
issn = {1949-0984},
mesh = {Humans ; *Immunoglobulin A/metabolism ; Animals ; Phylogeny ; *Campylobacter jejuni/physiology ; *Campylobacter Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Mice ; *Clostridiales/enzymology/genetics/classification ; Neutrophils/immunology/microbiology ; *Bacterial Proteins/genetics/metabolism ; China ; Phagocytosis ; Epithelial Cells/microbiology ; Serine Endopeptidases ; },
abstract = {Sutterella wadsworthensis is an enigmatic member of the microbiota, previously reported to be present in healthy humans yet also associated with certain gut diseases and their therapeutic outcomes. Here, we report on S. wadsworthensis classified to S. wadsworthensis_A that encodes an immunoglobulin A (IgA) protease that digests human IgA1 and IgA2 but not mouse IgA. The activity of this IgA protease could influence the trajectory of Campylobacter jejuni infection in human epithelial cells and phagocytosis in primary neutrophils. Comparative genomics and screening of metagenomic samples revealed that the protease shared sequence identity with an IgA protease from a bacterium that colonized other mammals and that S. wadsworthensis harboring IgA protease can be detected in individuals globally. Individuals positive for S. wadsworthensis IgA protease in China and Fiji (detection at >90% similarity) were found to have a different microbiome when compared to individuals where the protease was not detected. Phylogenetic analysis of pathogen IgA proteases along with IgA proteases from members of the microbiota suggested that there may be a unique subset of microbiota-derived IgA proteases. Our results highlight the importance of taxonomic resolution in microbiome studies and identify a subgroup of S. wadsworthensis that may be of potential clinical relevance.},
}

Humans
*Immunoglobulin A/metabolism
Animals
Phylogeny
*Campylobacter jejuni/physiology
*Campylobacter Infections/microbiology/immunology
*Gastrointestinal Microbiome
Mice
*Clostridiales/enzymology/genetics/classification
Neutrophils/immunology/microbiology
*Bacterial Proteins/genetics/metabolism
China
Phagocytosis
Epithelial Cells/microbiology
Serine Endopeptidases

@article {pmid41496455,
year = {2026},
author = {Ramesh, A and Subbarayan, R and Shrestha, R and Adtani, PN},
title = {Exploring Fecal Microbiota Transplantation: Potential Benefits, Associated Risks, and Challenges in Cancer Treatment.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {9},
number = {1},
pages = {e70455},
doi = {10.1002/cnr2.70455},
pmid = {41496455},
issn = {2573-8348},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods/adverse effects ; *Neoplasms/therapy/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Tumor Microenvironment/immunology ; Immunotherapy/methods ; Animals ; Risk Assessment ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has emerged as a groundbreaking strategy for modulating the gut microbiome and improving cancer treatment outcomes. This review synthesizes the current evidence on the role of FMT in oncology, focusing on its potential to enhance the efficacy of immunotherapy, restore microbiome homeostasis, and mitigate cancer-associated complications.

RECENT FINDINGS: Preclinical and clinical studies have demonstrated that FMT can reprogram the tumor microenvironment, augment immune checkpoint inhibitor responses, and reduce chemotherapy-induced toxicity. However, risks such as pathogen transmission, immune dysregulation, and unintended microbial shifts necessitate rigorous donor screening and a personalized approach. Challenges in standardization, regulatory frameworks, and mechanistic understanding further complicate their clinical translation. Emerging innovations, including precision microbial consortia, synthetic biology, and biomarker-driven strategies, have the potential to address these limitations.

CONCLUSION: While FMT holds transformative potential in cancer care, its integration into oncological practice requires robust clinical validation, long-term safety assessments, and interdisciplinary collaboration to harness its full therapeutic potential.},
}

Humans
*Fecal Microbiota Transplantation/methods/adverse effects
*Neoplasms/therapy/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Tumor Microenvironment/immunology
Immunotherapy/methods
Animals
Risk Assessment

@article {pmid41496451,
year = {2026},
author = {Wang, P and Jiang, F and Xue, Z and Bu, F and Zhu, W and Zhang, Y and Wen, T and Li, Y and Zhang, P and Cai, Y and Niu, C and Li, S and Zhou, Y and Cheng, X},
title = {The Medicago SPX1/3-PHR2 Network Relays Phosphate Signaling to Orchestrate Root Nodulation-dependent Nitrogen Acquisition by Controlling Flavonoid Biosynthesis.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101695},
doi = {10.1016/j.xplc.2026.101695},
pmid = {41496451},
issn = {2590-3462},
abstract = {The formation of symbiotic associations with rhizospheric microbes is an important strategy for sessile plants to acquire nitrogen and phosphorus from the soil. Root exudate plays a key role in shaping the rhizosphere microbiome. Depending on their needs for nitrogen or phosphorus, plants can adjust the composition of root exudate to attract the appropriate microbes. Flavonoids, a group of secondary metabolites, have been well studied for their role in shaping the root microbiome, particularly in mediating root nodule symbiosis in legumes. However, the mechanism by which plants regulate the absorption of microbe-mediated nitrogen and phosphorus remains unclear. Here, we show that the Medicago truncatula phosphate starvation response regulatory network SPX1/3-PHR2 controls flavonoid biosynthesis to recruit nitrogen-fixing microbes for nitrogen acquisition. Nitrogen-fixing microbes, including rhizobia, were fewer recruited in the rhizosphere of the spx1spx3 double mutant. This was caused by lower flavonoid levels in the root exudate compared to wild-type plants R108. Further results indicate that the control of flavonoid biosynthesis is exerted via PHR2, the interacting transcription factor of SPX1/3. Under phosphate-limiting conditions, PHR2 suppresses the expression of flavonoid biosynthetic genes to reduce root nodule symbiosis levels. Under phosphate-sufficient conditions, the interaction between SPX1/3 and PHR2 releases this suppression, thereby promoting root nodule symbiosis. We further showed that PHR2 can bind to the promoter regions of flavonoid biosynthetic genes in yeast. We propose that the SPX1/3-PHR2 network can modulate root nodule-dependent nitrogen acquisition in response to phosphate levels. Thus, the SPX1/3-PHR2 module contributes to maintaining a balance in microbe-mediated nitrogen and phosphorus acquisition for optimal plant growth.},
}

@article {pmid41496347,
year = {2026},
author = {Saghafi, S and Yaghoubi, MA and Safarpour, H and Raeisi, H and Mousavi, Z},
title = {Protecting the endocrine axis in immuno-oncology: GLP-1 receptor agonists as host-directed modulators in colorectal cancer.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {194},
number = {},
pages = {118948},
doi = {10.1016/j.biopha.2025.118948},
pmid = {41496347},
issn = {1950-6007},
abstract = {Immune checkpoint inhibitors (ICIs) have transformed colorectal cancer (CRC), particularly in microsatellite instability-high (MSI-H) and mismatch repair-deficient (dMMR) tumors, delivering durable responses and long-term survival. Yet this success is shadowed by immune-related adverse events (irAEs). Among them, endocrine toxicities including thyroiditis, hypophysitis, adrenalitis, and insulin-deficient diabetes are relatively frequent, irreversible, and frequently life-long. Survivors who might otherwise be considered cured remain tethered to chronic hormone replacement, underscoring a striking gap in immuno-oncology: management is reactive, supportive, and devoid of preventive strategies. Concurrently, glucagon-like peptide-1 receptor agonists (GLP-1RAs), introduced for type 2 diabetes (T2D) and obesity, are emerging as systemic modulators of inflammation, immunometabolism, and the gut microbiome. These three axes converge on mechanisms central to endocrine irAEs. Preclinical and epidemiologic data suggest that GLP-1RAs may also be associated with reduced cancer incidence and alterations in tumor-associated immune responses, raising the possibility of dual utility: mitigating endocrine autoimmunity while preserving or even augmenting anti-tumor efficacy. At the same time, their appetite-suppressing and weight-reducing effects highlight the countervailing risk of exacerbating cancer cachexia, demanding careful integration with nutritional and exercise strategies. Here, we synthesize current understanding of ICI-induced endocrine injury, delineate the immunobiology of GLP-1RAs, and develop a unified mechanistic framework linking these domains in CRC. We propose a translational roadmap spanning retrospective pharmacoepidemiology, biomarker-driven stratification, and prospective clinical trials. More broadly, GLP-1RAs exemplify host-directed therapies that may help shift the therapeutic focus of immuno-oncology toward preserving survivorship and endocrine health as integral endpoints of cancer care.},
}

@article {pmid41496313,
year = {2026},
author = {Sun, L and Sun, X and Qiao, C and Lu, Y and Li, Q and Wang, Q and Gao, H},
title = {Precision medicine in Crohn's disease: Navigating the path from biomarker discovery to clinical implementation.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {},
number = {},
pages = {},
pmid = {41496313},
issn = {1998-4049},
abstract = {Crohn's disease (CD) is a highly heterogeneous inflammatory bowel disorder. Despite an expanding therapeutic arsenal, treatment selection remains largely empirical, often leading to delayed effective control and suboptimal outcomes. Precision medicine, which tailors therapy to individual patient characteristics, offers a promising alternative. Advances in biomarker discovery are enabling more personalized approaches. Research has moved beyond conventional markers to high-dimensional data from genomics, proteomics, and microbiome studies. Over 200 genetic susceptibility loci have been identified, and dysbiosis is recognized as a key modulator of disease and treatment response. Integrating these multi-omics data is crucial for building predictive models, a task increasingly aided by artificial intelligence and machine learning. However, translating these discoveries into clinical practice faces significant hurdles. These include insufficient validation across diverse populations, methodological heterogeneity, and a lack of real-world evidence. Biomarker performance may vary significantly across genetically diverse patient cohorts, raising concerns that precision medicine tools validated only in homogeneous populations could inadvertently propagate health disparities. It is also important to consider regional contexts, such as the Middle East and Saudi Arabia, where rising IBD incidence due to urbanization and unique genetic architectures may affect biomarker performance and therapy response. This review synthesizes recent progress, outlines the major barriers to implementation, and discusses future directions, such as leveraging digital health technologies and international collaborations, to accelerate the adoption of precision medicine and improve outcomes for CD patients.},
}

@article {pmid41496250,
year = {2026},
author = {Anyango, OV and Aool, OW and Lukindu, M and Nakayiki, T and Lutwama, J and Kayondo, JK and Phillips, CD and Lutomiah, J and Mutisya, J and Brelsfoard, CL and Onyango, MG},
title = {Molecular detection of medically important rickettsiae, including Rickettsia prowazekii in Rhipicephalus appendiculatus and Hyalomma rufipes: A microbiome perspective.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {1},
pages = {102596},
doi = {10.1016/j.ttbdis.2025.102596},
pmid = {41496250},
issn = {1877-9603},
abstract = {The East African region hosts more than 50 % of Africa livestock and 9 % of global cattle, creating an ideal environment for ticks to thrive and transmit pathogens. Little is known of the full spectrum of tick-associated bacterial pathogens that circulate in the vast pastoralist-intense regions of East Africa, the range of the pathogens and their genetic relationships. To define this, we need to first delineate the microbial composition of the medically and veterinary important East African tick species. This study focused on the likely vectors of Orthonairovirus haemorrhagiae in Kenya and Uganda, specifically H. rufipes and R. appendiculatus. To characterize the bacterial microbiome associated with these two tick species, the V3-V4 hypervariable region of the 16S rRNA gene was sequenced from a total of 25 R. appendiculatus and 24 H rufipes specimens using the Illumina MiSeq platform. Microbial abundance and diversity were subsequently analysed to assess the composition and structure of their bacterial communities. We observed a richer and balanced bacterial microbiome profile among the H. rufipes compared to that of the R. appendiculatus, which was mainly dominated by Coxiella-like endosymbionts. Furthermore, a few bacterial taxa were unique to each sampling site, while several were common across all sampling sites. This study identified several medically important Rickettsia species, including R. aeschlimannii, R. conorii, and, for the first time, R. prowazekii, the causative agent of epidemic typhus, in H. rufipes sampled from Northeast Kenya. Furthermore, our findings demonstrate that R. africae exhibits a broad tick host tropism. Our present findings provide insights into the microbial community of medically important tick species of East Africa. The observation of a significant level of Coxiella-like endosymbionts in R. appendiculatus warrants an investigation into their transmissibility and impacts on the transmission of other pathogens. The identification of R. prowazekii in H. rufipes suggest that R. prowazekii is broadening its host tropism in Kenya.},
}

@article {pmid41496086,
year = {2026},
author = {Gao, Y and Yu, X},
title = {Acupuncture treatment for insomnia based on the microbiome-gut-brain axis theory: A review.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46967},
pmid = {41496086},
issn = {1536-5964},
mesh = {Humans ; *Sleep Initiation and Maintenance Disorders/therapy/microbiology ; *Acupuncture Therapy/methods ; *Gastrointestinal Microbiome/physiology ; Brain ; *Brain-Gut Axis/physiology ; },
abstract = {Insomnia, a prevalent sleep disorder, significantly impacts patient social function and quality of life, creating a substantial burden on individuals. This underscores the need for effective treatments. Acupuncture, an essential part of complementary and alternative medicine, has received increasing attention for its therapeutic effect on insomnia, although its mechanism is still not fully understood. In recent years, some studies have focused on the microbiome-gut-brain axis, a promising area of study that may shed light on how acupuncture alleviates insomnia. This review explores the possible mechanisms by which acupuncture therapy improves insomnia through the microbiome-gut-brain axis. These mechanisms include adjusting the types and diversity of intestinal microbiome and altering short-chain fatty acid levels, inhibiting inflammatory responses, improving the tight connection of the intestinal mucosal barrier, controlling the release and production of brain-gut peptides, and regulating the pathways associated with the hypothalamic-pituitary-adrenal axis and the vagus nerve. The findings aim to provide a more objective basis for the use of acupuncture and moxibustion in treating insomnia.},
}

Humans
*Sleep Initiation and Maintenance Disorders/therapy/microbiology
*Acupuncture Therapy/methods
*Gastrointestinal Microbiome/physiology
Brain
*Brain-Gut Axis/physiology

@article {pmid41496083,
year = {2026},
author = {Wang, X and Qin, W},
title = {Effect of gut microbiome and blood metabolites on colorectal cancer: A bidirectional Mendelian randomization and mediation analysis based on STROBE-MR guidelines.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46936},
pmid = {41496083},
issn = {1536-5964},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Colorectal Neoplasms/blood/genetics/microbiology ; Mendelian Randomization Analysis/methods ; Genome-Wide Association Study ; Mediation Analysis ; },
abstract = {Previous studies have shown that gut microbiome as well as blood metabolites are involved in the development of colorectal cancer (CRC). Therefore, this study attempted to discover the causal effects of gut microbiome and blood metabolites on CRC. Using genetic data from published genome-wide association studies, the 2-sample Mendelian randomization (MR) and 2-step MR analyses were applied to evaluate the causal connections between gut microbiome (exposure) and CRC (outcome) with blood metabolites as the mediators, as well as between blood metabolites (exposure) and CRC (outcome) with gut microbiome as the mediators. Moreover, a reverse MR analysis was done to measure the impact of CRC on gut microbiome and blood metabolites. The inverse variance weighted method was primarily utilized to analyze causal effects, with the robustness of the findings further assessed by sensitivity analyses. The 2-sample MR analyses illustrated that 14 gut microbes, 23 gut bacterial pathways, and 96 blood metabolites exerted an evidence of causal effect on CRC. However, there were no causal relationships between CRC and gut microbes and blood metabolites. Additionally, mediation analyses revealed that 5 gut microbiome (three gut microbes and 2 gut bacterial pathway abundance) influenced CRC through 4 blood metabolites, and 9 blood metabolites influenced CRC through 7 gut microbiome (four gut microbes and 3 gut bacterial pathways). Sensitivity analyses indicated that all results were reliable. Our study further highlights the complex relationship among gut microbiome, blood metabolites, and CRC and provides insights into clinical interventions for CRC.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
*Colorectal Neoplasms/blood/genetics/microbiology
Mendelian Randomization Analysis/methods
Genome-Wide Association Study
Mediation Analysis

@article {pmid41496069,
year = {2026},
author = {Zhao, Y and Wang, H and Lu, Y and Lou, D},
title = {Evolving landscapes in childhood asthma-gut microbiota research: A bibliometric analysis from 2000 to 2024.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46594},
pmid = {41496069},
issn = {1536-5964},
support = {ZHGF2024-1//The Key Construction Discipline of Immunology and Pathogen biology in Zhuhai Campus of Zunyi Medical University/ ; NO. QKHRC-CXTDã€"2025〕046//The Program for High level Innovative Talents in the Guizhou Province/ ; },
mesh = {Humans ; *Asthma/microbiology/immunology ; *Bibliometrics ; *Gastrointestinal Microbiome ; Child ; Dysbiosis ; *Biomedical Research/trends ; },
abstract = {BACKGROUND: Pediatric asthma, a chronic inflammatory airway disorder, is increasingly recognized for its association with gut microbiota dysbiosis, mediated through immune dysregulation and systemic inflammation. Recent advancements in multi-omics technologies and the "gut-lung axis" hypothesis have propelled this field into a research frontier. This bibliometric study delineates global research trends, collaborative networks, and emerging directions in pediatric asthma-gut microbiota research.

METHODS: Publications from the Web of Science Core Collection (2000-2024) were systematically retrieved using keywords related to asthma, children, and gut microbiota. Data from 635 articles (392 original studies, 243 reviews) were analyzed via CiteSpace and VOSviewer to map country/institutional contributions, author networks, citation metrics, and keyword clusters. Non-English publications, patents, and conference abstracts were excluded.

RESULTS: Global output demonstrated exponential growth, with 62% of articles published between 2018 to 2022. The United States led in productivity (180 articles, 28.35%) and citations (10,851), while Canada achieved the highest citation impact (121.12 citations/article). Key contributors included Prof Stuart E. Turvey (19 articles, 2463 citations) and Prof B. Brett Finlay (140.07 citations/article). The University of British Columbia dominated institutional contributions (28 articles, 149.11 citations/article). The Journal of Allergy and Clinical Immunology emerged as the top journal (33 articles, 126.48 citations/article). Seminal works highlighted early-life gut dysbiosis (e.g., reduced Lachnospira and Faecalibacterium) and cesarean delivery's role in asthma risk. Keyword clustering revealed 6 themes: disease phenotypes (asthma-allergy comorbidity), microbiota dynamics (dysbiosis, short-chain fatty acids [SCFAs]), immune mechanisms (T helper 17 cells/Treg imbalance, gut-lung axis), developmental exposures (antibiotics, breastfeeding), methodologies (metagenomics), and therapeutic strategies.

CONCLUSION: This study underscores a paradigm shift from descriptive microbial profiling to mechanistic exploration of microbiota-derived metabolites (e.g., SCFAs) and early-life interventions. Future priorities include elucidating causal pathways via longitudinal cohorts, developing microbiota-targeted therapies, and leveraging multi-omics integration. Despite limitations in database scope, this analysis highlights accelerating translation from basic research to clinical applications through global collaboration. Researchers should prioritize interdisciplinary studies to unravel the "microbiome-immune-development" triad and optimize personalized asthma management.},
}

Humans
*Asthma/microbiology/immunology
*Bibliometrics
*Gastrointestinal Microbiome
Child
Dysbiosis
*Biomedical Research/trends

@article {pmid41496014,
year = {2026},
author = {Yan, Y and Hu, M and Liu, C and Liu, Q and Xiong, T and Su, K},
title = {Unveiling the causal relationships between gut microbiota, circulating metabolic biomarkers, and benign prostate hyperplasia: A Mendelian randomization study.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46466},
pmid = {41496014},
issn = {1536-5964},
mesh = {Male ; Humans ; *Prostatic Hyperplasia/microbiology/blood/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Mendelian Randomization Analysis ; Biomarkers/blood ; *Dysbiosis/microbiology/complications ; Genome-Wide Association Study ; Risk Factors ; },
abstract = {The complex roles of gut microbiome (GM) dysbiosis and circulating metabolites in benign prostatic hyperplasia (BPH) pathogenesis have been widely hypothesized but lacked causal evidence. Critically, no Mendelian randomization (MR) study has established whether GM and metabolites exert direct causal effects or act through mediating pathways in BPH development. Using genome-wide association studies data, we conducted comprehensive 2-sample and mediation MR analyses. Causal effects were estimated via inverse-variance weighted methods with sensitivity analyses. Six bacterial phyla/genera showed significant causal links to BPH, including Actinobacteria (genus Bifidobacterium), Bacteroidetes (genus Bacteroides), Firmicutes (genera Blautia, Holdemania), and Proteobacteria (genus Comamonas). Additionally, 2 circulating metabolites - the mean diameter of low-density lipoprotein (LDL) particles and the free cholesterol to total lipids ratio in small very LDL - were significantly associated with BPH. However, no mediation effect was found for any circulating metabolites on BPH. In summary, our 2-sample and mediation MR analysis revealed 18 GM and 2 circulating metabolites significantly linked to BPH, highlighting their potential as risk factors. While no mediation effects for circulating metabolites were detected, these findings enhance our understanding of preventive strategies for BPH, emphasizing the intricate relationship between GM dysbiosis, circulating lipid metabolites, and disease onset.},
}

Male
Humans
*Prostatic Hyperplasia/microbiology/blood/genetics
*Gastrointestinal Microbiome/physiology/genetics
Mendelian Randomization Analysis
Biomarkers/blood
*Dysbiosis/microbiology/complications
Genome-Wide Association Study
Risk Factors