@article {pmid41260033,
year = {2025},
author = {Zhang, Q and Zhang, S and Cao, X and Zhi, Y and Guo, Y},
title = {The gut microbiota in post-stroke depression: A systematic review of microbial mechanisms and therapeutic targeting of neuroinflammation.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128391},
doi = {10.1016/j.micres.2025.128391},
pmid = {41260033},
issn = {1618-0623},
abstract = {Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.},
}

@article {pmid41259916,
year = {2025},
author = {Shi, R and Liu, W and Shi, X and Li, X and Ge, Y and Liu, J and Zeb, A and Zhao, Y and Sun, Y and An, J},
title = {Earthworm intestine orchestrates dual host-microbiome detoxification of 6PPD-quinone.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140527},
doi = {10.1016/j.jhazmat.2025.140527},
pmid = {41259916},
issn = {1873-3336},
abstract = {The highly toxic tire-derived compound N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) poses emerging environmental risks, yet its fate within soil invertebrates remains unclear. Here, we investigate the tissue distribution, elimination kinetics, biotransformation, and detoxification of 6PPD-Q in earthworms. 6PPD-Q showed tissue-specific accumulation, with the highest levels in the lipid-rich intestine (48.30 ± 4.06 ng/g; bioaccumulation factor (BAF) = 0.489 ± 0.156). We identified 17 metabolites generated through classical phase I and II detoxification pathways, mainly mediated by cytochrome P450 (CYP450) enzymes. 6PPD-Q exposure enriched detoxifying microbes (e.g., Paenibacillus and Pseudarthrobacter) and shifted microbial dynamics from deterministic to stochastic processes. Network analysis revealed enhanced microbial connectivity and functional resilience, which correlated strongly with degradation efficiency (p < 0.001). In vitro assays further confirmed microbial transformations yielding unique hydroxylated, acetylated, and methylated products. These findings highlight the intestine as both a reservoir and a bioreactor, emphasizing host-microbiota synergy in 6PPD-Q detoxification and offering new insights into contaminant bioremediation in soil invertebrates.},
}

@article {pmid41259824,
year = {2025},
author = {Fan, X and Wei, Y and Zang, T and Tu, Y and Liu, L and Tian, H and Li, X and Cheng, H and Bai, J and Liu, Y},
title = {Gut feelings: Dysbiosis of gut microbiota and short-chain fatty acids associated with prenatal depression, pregnancy-related anxiety, and prenatal combined depression and anxiety.},
journal = {Psychoneuroendocrinology},
volume = {184},
number = {},
pages = {107686},
doi = {10.1016/j.psyneuen.2025.107686},
pmid = {41259824},
issn = {1873-3360},
abstract = {OBJECTIVES: The role of the gut microbiota and short-chain fatty acids (SCFAs) in psychiatric disorders in pregnant women has not been fully elucidated. Therefore, this study aimed to investigate the association between the gut microbiota and its metabolite SCFAs and prenatal depression, pregnancy-related anxiety, and prenatal combined depression and anxiety.

METHODS: In total 200 pregnant women in the third trimester were recruited for this study. The Edinburgh Postnatal Depression Scale and Pregnancy-Related Anxiety Questionnaire Revised-2 were used to evaluate pregnant women's anxiety and depression, and stool samples were collected for gut microbiome and SCFAs.

RESULTS: This study found that reduced abundance of Allobaculum and Cetobacterium were associated with pregnancy-related anxiety in women. Furthermore, the enrichment of Anaerofustis, Gemella, and Staphylococcus and the reduction of Tyzzerella and unclassified_f_UCG-011 were associated with prenatal depression. This study was the first to indicate that women with comorbid prenatal anxiety and depression share similarities in gut microbiota and SCFAs with women with prenatal depression (Anaerofustis, Gemella, Staphylococcus, Tyzzerella, and isohexanoic acid). This study also found that certain gut microbial profiles were associated with prenatal comorbid anxiety and depression. While receiver operating characteristic analysis suggests a limited ability of the gut microbiota alone to predict prenatal psychological distress problems, the integration of phenotypic variables into the model significantly improved the model's predictive ability.

CONCLUSION: Our findings suggested that dysbiosis of gut microbiota and SCFAs are associated with prenatal psychiatric disorders. Alterations of the gut microbiota may have the potential as biomarkers for distinguishing prenatal psychiatric disorders.},
}

@article {pmid41259688,
year = {2025},
author = {Alizon, S and Tamarelle, J},
title = {[The scientific, health et social significance of the vaginal microbiome].},
journal = {Medecine sciences : M/S},
volume = {41},
number = {10},
pages = {760-769},
doi = {10.1051/medsci/2025139},
pmid = {41259688},
issn = {1958-5381},
mesh = {Humans ; Female ; *Microbiota/physiology ; *Vagina/microbiology/physiology ; Sexually Transmitted Diseases/microbiology/epidemiology ; },
abstract = {The vaginal microbiome is an ideal study system given the diversity of bacteria it harbors, its communities that can be structured into large, stable types, the ease of sampling, and the well-characterized environment. The microbiome is also dynamic and varying according to life stage, biological mechanisms such as hormonal cycles or menstruation, and specific exposures (e.g.; antibiotics, sexual practices). The associations between vaginal microbiota and health are strong, including its role in sexually transmitted infections, fertility, and general well-being. This raises questions about prevention and therapies, while avoiding the risk of excessive pathologization.},
}

Humans
Female
*Microbiota/physiology
*Vagina/microbiology/physiology
Sexually Transmitted Diseases/microbiology/epidemiology

@article {pmid41259558,
year = {2025},
author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A},
title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.},
journal = {Journal of applied oral science : revista FOB},
volume = {33},
number = {},
pages = {e20250476},
doi = {10.1590/1678-7757-2025-0476},
pmid = {41259558},
issn = {1678-7765},
mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; },
abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.

METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.

RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p≤0.05, LDA≥2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.

CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.},
}

Humans
*Dental Caries/microbiology
Adolescent
Male
*Microbiota/genetics
Female
Child
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
DMF Index
Reference Values

@article {pmid41259413,
year = {2025},
author = {Triadafilopoulos, G},
title = {Lessons learned: endoscopy with 96-hour ambulatory esophageal pH monitoring as a tool to avoid proton pump inhibitor use in cancer patients with refractory gastroesophageal reflux.},
journal = {Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus},
volume = {38},
number = {6},
pages = {},
doi = {10.1093/dote/doaf102},
pmid = {41259413},
issn = {1442-2050},
mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/adverse effects ; *Gastroesophageal Reflux/drug therapy/etiology/complications/diagnosis ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Esophageal pH Monitoring/methods ; Aged ; *Neoplasms/complications ; *Heartburn/etiology/drug therapy ; *Esophagoscopy/methods ; Adult ; },
abstract = {The proton pump inhibitors (PPIs) are extensively prescribed for the empirical treatment of epigastric pain and heartburn in cancer patients. However, they carry the potential for drug interactions with antineoplastic agents during active cancer therapy, and osteopenia, opportunistic infections, adverse cardiovascular outcomes, and altered gut microbiome in long-term users in survivorship. Herein, we examined the use of endoscopy with esophageal 96-hour ambulatory pH monitoring in guiding clinicians in safely prescribing PPI in 21 such patients. We retrospectively studied patients with active cancer or in survivorship, presenting with PPI-refractory heartburn. All underwent an endoscopy with esophageal ambulatory pH monitoring performed "off" PPI therapy for 96 hours, following a "liberal diet" for the first 48, and a "restrictive diet" for the latter 48 hours. Acid exposure time (AET) ≥ 6% per 24 hours was defined as abnormal. For each patient, the average AET from the first 2 days was considered as baseline and was compared with that from the latter 2 days (on restrictive diet). We concluded that ambulatory 96-hour pH monitoring, identifies 48% of patients with normal AET, who may not need PPI. Esophageal pH monitoring on restrictive diet normalizes AET in 73% of patients, thereby allowing esophageal acid control to be achieved with diet alone.},
}

Humans
*Proton Pump Inhibitors/therapeutic use/adverse effects
*Gastroesophageal Reflux/drug therapy/etiology/complications/diagnosis
Male
Female
Retrospective Studies
Middle Aged
*Esophageal pH Monitoring/methods
Aged
*Neoplasms/complications
*Heartburn/etiology/drug therapy
*Esophagoscopy/methods
Adult

@article {pmid41259398,
year = {2025},
author = {Yadav, A and Ali, R and Devi, P and Kumari, P and Soni, J and Garima, and Tarai, B and Budhiraja, S and Shamim, U and Pandey, R},
title = {Non-canonical Metatranscriptomic analysis of COVID-19 and Dengue reveals an expanded microbial and AMR landscape in COVID-19 mortality patients.},
journal = {PLoS pathogens},
volume = {21},
number = {11},
pages = {e1013703},
doi = {10.1371/journal.ppat.1013703},
pmid = {41259398},
issn = {1553-7374},
mesh = {Humans ; *COVID-19/mortality/microbiology ; *Dengue/microbiology/mortality ; *Microbiota/genetics ; SARS-CoV-2 ; Female ; Male ; Middle Aged ; Transcriptome ; Adult ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; },
abstract = {AMR is a growing concern in viral infections, where microbiome shifts contribute to resistance gene dissemination. While dengue and COVID-19, caused by ssRNA viruses, are not bacterial-driven, their resistome and microbial communities influence disease progression and AMR burden. This study analyzes the resistome and microbiome in 251 COVID-19 and 112 dengue patients using non-canonical metatranscriptomics. By mapping antimicrobial resistance genes (ARGs) and their transcriptionally active microbes (TAMs) hosts, we uncover greater ARG burden in COVID-19, particularly during mortality, with a diverse set of associated TAMs compared to dengue. MDR genes were prevalent, with beta-lactamase ARGs commonly detected in both infections. COVID-19 exhibited higher carbapenemase resistance genes (NDM, OXA, VIM), while dengue was associated with TEM variants. Escherichia coli and Klebsiella pneumoniae were dominant ARG hosts, with Acinetobacter baumannii in COVID-19 mortality and Bacillus cereus in severe dengue. These findings highlight resistome dynamics and emphasize the need for AMR surveillance in high-burden infections.},
}

Humans
*COVID-19/mortality/microbiology
*Dengue/microbiology/mortality
*Microbiota/genetics
SARS-CoV-2
Female
Male
Middle Aged
Transcriptome
Adult
Anti-Bacterial Agents/pharmacology/therapeutic use
*Drug Resistance, Bacterial/genetics

@article {pmid41259328,
year = {2025},
author = {Custodio, R and Alseth, EO and Brockhurst, MA and Brown, SP and Westra, ER},
title = {Bacterial immune systems as causes and consequences of microbiome structure.},
journal = {PLoS biology},
volume = {23},
number = {11},
pages = {e3003489},
doi = {10.1371/journal.pbio.3003489},
pmid = {41259328},
issn = {1545-7885},
mesh = {*Microbiota/immunology/genetics ; *Bacteria/immunology/genetics ; Humans ; Interspersed Repetitive Sequences ; Animals ; },
abstract = {Attacks from molecular parasites such as mobile genetic elements (MGEs) have driven the evolution of defense systems in bacterial genomes. Yet, despite significant advances in understanding the molecular mechanisms of these bacterial immune systems, we have only a rudimentary understanding of their ecology and evolution. Bacteria exist as part of complex microbiomes, but community ecology and microbiome research has yet to characterize the impacts of interactions between MGEs and defense mechanisms upon the structure, dynamics and evolution of microbiomes. This Essay introduces and discusses the interplay between bacterial community dynamics and bacterial immune systems, speculating about how these reciprocal interactions may shape microbial community structure and function.},
}

*Microbiota/immunology/genetics
*Bacteria/immunology/genetics
Humans
Interspersed Repetitive Sequences
Animals

@article {pmid41259124,
year = {2025},
author = {Todt, T and van Bussel, I and Afman, L and Brennan, L and Ivanova, DG and Kiselova-Kaneva, Y and Thomas, EL and Rühl, R},
title = {Transcriptome-driven Health-status Transversal-predictor Analysis for health, food, microbiome and disease markers for understanding of lifestyle diseases.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00026.2025},
pmid = {41259124},
issn = {1531-2267},
support = {EU FP7 nutritech//all except Tilman/ ; },
abstract = {We developed a novel artificial intelligence (AI) approach based on machine-learning to predict general health and food-intake parameters. This approach, named Transcriptome-driven Health-status Transversal-predictor Analysis (THTA) is relevant for markers of diabesity and is based on a non-transcriptomic, mathematics-driven approach. The prediction was based on values derived from food consumption, dietary lipids and their bioactive metabolites, peripheral blood mononuclear cell (PBMC) mRNA-based transcriptome signatures, magnetic resonance imaging (MRI), energy metabolism measurements, microbiome analyses, and baseline clinical parameters, as determined in a cohort of 72 subjects. Our novel machine learning approach incorporated transcriptome data from PBMCs as a "one-method" approach to predict 77 general health-status markers for the broad stratification of the diabesity phenotype. These markers would usually necessitate measurements using 16 different methods. The PBMC transcriptome was used to determine these 77 basic and background health markers with very high accuracy in a transversal-predictor establishment group (Pearson correlations are r = 0.98 ranging from 0.94 to 0.99). These collected variables provide valuable insides into which individual factor(s) are mainly target diabesity. Based on the "establishment group" prediction approach a further "confirmation group" prediction approach was performed, achieving a predictive potential r = 0.59 (ranging from 0.19 to 0.98) for these 77 variables. This "one-method" approach enables the simultaneous monitoring of a large number of health-status variables relevant to diabesity and may facilitate the monitoring of therapeutic and preventive strategies. In summary, this novel technique, which is based on PBMC transcriptomics from human blood, can predict a wide range of health-related markers.},
}

@article {pmid41258884,
year = {2025},
author = {Ni, D and Pinget, G and Santner-Nanan, B and Tan, J and Reyes, JGA and Lai, CL and Wang, Y and Tran, C and Clarke, JM and Macia, L and Campbell, DE and Hsu, P and Nanan, R},
title = {Effects of Butyrylated High Amylose Maize Starch (HAMSB) as an Adjuvant for Oral Immunotherapy.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70161},
pmid = {41258884},
issn = {1398-9995},
support = {//National Health and Medical Research Council/ ; //Norman Ernest Bequest Fund/ ; },
}

@article {pmid41258872,
year = {2025},
author = {Scheelings, TF and Kodikara, S and Beale, DJ and Van, TTH and Moore, RJ and Skerratt, LF},
title = {Unravelling the impacts of captivity on saltwater crocodile (Crocodylus porosus) cloacal bacterial communities and physiology.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf114},
pmid = {41258872},
issn = {1574-6941},
abstract = {This study addresses a significant research gap in understanding the impacts of captivity on the bacteriome and physiology of saltwater crocodiles (Crocodylus porosus). Despite their ecological and cultural significance, crocodilians are a taxon that remains underexplored in microbiome research. We investigated cloacal bacteriome samples from both wild and captive populations to identify compositional and functional differences resulting from captivity. Our findings reveal significant alterations in bacterial diversity and community structure in captive crocodiles, with notable shifts at both phylum and family levels; specifically, Bacteroidota and Fusobacteriota dominate in captivity, whereas wild crocodiles exhibit a higher prevalence of Pseudomonadota and Bacillota. The Shannon diversity index indicates a significant reduction in bacterial diversity among captive individuals, likely due to husbandry practices that foster a microbially depauperate environment. Additionally, serum metabolomics analysis shows an enrichment of alcohol sugars in captive crocodiles, alongside a decrease in pantothenic acid. While this is the first study to characterize these traits in saltwater crocodiles, further research is necessary to determine the physiological consequences of these bacterial and metabolic changes on host fitness and adaptability. Longitudinal studies are essential for understanding how bacterial communities evolve over time and in response to environmental factors, which will inform conservation strategies and improve the management of captive populations of crocodilians intended for reintroduction into the wild.},
}

@article {pmid41258857,
year = {2025},
author = {Wang, M and Hou, H and Sang, W and Li, P and Yang, X and Qi, P and Ma, Y},
title = {Bile Microbiome and Metabolic Characteristics in Primary Common Bile Duct Stone Patients with Juxtapapillary Duodenal Diverticula: A Clinical Investigation.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf280},
pmid = {41258857},
issn = {1365-2672},
abstract = {OBJECTIVE: This study aimed to characterize the bile microbiome and metabolome in patients with common bile duct stones (CBDs), with versus without juxtapapillary duodenal diverticulum (JPDD), to identify potential factors associated with stone formation.

METHODS: From January to May 2024, CBDs patients undergoing endoscopic retrograde cholangiopancreatography at our hospital were prospectively enrolled. Bile samples were collected for 16SrRNA sequencing and LC-MS/MS metabolomics analysis. Patients were divided into JPDD (n = 15) and CBDs (n = 15) groups.

RESULTS: The JPDD group had larger stone and bile duct diameters (P < 0.05). Although Proteobacteria dominated the bile microbiota in both groups, the JPDD group showed higher abundances of Escherichia-Shigella, Enterococcus, and Escherichia coli. Beta diversity differed significantly between groups (P < 0.05), and LEfSe identified 25 differentially abundant bacterial taxa. Enterococcus, Klebsiella, and Gemellaceae were more abundant in the JPDD group, while Peptococcaceae, Roseburia, and Alistipes were more prevalent in the CBDs group. Enterococcaceae and Enterococcus abundances were positively correlated with stone and duct sizes in the JPDD group (P < 0.05), whereas Peptococcaceae and Acinetobacter showed negative correlations. Metabolomic analysis identified ten differentially enriched pathways-including phenylalanine and alanine metabolism-and higher levels of bilirubin glucuronide and taurochenodeoxycholic acid in the JPDD group. Enterococcus abundance was correlated with bile acid metabolites such as chenodeoxycholylasparagine (P < 0.05).

CONCLUSIONS: JPDD is associated with distinct microbial and metabolic profiles in bile. Enrichment of Enterococcus and Klebsiella in the JPDD group, along with changes in metabolic pathways and bile acid metabolites, suggests a potential link to CBD stone formation and growth.},
}

@article {pmid41258716,
year = {2025},
author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME},
title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/msphere.00683-25},
pmid = {41258716},
issn = {2379-5042},
abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.},
}

@article {pmid41258692,
year = {2025},
author = {Lukacz, ES and McDonald, D and Bryant, M and Putnam, S and Rudser, K and Brennan, C and Meister, M and Fok, CS and Mueller, MG and Knight, R and Brubaker, L and , },
title = {Concordance of Urogenital Microbiome From Sequentially Self-collected Specimens.},
journal = {Urogynecology (Philadelphia, Pa.)},
volume = {31},
number = {11},
pages = {1033-1042},
pmid = {41258692},
issn = {2771-1897},
mesh = {Humans ; Female ; *Microbiota ; Longitudinal Studies ; Middle Aged ; Adult ; RNA, Ribosomal, 16S ; *Specimen Handling/methods ; *Urogenital System/microbiology ; Aged ; },
abstract = {IMPORTANCE: Population-based research is necessary to understand the relationship between the urobiome and bladder health.

OBJECTIVE: Using advanced contamination controls and ecological metrics, we aimed to evaluate the concordance of microbiota in self-collected urogenital specimens from home versus a clinical research setting.

STUDY DESIGN: A subset of community-dwelling women was enrolled in a longitudinal cohort study, self-collected urogenital samples at 3 time points: 1-day prior, the day of and during an in-person evaluation. Samples were sequenced with V4 16S rRNA and KatharoSeq removed samples indistinguishable from background contamination. Data were matched to Greengenes2-2022.10 and rarefied to 1000 seqs/sample. Intersample concordance pairs above the KatharoSeq threshold were assessed between samples. Unweighted UniFrac distances, Mantel Pearson correlations, Kruskal-Wallis, and chi-square tests were used for comparisons.

RESULTS: Detectable sequences were obtained in 261 samples from the 114 participants with 186 (71%) above the KatharoSeq threshold. Escherichia_710834, Lactobacillus, and Prevotella were most prevalent. Intersample concordance was determined for samples above the threshold from 38 participants with 2 home samples and 47 with home and clinic samples. Correlations between 2 home and between home and clinic were significant (r = 0.43, P = 0.001; r = 0.362, P = 0.001, respectively). There were no significant differences across time points (X2 = 2.72, P = 0.256).

CONCLUSIONS: Home-collected urine samples for urogenital microbiome ecological analysis have sufficient short-term similarity and concordance with self-collected urine samples from a research clinic setting for use in population-based research, which may facilitate inclusion of participants with limited access to clinic-based research.},
}

Humans
Female
*Microbiota
Longitudinal Studies
Middle Aged
Adult
RNA, Ribosomal, 16S
*Specimen Handling/methods
*Urogenital System/microbiology
Aged

@article {pmid41258538,
year = {2025},
author = {Brubaker, L and Horsley, H and Khasriya, R and Wolfe, AJ},
title = {Microbiologist in the Clinic: Pregnant Microbiologist with Asymptomatic Bacteriuria.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {41258538},
issn = {1433-3023},
abstract = {In this fourth episode of the Microbiologist in the Clinic series, clinicians and laboratory scientists share their perspectives about a 26-year-old microbiologist G1P0 who is 20 weeks pregnant. She is questioning her obstetrician's recommendation to take systemic antibiotics for a positive urine culture obtained, as her research work focuses on the effect of antibiotics on young children. She hopes to avoid exposing her child to systemic antibiotics if possible.},
}

@article {pmid41258495,
year = {2025},
author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A},
title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02652-8},
pmid = {41258495},
issn = {1432-184X},
support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; },
abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.},
}

@article {pmid41258493,
year = {2025},
author = {Xu, Q and Lin, A and Jiang, A and Chen, L and Zhu, L and Mou, W and Liu, Z and Zhang, J and Cheng, Q and Miao, K and Luo, P},
title = {Circadian rhythms as a modulator of gut microbiota-tumor microenvironment crosstalk.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {409},
pmid = {41258493},
issn = {1420-9071},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Tumor Microenvironment ; Animals ; *Neoplasms/microbiology/pathology/therapy ; Dysbiosis/microbiology ; },
abstract = {Circadian rhythms play a pivotal role in regulating diverse physiological functions, notably the composition and activity of gut microbiota. Accumulating evidence indicates that circadian rhythm disruption can induce dysbiosis of the gut microbiome, which in turn is implicated in influencing the tumor microenvironment (TME) and facilitating cancer progression. This review integrates and analyzes recent advances elucidating the complex interplay where circadian rhythms modulate gut microbiota, and how these circadian-driven microbial changes affect the TME. This review analyzes recent advances in elucidating the complex interplay among circadian rhythms, gut microbiota, and the TME. We examine how circadian disruption modifies the diversity and metabolic functions of gut microbiota, resulting in alterations of microbial metabolites, including but not limited to short-chain fatty acids and secondary bile acids. These metabolic alterations have the potential to modulate immune cell function, vascular remodeling, and tumor cell metabolism within the TME. We investigate the potential mechanisms through which gut microbial dysbiosis induced by circadian misalignment could promote an immunosuppressive TME and accelerate tumor growth. Additionally, we evaluate emerging therapeutic strategies that leverage the circadian-microbiome axis, encompassing chronotherapy, probiotic supplementation, and fecal microbiota transplantation. The integration of circadian biology, microbiology, and cancer immunology presents promising avenues for the development of novel diagnostic and therapeutic approaches. However, significant challenges persist in translating these findings into viable clinical applications. Further research is imperative to elucidate the molecular pathways interconnecting circadian rhythms, gut microbiota, and the TME, and to develop personalized chronobiological interventions for cancer prevention and treatment.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Circadian Rhythm/physiology
*Tumor Microenvironment
Animals
*Neoplasms/microbiology/pathology/therapy
Dysbiosis/microbiology

@article {pmid41258378,
year = {2025},
author = {Liu, L and Wang, H and Minichino, A and Xiao, R and Du, Y and Wang, L and He, D and Guo, S and Mo, X and Xiang, Y and Wu, J and McGuire, P and Yue, W and Lu, L and Cipriani, A and Xie, P},
title = {Mapping the reciprocal interactions between antidepressants and the gut microbiome: novel targets for the personalisation and optimization of drug response.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {41258378},
issn = {1476-5578},
support = {82201683//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401814//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82288101//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Although accumulating evidence suggests a role of the gut microbiome in the response to antidepressant medications, its mechanistic basis is largely unknown. We performed a comprehensive analysis and presented an up-to-date atlas of the relationship between antidepressants and gut microbiome. The main findings were: 1. Treatment with antidepressants increases the abundance of anti-inflammatory species (e.g., Bifidobacterium) and decreases that of pro-inflammatory species (e.g., Escherichia_coli); 2. The nature of microbiome at baseline and of its changes following the start of treatment can be used to predict the efficacy of individual antidepressants. 3. Two sets of bacterial taxa (termed "Microhancers" and "Microlencers") are candidate pre-treatment targets for optimizing the therapeutic response. Two mechanisms that appear to underlie the modulation of the antidepressant treatment response are biotransformation and bioaccumulation, and these appear to be mediated by specific bacterial strains. These findings could support the personalisation of treatment by informing the selection of the best antidepressant for each individual. In addition, they suggest that the therapeutic response to antidepressants may be optimised by manipulating the gut microbiome prior to treatment.},
}

@article {pmid41258153,
year = {2025},
author = {Cheng, YC and Krieger, M and Korves, AM and Camarinha-Silva, A},
title = {The chicken gut microbiome in conventional and alternative production systems.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {153},
pmid = {41258153},
issn = {1674-9782},
support = {FKZ 2821OE034//Bundesministerium für Ernährung und Landwirtschaft/ ; },
abstract = {The poultry gut microbiome plays a key role in nutrient digestion, immune function, and overall health. Differences among various farming systems, including conventional, antibiotic-free, free-range, and organic systems, influence microbial composition and function through variations in diet, genetic selection, environmental exposure, and antibiotic use. Conventional systems typically rely on formulated diets and controlled housing conditions, often with routine antimicrobial use. In contrast, organic systems emphasize natural feed ingredients, including roughage, outdoor access, and strict limitations on the use of antibiotics. These divergent practices shape the gut microbiota differently, with organic systems generally associated with greater exposure to environmental microbes and, consequently, greater microbial diversity. However, the implications of this increased diversity for poultry health and performance are complex, as organic systems may also carry a higher risk of pathogen exposure. This review summarizes current findings on the chicken gut microbiome across conventional and alternative production systems (antibiotic-free, free-range, and organic), focusing on microbial diversity, functional potential, and disease resilience. The need for standardized methodologies and consistent nomenclature in microbiome research is also discussed to improve comparability across studies. Understanding how production systems influence the gut microbiota is essential for improving poultry health and productivity while addressing challenges related to antimicrobial resistance and sustainable farming practices.},
}

@article {pmid41258106,
year = {2025},
author = {Zhang, Y and Ju, M and Chen, S and Yang, W and Cai, Y and Yu, X and Chen, G and Shen, Z and Bai, Y and Ren, H and Li, Y and Shen, L and Li, J and Shi, P and Yuan, Y and Han, B and Yao, H},
title = {Migration of CD8 + TSCM cells into intestine via PPBP-CXCR2 axis increases host stress susceptibility by inhibiting gut microbiome-derived homovanillic acid.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10165},
pmid = {41258106},
issn = {2041-1723},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *CD8-Positive T-Lymphocytes/immunology/metabolism ; Humans ; Mice ; Male ; Mice, Inbred C57BL ; *Stress, Psychological/immunology/metabolism ; Female ; Cell Movement ; *Memory T Cells/immunology/metabolism ; *Intestines/immunology/microbiology ; Adoptive Transfer ; },
abstract = {Psychosocial stress impacts immune system and brain function, yet mechanisms linking peripheral immune dysregulation to major depressive disorder remain unclear. Here, we demonstrate that a specific subset of T cells, the stem cell-like memory CD8[+] T (TSCM) cells, is elevated in patients and stress-susceptible mice. CD8[+] TSCM cells from patients display unique transcriptional programs and correlated with depression severity. Adoptive transfer of stress-derived CD8[+] TSCM cells induced depressive-like behavior and neuroinflammation in recipients, without brain migration. Employing a whole-body immunolabeling technology, we discover CD8[+] TSCM cells migrated to intestine via the interaction of pro-platelet basic protein and C-X-C motif chemokine receptor 2. CD8[+] TSCM cells decrease the abundance of tyrosine-metabolizing bacteria to reducing homovanillic acid production, triggered neuroinflammation and depressive symptoms. Thus, our findings uncover a complex interplay between CD8[+] TSCM cells and gut microbial metabolism, shedding light on potential mechanisms underlying depression and suggesting avenues for therapeutic intervention.},
}

Animals
*Gastrointestinal Microbiome/immunology
*CD8-Positive T-Lymphocytes/immunology/metabolism
Humans
Mice
Male
Mice, Inbred C57BL
*Stress, Psychological/immunology/metabolism
Female
Cell Movement
*Memory T Cells/immunology/metabolism
*Intestines/immunology/microbiology
Adoptive Transfer

@article {pmid41257857,
year = {2025},
author = {Knudsen, KS and Husebø, G and Nielsen, R and Paytuvi-Gallart, A and Malinverni, R and Sanseverino, W and Lehmann, S and Eagan, TM},
title = {Whole genome sequencing of the pulmonary microbiome in interstitial lung disease subtypes.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {324},
pmid = {41257857},
issn = {1465-993X},
mesh = {Humans ; Male ; *Lung Diseases, Interstitial/microbiology/genetics/diagnosis ; Female ; Middle Aged ; *Microbiota/genetics ; *Lung/microbiology ; Aged ; *Whole Genome Sequencing/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Dysbiosis/genetics ; },
abstract = {BACKGROUND: Interstitial lung diseases (ILDs) represent a heterogeneous group of lung disorders, some of which remain unclassifiable. The pulmonary microbiome may contribute to ILD pathogenesis, yet research is limited. Whole genome sequencing (WGS) offers enhanced microbial characterization. Here we evaluate the dysbiosis index (DI) as a potential biomarker to refine the classification of unclassifiable ILD.

METHODS: Protected bronchoalveolar lavage (PBAL) samples were collected from the right middle lobe of 12 IPF patients, 34 sarcoidosis patients, 11 unclassifiable ILD patients and 100 healthy controls. WGS was performed with the Illumina NovaSeq platform. Operational Taxonomic Units (OTU) were identified with GAIA 2.0 software, and statistical analyses were performed in R. The DI was calculated based on differential abundant species.

RESULTS: Alpha diversity was significantly higher in IPF and sarcoidosis patients compared to healthy controls. Beta diversity analysis revealed distinct microbial composition in IPF, sarcoidosis and unclassifiable ILD groups relative to controls. Differential abundance analysis identified several taxa with significant variation across groups. Notably, the dysbiosis index demonstrated high sensitivity and specificity in distinguishing IPF and sarcoidosis from healthy controls and provided further insight into the microbial characterization of unclassifiable ILD.

CONCLUSIONS: The pulmonary microbiome in unclassifiable ILD patients differed from healthy controls, and the dysbiosis index may provide exploratory insights for future ILD characterization.},
}

Humans
Male
*Lung Diseases, Interstitial/microbiology/genetics/diagnosis
Female
Middle Aged
*Microbiota/genetics
*Lung/microbiology
Aged
*Whole Genome Sequencing/methods
Bronchoalveolar Lavage Fluid/microbiology
Dysbiosis/genetics

@article {pmid41257762,
year = {2025},
author = {Linton, S and Hossenbaccus, L and Davis, A and Thiele, J and Garvey, S and Botting, H and Steacy, L and Sheth, PM and Ellis, AK},
title = {Staphylococcus aureus nasal carriage is associated with faster symptom resolution following nasal allergen challenge in ragweed-allergic participants: a subset of the Allergic Rhinitis Microbiome Study.},
journal = {Allergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology},
volume = {21},
number = {1},
pages = {48},
pmid = {41257762},
issn = {1710-1484},
abstract = {In this letter, we report that ragweed-allergic participants with nasal Staphylococcus aureus carriage (n = 7) exhibited significantly smaller reductions in Peak Nasal Inspiratory Flow from baseline at 3 h (P = 0.013) and 5 h (P = 0.008) post-nasal allergen challenge compared to non-carriers (n = 12). There was no significant difference between carriers and non-carriers in the initial response within the first three hours following the challenge (all P > 0.05). Carriers also reported significantly lower Total Nasal Symptom Scores (P = 0.015) and Total Rhinoconjunctivitis Symptom Scores (P = 0.021) at 48 h. These findings suggest that S. aureus carriage does not exacerbate allergic responses and may instead be associated with more rapid symptom resolution.},
}

@article {pmid41257759,
year = {2025},
author = {Flintham, L and Dack, C and Koumanov, F and Feil, E and Ainsworth, B},
title = {A qualitative evaluation of older people's perceptions towards optimal diet management in the context of antimicrobial resistance.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {4060},
pmid = {41257759},
issn = {1471-2458},
}

@article {pmid41257564,
year = {2025},
author = {Zou, F and Chen, H and Yu, X and Hu, D and Dong, Y and Zhou, X and Si, X},
title = {Oral microbial profile polymorphisms predict early Siewert II adenocarcinoma of esophagogastric junction.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {764},
pmid = {41257564},
issn = {1471-2180},
support = {JSPH-MB-2021-13//the Clinical Capacity Enhancement Project of the First Affiliated Hospital of Nanjing Medical University/ ; },
mesh = {Humans ; *Esophagogastric Junction/pathology/microbiology ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology/pathology/diagnosis ; *Esophageal Neoplasms/microbiology/pathology/diagnosis ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Aged ; *Microbiota/genetics ; *Mouth/microbiology ; *Stomach Neoplasms/microbiology ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Dysbiosis of the oral microbiota has been shown to be associated with the development of esophageal and gastric cancer. Nevertheless, little research explores how oral microbiota might contribute to the occurrence and progression of adenocarcinoma of the esophagogastric junction (AEG).

METHOD: 16 S rRNA V3-V4 amplicon sequencing was performed on 106 oral microbiota samples from 55 AEG patients and 51 controls. To determine key microbial indicators, Linear Discriminant Analysis Effect Size (LEfSe) analysis, Random Forest model, and species composition heatmaps were utilised. Spearman correlation analysis assessed the relationship between oral microbiota and clinicopathological variables. PICRUSt2 was employed to predict microbial functions and investigate the association with KEGG metabolic pathways.

RESULTS: A total of 584 oral genera and 647 oral species were observed in AEG and controls, excluding unidentified species. The abundance of 24 oral genera significantly increased in AEG patients, with Neisseria, Streptococcus, Rothia, Gemella, and Capnocytophaga being the five most abundant. Lefse, RF model and Species composition heatmap identified that genera enriched in the AEG group including Streptococcus, Neisseria, Rothia, Gemella, and genera depleted including Prevotella, Veillonella, Centipeda, Nanosynbacter were determined as biological markers to distinguish AEG from healthy controls. The genera with decreased abundance in AEG patients showed a positive association with WBC levels, neutrophil levels, and CA724 levels in the Mantel correlation test. PICRUSt analysis revealed significant differences in the abundance of 12 KEGG pathways. Carbohydrate metabolism, drug resistance, infectious diseases, lipid metabolism, nucleotide metabolism, and membrane transport pathways were positively correlated with genera enriched in the AEG group such as Streptococcus and Rothia, while negatively correlated with depleted genera like Prevotella.

CONCLUSION: Our research may suggest that dysbiosis of the oral microbiota and alterations in the KEGG metabolic pathway are linked to the development of AEG. In the future, we will conduct comprehensive verification through animal experiments and large-scale multicentre studies.},
}

Humans
*Esophagogastric Junction/pathology/microbiology
Male
Female
Middle Aged
*Adenocarcinoma/microbiology/pathology/diagnosis
*Esophageal Neoplasms/microbiology/pathology/diagnosis
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Aged
*Microbiota/genetics
*Mouth/microbiology
*Stomach Neoplasms/microbiology
Dysbiosis/microbiology

@article {pmid41257545,
year = {2025},
author = {Vazquez-Ortiz, K and Rivera-Orduña, FN and Zúñiga, G},
title = {Comparative genomics of dominant members of the gut core microbiome of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) reveals potential functional complementarity in the detoxification process.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {1064},
pmid = {41257545},
issn = {1471-2164},
support = {891748//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
}

@article {pmid41256608,
year = {2025},
author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI},
title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.02.680046},
pmid = {41256608},
issn = {2692-8205},
abstract = {UNLABELLED: Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, 'reverse translation' experiments are performed where intact fecal microbiomes collected from trial participants prior to and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because 'no treatment' control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes microbial gene expression consistent with a less virulent gut ecosystem and changes in expression of (i) components of gut epithelial cell junctions in the enterocytic and goblet cell lineages, (ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and (iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.

SIGNIFICANCE STATEMENT: Undernutrition is a global health problem. Recent clinical trials of a gut microbiome-directed complementary food (MDCF-2) designed to repair the perturbed gut microbiomes of undernourished Bangladesh children produced superior growth outcomes versus a standard nutritional supplement. Given ethical considerations and tissue sampling constraints associated with these types of studies, we colonized gnotobiotic mice postnatally with microbiome samples obtained from trial participants before and after treatment to model "unrepaired" and "repaired" gut ecosystems. Using a multi-omics approach, we uncover heretofore unappreciated changes in expressed chemosensory tuft cell, mucus-producing goblet cell and absorptive enterocytic functions and interactions accompanying microbiome repair. Extending microbiome clinical trials back to preclinical models ('reverse translation') provides mechanistic insights that can inform design/interpretation of future interventions.},
}

@article {pmid41256588,
year = {2025},
author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandon, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR},
title = {Pre-treatment Microbiome Diversity and Function is associated with Expansion of Cytotoxic and Regulatory Immune Populations after N-803 treatment in People with HIV.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.01.679827},
pmid = {41256588},
issn = {2692-8205},
abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.

METHODS: In this longitudinal metagenomic study, we analyzed fecal microbiomes from ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.

RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii increased significantly after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8 [+] and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA [+] cells. MaAsLin2 analyses further associated short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.

CONCLUSIONS: These results indicate that gut microbiome diversity prior to immunotherapy influences host response and suggest that microbiome-based strategies could improve efforts to cure HIV.},
}

@article {pmid41256397,
year = {2025},
author = {Chakraborty, M and Shi, SM and Porter, IE and Richard, DJ and Marinov, GK and Moore, AA and Blum, JLE and Natarajan, A and Jahng, JW and Wu, JC and Lu, SX and Davidson, SM and Greenleaf, WJ and Saw, NL and Shamloo, M and Brunet, A and Wyss-Coray, T and Bhatt, AS},
title = {Age-related microbiome metabolites alter RNA splicing and chromatin accessibility in the brain.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.03.680371},
pmid = {41256397},
issn = {2692-8205},
abstract = {The gut microbiome generates diverse metabolites that can enter the bloodstream and alter host biology, including brain function. Hundreds of physiologically relevant, gut-brain signaling molecules likely exist; however, there has been no systematic, high-throughput effort to identify and validate them. Here, we integrate computational, in vitro , and in vivo approaches to pinpoint microbiome-derived metabolites whose blood levels change during aging, and that induce corresponding changes in the mouse brain. First, we mine large-scale metabolomics datasets from human cohorts (each n ≥ 1200) to identify 30 microbiome-associated metabolites whose blood levels change with age. We then screen this panel in an in vitro transcriptomic assay to identify metabolites that perturb genes linked to age-related neurodegeneration. We then test four metabolites in an acute-exposure mouse model, and use multi-omic approaches to evaluate their impact on cellular functions in the brain. We confirm the known neurodegeneration-promoting effects of trimethylamine N-oxide (TMAO), including mitochondrial dysfunction, and further discover its disruptive impact on the pathways of glycolysis, GABAergic signaling, and RNA splicing. Additionally, we identify glycodeoxycholic acid (GDCA), a microbiome-derived secondary bile acid, as a potent regulator of chromatin accessibility and suppressor of genes that protect the brain from age-related, neurodegeneration-promoting insults. GDCA also acutely reduces mobility. In summary, we present a scalable framework for linking microbiome metabolites to host pathologies, and apply it to identify microbial metabolites that induce molecular changes related to neurodegeneration.},
}

@article {pmid41256368,
year = {2025},
author = {Gao, A and Newhart, V and Flory, M and Alam, A},
title = {Pro-restitutive Bacteroides thetaiotaomicron reprograms the transcriptome of intestinal epithelial cells by modulating the expression of genes essential for proliferation and migration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.30.679439},
pmid = {41256368},
issn = {2692-8205},
abstract = {The mammalian intestine harbors a highly complex, very diverse, and numerically vast community of symbiotic microorganisms, which profoundly influence the development and maintenance of the intestinal barrier function. Alterations in microbial composition, known as dysbiosis, are observed in Inflammatory Bowel Disease (IBD), colorectal cancer (CRC), and gastrointestinal infections; however, the exact causal relationship between these changes and the resolution of intestinal inflammation and the repair of damaged mucosa remains unclear. Notably, IBD is not only marked by dysbiosis but also by changes in microbial metabolic pathways and metabolite landscape in the intestinal lumen. The small molecules and microbial metabolites present in the intestinal lumen have emerged as potential regulators of gut pathology, cancer, and mucosal repair. Investigating how altered microbiota and microbial metabolic activities influence intestinal epithelial cells (IEC) can provide insights into their role in the regeneration of mucosal epithelia and restoration of gut barrier functions. This knowledge can be harnessed to promote intestinal homeostasis, prevent relapse, and prolong remission of IBD. To dissect the complex interplay between the gut microbiome and IEC, we focused on the overrepresented bacterium Bacteroides thetaiotaomicron . Here, we show that B. thetaiotaomicron and Akkermansia muciniphila , the dominant members of gut microbiota, expand during the repair & resolution phase of the chemically induced acute murine colitis. Furthermore, our bioinformatics analysis demonstrated that the elevated relative abundance of B. thetaiotamicron was also accompanied by rewiring of bacterial metabolic programs towards the essential amino acid metabolism, polyamine synthesis and utilization, stress response mechanisms, cell envelope biogenesis, and nutrient scavenging. Our RNA sequencing and transcriptomic analysis of primary human colonic epithelial cells cocultured with B. thetaiotaomicron showed that B. thetaiotaomicron stimulates the expression of genes and pathways involved in different cellular functions, including proliferation, differentiation, adhesion, lipid metabolism, migration, chemotaxis, and receptor expression. Our study emphasizes the crucial functions of the gut microbiome and metabolic activities in regulating the functions of intestinal epithelial cells during the repair of injured gut mucosa. Thus, these microorganisms and their metabolism hold promise as potential therapeutic agents.},
}

@article {pmid41256293,
year = {2025},
author = {Agrawal, H and Agarwal, N and Gupta, N},
title = {Impact of gut microbiome on outcomes following endoscopic interventions in gastrointestinal disease.},
journal = {World journal of gastrointestinal endoscopy},
volume = {17},
number = {11},
pages = {110207},
pmid = {41256293},
issn = {1948-5190},
abstract = {BACKGROUND: Endoscopic interventions play a vital role in diagnosing and managing gastrointestinal diseases, but complications such as bleeding, infection, and delayed healing can adversely affect patient outcomes. The influence of the gut microbiome on these outcomes is increasingly being recognized.

AIM: To evaluate the role of the gut microbiome in influencing clinical outcomes after endoscopic interventions, focusing on microbial diversity, specific taxa, metabolic functions, and emerging predictive models.

METHODS: A systematic literature search was conducted in PubMed, EMBASE, and Cochrane databases up to May 2025, selecting human studies that analyzed gut microbiome composition or function in relation to endoscopic interventions and clinical outcomes. Microbiome analysis techniques included 16S rRNA gene sequencing, metagenomics, and metabolomics.

RESULTS: Forty-two studies met the inclusion criteria. Our review identifies key beneficial microbes, such as Faecalibacterium prausnitzii and Bacteroides spp., which support mucosal healing. In contrast, dysbiosis (e.g., an increased abundance of Proteo bacteria) is associated with poorer healing and higher complication rates. Notably, microbiome-informed predictive models have shown strong potential for forecasting post-procedural complications, offering a pathway to personalized treatment strategies. Probiotics have also emerged as a promising intervention, helping to restore microbial balance and reduce complications such as infection and delayed healing.

CONCLUSION: The gut microbiome plays a significant role in recovery after endoscopy. Integrating microbiome analysis into clinical decision-making could improve outcomes through personalized predictions and targeted therapies. Future research should focus on standardizing microbiome assessment protocols and validating predictive models to optimize patient care.},
}

@article {pmid41256169,
year = {2025},
author = {Band, VI and LaPoint, P and Levy, S and Krausfeldt, L and Lacroix, IS and Chong, A and Brandes, NT and Schwarz, B and Mistry, S and Burns, AS and Bacorn, M and Banks, K and Strength, R and Chen, Q and Romero-Soto, HN and Prasad, R and Apps, R and Wang, L and Douagi, I and Polanco, JJ and Kotekar, A and Mukherjee, A and Koroleva, G and Compean, A and Sellers, B and Langowski, T and Rose, K and Roy, S and Namasivayam, S and Perez-Chaparro, PJ and Chau, J and Stacy, A and Belkaid, Y and Hourigan, SK},
title = {Bismuth subsalicylate profoundly alters gut microbiome and immunity with increased susceptibility to infection.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.01.25337000},
pmid = {41256169},
abstract = {Bismuth subsalicylate (BSS) is a commonly used over-the-counter medication for a variety of gastrointestinal symptoms. BSS sequesters gut sulfides, which have been shown in murine studies to be key regulators of gut microbiota. Here, we investigated the impact of BSS on human gut microbiome, immunity and susceptibility to enteric pathogens. We observed a significant shift in microbiome composition after BSS usage, with a profound expansion in bacteria with pathogenic potential including Pseudomonadota. Metabolite composition was greatly altered with increased amino acid levels and decreased short chain fatty acids and secondary bile acids. Notably, there was a collapse of key CD4 T cell subsets in the ileum. Finally, mouse and ex vivo human models revealed that BSS treatment increases susceptibility to colonization with the enteric pathogen Salmonella enterica . This study underlines the key role of sulfides in human gut microbiome and immunity and warrants further investigation into commonly used sulfide-depleting drugs.},
}

@article {pmid41255946,
year = {2025},
author = {Cui, L and Wang, Q and Sun, S and Li, W and Li, L and Sun, K and Zhou, Y and Tu, G and Liu, R and Li, L and Yu, Z and Zhang, C and Wu, X and Pan, T},
title = {The Role of Semi-Wild Habitats in the Physical Conditions of Juvenile Alligators: Implications for Conservation.},
journal = {Ecology and evolution},
volume = {15},
number = {11},
pages = {e72451},
pmid = {41255946},
issn = {2045-7758},
abstract = {The number and survival rate of juveniles play a key role in the recovery of Chinese alligators (Alligator sinensis). The differences between artificial and semi-wild environments can directly affect the growth and development of juvenile alligators. This study analyzed the physical conditions (lengths and weights) and cloacal microbial communities of juvenile alligators in both artificial breeding (DJ, ZX) and semi-wild (GJM) environments to reveal the significant effects of environmental pressure on their physiological state and microbiome. The results revealed that the body length (23.15 ± 1.06 cm) and weight (22.8 ± 3.08 g) of juvenile alligators in the GJM were significantly lower than those in the artificial environment (body length = 29.5 cm, weight = 68.6 g; p < 0.01). Moreover, the microbial α diversity (ACE, Shannon) of the GJM was significantly reduced, and the community structure was significantly separated (NMDS analysis), suggesting that the pressure of the semi-wild environment inhibited growth. In terms of microbial composition, the relative abundance of Actinobacteria in the GJM group was significantly, increased, whereas that of Bacteroidetes was decreased, and Microbacteria and Cyanobacteria were unique; at the genus level, environmentally specific marker genera were identified (such as Limnohabitans and Pseudomonas in GJM and Fluviicola and Deinococcus in the artificial environments). LEfSe analysis further elucidated the differential marker microbiota (such as Actinobacteria/Cyanobacteria in GJM). In summary, stress (such as food shortages) in semi-wild environments affects the growth and development of juvenile alligators by changing their microbial communities (such as enriched actinomycetes), This finding provides a microbial ecological basis for optimizing the conservation strategy of the Chinese alligator.},
}

@article {pmid41255677,
year = {2025},
author = {Devulapalli, CS},
title = {Modulatory role of vitamin D in atopic dermatitis and allergic rhinitis.},
journal = {World journal of clinical pediatrics},
volume = {14},
number = {4},
pages = {112145},
pmid = {41255677},
issn = {2219-2808},
abstract = {Vitamin D, beyond its classical role in calcium homeostasis, has emerged as a key regulator of immune function and epithelial barrier integrity. Its deficiency during early childhood-a critical period for immune maturation-has been increasingly implicated in the development of atopic diseases. While extensively studied in asthma, its role in non-respiratory allergic conditions such as atopic dermatitis (AD) and allergic rhinitis (AR) remains comparatively underexplored. This minireview synthesizes current mechanistic and clinical evidence on vitamin D in pediatric AD and AR. In AD, vitamin D promotes epidermal barrier function through upregulation of filaggrin and ceramide synthesis, and enhances antimicrobial defense via induction of antimicrobial peptides. Observational studies consistently report lower serum 25-hydroxyvitamin D in affected children, particularly those with allergic sensitization. Select randomized controlled trials suggest clinical improvement with supplementation, especially at doses > 2000 IU/day in deficient individuals. In AR, epidemiological data indicate stronger inverse associations with seasonal (pollen-induced) disease. Proposed mechanisms include modulation of dendritic cells, regulatory T cells, T helper 2 cytokines, and mucosal barrier integrity. The shared immunopathogenesis of AD and AR underscores vitamin D's relevance. Although promising, clinical evidence remains heterogeneous. Future research should prioritize phenotype-stratified trials to clarify optimal dosing, timing, and individual response determinants, including genetics and microbiome composition.},
}

@article {pmid41255658,
year = {2025},
author = {Nagoba, BS and Dhotre, SV and Sonar, MN and Mumbre, SS and Gavkare, AM and Dhotre, PS},
title = {Neonatal and pediatric sepsis: Microbiological insights, diagnostic innovations, and antimicrobial challenges.},
journal = {World journal of clinical pediatrics},
volume = {14},
number = {4},
pages = {107974},
pmid = {41255658},
issn = {2219-2808},
abstract = {Neonatal and pediatric sepsis remains a major global health concern, contributing significantly to morbidity and mortality among children under 5 years of age. The clinical and microbiological characteristics of sepsis differ markedly in neonates and children, necessitating tailored diagnostic and treatment approaches. This mini-review explores the evolving microbiological landscape, recent advancements in diagnostic methodologies, and challenges posed by antimicrobial resistance (AMR) in managing neonatal and pediatric sepsis. Emerging pathogens, including multidrug-resistant Gram-negative bacilli and fungal organisms, are reshaping the epidemiology of sepsis. Innovations in molecular diagnostics, including polymerase chain reaction-based platforms, next-generation sequencing, and artificial intelligence-integrated tools, are revolutionizing early pathogen detection and resistance profiling. However, implementation gaps persist, particularly in low- and middle-income countries. Therapeutic challenges are compounded by limited pediatric data on newer antimicrobials and rising AMR rates. Infection prevention strategies, especially in intensive care units, are crucial to outbreak containment. An integrated approach combining microbiological surveillance, rapid diagnostics, and antimicrobial stewardship is critical for improving sepsis outcomes. Future research should focus on context-specific implementation of diagnostic tools and optimizing treatment strategies for resource-limited settings.},
}

@article {pmid41255540,
year = {2025},
author = {Tseyslyer, Y and Malyi, V and Saifullina, M and Tsyryuk, O and Shvets, Y and Penchuk, Y and Kovalchuk, I and Kovalchuk, O and Korotkyi, O and Bulda, V and Lazarieva, O},
title = {Harnessing gut-derived bioactives and AI diagnostics for the next generation of type 2 diabetes solutions.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1699954},
pmid = {41255540},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/diagnosis/therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Artificial Intelligence ; Quality of Life ; },
abstract = {INTRODUCTION: The prevalence of type 2 diabetes (T2D) has significantly increased over the past 20 years, currently affecting over 500 million people worldwide. Projections suggest that this number could rise to over 700 million in the next two decades. Despite advancements in medication and global health strategies that promote healthy lifestyles, T2D remains a complex disease that impacts the quality of life. Traditional treatment methods are becoming less effective, highlighting the need for innovative approaches to prevention, diagnosis, and treatment.

METHODS: Two promising areas of research that could transform the management of T2D are the use of biologically active substances derived from the intestines and the integration of artificial intelligence (AI) in clinical diagnostics. The human intestinal microbiota plays a crucial role in metabolic processes, including glucose regulation and insulin sensitivity. Microbial metabolites, including bile acids and short-chain fatty acids, have potential as therapeutic agents for metabolic disorders. As digital medicine advances, AI is increasingly utilized for real-time monitoring and personalized risk assessments. The medical field is evolving from merely using biosensors for glucose tracking to employing machine learning to analyze various biological indicators and electronic medical records.

RESULTS: Recent research at the intersection of microbiome studies and AI may improve diagnostic accuracy and support tailored treatment strategies. This study aims to analyze global experiences with the implementation of bioactive substances from the intestines and the diagnostic potential of AI in developing a new approach to enhancing the quality of life and treating T2D.

DISCUSSION: We examine the diverse functions of microbial metabolites and the current landscape of their therapeutic applications. Additionally, the review examines the current state of AI in diagnostics, with a particular focus on microbiome parameters. As a result, we propose a novel model that combines these two fields into an adaptive and personalized approach to treating patients with T2D and improving their quality of life.},
}

Humans
*Diabetes Mellitus, Type 2/diagnosis/therapy/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
*Artificial Intelligence
Quality of Life

@article {pmid41255529,
year = {2025},
author = {Horiachok, M and Potapova, K and Ivanykovych, T and Yerokhovych, V and Ilkiv, Y and Sokolova, L},
title = {Integrating gut microbiota into multidisciplinary perspectives on diabetic neuropathy.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1710868},
pmid = {41255529},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Neuropathies/microbiology/therapy/metabolism ; *Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; },
abstract = {Diabetic neuropathy (DN) is one of the most common and debilitating complications of diabetes mellitus, yet its precise pathogenesis remains incomplete. Emerging evidence highlights the gut microbiome as a key factor linking metabolic dysfunction, immune activation, and neuronal damage. Even minor dysbiosis may interfere with microbial metabolite balance and disrupt intestinal integrity, leading to local and, consequently, systemic inflammation, which in turn drives altered pain response via the gut-brain-immune axis. Recent clinical and preclinical data show that reduced short-chain fatty acid availability, altered bile acid and tryptophan metabolism, let alone expansion of pro-inflammatory species collaboratively contribute to DN onset and progression. Moreover, advances in metagenomics and metabolomics reveal reproducible microbiome-derived biomarkers that could predict neuropathy risk and pain phenotypes independent of glycemic control, supporting the microbiome as both a mechanistic driver and a measurable potential diagnostic tool. In the context of management, microbiota-affected interventions, such as probiotics, synbiotics, omega-3 supplementation, and fecal microbiota transplantation, show early promise in alleviating symptoms and improving nerve function. This mini-review synthesizes current evidence on the microbiome's role in DN, emphasizing its dual potential as a biomarker for early diagnosis and a therapeutic target for precision microbiome-based interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diabetic Neuropathies/microbiology/therapy/metabolism
*Dysbiosis/microbiology
Animals
Probiotics/therapeutic use

@article {pmid41255342,
year = {2025},
author = {Miller, DM and McCauley, KF and Dunham-Snary, KJ},
title = {Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD): Mechanisms, Clinical Implications and Therapeutic Advances.},
journal = {Endocrinology, diabetes & metabolism},
volume = {8},
number = {6},
pages = {e70132},
doi = {10.1002/edm2.70132},
pmid = {41255342},
issn = {2398-9238},
support = {202303PJT-190103/CAPMC/CIHR/Canada ; CRC-2020-00192//Tier II Canada Research Chair in Mitochondrial and Metabolic Regulation in Health and Disease/ ; 41511//Canada Foundation for Innovation/ ; 6035577//Banting Research Foundation and Mitacs/ ; 6032495//Queen's University, Kingston, Ontario, Canada/ ; 6034430//Queen's University, Kingston, Ontario, Canada/ ; },
mesh = {Humans ; *Fatty Liver/therapy/epidemiology/etiology/metabolism ; *Metabolic Syndrome/complications/epidemiology ; *Non-alcoholic Fatty Liver Disease/therapy/epidemiology ; Prevalence ; Insulin Resistance ; },
abstract = {INTRODUCTION: Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) has emerged as the most prevalent chronic liver disease worldwide, affecting ~25%-30% of the adult population, with higher prevalence observed in individuals with obesity and type 2 diabetes. Among reported MASLD cases, prevalence is consistently higher in men than in women, and global incidence has risen by ~50% over the past two decades, mirroring the global rise in obesity and metabolic syndrome. MASLD encompasses a spectrum of hepatic pathologies ranging from simple steatosis to steatohepatitis, fibrosis and cirrhosis. Despite its high prevalence, the heterogeneity in disease progression and relative absence of approved pharmacological therapies pose challenges for effective clinical management.

METHODS AND RESULTS: This review synthesises current literature on MASLD across epidemiology, pathophysiology, clinical presentation and treatment. Key molecular mechanisms, including lipid metabolism dysregulation, insulin resistance and mitochondrial dysfunction, are examined with a focus on understanding the basis for progression to metabolic dysfunction-associated steatohepatitis (MASH). Clinical manifestations, diagnostic tools and risk stratification systems for MASLD are summarised. Current and emerging therapies such as lifestyle interventions, pharmacological agents and microbiome-targeted strategies are reviewed. The review also highlights ongoing challenges, including diagnostic limitations, disease heterogeneity and disparities in care.

CONCLUSION: MASLD is a complex, multifactorial liver disease with a growing public health impact, driven by the rising prevalence of metabolic syndrome. Mitochondrial dysfunction is a critical nexus linking genetic susceptibility to metabolic stress and inflammatory responses. Preclinical models that capture these mitochondrial contributions are vital for therapeutic discovery and for advancing personalised medicine approaches in MASLD care.},
}

Humans
*Fatty Liver/therapy/epidemiology/etiology/metabolism
*Metabolic Syndrome/complications/epidemiology
*Non-alcoholic Fatty Liver Disease/therapy/epidemiology
Prevalence
Insulin Resistance

@article {pmid41255157,
year = {2025},
author = {Chen, J and Wu, C and Yang, R and Chen, Z and Yang, X and Xu, Y and Cheng, X and Sui, H and Zhang, S and Zhu, X and Wu, M and Huang, Y and Chen, X and Liu, H and Yang, J and Tan, X and Chen, F and Cheng, C and Shao, D and Han, X and Shi, B and Yang, C and Leong, KW and Huang, H},
title = {LPS-Binding Hydrogel for TLR4-Mediated Microbiota-Immune Modulation.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e14484},
doi = {10.1002/adma.202514484},
pmid = {41255157},
issn = {1521-4095},
support = {82301148//National Natural Science Foundation of China/ ; 82470955//National Natural Science Foundation of China/ ; 2024T170605//China Postdoctoral Science Foundation/ ; RD-02-202511//Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; 2025ZNSFSC0758//Sichuan Province Science and Technology Support Program/ ; RCDWJS2024-7//West China School of Stomatology, Sichuan University/ ; 24QNMP060//Health Commission of Sichuan Province/ ; TB2022005//Sichuan Provincial Postdoctoral Science Foundation/ ; },
abstract = {Lipopolysaccharide (LPS), a conserved component of Gram-negative bacteria, is a potent immune activator that disrupts tissue repair when released during microbial dysbiosis. LPS-scavenging strategies are often limited by the poor accessibility of lipid A, the bioactive core of LPS, which is shielded by variable oligosaccharide structures and embedded in bacterial membranes. To address this, a synergistic LPS-binding hydrogel (OCMC-PMBP) is developed, combining polymyxin B (PMB) for lipid A-targeted bacterial lysis and polyethyleneimine (PEI) for electrostatic LPS capture. This system is applied to oronasal-perforating wounds, a complex and infection-prone condition associated with cleft palate repair. Clinical microbiome analysis and murine models reveal that LPS-TLR4 signaling contributes to immune dysregulation and impaired healing. OCMC-PMBP treatment reduces LPS levels, restores microbiota balance, suppresses inflammation, and accelerates epithelial regeneration and collagen remodeling. Integrated 16S rRNA sequencing, metagenomics, and single-cell transcriptomics show that the hydrogel reprograms immune cell phenotypes and modulates macrophage interactions with neutrophils, epithelial cells, and fibroblasts across healing phases. This study introduces a biomaterials design combining antimicrobial and immunomodulatory functions to resolve dysbiosis-induced inflammation and enhance regenerative healing in complex mucosal wounds.},
}

@article {pmid41255097,
year = {2025},
author = {van Heule, M and Verstraete, M and Norris, JK and Graniczkowsa, KB and Scoggin, KE and Ali, HE and Ball, BA and De Spiegelaere, W and Daels, P and Weimer, BC and Dini, P},
title = {Beyond nocardioform: Transcriptionally active microbes and host responses in equine mucoid placentitis.},
journal = {Equine veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/evj.70112},
pmid = {41255097},
issn = {2042-3306},
support = {//UC Davis Center for Equine Health/ ; //Special Research Fund at University of Ghent (BOF)/ ; //Clay Endowment at UKY/ ; //John Hughes Endowment at UCDavis/ ; //Foundation for the Horse/ ; //Grayson-Jockey Club Research Foundation/ ; },
abstract = {BACKGROUND: Nocardioform placentitis (NP) is an understudied form of equine placentitis historically attributed to nocardioform bacteria, yet it remains uncertain whether these organisms are the sole pathogens involved.

OBJECTIVES: To elucidate the pathophysiology of NP and the host-pathogen interaction.

STUDY DESIGN: In vivo clinical multi-omics study.

METHODS: Dual RNA sequencing was performed to profile transcriptionally active microbial communities and concurrent placental transcriptome responses in samples from 31 placentas with and without NP. Untargeted metabolomics was performed to study the associated metabolites in the placenta.

RESULTS: The most abundant microbial transcripts belonged to Amycolatopsis, Crossiella, Lentzea, Enterococcus, and Mycobacterium. Bacterial gene expression in NP-affected placentas was enriched in pathways related to ribosomal activity and metabolic processes involving amino acid, carbohydrate, and glycosphingolipid metabolism. Concurrently, placental transcripts demonstrated significant upregulation of inflammatory pathways and downregulation of pathways associated with blood vessel formation. Untargeted metabolomics highlighted an elevated abundance of metabolites such as beta-D-fucose, nervonic acid, and zymostenol in the placentitis samples. Significant correlations were found between microbial genes (mraW, rlmB, amy, afuA, and cysC) and host inflammation genes (CXCL14, IL15RA, TASL, and IFIH1). Additionally, elevated beta-D-fucose, a microbe-specific metabolite, showed a strong correlation with microbial genes involved in stress-adaptive metabolism and DNA repair (ydhP, ybgC, serC, puuE, and radA). The bacterial enzymes involved in beta-D-fucose were notably upregulated and predominantly expressed by Amycolatopsis and Lentzea.

MAIN LIMITATIONS: Classification based on RNA abundance limited the number of Crossiella cases (n = 3).

CONCLUSIONS: Both nocardioform and non-nocardioform bacteria are involved in NP-diagnosed cases, challenging the current generalisation of the term 'nocardioform placentitis' and supporting the need to broaden diagnostic protocols for mucoid placentitis. Multi-omics profiling revealed potential host-microbe interactions mediated by microbial metabolites, offering mechanistic insights and opportunities for improved diagnostic strategies.},
}

@article {pmid41254816,
year = {2025},
author = {Chen, CY and Kuo, HC and Fang, YT and Lu, CW and Chen, SK and Hung, CM},
title = {Microbiota-gut-brain axis in avian parenting: gut microbiome associates with nest-construction behavior and neural gene expression in a songbird.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {120},
pmid = {41254816},
issn = {2524-4671},
support = {NSTC 112-2311-B-001-039-MY3//National Science and Technology Council/ ; NSTC 112-2811-B-001-025//National Science and Technology Council/ ; AS-CDA-108-L05//Academia Sinica/ ; },
}

@article {pmid41254708,
year = {2025},
author = {Liu, Y and Liu, Y and Huang, W and Liu, Y and Sun, J},
title = {An inflammation-responsive therapeutic gel for precise microbiota modulation in colitis.},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {719},
pmid = {41254708},
issn = {1477-3155},
support = {82304903//National Natural Science Foundation of China/ ; 82204678//National Natural Science Foundation of China/ ; 22202206//National Natural Science Foundation of China/ ; XYD2024GR03//National Research Innovation Talents Cultivation Project/ ; },
mesh = {Animals ; Mice ; *Colitis/drug therapy/microbiology/chemically induced ; Gels/chemistry/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Inflammation/drug therapy ; Nanofibers/chemistry ; Humans ; Tungsten/chemistry/pharmacology ; Male ; Cytokines/metabolism ; Leukocyte L1 Antigen Complex/metabolism ; Dextran Sulfate ; },
abstract = {Microbiome dysbiosis is a hallmark of inflammatory bowel disease (IBD), and its reprogramming represents a promising intervention strategy. Existing treatments are often limited by gastrointestinal instability and non-specific microbial toxicity, leading to suboptimal outcomes and potential aggravation of IBD symptoms. Herein, we construct a calcium phosphotungstate gel (CPW), characterized by tortile nanofibers (length > 5 μm, diameter ~ 20 nm) forming a stable 3D network, which remains structurally intact in gastrointestinal fluid for over 24 h and exhibits commendable resistance to gastric acid and digestive enzymes. Furthermore, CPW disintegrates specifically in response to the inflammatory biomarker calprotectin (CAL), releasing over 54% of tungsten payloads within 12 h (versus < 6% without CAL). The locally released tungsten ions selectively inhibit nitrate respiratory enzymes and induce apoptosis in approximately 50% of nitrate-dependent pathogens within 24 h, enabling precise microbiome modulation. As a versatile carrier, CPW demonstrated exceptional protection for diverse therapeutics (DIO, peptides, nucleic acids) against digestive enzymes, enabling > 70% cargo release specifically at inflamed sites. In DSS-induced colitis mice, DEX-loaded CPW (DEX@CPW) significantly improved colon length (comparable to healthy controls), reduced pro-inflammatory cytokines (IL-1β, IL-6, TNF-α by 2.1-3.3 fold), and restored beneficial microbiota. Crucially, CPW reduced systemic tungsten exposure by 62.7% in kidneys while increasing intestinal tungsten retention by 1.67-fold, demonstrating superior targeting. This dual-function platform-integrating pathogen-selective metallotherapy and inflammation-triggered drug release-represents a promising clinical approach for IBD by simultaneously modulating dysbiosis and ameliorating inflammation.},
}

Animals
Mice
*Colitis/drug therapy/microbiology/chemically induced
Gels/chemistry/pharmacology
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Inflammation/drug therapy
Nanofibers/chemistry
Humans
Tungsten/chemistry/pharmacology
Male
Cytokines/metabolism
Leukocyte L1 Antigen Complex/metabolism
Dextran Sulfate

@article {pmid41254590,
year = {2025},
author = {Schwob, G and Delleuze, M and Motreuil, S and Marschal, C and Saucède, T and Orlando, J and Poulin, E and Cabrol, L},
title = {Gut microbiome plasticity and host resistance in response to ocean warming in sub-Antarctic sea urchins.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {343},
pmid = {41254590},
issn = {1741-7007},
support = {program No. 1044 PROTEKER//French Polar Institute-IPEV/ ; Millennium Institute BASE, grant #ICN2021_002//Millennium Science Initiative Program - Chilean National Agency of Research and Innovation (ANID)/ ; 1211672//Regular FONDECYT - Chilean National Agency of Research and Innovation (ANID)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Climate Change ; *Sea Urchins/microbiology/physiology ; Antarctic Regions ; RNA, Ribosomal, 16S/genetics ; Seawater ; Acclimatization ; *Global Warming ; Oceans and Seas ; Temperature ; },
abstract = {BACKGROUND: Sub-Antarctic marine ecosystems are highly vulnerable to climate change, with rising ocean temperatures threatening key benthic species. Abatus cordatus, an endemic sea urchin of the Kerguelen Islands with limited dispersal capacity, has been hypothesised to possess a narrow thermal niche, which would render it particularly susceptible to environmental shifts. However, microbiome-mediated acclimation may provide a potential mechanism of resilience to ocean warming. To test these hypotheses, this study evaluates host survival and gut microbiome responses of A. cordatus to medium-term seawater warming under near-future temperature scenarios using 16S rRNA gene sequencing to compare these changes with those observed in sediment microbiomes.

RESULTS: Host mortality remained relatively low across all temperatures, showing no association with warming intensity and thereby suggesting thermal tolerance. While gut microbiome alpha-diversity remained stable, its composition shifted and variability increased with experiment duration and temperature, leading to greater inter-individual divergence and a decline in both the richness and abundance of core taxa. In contrast, sediment microbiomes remained more stable, exhibiting more deterministic assembly and increased core stability over time. At the taxonomic level, specific gut bacterial ASVs showed temperature-dependent abundance shifts, with greater flexibility at moderate thermal stress. Notably, the depleted and enriched ASVs were affiliated to known sulphate-reducing and fermentative taxa, respectively, suggesting a possible functional shift.

CONCLUSIONS: Overall, our findings suggest that A. cordatus can tolerate medium-term warming, with gut microbiome plasticity representing a potential mechanism supporting host resilience.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Climate Change
*Sea Urchins/microbiology/physiology
Antarctic Regions
RNA, Ribosomal, 16S/genetics
Seawater
Acclimatization
*Global Warming
Oceans and Seas
Temperature

@article {pmid41254344,
year = {2025},
author = {Distante, A and Garino, D and Cerrato, C and Perez-Ardavin, J and Flores, FQ and Lopetuso, L and Mir, MC},
title = {The role of the human microbiome in prostate cancer: a systematic review from diagnosis to treatment.},
journal = {Prostate cancer and prostatic diseases},
volume = {},
number = {},
pages = {},
pmid = {41254344},
issn = {1476-5608},
abstract = {BACKGROUND: Prostate cancer (PC) heterogeneity and treatment resistance remain major clinical challenges, with emerging evidence implicating the microbiome as a key modulator of disease pathogenesis. While microbial dysbiosis has been linked to PC diagnosis, progression, and therapeutic outcomes, the mechanisms underlying these associations are poorly understood. This review synthesizes current evidence on the diagnostic, prognostic, and therapeutic potential of the microbiome in PC.

METHODS: A systematic search of PubMed, Embase, and Cochrane Central Register of Controlled Trials (through April 2024) was conducted following PRISMA guidelines (PROSPERO: CRD42024534899). Controlled and observational studies investigating microbial roles in PC diagnosis (e.g., ISUP grading group), prognosis, or treatment response were included. Data extraction and quality assessment used the QUIPS tool. From 810 screened records, 42 studies met inclusion criteria.

RESULTS: Distinct microbial profiles differentiated PC from controls, with Mycoplasma genitalium and Staphylococcus spp. enriched in prostate tumors (3.1- and 2.7-fold, respectively) and correlated with inflammation (IL-6: r = 0.38, p = 0.002). Urinary microbiota showed diagnostic potential (sensitivity: 58-82%), though sampling methods influenced variability. Prognostically, Betaproteobacteria gut enrichment predicted earlier castration-resistant progression (5.2 months; HR 1.8, 95% CI 1.3-2.5), while ADT-induced dysbiosis (e.g., Klebsiella overgrowth) accelerated resistance (2.1-fold risk). Therapies altered microbial ecology: radiotherapy depleted Bacteroides (linked to proctitis; OR 3.1), and immunotherapy responders harbored higher Akkermansia muciniphila. Microbial androgen synthesis and endotoxin production emerged as resistance mechanisms.

CONCLUSIONS: The microbiome influences PC detection, aggressiveness, and treatment efficacy through direct (tissue-resident) and indirect (gut-derived) mechanisms. Standardized profiling and microbiome-modulating strategies (e.g., probiotics during ADT) may personalize management. Prospective trials are needed to validate causality and translate microbial biomarkers into clinical practice.},
}

@article {pmid41254308,
year = {2025},
author = {Nicola, T and Wenger, NM and Seidman, K and Evans, M and Yang, Y and Chen, D and Van Der Pol, WJ and Walia, A and Lefkowitz, EJ and Wang, J and LeMoire, A and Lin, L and Morrow, C and Ambalavanan, N and Gaggar, A and Lal, CV},
title = {Double-Blind Randomized Placebo-Controlled Trial of a Lactobacillus Probiotic Blend in Chronic Obstructive Pulmonary Disease.},
journal = {Pulmonary therapy},
volume = {},
number = {},
pages = {},
pmid = {41254308},
issn = {2364-1746},
support = {K08 HL141652/HL/NHLBI NIH HHS/United States ; R44HL164156/HL/NHLBI NIH HHS/United States ; UM1TR004771/TR/NCATS NIH HHS/United States ; },
abstract = {INTRODUCTION: Gut microbiota modulate systemic anti-inflammatory and immune responses in the lungs, suggesting a potential to support lung health through probiotic supplementation. We hypothesized that a probiotic blend (Lactobacilli) combined with herbal extracts (resB[®]) could improve quality of life in patients with chronic obstructive pulmonary disease (COPD).

METHODS: We conducted a randomized, double-blinded, placebo-controlled study (NCT05523180) evaluating the safety and impact of resB[®] on quality of life in volunteers with COPD. Participants took resB[®] or placebo (two capsules daily) for 12 weeks. The primary endpoint was change in quality of life by Saint George's Respiratory Questionnaire (SGRQ). Secondary outcomes included safety, serum and sputum biomarkers, and microbiome analysis. resB[®] was well tolerated with no related adverse events.

RESULTS: Participants receiving resB[®] showed significant improvement in SGRQ symptom scores (P < 0.05), while placebo recipients did not. In the resB[®] group, serum and sputum levels of matrix metalloproteinase 9, C-reactive protein, and interleukin 6 decreased (P < 0.05), correlating with increased stool Lactobacilli. Additionally, Veillonella abundance increased in both stool and sputum.

CONCLUSION: These findings suggest that resB[®] improves respiratory symptoms and reduces inflammation in patients with COPD, potentially by modulating gut and lung microbiota.

TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT05523180.},
}

@article {pmid41254244,
year = {2025},
author = {Mekadim, C and Mrázek, J and Vodička, M and Ergang, P and Fliegerová, KO and Mahayri, TM and Chawengsaksophak, K and Pácha, J},
title = {Impact of Sex, Gonadectomy, and Repeated Restraint Stress on Gut Microbiome in Mice.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {80},
pmid = {41254244},
issn = {1559-1182},
support = {Grant 21-10845S//Czech Science Foundation/ ; PPLZ Project: L200112201//Czech Academy of Science/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Restraint, Physical ; *Stress, Psychological/microbiology/blood ; *Sex Characteristics ; Mice, Inbred C57BL ; Mice ; *Castration ; Corticosterone/blood ; RNA, Ribosomal, 16S/genetics ; Cecum/microbiology ; Colon/microbiology ; },
abstract = {Recently, the bidirectional connection between the gastrointestinal microbiota and the brain has gained interest in many research studies. Findings have highlighted the potential role of stress and sex hormones in modulating the gut microbiome. To our knowledge, no study has investigated the effect of sex hormone perturbations on the gut microbiota in response to stress. To understand how stress may alter the gut microbiota differently depending on sex, gonadectomized and sham-operated male and female mice were subjected to 2 h of daily restraint stress for seven consecutive days. Body weight and plasma level of corticosterone were evaluated. Bacterial diversity and composition of colon and cecum were analyzed by sequencing of 16S rRNA gene. The bacterial communities were strongly altered by stress in the colon than in the cecum. A profound dysregulation of several metabolic and functional pathways was observed in sham mice. Alterations in the gut microbiome diversity and its functional pathways due to stress were more pronounced in males than in females. The present results provide potential sex-specific biomarkers and novel metabolic signatures in the gut microbiota related to stress disorders which may be used as potential targets in diagnostic and therapeutic approaches in neurogastroenterological diseases.},
}

Animals
*Gastrointestinal Microbiome/physiology
Male
Female
*Restraint, Physical
*Stress, Psychological/microbiology/blood
*Sex Characteristics
Mice, Inbred C57BL
Mice
*Castration
Corticosterone/blood
RNA, Ribosomal, 16S/genetics
Cecum/microbiology
Colon/microbiology

@article {pmid41254155,
year = {2025},
author = {Ayayee, P and Custer, G and Clayton, JB and Price, J and Ramer-Tait, A and Larsen, T},
title = {Assessing gut microbial provisioning of essential amino acids to host in a mouse model with reconstituted gut microbiomes.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1604},
pmid = {41254155},
issn = {2399-3642},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Amino Acids, Essential/metabolism ; Mice, Inbred C57BL ; Male ; Carbon Isotopes ; },
abstract = {Gut microbial provisioning of essential amino acids (EAAs) represents a critical but poorly understood aspect of mammalian nutrition, with direct implications for host metabolism, growth, and disease resistance. While advances in microbiome research have highlighted the potential significance of these microbial-host nutritional interactions, direct empirical evidence quantifying actual microbial contributions to host EAA supply remains surprisingly limited, particularly under controlled experimental conditions. Here, we show using stable carbon isotope analysis of six EAAs across brain, kidney, liver, and muscle tissues that germ-free mice maintained on a high-protein diet and conventionalized mice with reconstituted gut microbiomes fed a low-protein diet for twenty days exhibit no significant differences in δ[13]C-EAA values. Our results reveal no detectable microbial contribution to host EAA pools, as δ[13]C-EAA patterns remain nearly identical between treatment groups across all organs examined. Microbial profiling confirms that conventionalized mice successfully established diverse gut microbiota communities dominated by typical Firmicutes and Bacteroidetes phyla. These findings contrast with recent δ[13]C-EAA based studies that reported substantial microbial EAA contributions in wild-type mice, raising important questions about functional restoration of reconstituted gut microbiomes and underscoring the need to critically revisit experimental designs and analytical frameworks to better understand microbial nutrient provisioning dynamics.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
*Amino Acids, Essential/metabolism
Mice, Inbred C57BL
Male
Carbon Isotopes

@article {pmid41254023,
year = {2025},
author = {Liu, Y and Wu, W and Liang, Q and Diao, J and Yang, W and Zheng, S and Han, Y and Yuan, C},
title = {Metabolic and microbial alterations in oral potentially malignant disorders versus oral squamous cell carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40637},
pmid = {41254023},
issn = {2045-2322},
support = {PKUSS-2023CRF304//Peking University School and Hospital of Stomatology series of clinical research projects/ ; 2022YFE0118300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Mouth Neoplasms/metabolism/microbiology/diagnosis/pathology ; Male ; Female ; Middle Aged ; Saliva/metabolism ; *Carcinoma, Squamous Cell/metabolism/microbiology ; Aged ; Metabolomics/methods ; Biomarkers, Tumor/metabolism ; Adult ; Microbiota ; Metabolome ; },
abstract = {Oral potentially malignant disorders (OPMDs) are oral mucosal conditions associated with an increased risk of oral squamous cell carcinoma (OSCC), and their clinical manifestations may be subtle and insidious. The primary aim of this study was to identify metabolite-based biomarkers for early, non-invasive detection of tumor-related metabolic signals in this at-risk population. We enrolled 21 OPMD and 46 OSCC patients, collecting saliva and plasma from all participants and tissue samples from a subset of the same cohort (12 OPMD and 5 OSCC). Untargeted metabolomics identified 491 and 303 differential metabolites in saliva and plasma, respectively. Five metabolites-dodecanoic acid, tetradecanedioic acid, porphobilinogen, uridine, and isocitrate-were significantly altered in both biofluids. Tissue validation showed significant alterations in dodecanoic acid, tetradecanedioic acid, and isocitrate. Using all biologically annotated differential metabolites, AUCs were 0.888 (saliva) and 0.994 (plasma), while the tissue-anchored three-metabolite classifier yielded 0.694 (saliva) and 0.852 (plasma). Full-length 16S rDNA sequencing and integrative microbiome-metabolome analysis indicated potential correlations between microbial shifts and metabolite profiles. Our findings highlight metabolic alterations and cross-compartment associations across saliva, plasma, and tissue in OPMDs and OSCC. Notably, despite the higher internal discrimination of all-differential models, the tumor-informed three-metabolite model captures tissue-aligned metabolic changes detectable in saliva and plasma, providing a specific, non-invasive readout for early detection.},
}

Humans
*Mouth Neoplasms/metabolism/microbiology/diagnosis/pathology
Male
Female
Middle Aged
Saliva/metabolism
*Carcinoma, Squamous Cell/metabolism/microbiology
Aged
Metabolomics/methods
Biomarkers, Tumor/metabolism
Adult
Microbiota
Metabolome

@article {pmid41253982,
year = {2025},
author = {Chiba, N and Limviphuvadh, V and Ng, CH and Koyagi, R and Kino, Y and Nakamura, Y and Yamada, T},
title = {Preliminary study of gut microbiome influence on black Ivory coffee fermentation in Asian elephants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40548},
pmid = {41253982},
issn = {2045-2322},
support = {KAKENHI JP16H06279//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Elephants/microbiology ; *Fermentation ; *Coffee/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; *Coffea/metabolism ; },
abstract = {Black Ivory Coffee (BIC), produced through the digestion of Arabica coffee beans by Asian elephants, is recognized for its smooth, chocolaty flavor and low bitterness. However, the biological mechanisms underlying its unique taste remain poorly understood. In this study, we conducted a preliminary analysis of the gut microbiome of BIC-producing elephants and compared it with that of control elephants. 16S rRNA gene sequencing analysis revealed significant differences in microbial community structure, including the enrichment of specific bacterial genera such as Acinetobacter and family such as Izemoplasmataceae in the BIC group. Functional prediction using PICRUSt2 indicated that the BIC elephant gut microbiome harbors key enzymes involved in the degradation and utilization of pectin and cellulose-major components of coffee cherries and beans. Notably, genes related to pectin transport and downstream metabolism, including K08191 and K01812, were significantly more abundant in BIC elephants. These pathways may contribute to the degradation of specific compounds, such as 2-furfuryl furan, which has been previously shown to decrease after gastrointestinal passage. Comparative analysis with other animals revealed that only elephants harbored a complete set of pectin-degrading genes. Our findings suggest that the gut microbiota of BIC elephants facilitates microbial fermentation of coffee components, potentially influencing the chemical profiles of Black Ivory Coffee.},
}

Animals
*Gastrointestinal Microbiome
*Elephants/microbiology
*Fermentation
*Coffee/metabolism
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
*Coffea/metabolism

@article {pmid41253951,
year = {2025},
author = {Palladino, G and Marangi, M and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M},
title = {Gut microbiome structure in asylum seekers newly arrived in Italy from Africa.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40596},
pmid = {41253951},
issn = {2045-2322},
mesh = {Humans ; *Refugees ; Italy ; *Gastrointestinal Microbiome/genetics ; Africa ; Adult ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Middle Aged ; Young Adult ; Feces/microbiology ; },
abstract = {The global landscape of migration has evolved significantly, with international migrants tripling since 1970, reaching approximately 281 million by 2020. This rise includes a notable surge in forcibly displaced individuals due to conflicts, wars, and human rights violations. Additionally, climate change is reshaping migration patterns by environmental degradation and extreme weather events, with projections indicating that 143 million individuals may be uprooted by climate catastrophes over the next three decades. In this context, migrants experience chronic stress due to the uncertainties of their journey, exposure to trauma, and changes in living conditions, possibly exacerbating health issues, including through impairment of the gut microbiome. Our study focuses on the characterization-by 16 S rRNA gene amplicon sequencing-of intestinal microbiome in 79 asylum seekers newly arrived in Italy from African countries through their comparison with publicly available datasets of worldwide populations encompassing different origin and lifestyle. This microbiological surveillance, conducted as cross-sectional sampling over one year, aimed to provides some glimpses on how the forced migration journey and the associated stressors affect refugees' gut microbiome composition. Our findings suggest significant deviations in the gut microbiome composition of refugees compared to traditional rural populations, possibly driven by stressors such a psychological trauma and dietary changes. The loss of microbial diversity may increase susceptibility to health issues, highlighting the need for targeted public health strategies for refugee populations.},
}

Humans
*Refugees
Italy
*Gastrointestinal Microbiome/genetics
Africa
Adult
Male
Female
RNA, Ribosomal, 16S/genetics
Cross-Sectional Studies
Middle Aged
Young Adult
Feces/microbiology

@article {pmid41253868,
year = {2025},
author = {Li, J and Yu, L and Wang, Y and Yuan, C and Wang, K and Ma, X},
title = {Alterations in urinary microbiota composition in children with overactive bladder: insights from 16S rRNA gene sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40455},
pmid = {41253868},
issn = {2045-2322},
support = {2024NSFSC1499//Natural Science Foundation of Sichuan Province/ ; 2023YFS0101//Sichuan Science and Technology Program/ ; },
mesh = {Humans ; Child ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; *Urinary Bladder, Overactive/microbiology/urine ; *Microbiota/genetics ; Adolescent ; Child, Preschool ; *Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {This study aimed to characterize the urinary microbiota profiles in pediatric patients with overactive bladder (OAB) compared to healthy controls, identify differentially enriched microbial taxa, and explore their associations with clinical symptoms and functional pathways. Urine samples were collected from 87 children (39 OAB patients, 48 controls) aged 5-14 years. Microbial DNA was extracted, and the V3-V4 regions of the 16 S rRNA gene were sequenced using the Illumina NovaSeq6000 platform. To delineate microbial community variations and functional associations, bioinformatics pipelines and statistical approaches-including permutational multivariate ANOVA (PERMANOVA), principal coordinates analysis (PCoA), linear discriminant analysis effect size (LEfSe), and Spearman's correlation-were applied to assess α/β-diversity, taxon-specific disparities, and clinical phenotype linkages in 16 S rRNA sequencing datasets. Clinical parameters, such as urinary urgency severity, nocturnal enuresis, and residual urine, were correlated with microbial composition. While no significant differences in α-diversity were observed between groups, β-diversity analysis revealed distinct clustering of microbial communities (ANOSIM, P = 0.001). OAB patients (OABs) exhibited enrichment in Proteobacteria, Gammaproteobacteria, Enterobacterales, Sphingomonas, and Escherichia-Shigella, whereas controls showed higher abundances of Clostridia, Bacteroidales, and Prevotella. Positive correlations were detected among Defluviitoga, Escherichia-Shigella, and Ligilactobacillus, while Defluviitoga negatively correlated with Bacteroides. Functional prediction highlighted OAB-associated upregulation of antibiotic resistance, biofilm formation, and bacterial secretion pathways. Subgroup analyses further linked severe OAB symptoms to elevated inflammatory taxa (e.g., Enterobacteriaceae) and residual urine to Gammaproteobacteria dominance. Pediatric OAB is associated with a dysbiotic urinary microbiota characterized by pro-inflammatory bacteria and altered metabolic functions. Specific microbial signatures, such as Escherichia-Shigella and Enterobacterales, may contribute to pathogenesis, while Prevotella and Clostridia in controls suggest protective roles. Specific microbial signatures associate with disease severity and possess functional capacities linked to inflammation, urothelial invasion, and immune evasion. Our findings underscore the urinary microbiome's contribution to pediatric OAB pathogenesis, suggesting promise for microbiome-informed diagnostic and therapeutic strategies.},
}

Humans
Child
*RNA, Ribosomal, 16S/genetics
Female
Male
*Urinary Bladder, Overactive/microbiology/urine
*Microbiota/genetics
Adolescent
Child, Preschool
*Bacteria/genetics/classification
Case-Control Studies

@article {pmid41253756,
year = {2025},
author = {Knoll, RL and Brauny, MM and Robert, E and Cloos, L and Waser, L and Hilbert, K and Ulmer, N and Hillen, B and Birkner, T and Bartolomaeus, TUP and Nitsche, O and Jarquín-Díaz, VH and Lynch, S and Gehring, S and Maier, L and Poplawska, K and Forslund-Startceva, SK},
title = {CFTR modulator therapy drives microbiome restructuring through improved host physiology in cystic fibrosis: the IMMProveCF phase IV trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10111},
pmid = {41253756},
issn = {2041-1723},
support = {551589343//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FO 1279/6-1, Project ID 431232613 - SFB 1449 (//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Humans ; *Cystic Fibrosis/drug therapy/microbiology/genetics/physiopathology ; *Cystic Fibrosis Transmembrane Conductance Regulator/genetics/metabolism ; *Quinolones/therapeutic use/pharmacology ; Male ; Female ; *Aminophenols/therapeutic use/pharmacology ; Adult ; Sputum/microbiology ; Gastrointestinal Microbiome/drug effects ; *Benzodioxoles/therapeutic use/pharmacology ; Indoles/therapeutic use/pharmacology ; Feces/microbiology ; Longitudinal Studies ; Young Adult ; *Microbiota/drug effects/genetics ; *Pyrroles/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Adolescent ; Pyridines/therapeutic use/pharmacology ; Drug Combinations ; Dysbiosis/drug therapy/microbiology ; Pyrrolidines/therapeutic use/pharmacology ; Pyrazoles ; },
abstract = {Cystic fibrosis (CF) is a genetic disorder caused by mutations in the CFTR gene, leading to impaired CFTR function, mucus accumulation, chronic infections, and inflammation. The triple combination elexacaftor/tezacaftor/ivacaftor (ETI) has transformed CF treatment by restoring CFTR function. However, how ETI-induced physiological improvements affect long-standing dysbiosis and pathogen colonization across microbiome habitats remains poorly understood. In this prospective longitudinal study (DRKS00023862), we analyzed sputum, throat, and stool microbiomes of pwCF (n = 35) before and after ETI initiation, alongside healthy controls (n = 49). The primary endpoint was longitudinal change in diversity, species richness, and microbial composition in the respiratory and intestinal microbiome, profiled by 16S rRNA gene sequencing. Secondary endpoints included changes in lung function, systemic and gastrointestinal inflammation. We show how improved CFTR function and direct antibacterial effects of ETI create a niche disadvantage for Staphylococcus in the sputum microbiome. Respiratory microbiome shifts were immediate, while gut changes emerged gradually. Escherichia abundance in stool, initially elevated in pwCF, decreased post-ETI and correlated with lower fecal calprotectin. These findings demonstrate that ETI can partially reverse CF-associated dysbiosis through improved host physiology. They offer insights into host-microbiome dynamics under therapeutic modulation and emphasize the need for confounder-aware models in complex clinical populations.},
}

Humans
*Cystic Fibrosis/drug therapy/microbiology/genetics/physiopathology
*Cystic Fibrosis Transmembrane Conductance Regulator/genetics/metabolism
*Quinolones/therapeutic use/pharmacology
Male
Female
*Aminophenols/therapeutic use/pharmacology
Adult
Sputum/microbiology
Gastrointestinal Microbiome/drug effects
*Benzodioxoles/therapeutic use/pharmacology
Indoles/therapeutic use/pharmacology
Feces/microbiology
Longitudinal Studies
Young Adult
*Microbiota/drug effects/genetics
*Pyrroles/therapeutic use/pharmacology
RNA, Ribosomal, 16S/genetics
Prospective Studies
Adolescent
Pyridines/therapeutic use/pharmacology
Drug Combinations
Dysbiosis/drug therapy/microbiology
Pyrrolidines/therapeutic use/pharmacology
Pyrazoles

@article {pmid41253509,
year = {2025},
author = {Acire, PV and Brown, SC and Day, AS},
title = {The role of the Mediterranean diet in the management of inflammatory bowel disease: a narrative review.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2025.00043},
pmid = {41253509},
issn = {1598-9100},
abstract = {Inflammatory bowel disease (IBD) is characterized by the presence of gastrointestinal inflammation, that in some individuals leads on to complications, including strictures. IBD can be associated with significant morbidity with disruption of daily activities. Although the precise cause of IBD is unknown, epidemiologic studies indicate that diet is one contributory factor. Furthermore, various specific nutritional interventions have roles in the management of IBD. While the contribution of the Mediterranean diet (MedDiet) to the development or management of IBD has not yet been clearly delineated, available data are generally supportive. The MedDiet includes the consumption of a pattern of particular foods, such as plentiful vegetables, fruit, seafood, and olive oil, along with lifestyle features. Adherence to a MedDiet is associated with enrichment of beneficial components of the intestinal microbiome and enhanced barrier function: outcomes that are likely beneficial to individuals with IBD. The focus of this review was to highlight the evidence for the MedDiet in the setting of IBD, whilst giving an overview of the underlying health impacts of the MedDiet and the putative mechanisms of this dietary approach.},
}

@article {pmid41253445,
year = {2025},
author = {Chen, YL and Meng, LL and Wu, JY and Yang, XY and Ouyang, L and Wu, BF and Xu, HX and Gu, JL and Wang, YL and Jing, XY and Lu, SF and Fu, SP},
title = {Electroacupuncture Reprograms Gut Microbiota and Confers Cerebral Protection After Stroke through Enhanced Regulatory T Cell Response.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-24},
doi = {10.1142/S0192415X25500855},
pmid = {41253445},
issn = {1793-6853},
abstract = {Ischemic stroke seriously endangers both the health and quality of life of patients. The gut microbiota, which plays a crucial role in modulating communication between the gut and the nervous system, has emerged as a promising target for therapeutic interventions in stroke. Electroacupuncture (EA), which is associated with intestinal immunity, has been proven to exert significant beneficial effects in ischemic stroke, but its exact mechanism remains unclear. In this study, we investigated the regulatory mechanism of EA on the microbiome-gut-brain axis following ischemic stroke. In rat models of ischemic stroke, EA treatment significantly reduced cerebral infarct volume and neuronal damage following cerebral ischemia-reperfusion injury, and also modulated the composition, diversity, and taxonomic distribution of the gut microbiota. Fecal microbiota transplantation from EA-treated donors significantly reduced cerebral infarct volume and neuronal damage in the ischemic hemisphere of recipient mice, and likewise upregulated Treg cell expression to suppress immune-inflammatory responses in the brain. These results indicate that, through modulation of the gut microbiota, which in turn regulates Treg-mediated immune-inflammatory responses, EA ameliorates cerebral ischemic injury to thereby improve the prognosis of ischemic stroke patients. This study provides new perspectives on the efficacy of EA in the treatment of ischemic stroke.},
}

@article {pmid41249928,
year = {2025},
author = {Meng, F and Yu, T and Xie, M and Chen, M and Chen, X},
title = {Postoperative wound microbiota in diabetic patients with perianal abscess: a 16s rRNA gene sequencing study.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {756},
pmid = {41249928},
issn = {1471-2180},
abstract = {BACKGROUND: Perianal abscesses are common in colorectal surgery, requiring surgical drainage and wound care. Diabetic patients often experience delayed wound healing and increased infection risk due to systemic factors and altered microbiota. This study investigated the postoperative wound microbiota in diabetic patients with perianal abscesses using 16s rRNA sequencing, aiming to identify potential microbial contributions to wound healing outcomes.

RESULTS: The study compared wound microbiota between 22 diabetic patients and 22 non-diabetic patients undergoing perianal abscess surgery. Diabetic patients exhibited significantly lower microbial diversity and richness compared to non-diabetic patients. Specific bacterial taxa were enriched in the diabetic group, including Enterobacteriaceae, Streptococcus, and Lactobacillales, while beneficial bacteria like Bacteroides and Ruminococcaceae were reduced. Functional prediction analysis revealed significant differences in metabolic pathways, with diabetic wounds showing increased carbohydrate metabolism and chitin biosynthesis, and decreased energy metabolism and endocrine system function.

CONCLUSIONS: This study highlights the distinct wound microbiota characteristics of diabetic patients with perianal abscesses, suggesting potential microbial contributions to delayed wound healing. The findings underscore the importance of considering the wound microbiome in managing postoperative wound care for diabetic patients. Strategies to modulate the wound microbiota, such as probiotics or antibiotics, may be beneficial in improving healing outcomes. Further research is needed to understand the specific mechanisms driving the observed microbial dysbiosis and its impact on wound healing in diabetic patients.},
}

@article {pmid41253270,
year = {2025},
author = {Ding, L and Xu, JY and Zhang, LL and Liu, Y and Gu, KT and Liang, YZ and Hidayat, K and Wan, Z and Chen, GC and Qin, LQ},
title = {Lactoferrin alleviates non-alcoholic steatohepatitis via remodeling gut microbiota to regulate serotonin-related pathways.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.11.034},
pmid = {41253270},
issn = {2090-1224},
abstract = {INTRODUCTION: Lactoferrin (LF), a multifunctional glycoprotein, has been implicated in the regulation of glucose and lipid metabolism.

OBJECTIVES AND METHODS: This study employed in vivo and in vitro models to investigate the direct effects of LF on non-alcoholic steatohepatitis (NASH) and to elucidate its underlying mechanisms.

RESULTS: LF intervention alleviated hepatic lipid metabolic disorders and liver injury in high-fat, high-cholesterol cholate-containing diet (HFCCD)-fed mice by mitigating oxidative stress, suppressing the inflammatory cGAS/STING pathway, and reducing M1 proinflammatory macrophage polarization. These effects were validated in free fatty acid (FFA)-treated HepG2 cells and AML12 cells. Furthermore, LF ameliorated HFCCD-induced gut microbiota dysbiosis and increased short-chain fatty acid levels. The critical role of gut microbiota in mediating the hepatoprotective effects of LF was confirmed through antibiotic-induced microbiome depletion and fecal microbiota transplantation. Mechanistically, LF modulated gut-liver serotonin signaling and promoted fatty acid β-oxidation through the HTR2A-PPARα-CPT-1A pathway, an effect abolished by the HTR2A agonist DOI. In a co-culture system, LF treatment of the Caco-2/HT29 monolayer alleviated lipid accumulation and regulated the HTR2A-PPARα-CPT-1A pathway in FFA-treated HepG2 cells.

CONCLUSIONS: These findings indicate that LF attenuates NASH by remodeling gut microbiota to modulate microbiota-derived serotonin signaling and enhance fatty acid oxidation.},
}

@article {pmid41253145,
year = {2025},
author = {Shi, H and Newton, DP and Nguyen, TH and Estrela, S and Sanchez, J and Tu, M and Ho, PY and Zeng, Q and DeFelice, BC and Sonnenburg, JL and Huang, KC},
title = {Nutrient competition predicts gut microbiome restructuring under drug perturbations.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.10.038},
pmid = {41253145},
issn = {1097-4172},
abstract = {Human gut bacteria are routinely exposed to stresses, and community-level responses are difficult to predict. To interrogate these effects, we screened stool-derived in vitro communities with 707 clinically relevant drugs. Across ∼5,000 community-drug conditions, compositional and metabolomic responses were shaped by nutrient competition, with certain species expanding due to the suppression of competitors. Most compositional changes arose from strain extinction and were reversed by reintroducing extinct species, although certain drugs promoted alternative states long after treatment. Despite strong selection pressures, resistance emergence was infrequent. Responses to drugs were qualitatively conserved across communities, while nutrient competition quantitatively tuned species abundances, consistent with consumer-resource model predictions. Together, nutrient competition provides a predictive framework to anticipate and potentially mitigate drug side effects on the gut microbiota.},
}

@article {pmid41252854,
year = {2025},
author = {Chen, X and Huang, Y and Zhu, X and Gan, C and An, W and Liu, Y and Zhou, S and Xu, M},
title = {Global biogeographic patterns and assembly processes of landfill leachate microbiomes.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124922},
doi = {10.1016/j.watres.2025.124922},
pmid = {41252854},
issn = {1879-2448},
abstract = {Approximately 95 % of municipal solid waste is disposed of in landfill globally, generating leachate that is known as a complex mixture of biodegradable and persistent toxic compounds. Microbes are main forces for tackling the toxic leachate but the patterns of microbial assembly in such treatments are largely unknown, limiting the proper optimization of leachate treatment efficiency. This study, for the first time, presents a global-scale analysis involving 151 landfill leachate treatment samples for uncovering mechanisms of microbial assembly from an ecological perspective. The information of microbiome from 97 treatments in Asia, 41 treatments in Europe, and 13 treatments in North America were collected. The results revealed pronounced biogeographic divergence, with Asian samples (particularly those from India) exhibiting lower microbial diversity and richness compared to Europe and North America counterparts. Geographical-climatic and socio-economic factors significantly influenced microbial composition, with elevation and per capita GDP being primary drivers. Further, the community assembly was predominantly governed by deterministic processes. Co-occurrence network analyses demonstrated distinct microbial interaction patterns across continents, with Asian networks being more vulnerable to collapse under external disturbances. This study provides critical insights into the global microbial ecology of landfill leachate treatment, offering a foundation for developing targeted bioremediation strategies.},
}

@article {pmid41252749,
year = {2025},
author = {Welsh, TB and Dundas, CM},
title = {Genetically Reprogramming Crops and Rhizobacteria for Nutritional Iron Biofortification.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00614},
pmid = {41252749},
issn = {2161-5063},
abstract = {Iron is a critical micronutrient for both plants and humans, yet its declining availability across agricultural systems threatens global food security and health. Biofortification of food crops has emerged as a promising strategy to combat iron deficiency and anemia, leveraging both crop breeding and microbiome-based approaches to enhance iron mobilization and uptake. Advances in plant and bacterial synthetic biology could enable the precise programming of iron homeostasis and acquisition mechanisms, offering tailored solutions across diverse species and environments. Here, we outline key biomolecules, genes, and biosynthetic and transport pathways that represent underexplored synthetic biology targets for improving crop iron acquisition. We highlight opportunities to tune expression strength, tissue specificity, and cross-host pathway transfer to enhance chelation- and reduction-mediated solubilization of soil iron and augment plant uptake. Finally, we emphasize the broader importance of developing plant-microbe-metal actuators as modular components in genetic circuit design and discuss how their deployment across diverse plant and microbial chassis could accelerate agricultural biofortification and improve global nutrition.},
}

@article {pmid41252568,
year = {2025},
author = {Severino, A and Marchitto, SA and Bisegna, P and Porcari, S and Rondinella, D and Schepis, T and Barbaro, F and Pecere, S and Maida, M and Spada, C and Gasbarrini, A and Cammarota, G and Facciorusso, A and Ianiro, G},
title = {Measuring gut microbiome as a colorectal cancer screening tool: potential and challenges.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2592078},
pmid = {41252568},
issn = {1747-4132},
abstract = {INTRODUCTION: Colorectal cancer (CRC) represents a global public health challenge, ranking as the third most prevalent cancer globally. Population-based screening programs for average-risk populations have proven effective in reducing incidence and mortality of CRC through early detection of cancer. The fecal immunochemical test (FIT), the standard diagnostic method in many nations, still falls short in diagnostic effectiveness, resulting in undetected adenomas and, more significantly, unnecessary colonoscopies.

AREAS COVERED: One of the primary research focuses in the field of CRC is the discovery of new, noninvasive biomarkers. Recent studies, including metagenomic meta-analyses, have discovered common microbial signatures able to reproducibly discriminate between patients with CRC and healthy controls. Based on this evidence, international guidelines have recently recommended the use of microbiome-based biomarkers for CRC screening in clinical settings, although such studies have yet to be conducted.

EXPERT OPINION: This field of research needs considerable multidisciplinary efforts, including large and geographically different meta-cohorts, and the application of state-of-the-art computational approaches, to identify reproducible signatures able to predict early lesions. Such diagnostic tool would revolutionize CRC screening. More widely, it would provide a mind-set shift in the clinical and scientific community promoting the exploitation of diagnostic and therapeutic microbiome tools in clinical practice.},
}

@article {pmid41252467,
year = {2025},
author = {Soffa, DR and Hickman, KJ and Cain, JW and Spencer, JA and Poole, RK},
title = {Vaginal microbiota and circulating interferon-stimulated genes in lactating dairy cows at and following time of artificial insemination.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf399},
pmid = {41252467},
issn = {1525-3163},
abstract = {Reproductive tract microbiota has been shown to shift during early gestation in cattle. However, characterization of the vaginal microbiota during the establishment of pregnancy in lactating dairy cows has yet to be fully determined. Therefore, the objectives of this study were to characterize shifts in the vaginal microbiota from time of artificial insemination (AI) to maternal recognition of pregnancy and analyze its relationship with interferon-stimulated genes (ISGs) in lactating dairy cows. Vaginal swab samples for microbiota analysis and blood were collected from lactating Holstein dairy cows (n = 40) on day 0 (d0; time of AI) and day 18 (d18; post-AI during the time of maternal recognition of pregnancy). Pregnancy status was determined via transrectal ultrasonography on d32 (Open, n = 18 and Pregnant, n = 22). Microbiota analysis for phylum and genus taxonomic classification, as well as α- and β-diversity, was conducted targeting the V4 hypervariable region of the 16S rRNA gene on d0 and d18. RT-qPCR analysis was conducted to analyze expression of ISGs, interferon-stimulated gene 15 kDa (ISG15) and myxovirus resistance 2 (MX2), on d0 and d18. Phyla and genera greater than 1% relative abundance did not differ between Open and Pregnant cows (P > 0.10). Shifts in certain bacterial phyla and genera between d0 and d18 (P < 0.05), along with lower α-diversity matrices of Simpson's diversity index (P = 0.02) and Shannon's diversity index (P = 0.009) on d18, indicate that time-dependent shifts in bacterial communities may alter reproductive success. This is further supported by the difference between days for the weighted UniFrac β-diversity matrix (P = 0.005). Reduced MX2 expression on d18 (P = 0.002), and its correlation with Fusobacteria (r = -0.35; P = 0.09), may be indicative of pregnancy failure and thus result in Open cows. These results indicate that shifts in microbiota from day of AI to d18 may influence successful establishment of pregnancy in lactating dairy cows.},
}

@article {pmid41252442,
year = {2025},
author = {Zentgraf, J and Schmitz, JE and Rahmann, S},
title = {Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf632},
pmid = {41252442},
issn = {1367-4811},
abstract = {MOTIVATION: The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome data containing partly human data cannot be easily further processed or published. Second, human contamination may cause problems in downstream analysis, such as metagenomic binning or genome assembly. For large-scale metagenomics projects, fast and accurate removal of human contamination is therefore critical.

RESULTS: We introduce Cleanifier, a fast and memory frugal alignment-free tool for detecting and removing human contamination based on gapped k-mers, or spaced seeds. Cleanifier uses a pangenome index of known human gapped k-mers, and the creation and use of alternative references is also possible. Reads are classified and filtered according to their gapped k-mer content. Cleanifier supports two filtering modes: one that queries all gapped k-mers and one that queries only a sample of them. A comparison of Cleanifier with other state-of-the-art tools shows that the sampling mode makes Cleanifier the fastest method with comparable accuracy. When using a probabilistic Cuckoo filter to store the complete k-mer set, Cleanifier has similar memory requirements to methods that use a sampled minimizer index. At the same time, Cleanifier is more flexible, because it can use different sampling methods on the same index.

Cleanifier is available via gitlab (https://gitlab.com/rahmannlab/cleanifier), PyPi (https://pypi.org/project/cleanifier/) and Bioconda (https://anaconda.org/bioconda/cleanifier). The pre-computed human pangenome index is available at Zenodo (https://doi.org/10.5281/zenodo.15639519).

SUPPLEMENTARY INFORMATION: Available online.},
}

@article {pmid41252333,
year = {2025},
author = {Bahji, A and Brietzke, E and Cooke, NCA and Clement, F and Frey, BN and Hofmeister, M and Kennedy, SH and Lam, R and Milev, R and Moinul, D and Parikh, SV and Patten, S and Ravindran, A and Rosenblat, JD and Samaan, Z and Schaffer, A and Saleem, A and Beaulieu, S and Tourjman, V and Van Ameringen, M and Vigod, S and Yatham, L and Taylor, V and , },
title = {The Canadian Network for Mood and Anxiety Treatments Task Force Recommendations for the Use of Probiotics, Prebiotics, Synbiotics, and Fecal Microbiota Transplants in Adults With Major Depressive Disorder: Recommandations du Groupe de travail du Réseau canadien pour le traitement des troubles de l'humeur et de l'anxiété (Canadian Network for Mood and Anxiety Treatments, CANMAT) concernant l'utilisation des probiotiques, des prébiotiques, des symbiotiques et de la transplantation de microbiote fécal chez les adultes atteints de trouble dépressif majeur.},
journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie},
volume = {},
number = {},
pages = {7067437251394363},
doi = {10.1177/07067437251394363},
pmid = {41252333},
issn = {1497-0015},
abstract = {BackgroundApproximately one-third of adults with major depressive disorder (MDD) experience limited response or intolerable side effects with existing pharmacotherapies. As such, innovative treatments targeting novel biological pathways are under investigation. One promising area of research is the gut microbiome and its influence on mood through the microbiota-gut-brain axis. Clinical studies have begun evaluating microbiome-targeted interventions such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) as potential treatments for MDD. The Canadian Network for Mood and Anxiety Treatments (CANMAT) convened a task force to evaluate the evidence for microbiome-targeted interventions in adults with MDD and to provide updated clinical recommendations.MethodsA systematic review of randomized controlled trials (RCTs) and meta-analyses was conducted, assessing interventions such as probiotics, prebiotics, synbiotics, and FMT in adults with MDD. The CANMAT methodology was used to determine levels of evidence and treatment line recommendations, which were presented in a question-and-answer format.ResultsTwenty-three RCTs and eight meta-analyses were included. Probiotics have been the most extensively studied and have demonstrated modest improvements in depressive symptoms, particularly when used in an adjunctive manner. However, recent high-quality trials yielded mixed results. Evidence for prebiotics and FMT was limited and inconclusive, while synbiotics were assessed in only one small RCT. Most interventions were well tolerated, with few serious adverse events.ConclusionsProbiotics may be cautiously considered as third-line adjunctive treatments for MDD, though findings remain inconsistent. There is currently insufficient evidence to recommend prebiotics, synbiotics, or FMT in clinical practice. Further large-scale, well-controlled trials are needed to clarify efficacy, safety, and optimal patient subgroups.},
}

@article {pmid41252249,
year = {2025},
author = {Febinia, CA and Luqman, H and Kusuma, P and Priliani, L and Lewis, J and Wihandani, DM and Pinatih, GN and Sudoyo, H and Almeida, A and Malik, SG and Jacobs, GS},
title = {From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116573},
doi = {10.1016/j.celrep.2025.116573},
pmid = {41252249},
issn = {2211-1247},
abstract = {Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.},
}

@article {pmid41252227,
year = {2025},
author = {van Loenen, MR and Remie, LB and van Trijp, MP and Jansen, MG and Marques, JP and Claassen, JA and van de Rest, O and Vermeiren, Y and Smidt, N and Sikkes, SA and Deckers, K and Zwan, MD and van der Flier, WM and Köhler, S and Steegenga, WT and Oosterman, JM and Aarts, E},
title = {The Effects of a Multidomain Lifestyle Intervention on Brain Function and Its Relation With Immunometabolic Markers and Intestinal Health in Older Adults at Risk of Cognitive Decline: Study Design and Baseline Characteristics of the HELI Randomized Controlled Trial.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e69814},
doi = {10.2196/69814},
pmid = {41252227},
issn = {1929-0748},
mesh = {Humans ; Aged ; *Cognitive Dysfunction/prevention & control/physiopathology ; *Brain/physiology/physiopathology ; Male ; Female ; *Life Style ; Biomarkers/blood ; Netherlands ; Exercise/physiology ; Magnetic Resonance Imaging ; Middle Aged ; },
abstract = {BACKGROUND: Studies of multidomain lifestyle interventions show mixed results on preventing or delaying cognitive decline in aging. A better understanding of central and peripheral mechanisms underlying these interventions could help explain these mixed findings.

OBJECTIVE: The HELI (Hersenfuncties na LeefstijlInterventie) study aims to investigate the brain and peripheral mechanisms of a multidomain lifestyle intervention in older adults at risk of cognitive decline.

METHODS: The HELI study is a 6-month multicenter, randomized, controlled multidomain lifestyle intervention trial powered to include 104 Dutch older adults at risk of cognitive decline. Individuals were deemed at risk when scoring ≥2 points on a lifestyle-modifiable risk factor scale (eg, overweight, physical inactivity, hypertension, and hypercholesterolemia). The intervention consisted of 5 domains (diet, physical activity, stress management and mindfulness, cognitive training, and sleep) and participants were randomized to one of two groups: (1) a high-intensity coaching group with weekly supervised online and on-site group meetings, exercises, and lifestyle-specific course materials, and (2) a low-intensity coaching group receiving general lifestyle health information sent through email every 2 weeks. The primary study outcomes are changes between baseline and 6-month follow-up in (1) brain activation in dorsolateral prefrontal cortex (dlPFC) and hippocampus and task accuracy during a functional magnetic resonance imaging (fMRI) working memory task, (2) arterial spin labeling-quantified cerebral blood flow in dlPFC and hippocampus, (3) systemic inflammation from blood plasma (interleukin-6, tumor necrosis factor-α, high-sensitivity C-reactive protein) and (4) microbiota profile from feces (gut microbiome diversity [Shannon and phylogenetic diversity] and richness [Chao1]). In addition, we will investigate intervention-induced gut-immune-brain links by assessing relations between effects in primary brain and gut outcomes. Secondary study outcomes include (1) structural and neurochemical magnetic resonance imaging (MRI), (2) anthropometric measurements, (3) neuropsychological test battery scores, (4) lifestyle-related questionnaire and smartwatch measures, and peripheral measures from (5) fecal, (6) blood, and (7) breath analyses.

RESULTS: This work was supported by a Crossover grant (Maintaining Optimal Cognitive Functioning In Aging [MOCIA] 17611) of the Dutch Research Council (NWO), granted in December 2019. The MOCIA program is a public-private partnership. Between April 2022 and October 2023, we successfully included 102 older Dutch adults (mean age 66.6, SD 4.3 years; 67/102, 65.7% female) with ≥2 lifestyle-modifiable risk factors of cognitive aging (median risk 3, IQR 2-3). The most common self-reported lifestyle-modifiable risk factors at baseline were overweight or obesity (76/102, 74.5%), followed by hypertension (58/102, 56.9%), hypercholesterolemia (57/102, 55.9%), and physical inactivity (57/102, 55.9%).

CONCLUSIONS: The HELI study aims to enhance our understanding of the working mechanisms of multidomain lifestyle interventions through its comprehensive characterization of central and peripheral markers. We intend to achieve this aim by assessing lifestyle intervention-induced changes in functional and structural MRI brain measures, as well as peripheral measures of the gut-immune-brain axis involved in cognitive aging.},
}

Humans
Aged
*Cognitive Dysfunction/prevention & control/physiopathology
*Brain/physiology/physiopathology
Male
Female
*Life Style
Biomarkers/blood
Netherlands
Exercise/physiology
Magnetic Resonance Imaging
Middle Aged

@article {pmid41252206,
year = {2025},
author = {Moreau, GB and Tian, J and Natale, NR and Naz, F and Young, MK and Nayak, U and Tanyüksel, M and Rigo, I and Madden, GR and Abhyankar, MM and Hagspiel, N and Brovero, S and Worthington, M and Behm, B and Marie, C and Petri, WA and Ramakrishnan, G},
title = {FMT promotes type 2 mucosal immune responses with colonic epithelium proliferation in recurrent CDI patients.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.195678},
pmid = {41252206},
issn = {2379-3708},
abstract = {BACKGROUND: Fecal Microbiota Transplantation (FMT) is the most effective therapy for recurrent Clostridioides difficile infection (rCDI), yet its mechanism of action remains poorly understood.

METHODS: We report the results of a clinical trial of subjects undergoing FMT therapy for rCDI (n=16), analyzing colon biopsies, plasma, peripheral blood mononuclear cells, and stool at the time of FMT and two-month follow-up. Plasma and colon biopsy samples were also collected from healthy controls for comparison with rCDI patients. Microbiome composition, colonic gene expression, and immune changes were evaluated through high-throughput sequencing and immunoprofiling via flow cytometry.

RESULTS: No subjects experienced recurrence at follow-up. FMT significantly altered the intestinal microbiome but had no significant impact on the systemic immune system. In contrast, FMT promoted broad changes in colonic transcriptional profiles compared to both pre-FMT and healthy control biopsies, inhibiting genes associated with pro-inflammatory signaling and upregulating type 2 immunity and proliferative pathways (Myc and mTORC1). FMT increased expression of IL-33 and the type 2 immune EGFR family ligand amphiregulin, potentially explaining upregulation of Myc and mTORC1 pathways. Spatial transcriptomics demonstrated that these changes were localized to the colonic epithelium. Comparison of transcriptional profiles with available single cell gene sets determined that post-FMT biopsies were enriched in signatures associated with proliferative cell types while repressing signatures of differentiated colonocytes.

CONCLUSIONS: We conclude that FMT promotes proliferation of the colonic epithelium in rCDI patients, which may drive regeneration and protect against subsequent CDI.

CLINICALTRIALS: gov NCT02797288.

FUNDING: NIH grants R01 AI152477, R01 AI124214, and K23 AI163368.},
}

@article {pmid41252027,
year = {2026},
author = {Vaila, C and Nikou, V and Mataragka, A and Katsenios, N and Zafeiriou, I and Kounani, K and Efthimiadou, A and Papakonstantinou, E and Fountas, S and Vlachakis, D},
title = {Adaptation to Climatic Change and Epigenetic Modifications of Soil Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1489},
number = {},
pages = {419-430},
pmid = {41252027},
issn = {0065-2598},
mesh = {*Soil Microbiology ; *Climate Change ; *Epigenesis, Genetic ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Rhizosphere ; Plants/microbiology ; *Adaptation, Physiological ; },
abstract = {The rhizosphere microbiome, and especially bacteria, is essential for the plant's life and health, forming different mutual beneficial relationships. Throughout evolution, bacteria have adapted to various habitats by adjusting their genomes in order to fit the changing environmental conditions, resulting in the development of additional functional traits. Epigenetic modifications in their DNA play a crucial role in their ability to thrive in such conditions. Climate change is a serious phenomenon, challenging the plant's health and soil microbiome's assembly, and bacteria must enhance their stability by using resistance, resilience, and redundancy, mainly by stress-driven epigenetic modifications. In this review, recent studies have been investigated in order to record the most abundant bacterial genera in the soil's rhizosphere of 11 plants and at the same time to locate the role each one of them plays in plant's health, which has also been regulated by epigenetic mechanisms, leading to the inheritance of diverse phenotypes. As a result, we propose that this field needs further investigation, and future research should be focused on testing the alterations of the abundance and possible epigenetic modifications on the DNA of the main bacterial genera in soil microbiome, from areas affected by the climate change consequences, in order to conclude to potential solutions for assisting the soil microbiome and plants to survive after such catastrophic conditions.},
}

*Soil Microbiology
*Climate Change
*Epigenesis, Genetic
*Microbiota/genetics
*Bacteria/genetics/classification
Rhizosphere
Plants/microbiology
*Adaptation, Physiological

@article {pmid41251823,
year = {2025},
author = {Della Mónica, IF and Godeas, AM and Scervino, JM},
title = {Hyphosphere interactions: P-solubilizing fungi modulate AMF phosphatase activity and mycorrhizal symbiosis via exudate-mediated communication.},
journal = {Mycorrhiza},
volume = {35},
number = {6},
pages = {66},
pmid = {41251823},
issn = {1432-1890},
support = {UBACyT 20020220400300BA//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; PIBAA 28720210100694CO//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; PICT 01283-2021//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación/ ; PINI 04/B253//Fundación de la Universidad Nacional del Comahue para el Desarrollo Regional/ ; },
mesh = {*Mycorrhizae/physiology/enzymology ; *Symbiosis ; Plant Roots/microbiology ; *Phosphorus/metabolism ; Acid Phosphatase/metabolism ; *Phosphoric Monoester Hydrolases/metabolism ; Daucus carota/microbiology ; *Glomeromycota/physiology/enzymology ; *Phosphates/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots, enhancing water and nutrient absorption. Phosphate-solubilizing fungi (PSF) can solubilize and mineralize phosphorus, an essential nutrient with low bioavailability, and eventually interact with AMF. However, the understanding of how they interact in the hyphosphere, where root influence is absent, remains limited. Furthermore, the effect of PSF on the phosphatase activity of AMF, related to the P efficiency in acquisition and utilization, within the hyphosphere and mycorrhizosphere zones, remains unclear. Therefore, this study aimed to assess the effect of three different PSF (Talaromyces flavus, T. helicus, and T. diversus) exudates on extracellular acid phosphatases and alkaline phosphatases associated with intra- and extraradical AMF structures in the hyphosphere and mycorrhizosphere, in vitro. To achieve this aim, the AMF Rhizophagus intraradices was cultured with Ri T-DNA transformed carrot roots in a system using Petri dishes that mimicked the hyphosphere (with 2 sections: (a) with roots and AMF, and (b) with only AMF) and the mycorrhizosphere (with roots and AMF in the same place). Different concentrations of PSF exudates were placed in either the hyphosphere or the mycorrhizosphere, and at the end of the experiment (8 weeks), the phosphatase activity of the AMF was measured. This research highlights that the enzymatic activity of AMF is modulated by PSF exudates, depending on whether these exudates are present in the hyphosphere or the mycorrhizosphere. Exudates in the hyphosphere, where PSF are directly associated with AMF hyphae, have a more pronounced effect on AMF extraradical alkaline phosphatases than acid phosphatases, and promote symbiosis efficiency. In contrast, PSF exudates in the mycorrhizosphere had a neutral or negative effect on symbiosis efficiency, improving the extraradical alkaline phosphatases of AMF and the acid phosphatases of the roots. Also, the effect depends on the fungal identity. AMF act as mediators in this context, improving communication between the roots and the hyphosphere microbiome. When exploring the soil, the hyphae encounter compounds produced by microorganisms, thus establishing a complex network of interactions. These interactions enhance the symbiotic efficiency of AMF, modulating the host plant without direct contact. These results show that microbial interactions not only influence the efficiency of phosphorus transfer to plants but also have broader implications for soil health and fertility management.},
}

*Mycorrhizae/physiology/enzymology
*Symbiosis
Plant Roots/microbiology
*Phosphorus/metabolism
Acid Phosphatase/metabolism
*Phosphoric Monoester Hydrolases/metabolism
Daucus carota/microbiology
*Glomeromycota/physiology/enzymology
*Phosphates/metabolism

@article {pmid41251489,
year = {2025},
author = {Ye, H and Šlipogor, V and Hanson, BT and Séneca, J and Hausmann, B and Herbold, CW and Pjevac, P and Bugnyar, T and Loy, A},
title = {Associations between gut microbiota and personality traits: insights from a captive common marmoset (Callithrix jacchus) colony.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0044325},
doi = {10.1128/spectrum.00443-25},
pmid = {41251489},
issn = {2165-0497},
abstract = {Recent studies have suggested associations between consistent inter-individual behavioral variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated associations between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status, and relatedness of 26 captive common marmosets (Callithrix jacchus), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genus Desulfovibrio were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene dsrB confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between identified microbial taxa and personality traits in captive common marmosets.IMPORTANCEThis study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential of the gut microbiome to reflect or be associated with personality differences. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.},
}

@article {pmid41251470,
year = {2025},
author = {Young, MG and Just, J and Lee, YJ and McMahon, T and Gonzalez, J and Fuentes, P and Noh, S and Angelini, DR},
title = {Seasonally increasing parasite load is associated with microbiota dysbiosis in wild bumblebees.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118425},
doi = {10.1128/msystems.01184-25},
pmid = {41251470},
issn = {2379-5077},
abstract = {UNLABELLED: Gut microbiota often influence host defense against infection, but this relationship is incompletely understood in wild bumblebees. These critical pollinators host a characteristic core gut microbiota, yet field studies have offered conflicting insights into its association with Crithidia bombi, a prevalent trypanosomid parasite. To address this gap in our knowledge, we conducted an 3 year field survey, profiling the gut microbiota of 638 bumblebees from 9 sympatric species across diverse sites in Maine using 16S rRNA amplicon sequencing and qPCR for C. bombi detection. We confirmed a robust core bumblebee microbiota, identifying novel host-specific phylogenetic associations of bacterial amplicon sequence variants even among closely related host species. C. bombi infection was common and showed significant seasonal increases. We also found spatial variation, with higher prevalence in coastal regions. Crucially, increasing C. bombi infection load was consistently associated with microbiome dysbiosis. This dysbiosis was characterized by a depletion of core bumblebee-associated microbial taxa, notably Apibacter and Gilliamella (previously shown to be protective), and a corresponding increase in opportunistic, environmentally derived microbes like Entomomonas. While the core microbiota's association with initial pathogen transmission appears minor, its depletion in severe infections strongly supports a correlation to host health in wild bumblebees.

IMPORTANCE: The community of microorganisms in close association with an animal, its microbiota, can be important to its health. Understanding how microbiota composition relates to health and disease is an important goal with broad potential implications. Like most animals, bumblebees have a characteristic core gut microbiota. We have conducted a broad survey of bumblebees over 3 years to examine the interactions of microbiota composition with infection by an endemic trypanosomatid parasite. We found that the relative abundances of core microbes were inversely related to infection load, and that increased pathogen load was associated with the prevalence of novel microbes. These results are evidence of strong associations between bumblebees and their core microbiota and suggest a role in providing resistance to severe parasitism.},
}

@article {pmid41250828,
year = {2025},
author = {Zhao, C and Lao, J and Cao, J and Yang, Y and Liu, C and Tang, F},
title = {Advances in Gut Microbiome and Metabolomics Research in the Comorbidity of Inflammatory Bowel Disease and Depressive Disorder.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70173},
pmid = {41250828},
issn = {1440-1746},
support = {202328057//Science and Technology Plan Project of Jinan/ ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic autoimmune disorder characterized by persistent inflammation of the gastrointestinal tract, with a substantial proportion of patients experiencing comorbid depressive disorders. This comorbidity profoundly affects patients' long-term prognosis and quality of life. Emerging evidence suggests that the interplay between IBD and depression may be mediated by disruptions in the gut microbiome and metabolome. Notably, alterations in gut microbial composition and metabolic profiles observed in both IBD and depression indicate potential shared pathophysiological mechanisms, which could inform novel therapeutic strategies. This review aims to summarize recent advances in gut microbiome and metabolomics research related to IBD comorbid with depression, highlighting their implications for disease management and treatment. First, we provide an overview of the epidemiological features of IBD comorbid with depressive disorder, as well as the underlying pathophysiological mechanisms that may contribute to their bidirectional relationship. Subsequently, we highlight key microbiome and metabolite alterations observed in comorbid patients, which may contribute to disease onset and progression. At last, we also discuss emerging microbiota- and metabolite-based therapeutic approaches that hold promise for improving both gastrointestinal and psychological outcomes. In conclusion, integrating microbiome and metabolomics perspectives provides novel insights into the shared pathophysiology of IBD and depressive disorders and may inform the development of more effective and personalized interventions.},
}

@article {pmid41250628,
year = {2025},
author = {Yathindra, MR and Badugu, R and Singh, SK and Paluri, S and Poudala, H and Swathi, NL},
title = {The role of the urinary microbiome in diabetes-associated UTIs: current understanding and future directions.},
journal = {Journal of basic and clinical physiology and pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41250628},
issn = {2191-0286},
abstract = {This review explores the interplay between type 2 diabetes mellitus (T2DM) and urinary microbiome dysbiosis, focusing on its role in urinary tract infections (UTIs). Once considered sterile, the urinary tract hosts a diverse microbiota that supports mucosal immunity and pathogen resistance. In T2DM, chronic hyperglycemia and glycosuria disrupt microbial balance, impair immune responses, and increase UTI susceptibility. Glycosuria promotes pathogenic colonization, biofilm formation, and microbial shifts, with studies reporting a threefold rise in Escherichia coli and a 56 % reduction in Lactobacillus spp. in diabetic women with recurrent UTIs. Diabetic urine shows reduced diversity, higher abundance of Klebsiella, Pseudomonas, and Enterococcus, and elevated IL-8. Microbiota-targeted interventions, including probiotics (Lactobacillus crispatus, Lactobacillus rhamnosus GR-1), prebiotics (astaxanthin), and phytotherapeutics (cranberry), demonstrate potential via lactic acid, hydrogen peroxide production, competitive exclusion, and NF-κB modulation. A 12-month RCT showed significant UTI recurrence reduction with probiotics. Advances in 16 S rRNA sequencing and metagenomics reveal microbial signatures associated with diabetic UTIs, though methodological heterogeneity limits comparability. A review of 1,200 publications (2000-2024) highlights the need for longitudinal studies and precision microbiota therapeutics to translate findings into clinical practice.},
}

@article {pmid41250602,
year = {2025},
author = {Cosic, A and Halwachs, B and Schild-Prüfert, K and Zechner, EL and Kienesberger, S},
title = {Refining microbiome resolution: KoSCAPEbio identifies Klebsiella oxytoca complex species in16S rRNA amplicon data and uncovers associations with NEC.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2582900},
doi = {10.1080/19490976.2025.2582900},
pmid = {41250602},
issn = {1949-0984},
mesh = {*Klebsiella oxytoca/genetics/classification/isolation & purification ; Humans ; RNA, Ribosomal, 16S/genetics ; Klebsiella Infections/microbiology ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; DNA, Bacterial/genetics ; Infant ; },
abstract = {Klebsiella are early colonizers and commensals of human hosts but are also opportunistic pathogens. Research has focused on Klebsiella pneumoniae due to its global contribution to nosocomial infection and antibiotic resistance. Yet Klebsiella oxytoca and several closely related species are increasingly recognized as clinically significant bacteria underlying enteric and respiratory disorders. Inadequate interspecies discrimination inhibits advancement of our understanding of these diseases including necrotizing enterocolitis (NEC) in infants. Here we leverage the taxonomic potential of the amplified V3 and V4 regions of the K. oxytoca species complex (KoSC) 16S rRNA genes. We developed a curated database of all 16S rRNA gene sequences available for KoSC genomes and the automated pipeline KoSCAPEbio for efficient interspecies discrimination. Sequence polymorphism in the V3-V4 area revealed 41 signature sequences unique to individual species. Six amplicon variants are unique to the KoSC but shared by two to three species within the complex. Genetic linkage of the specific variants to the clinically relevant tiI gene cluster provided a predictive marker for risk of enterotoxin exposure. Reiteration of the workflow with K. aerogenes complex genomes and phylogroups of the K. pneumoniae species complex (KpSC) added K. aerogenes-specific variant typing. We then applied KoSCAPEbio to interrogate publicly available datasets. Analyses resolved and quantified coresident Klebsiella in patient samples including species belonging to KoSC, K. aerogenes and the KpSC. The population structure thus delineated in this proof of principle research differs significantly in disease versus controls. NEC cases associate positively with exclusive presence of the KoSC and negatively with cooccurrence of both KoSC and KpSC, suggesting conflict within the Klebsiella may promote pathogenesis. Thus, KoSCAPEbio has potential to contribute to a better understanding of factors involved in the etiology of NEC and other Klebsiella spp. associated diseases.},
}

*Klebsiella oxytoca/genetics/classification/isolation & purification
Humans
RNA, Ribosomal, 16S/genetics
Klebsiella Infections/microbiology
Phylogeny
*Gastrointestinal Microbiome/genetics
DNA, Bacterial/genetics
Infant

@article {pmid41250148,
year = {2025},
author = {Lam, AY and Lau, CH and Tam, WY and Chan, CT and Lok, TM and Suen, LK and Lee, LK and Yeung, EY and Lam, TK and Cheung, WK and Chui, MW and Soong, HS and Chow, FW and Lam, SC and So, SN and Yuen, SK and Siu, GK},
title = {Targeted probe capture metagenomics-enabled surveillance of multidrug-resistant organisms and antimicrobial resistance genes in post-handwashing areas of public washrooms.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {143},
pmid = {41250148},
issn = {2524-6372},
support = {2023-00-51 CRG230402//Tung Wah College/ ; 1-ZVZL//The Hong Kong Polytechnic University/ ; },
abstract = {BACKGROUND: Public washrooms (toilets) are potential hubs for pathogen transmission, yet the risk of microbial re-contamination via post-handwashing surfaces remains understudied. We characterized the prevalence and distribution of multidrug-resistant organisms (MDROs) and antimicrobial resistance genes (ARGs) in post-handwashing areas by sampling four high-contact sites, including faucets, paper dispensers, hand dryers, and exit door handles, in public washrooms across healthcare, commercial, and recreational facilities.

RESULTS: From the 232 post-handwashing surface samples collected, we isolated 17 MDROs (7.33% prevalence) from cultures, including extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E, n = 10), carbapenem-resistant Pseudomonas aeruginosa (CRPA, n = 5), and methicillin-resistant Staphylococcus aureus (MRSA, n = 2). Additionally, we novelly employed targeted probe capture metagenomics (TCM), which utilizes oligonucleotide probes to enrich and detect low-abundance microbial species and ARG sequences. TCM revealed the detection of human pathogenic taxa in 65.2% of samples, including P. aeruginosa (78.4%), Acinetobacter baumannii (77.9%), and S. aureus (71.1%). Clinically critical ARGs, such as blaCTX-M (2.0%), blaNDM (2.9%), blaSHV (3.4%), and mecA (62.3%), were detected in 63.7% of samples, indicating a potential transmission within the post-handwashing area.

CONCLUSIONS: Our findings highlight the role of post-handwashing areas as underrecognized reservoirs for MDROs, particularly MRSA. Furthermore, this study demonstrates the utility of TCM in public health surveillance by enabling a sensitive detection of rare but high-risk microbial species and drug resistance determinants in low-biomass environmental samples. This study offers a comprehensive and nuanced view of the microbial and resistome landscape of washroom environments, offering a revolutionary approach for future environmental surveillance.},
}

@article {pmid41250096,
year = {2025},
author = {Zhang, Y and Le Guennec, A and Pussinen, P and Proctor, G and Niazi, SA},
title = {Successful endodontic treatment improves glucose and lipid metabolism: a longitudinal metabolomic study.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1195},
pmid = {41250096},
issn = {1479-5876},
support = {FDS Pump Priming Grant 2022//Royal College of Surgeons of England/ ; },
mesh = {Humans ; Longitudinal Studies ; Male ; Female ; *Metabolomics ; *Lipid Metabolism ; *Glucose/metabolism ; Middle Aged ; Adult ; Biomarkers/blood ; *Root Canal Therapy ; Metabolome ; Periapical Periodontitis/metabolism/blood/therapy ; },
abstract = {BACKGROUND: Apical periodontitis (AP) is one of the most prevalent dental diseases. Its presence can increase systemic inflammatory burden and is associated with cardiometabolic disorders including higher cardiovascular risks and impaired glycaemic control. There is currently a paucity of knowledge showing whether successful endodontic treatment is associated with systemic metabolic improvements. This study aims to identify the potential impact of successful endodontic treatment on patients' serum metabolomic profiles, and to evaluate how these impacts are associated with the metabolic syndrome (MetS) indicators, inflammatory biomarkers, as well as blood and intracanal microbiomes.

METHODS: This self-controlled two-year longitudinal cohort study investigated the metabolic improvements associated with successful endodontic treatment in 65 AP patients using nuclear magnetic resonance (NMR) spectroscopy on serum samples. The samples were collected at 5 time points including pre-operative baseline and 3 month, 6 month, 1 year, and 2 year reviews.

RESULTS: Significant postoperative changes were observed in 24 (54.5%) metabolites. The results suggested improved glucose and lipid metabolism as well as reduced inflammatory burdens, as evidenced by a significant reduction in branched-chain amino acids at the 3 month review, a significant decrease in glucose and pyruvate at the 2 year review, a short-term reduction in cholesterol, choline, and fatty acid levels, and a progressive increase in tryptophan. In addition, strong associations were found between metabolic profile and clinical metabolic syndrome indicators, inflammatory markers, and pre-operative blood and intracanal microbiome, underscoring the systemic impact of AP and its treatment. A dynamic Bayesian model identified that metabolites associated with the tricarboxylic acid (TCA) cycle are the key regulators in the longitudinal alterations of the metabolic profiles.

CONCLUSIONS: Successful endodontic treatment in AP patients is associated with improved glucose and lipid metabolic profiles, and a reduction in systemic inflammation, suggesting a potential role in mitigating cardiometabolic disease risk.},
}

Humans
Longitudinal Studies
Male
Female
*Metabolomics
*Lipid Metabolism
*Glucose/metabolism
Middle Aged
Adult
Biomarkers/blood
*Root Canal Therapy
Metabolome
Periapical Periodontitis/metabolism/blood/therapy

@article {pmid41250081,
year = {2025},
author = {Xu, J and Song, J and Fu, Z and Zhou, H and Zhang, Y and Shi, C},
title = {Unraveling gut microbiome interferences in cancer immunotherapy: a meta-analysis of diverse drug effects.},
journal = {BMC cancer},
volume = {25},
number = {1},
pages = {1776},
pmid = {41250081},
issn = {1471-2407},
support = {2023YFF1205000//National Key Research and Development Program of China/ ; Z-2018-35-2004//China International Medical Foundation/ ; 2023HT035//Industry, University and Research Projects of the Ministry of Education/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Immunotherapy/methods/adverse effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/immunology/microbiology/drug therapy/therapy ; Proton Pump Inhibitors/therapeutic use ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Probiotics/therapeutic use ; },
abstract = {Recent advancements in tumor therapy have centered on novel treatments, particularly immune checkpoint inhibitors (ICIs), which have transformed cancer treatment since their global approval in 2011. ICIs have demonstrated remarkable and substantial efficacy across a range of malignancies, including malignant melanoma, non-small cell lung cancer (NSCLC), head and neck cancers, renal carcinoma, and selected gastrointestinal cancers. Despite these promising outcomes, the challenges that during the clinical application, such as relatively low response rates and the occurrence of immune-related adverse events, can limit therapeutic benefits. Accumulating evidence highlights the gut microbiome as a critical modulator of cancer immunotherapy efficacy. Notably, alterations in gut microbiota composition observed in response to ICI therapy, and specific bacterial populations (such as an increased Clostridiales/ Baceroidales ratio, etc.) have been associated with improved responses in patients with NSCLC and renal cell carcinoma. However, the composition and function of the gut microbiome are influenced by a variety of factors, among which concomitant drug use plays a particularly prominent role. Medications commonly prescribed to cancer patients, such as antibiotics, proton pump inhibitors (PPIs), and probiotics, can significantly alter microbial communities, potentially impacting immunotherapy outcomes. Thus, there is a compelling need for rigorous research to elucidate how such drug-induced shifts in gut microbiota affect patient responses to ICIs. Thus, we conducted a meta-analysis which included 69 studies, 102 cohorts (22,568 patients were included) to systematically investigate the influence of drug interventions, including PPIs, antibiotics and probiotics on gut microbiome dynamics and ICI effectiveness. Progression-free survival (PFS), Overall survival (OS) and Objective response rate (ORR) were utilized as the main meta notions, while a subgroup analysis was determined based on: (1) tumor type; (2) exposure time window; (3) Treatment scheme as well. The total HR and 95% CI for PFS and OS are calculated separately for each intervention (probiotics, antibiotics, and PPIs) to compare their impact on ICI immunotherapy. Our research showed that the concurrent use of antibiotics or PPIs with ICIs was associated with significantly OS, PFS, and ORR. In contrast, probiotic supplementation demonstrated promising results with improved efficacy metrics. Besides, in subgroup analysis, patients using antibiotics within three months before or after the initiation of ICI therapy, OS, PFS, and ORR were significantly lower compared to those who did not receive antibiotics; the timing of antibiotic or PPI administration consistently resulted in poorer outcomes; a negative correlation between PPI use and OS, PFS, and ORR across treatment modalities was also exhibited. By elucidating the interplay between these factors, this study aims to provide robust evidence for optimizing ICI therapy, and to enlighten cancer treatment strategies more personalized, effective and safer, ultimately advancing patient care in oncology.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Immunotherapy/methods/adverse effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Neoplasms/immunology/microbiology/drug therapy/therapy
Proton Pump Inhibitors/therapeutic use
Anti-Bacterial Agents/therapeutic use/pharmacology
Probiotics/therapeutic use

@article {pmid41249904,
year = {2025},
author = {Zárate, A and Barrientos, L and Florez, JZ and Buschmann, AH and Pérez-Santos, I and Abanto, M and Bruna, P and Leyton, B and Vásquez, C and Inostroza, PA and Lundin, D and Borrego, CM and Balcázar, JL and Vila-Costa, M},
title = {Capturing the spatial structure of the benthic microbiome under an intensive aquaculture scenario in Chilean Patagonia.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {752},
pmid = {41249904},
issn = {1471-2180},
mesh = {Chile ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Aquaculture ; *Seawater/microbiology/chemistry ; Ecosystem ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; },
abstract = {BACKGROUND: Identifying the microbial taxa that structure assemblages in response to local disturbances along the Chilean Patagonian coast is critical for understanding community reorganization and ecological risk in this vulnerable marine environment. Here, we examined benthic microbial interactions across sixteen sites spanning 42-44°S in the Inner Sea of Chiloé and adjacent fjord systems. Using co-occurrence network analysis, we characterized spatial interaction patterns and identified keystone taxa whose relationships with environmental variables may serve as ecological indicators. The presence of keystone taxa supports the concept of microbial "seed banks," which sustain community stability and ecosystem functionality under stress. Networks revealed structured communities dominated by niche-specialist taxa, consistent with ecological processes of niche differentiation and environmental filtering.

RESULTS: The benthic environment was found to harbor niche-specialist taxa, including Flavobacteriaceae, Gemmataceae, Humimicrobiaceae, Clostridiaceae, and Sulfurovaceae, typically associated with organic enrichment and anthropogenic influence. These microbial families showed strong correlations with environmental gradients such as nitrate, phosphate, silicate, pH, salinity, and phaeopigments. Alpha-diversity analyses revealed greater microbial richness in FZ compared to the ISC, likely reflecting higher environmental heterogeneity and long-term adaptation to dynamic and fluctuating conditions. Beta-diversity analyses further supported the presence of distinct microbial assemblages between the two zones. Multivariate statistics and co-occurrence network analyses demonstrated that FZ communities display enhanced taxonomic interactions and greater network complexity, suggesting increased ecological stability. In contrast, microbial networks in the ISC exhibited reduced connectivity, potentially indicative of environmental stressors disrupting microbial spatial organization and network resilience. Moreover, the identification of indigenous bacterial isolates provided evidence for the presence of opportunistic host-associated pathogens, highlighting the utility of microbial biomarkers in detecting early ecological responses to human impacts.

CONCLUSION: Microbial co-occurrence patterns in northern Patagonian sediments reveal shifts in community assembly and increased network complexity that may enhance resilience to perturbations. The detection of strains harboring opportunistic pathogen biomarkers highlights risks under intense anthropogenic pressures. Monitoring keystone taxa thus offers early warning of functional decline. Broader spatio-temporal assessments remain essential to clarify microbial dynamics and their implications for ecosystem health and antimicrobial resistance.},
}

Chile
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Aquaculture
*Seawater/microbiology/chemistry
Ecosystem
Biodiversity
RNA, Ribosomal, 16S/genetics
*Geologic Sediments/microbiology

@article {pmid41249836,
year = {2025},
author = {Huang, Y and Sun, Y and Ronda, C and Mavros, CF and Li, J and Jacobse, J and Huang, LH and Resnick, SJ and Giddins, M and Freedberg, DE and Chavez, A and Goettel, JA and Wang, HH},
title = {Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41249836},
issn = {1546-1696},
support = {MCB-2025515//National Science Foundation (NSF)/ ; 1R01DK118044//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R21AI146817//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R01CA272898//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5U19AI067773//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R03DK123489//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; N00014-17-1-2353//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; HR00111920009//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; S-168-4X5-001//United States Department of Defense | United States Air Force | AFMC | Air Force Research Laboratory (AFRL)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; 1061046//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; 1513935//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; IRIS Award//Columbia University/ ; },
abstract = {Metagenomic sequencing and metabolomics of fecal matter have revealed the impact of the gut microbiome on health and disease. In addition to microbiota, feces also contain shed or exfoliated host epithelial, secretory and immune cells, but RNA profiling of these cells is challenging owing to degradation and cross-contamination. Here we introduce exfoliome sequencing (Foli-seq) to profile fecal exfoliated eukaryotic messenger RNAs (feRNAs) originating from the upper and lower gastrointestinal regions and show that this 'fecal exfoliome' harbors stable RNAs that reflect intestinal and immune function. By selectively amplifying targeted transcripts, Foli-seq demonstrates robust, accurate, sensitive and quantitative measurement of feRNAs. In murine colitis models, feRNA reveals temporal processes of epithelial damage, immune response and intestinal recovery specific to different types of gut inflammation. Simultaneous exfoliome and microbiome profiling uncovers a dense host-microbe interaction network. Moreover, we demonstrate stratification of patients with inflammatory bowel disease into subgroups that correlate with disease severity. Fecal Foli-seq is a noninvasive strategy to longitudinally study the gut and profile its health.},
}

@article {pmid41249780,
year = {2025},
author = {Kou, R and Li, A and Yu, M and Wang, J and Hu, Y and Zhang, B and Liu, J and Wang, S},
title = {Bifidobacterium bifidum FB3-12 attenuates ovalbumin-induced allergic diseases by enhancing intestinal barrier function and regulating gut microbiota.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {227},
pmid = {41249780},
issn = {2396-8370},
support = {32302096//the National Natural Science Foundation of China/ ; },
abstract = {The escalating environmental changes have exacerbated the physiological suffering and economic burden caused by allergic diseases worldwide. Bifidobacterium bifidum (B. bifidum), due to its positive regulatory effects on the gut microenvironment, is considered a promising strategy for the prevention and treatment of allergies. Our study utilized the ovalbumin (OVA)-induced allergy mouse model to explore the anti-allergic potential of the self-screened strain B. bifidum FB3-12 (FB3-12) via intestinal intervention. The results demonstrated that a three-week FB3-12 treatment effectively suppressed the levels of immune markers, including OVA-specific immunoglobulin E (OVA-sIgE), mast cell protease-1 (Mcpt-1), and histamine (HIS) in the serum of allergic mice, and restored the Th2/Th1 immune response imbalance in the spleen. Furthermore, compared to the OVA group, FB3-12 intervention ameliorated intestinal damage and inflammation, significantly increasing the relative expression of Mucin-2 and tight junction proteins. Analysis of the gut microbiota profile revealed a distinct shift in the enterotype of OVA-challenged mice, characterized by a decreased Firmicutes/Bacteroidetes (F/B) ratio and a marked increase in the relative abundance of Akkermansia. FB3-12 intervention significantly enriched beneficial genera such as Lactobacillus and Colidextribacter, and upregulated the levels of short-chain fatty acids (SCFAs) and associated G protein-coupled receptors (GPRs) in the intestine. These findings underscore the therapeutic potential and application value of FB3-12 in alleviating allergic diseases through modulation of the gut microbiome.},
}

@article {pmid41249722,
year = {2025},
author = {Xu, N and He, Y and Yang, G and Huang, X},
title = {Exploring the Role of Gut Microbiota in Chronic Spontaneous Urticaria: Mechanisms and Potential Therapeutic Implications.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41249722},
issn = {1867-1314},
support = {no. 82103751//National Natural Science Foundation of China/ ; },
abstract = {Gut microbiota dysbiosis has emerged as a significant factor in the pathogenesis of chronic spontaneous urticaria (CSU), a condition characterized by immune dysregulation and skin inflammation. This review summarizes the current understanding of the role of gut microbiota in CSU pathogenesis, highlighting the alterations in microbial composition and function, the mechanisms by which dysbiosis triggers systemic inflammation and skin mast cell activation, and the impact of microbial metabolites. We critically evaluate the potential of gut microbiota-targeted therapies, such as probiotics, prebiotics, and fecal microbiota transplantation (FMT), as novel treatment strategies for CSU. Despite the evident promise of these approaches, significant challenges persist, including the necessity for personalized interventions, the collection of long-term efficacy and safety data, and a more profound understanding of the complex interplay between the gut and skin. Future research endeavors must prioritize the execution of clinical trials that evaluate the efficacy of gut microbiota modulation in CSU patients and the identification of biomarkers that can effectively predict treatment response.},
}

@article {pmid41249638,
year = {2025},
author = {Tinning, Z and Kaestli, M and Nowland, SJ and Siboni, N and Seymour, JR and Gibb, KS and Padovan, AC},
title = {Dynamics of Bacterial and Vibrio Communities in Blacklip Rock Oysters in the Seasonal Tropics.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {125},
pmid = {41249638},
issn = {1432-184X},
support = {2020-043//Fisheries Research and Development Corporation/ ; Discovery Project DP240100370//Australian Research Council/ ; },
mesh = {Animals ; *Vibrio/isolation & purification/genetics/classification ; *Ostreidae/microbiology ; Seasons ; Aquaculture ; Seawater/microbiology ; *Microbiota ; Australia ; Tropical Climate ; Shellfish/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Humans ; },
abstract = {Cultivation of the tropical Blacklip Rock Oyster (BRO) (Saccostrea spathulata) is an emerging Indigenous-led aquaculture industry in the seasonal tropics of northern Australia. However, little is currently known about the potential for pathogen outbreaks in this species. We conducted a year-long study to establish a microbial baseline to identify potential oyster and human health risks to inform future food safety decision making in this nascent industry. In healthy oysters, we identified both the core microbiome of this oyster species and the presence of potential oyster and human pathogens. The core bacteriome comprised nine bacterial families, while the core vibriome comprised the animal pathogens Vibrio harveyi and V. owensii. The potential human pathogen V. parahaemolyticus was detected in some oysters during the wet season, during periods of increased rainfall, turbidity and total nitrogen. The bacteriome and vibriome of oysters were significantly different to the adjacent seawater and therefore we concluded that seawater is not an appropriate surrogate for pathogen risk surveillance in this developing industry. These results provide new knowledge on the microbiology of a previously understudied oyster species and will inform monitoring methods, harvesting and shellfish quality compliance in this emerging Indigenous-led industry.},
}

Animals
*Vibrio/isolation & purification/genetics/classification
*Ostreidae/microbiology
Seasons
Aquaculture
Seawater/microbiology
*Microbiota
Australia
Tropical Climate
Shellfish/microbiology
*Bacteria/classification/genetics/isolation & purification
Humans

@article {pmid41249613,
year = {2025},
author = {Zhang, X and Jia, L and Lin, X and Zhou, L},
title = {The gut-bone axis in ankylosing spondylitis: mechanistic insights and the translational gap.},
journal = {Clinical and experimental medicine},
volume = {26},
number = {1},
pages = {12},
pmid = {41249613},
issn = {1591-9528},
support = {No. 202101//Wuxi Taihu Lake Talent Plan, Supports for Leading Talents in Medical and Health Profession/ ; },
mesh = {*Spondylitis, Ankylosing/drug therapy/immunology/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Bone and Bones/pathology/immunology ; Dysbiosis ; Interleukin-23/antagonists & inhibitors ; },
abstract = {The gut-bone axis is pivotal in the pathogenesis of ankylosing spondylitis (AS), with gut dysbiosis and mucosal immune activation driving skeletal pathology. However, translating these mechanistic insights into effective therapies remains challenging. This review critically analyzes this translational gap, arguing that the therapeutic paradoxes seen with cytokine inhibitors and microbiome-targeted therapies are a direct consequence of the disease's significant variability. We focus on the unexpected failure of IL-23 inhibitors and the dual effects of IL-17 blockade to illustrate the need for a nuanced understanding of tissue-specific immunity. We then propose a biomarker-driven, AI-assisted therapeutic framework that integrates multi-omic data to personalize AS treatment, aiming to bridge the gap between mechanistic insights and clinical success and offer a path toward progression-free remission.},
}

*Spondylitis, Ankylosing/drug therapy/immunology/microbiology/pathology
Humans
*Gastrointestinal Microbiome/drug effects
*Bone and Bones/pathology/immunology
Dysbiosis
Interleukin-23/antagonists & inhibitors

@article {pmid41249586,
year = {2025},
author = {Zhou, S and Bi, J and Zhou, S and Luo, L and Yan, X and Zou, J and Ji, Y and Zhao, S and Qiu, J and Liu, Z and Jiang, J and Wang, B and Liu, X},
title = {Community Assembly Mechanisms Underlying Divergent Responses of Indica and Japonica Rice Rhizosphere Microbiota to Drought Stress.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {126},
pmid = {41249586},
issn = {1432-184X},
support = {2022YFD2300302//National Key Research and Development Program of China/ ; 42277304//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; XUEKEN2022003//Fundamental Research Funds for the Central Universities/ ; BX20240168//National Postdoctoral Program for Innovative Talents/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {*Oryza/microbiology/growth & development/physiology/genetics/classification ; *Rhizosphere ; *Droughts ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; Agricultural Irrigation ; },
abstract = {Drought stress markedly reduces rice yield, with notable genotypic variation in drought tolerance. While the rhizosphere microbiome is regarded as the second genome of plants, how the indica and japonica rice rhizosphere microbial communities respond to deficit irrigation and their relationship with yield remain to be elucidated. Here, we conducted field experiments using 12 indica and 12 japonica rice varieties under full and deficit irrigation regimes. Yield-related traits, including filled grain number, seed setting rate, two-plant yield, and thousand grain weight, were measured, and the rhizosphere microbial communities were characterized by 16S rRNA gene sequencing. In line with previous studies, japonica varieties showed superior drought resistance in terms of yield performance. Both rice genotype and irrigation regime significantly influenced the composition and functional potential of the rhizosphere microbiome. Compared to indica rice, the japonica rice rhizosphere was enriched with more beneficial microorganisms. Enrichment of nitrogen‑metabolism‑related groups, such as Microvirga and Nitrososphaeraceae, may contribute to rhizosphere nitrogen cycling and support nitrogen availability for the rice. Similarly, higher abundance of Streptomyces in japonica varieties under drought conditions may be associated with improved drought tolerance. These microbial genera were closely associated with rice yield. Moreover, the japonica rhizosphere microbiome was less disturbed by water limitation, showing higher stability. Overall, the rhizosphere microbiome of japonica rice exhibited functional optimization under drought stress by promoting the enrichment of beneficial and nitrogen-cycling microbes, thereby enhancing drought resistance and yield stability. This study demonstrated a significant correlation between rhizosphere microbial communities and rice yield, providing fundamental insights that may contribute to future strategies for optimizing crop productivity through microbiome management in sustainable agriculture.},
}

*Oryza/microbiology/growth & development/physiology/genetics/classification
*Rhizosphere
*Droughts
*Microbiota
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
Stress, Physiological
Agricultural Irrigation

@article {pmid41249582,
year = {2025},
author = {Qu, W and Wang, Z and Zhu, T and Cui, H and Bing, Z and Shen, S and Shen, Y and Yu, S and Zhuang, H and Wang, T},
title = {Aspergillus fumigatus promotes tumor angiogenesis via SLC7A11 on myeloid-derived suppressor cells.},
journal = {EMBO reports},
volume = {},
number = {},
pages = {},
pmid = {41249582},
issn = {1469-3178},
support = {BK20211508//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; 82273011//MOST | National Natural Science Foundation of China (NSFC)/ ; 021414380472//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; },
abstract = {The microbiome is increasingly recognized as playing a critical role in lung cancer prevention, diagnosis, and treatment. While bacteria are essential for tumor angiogenesis, the impact of fungi on this process remains largely unexplored. In this study, we investigate effects of Aspergillus fumigatus (A. fumigatus) on lung cancer. We show that inhalation of A. fumigatus increases tumor burden and angiogenesis in mouse models. Interestingly, A. fumigatus does not directly affect the proangiogenic abilities of tumor cells or endothelial cells. Instead, A. fumigatus promotes the accumulation of myeloid-derived suppressor cells (MDSCs), particularly G-MDSCs, in tumor tissues. A. fumigatus increases VEGF-A secretion from tumor-associated MDSCs, promoting tumor angiogenesis. Furthermore, we identify solute carrier family 7 member 11 (SLC7A11) as a key player in regulating this proangiogenic function through an interaction with High Mobility Group Box 1 (HMGB1) in MDSCs. Our results shed light on the mechanisms by which A. fumigatus influences MDSCs to promote angiogenesis and demonstrate that commensal fungi influence host immunity and support tumor progression.},
}

@article {pmid41249559,
year = {2025},
author = {Liu, B and Sondervorst, K and Nesporova, K and Faust, K and Govers, SK},
title = {Growth stage and interspecies interactions shape the cell biology and cell cycle characteristics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1580},
pmid = {41249559},
issn = {2399-3642},
support = {STG/21/068//KU Leuven (Katholieke Universiteit Leuven)/ ; 101040800//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 1110925N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 1251624N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 101105027//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteroides thetaiotaomicron/growth & development/genetics/cytology/physiology/metabolism ; *Cell Cycle ; *Clostridiales/growth & development/genetics/physiology ; Peptidoglycan/biosynthesis ; },
abstract = {The human gut is a densely populated environment where microbial cells face frequent nutrient fluctuations. While previous studies have identified changes in gene expression, protein concentrations, and metabolite levels, less is known about how gut bacteria respond to nutrient fluctuations at the cellular level. Here, we compared cell biological properties of B. thetaiotaomicron and R. intestinalis, two prevalent human gut microbiome members. Our comparison revealed distinct cellular properties of both bacteria during exponential growth in vitro, including a unique zonal peptidoglycan synthesis pattern in R. intestinalis. Upon nutrient depletion in stationary phase, we observed different cell morphological alterations, with B. thetaiotaomicron cells becoming wider and R. intestinalis cells shorter, accompanied by distinct intracellular changes. These alterations extended to other B. thetaiotaomicron strains, but not Roseburia species. By re-analyzing an existing RNA-seq dataset, we could link the cell biological response of both species to different alterations in gene expression in stationary phase. Finally, coculture experiments revealed a significant impact of interspecies interactions on cell morphological and transcriptomic properties of both bacteria. Together, our work provides insight into the unexplored cell biology of representative human gut microbiome members and how this is shaped by nutrient fluctuations and the presence of other species.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bacteroides thetaiotaomicron/growth & development/genetics/cytology/physiology/metabolism
*Cell Cycle
*Clostridiales/growth & development/genetics/physiology
Peptidoglycan/biosynthesis

@article {pmid41249313,
year = {2025},
author = {Kok, PJR and Wisse, BB and Kapuściak, M and Lampo, M},
title = {Amphibian supercooling capacity is not limited to sub-zero thermal environments.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40311},
pmid = {41249313},
issn = {2045-2322},
support = {2020/39/D/NZ8/02399//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Freezing ; *Amphibians/physiology ; Skin/microbiology ; Cold Temperature ; Acclimatization ; Microbiota ; },
abstract = {Freeze-tolerant amphibians initiate controlled freezing using ice nucleators and survive internal ice formation by accumulating cryoprotectants. In contrast, freeze-avoidant (supercooling) species rely on the inhibition of ice nucleators to prevent freezing altogether. All confirmed supercooling species are native to the Northern Hemisphere and regularly endure negative temperatures. The occurrence, ecological role, and underlying mechanisms of supercooling in amphibians remain poorly understood. Here, we demonstrate for the first time that amphibian supercooling capacity may be present even if not expressed (i.e., latent) and not limited to freezing thermal environments. Exploratory metagenomic data allow us to evaluate whether skin-associated bacteria could contribute to freeze avoidance. In addition, using field experiments, we assess cold and dehydration tolerance limits in two syntopic amphibian species from a high tepui summit (Roraima-tepui in Venezuela) and explore the potential role of cryoprotective dehydration in facilitating supercooling. Despite being syntopic, these species showed striking differences in thermal and dehydration tolerance. Physiological freeze avoidance in tropical montane amphibians is shown to be associated with low critical thermal minima, high dehydration tolerance and possibly antifreeze-producing skin microbiota, although the latter needs further investigation. These traits may determine species persistence under shifting climatic regimes, particularly in thermally variable montane systems.},
}

Animals
Freezing
*Amphibians/physiology
Skin/microbiology
Cold Temperature
Acclimatization
Microbiota

@article {pmid41249223,
year = {2025},
author = {Li, CM and Cheng, TH and Chen, YJ and Liang, YR and Huang, CL},
title = {Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40115},
pmid = {41249223},
issn = {2045-2322},
support = {108AS-8.5.2-PI-P2//Ministry of Agriculture, Taiwan/ ; Higher Education Sprout Project//Ministry of Education, Taiwan/ ; },
mesh = {Animals ; *Soil Microbiology ; *Cucumis sativus/parasitology/growth & development ; *Microbiota/drug effects ; *Nitrification/drug effects ; Plant Roots/parasitology ; *Tylenchoidea ; Soil/chemistry ; *Plant Diseases/parasitology/prevention & control ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Brachyura/chemistry ; },
abstract = {With growing environmental awareness, eco-friendly agricultural practices are gaining increased attention. Among these, crab shell meal (CSM) is recognized for its potential to suppress root-knot nematodes (Meloidogyne spp.), largely through the enrichment of chitinolytic bacteria, particularly members of the phylum Actinobacteriota. However, the broader effects of CSM on the soil microbiome remain poorly understood. This study employed 16S amplicon metagenomics to investigate the impact of CSM application on the soil bacterial community associated with root-knot nematode-infected cucumber (Cucumis sativus L.) in a pot experiment. Plant growth parameters and soil chemical properties were also assessed. CSM application at concentrations ranging from 0% to 4% significantly altered the soil microbiome, increasing in the relative abundances of Firmicutes and Actinobacteriota in a dose-dependent manner. These microbial shifts were associated with enhanced cucumber growth and reduced nematode infection severity. Functional predictions indicated that CSM-enriched microbial communities exhibited higher potential for chitin hydrolysis and nitrification, processes that likely contributed to nematode suppression and plant growth promotion. By contrast, the introduction of Streptomyces as a biocontrol agent was less effective, as this strain struggled to establish within the potting system. Overall, the application of CSM successfully enhanced the abundance of chitinolytic bacteria and soil nitrification, providing a dual benefit of nematode control and improved plant growth.},
}

Animals
*Soil Microbiology
*Cucumis sativus/parasitology/growth & development
*Microbiota/drug effects
*Nitrification/drug effects
Plant Roots/parasitology
*Tylenchoidea
Soil/chemistry
*Plant Diseases/parasitology/prevention & control
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
*Brachyura/chemistry

@article {pmid41249215,
year = {2025},
author = {Oliva-Arancibia, B and Villanueva, P and Ugalde, JA},
title = {Profiling of vaginal microbial communities in Chilean women via self-sampling and nanopore sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40093},
pmid = {41249215},
issn = {2045-2322},
support = {National Doctorate Scholarship 21240354//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt Regular 1221209//Agencia Nacional de Investigación y Desarrollo/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; Chile ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Adult ; *Nanopore Sequencing/methods ; Young Adult ; Lactobacillus/genetics/isolation & purification/classification ; },
abstract = {The vaginal microbiota is a dynamic ecosystem that plays a central role in women's reproductive health, with Lactobacillus species typically dominating in healthy individuals. Disruptions to this microbiota can lead to dysbiosis, increasing susceptibility to infections such as bacterial vaginosis and contributing to adverse reproductive outcomes. Despite growing global interest in vaginal microbiome research, studies in Latin American populations remain limited, particularly in Chile. In this exploratory study, we aimed to characterize the vaginal microbiota of Chilean women using a combination of self-sampling and full-length 16S rRNA gene sequencing with Oxford Nanopore Technologies (ONT). We implemented a customized bioinformatic pipeline using the Emu classifier to achieve species-level taxonomic resolution. Our analysis revealed that most participants had microbiota dominated by Lactobacillus species, while a subset exhibited diverse microbial communities consistent with Community State Type (CST) IV. Alpha and beta diversity metrics supported these classifications and demonstrated that species-level resolution enhances the ability to distinguish CSTs. These findings provide the first species-level characterization of vaginal microbiota in Chilean women and demonstrate the utility of ONT sequencing and self-sampling in underrepresented populations. This work contributes essential baseline data for the region and highlights the importance of inclusive microbial profiling in advancing personalized approaches to women's health.},
}

Female
Humans
*Vagina/microbiology
Chile
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Adult
*Nanopore Sequencing/methods
Young Adult
Lactobacillus/genetics/isolation & purification/classification

@article {pmid41249202,
year = {2025},
author = {Gómez-Repollés, A and Villa-Rodríguez, E and Blahovska, Z and Ferguson, S and Radutoiu, S},
title = {High-quality genome assemblies of 152 root commensal bacteria from the model legume Lotus japonicus.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1793},
pmid = {41249202},
issn = {2052-4463},
support = {NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
mesh = {*Lotus/microbiology ; *Genome, Bacterial ; *Plant Roots/microbiology ; *Microbiota ; *Bacteria/genetics ; Symbiosis ; },
abstract = {Bacterial culture collections represent a valuable tool for mechanistic understanding of microbiome assemblies and are increasingly used to assemble tailored synthetic communities to characterize their microbe-microbe interactions and those with the environment. Given the size of these collections, short-read sequencing is primarily used to capture the encoded genetic information. Whilst sufficient for many microbiome studies, this approach is not amenable for understanding bacterial genome evolution or detailed genetic analyses at the entire genome level. Here we report the assembly of 152 full bacterial genomes from the Lj-SPHERE, the Lotus japonicus collection of root commensals. We performed long-read sequencing using Oxford Nanopore Technology and used this together with pre-existing Illumina sequences to de novo assemble these into high quality genomes with improved contiguity and quality. These genomes now provide a solid platform for detailed, mechanistic understanding of microbiome assembly, dynamics, and evolution in plants.},
}

*Lotus/microbiology
*Genome, Bacterial
*Plant Roots/microbiology
*Microbiota
*Bacteria/genetics
Symbiosis

@article {pmid41249178,
year = {2025},
author = {Zhang, J and Yu, D and Zhang, L and Wang, T and Zhang, L and Yan, J},
title = {Quantifying the relative contributions of bacterial and fungal communities to carcass decomposition using a quantitative microbiome profiling approach.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {210},
pmid = {41249178},
issn = {2055-5008},
support = {82101977//the National Natural Science Foundation of China/ ; 82030058//the National Natural Science Foundation of China/ ; },
mesh = {*Bacteria/classification/metabolism/genetics/isolation & purification ; *Fungi/classification/metabolism/isolation & purification/genetics ; Soil Microbiology ; *Microbiota ; Animals ; Metabolomics/methods ; *Mycobiome ; Postmortem Changes ; },
abstract = {Carcass microbial decomposition plays a vital role in global elemental cycling. However, bacterial and fungal absolute abundance dynamics, as well as their contributions to carcass decomposition, remain unclear. Here, the questions were investigated through quantitative microbiome profiling (QMP) and metabolomics. Within the first 14 days postmortem, microbial copies in grave soil and tissue increased by several orders of magnitude. Comparison of QMP with relative microbiome profiling (RMP) revealed strikingly different, even opposing successional trends for major phyla. Bacteria drove more metabolite variation than fungi in the decomposition. Co-occurrence networks revealed that key bacterial and fungal decomposers formed two distinct modules that were highly interconnected and significantly associated with carcass-derived metabolites, suggesting a synergistic relationship in the breakdown of organic matter. Notably, using QMP did not substantially enhance the accuracy of postmortem interval estimation. Collectively, our findings provide critical insights into microbial ecological dynamics during carcass decomposition.},
}

*Bacteria/classification/metabolism/genetics/isolation & purification
*Fungi/classification/metabolism/isolation & purification/genetics
Soil Microbiology
*Microbiota
Animals
Metabolomics/methods
*Mycobiome
Postmortem Changes

@article {pmid41249177,
year = {2025},
author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y},
title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {209},
pmid = {41249177},
issn = {2055-5008},
support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&D Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; },
abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.},
}

Animals
*Gastrointestinal Microbiome/genetics
Feces/microbiology/chemistry
Metagenomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
*Conservation of Natural Resources/methods
Metabolomics/methods
Metabolome
*Colobinae/microbiology
Endangered Species
Multiomics

@article {pmid41248758,
year = {2025},
author = {Habimana-Griffin, L and Prusa, J and Wang, B and Strong, L and Ning, J and Tovar, ESR and Toth, K and Butler, B and Reynoso, FJ and Markovina, S and Ciorba, MA and Dantas, G},
title = {A novel focal duodenal radiation injury model reveals dose-, time-, and spatially-dependent microbiome perturbations after radiation injury.},
journal = {International journal of radiation oncology, biology, physics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijrobp.2025.11.011},
pmid = {41248758},
issn = {1879-355X},
abstract = {PURPOSE: The duodenum is a key organ at risk during stereotactic ablative radiotherapy (SABR). Understanding mechanisms of radiation-induced intestinal injury (RIII) could reveal novel strategies to reduce SABR toxicities. The gut microbiome contributes to RIII, however existing preclinical models either require surgical manipulation or fail to recapitulate high-dose conformal treatment fields used during SABR, confounding microbiome studies. We developed a non-invasive focal bowel irradiation model to assess microbiome dynamics in both the duodenum and the stool after high-dose duodenal irradiation.

MATERIALS AND METHODS: C57BL/6J mice received sham treatment or focal irradiation (12 or 18 Gy) to the proximal duodenum using a small animal irradiator. Stool and duodenal tissue samples were collected at days 4, 14, and 91 post-treatment and processed for bacterial 16S rRNA gene V4 region amplicon sequencing (Illumina MiSeq platform). Microbiome diversity metrics were calculated and multivariable linear mixed modeling identified bacterial taxa associated with radiotherapy.

RESULTS: Oral iodine contrast enabled duodenum visualization and 100% of mice survived until sacrifice. Focal duodenal irradiation led to dose- and time-dependent changes in duodenal bacterial community composition that were not observed in stool. At days 4 and 14 post-treatment, 18 duodenal taxonomic groups were significantly perturbed, while only 2 taxa were significantly altered in the stool.

CONCLUSIONS: Our focal duodenal irradiation model is safe, well-tolerated, and easy to implement. It enables characterization of microbiome perturbations during both the acute and late phases of injury and serves as a platform for testing new RIII mitigation strategies. Our findings reveal that irradiation-induced changes in the duodenal microbiome are dose-, time-, and spatially-dependent and are not reflected in stool samples. These results underscore the imperative of directly assessing tissue-associated microbiota, as relying solely on stool samples risks overlooking critical, localized microbial dynamics that may drive injury and repair.},
}

@article {pmid41249173,
year = {2025},
author = {Cheng, Q and Lv, S and Yin, N and Wang, J},
title = {Microbial regulators of physiological and reproductive health in women of reproductive age: their local, proximal and distal regulatory roles.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {207},
pmid = {41249173},
issn = {2055-5008},
support = {2022YFA1304102//National Key Research and Development Program of China/ ; T2341010//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; *Reproductive Health ; Pregnancy ; *Gastrointestinal Microbiome ; Fertility ; *Microbiota ; Homeostasis ; Reproduction ; },
abstract = {The female microbiome is emerging as a key regulator of gynecological and reproductive health. This review summarizes how local and gut microbes affect gynecological outcomes, fertility, and pregnancy through metabolic, immune, and hormonal pathways. We highlight underlying mechanisms and intervention strategies, emphasizing the restoration of microbial homeostasis as a promising avenue for advancing understanding, prevention, and management of women's physiological and reproductive health conditions.},
}

Female
Humans
*Reproductive Health
Pregnancy
*Gastrointestinal Microbiome
Fertility
*Microbiota
Homeostasis
Reproduction

@article {pmid41248824,
year = {2025},
author = {Desouky, MA and Eldahshan, W and Atawia, RT},
title = {Exploring the gut-lung-brain axis: Focus on endothelial dysfunction, impaired bioenergetics and strategies to mitigate lung and cognitive disorders.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124089},
doi = {10.1016/j.lfs.2025.124089},
pmid = {41248824},
issn = {1879-0631},
abstract = {Dysbiosis has emerged as a major determinant in the pathogenesis of many human disorders and is a continuously expanding area of research. Identification of several microbial populations and their derived products marks an important milestone in microbiome research. Interestingly, there is evidence that gut microbiota-derived products affect distant organs such as the brain and lungs. Although the effect of gut dysbiosis on several lung- and brain-related disorders has been demonstrated, our knowledge of the mechanisms and consequences of individual metabolites and products on specific cell types such as endothelial cells is still evolving. Endothelial dysfunction is a prominent feature in vascular dementia and several lung disorders. Specifically, alteration in endothelial bioenergetics is an emerging area of research. In this review, the evidence on the interconnection between dysbiosis in the gut and three lung disorders- asthma, COPD and ARDS is discussed. Additionally, the association between these respiratory disorders and cognitive impairment is examined with mechanistic insights. Moreover, data involving the direct impact of key microbial metabolites and products on endothelial cells is synthesized and potential therapeutic modalities are highlighted. We identify the impact of microbial metabolites on endothelial dysfunction and bioenergetics as a potential gap in knowledge and a plausible avenue for future research.},
}

@article {pmid41248397,
year = {2025},
author = {Korenblik, V and Korosi, A and Brul, S and Bockting, C and Nieuwdorp, M and Lok, A},
title = {Feasibility and acceptability of 8-week oral tributyrin supplementation as add on to antidepressant medication in patients with depression: a study protocol paper for a pilot, randomised controlled trial.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e108423},
doi = {10.1136/bmjopen-2025-108423},
pmid = {41248397},
issn = {2044-6055},
mesh = {Humans ; *Antidepressive Agents/therapeutic use/administration & dosage ; Pilot Projects ; Adult ; Feasibility Studies ; Double-Blind Method ; *Depressive Disorder, Major/drug therapy ; *Triglycerides/administration & dosage/therapeutic use ; Middle Aged ; Male ; *Dietary Supplements ; Female ; Young Adult ; Adolescent ; Administration, Oral ; Drug Therapy, Combination ; Aged ; Randomized Controlled Trials as Topic ; Gastrointestinal Microbiome ; Treatment Outcome ; },
abstract = {BACKGROUND: Major depressive disorder (MDD) is a severe mental health condition that profoundly affects both psychological and physical well-being. Growing evidence indicates that targeting the gut-brain axis could present new therapeutic opportunities for MDD, given the role of gut microbiota and their metabolites in its pathophysiology. One promising approach involves supplementation with butyrate, a short-chain fatty acid that has demonstrated antidepressant potential in preclinical models of depression. However, clinical research exploring the effects of butyrate supplementation in individuals with MDD remains lacking.

METHODS: This study is a double-blind, parallel, 1:1 randomised placebo-controlled trial. The primary aim of this pilot study is to assess the feasibility and acceptability of an 8-week oral supplementation with tributyrin, a triglyceride form of butyrate (4 g/day), added to usual treatment with antidepressant medication in 24 patients with mild-to-severe MDD aged 18-65 years. Secondary outcomes include changes in depressive symptoms, assessed weekly throughout the supplementation period and at 16 weeks post-supplementation during follow-up, as well as changes in anhedonia and affect, measured multiple times per day via a smartphone application throughout the supplementation period. Additional outcomes include changes in gastrointestinal symptoms, changes in faecal microbiome, metabolites in blood and faeces, inflammation, epigenetic markers, stress and intestinal permeability.

ETHICS AND DISSEMINATION: The study has been approved by the Medical Research Ethics Committee of the Amsterdam University Medical Centre, the Netherlands.

DISCUSSION: Should the pilot demonstrate feasibility and acceptability, a larger-scale study will be warranted to evaluate the efficacy of tributyrin supplementation in alleviating depressive symptoms. This pilot will provide valuable insights to guide sample size calculations and refine study design for subsequent trials. Ultimately, this research could lead to novel adjunctive treatments for MDD targeting gut-brain signalling, offering new therapeutic avenues for patients with MDD.

TRIAL REGISTRATION NUMBER: This trial has been registered in the International Clinical Trials Registry Platform (registry number: NL-OMON57116).},
}

Humans
*Antidepressive Agents/therapeutic use/administration & dosage
Pilot Projects
Adult
Feasibility Studies
Double-Blind Method
*Depressive Disorder, Major/drug therapy
*Triglycerides/administration & dosage/therapeutic use
Middle Aged
Male
*Dietary Supplements
Female
Young Adult
Adolescent
Administration, Oral
Drug Therapy, Combination
Aged
Randomized Controlled Trials as Topic
Gastrointestinal Microbiome
Treatment Outcome

@article {pmid41248372,
year = {2025},
author = {Fernando, SM and Muscedere, J and Rochwerg, B and Johnstone, J and Daneman, N and Marshall, JC and Lauzier, F and Rudkowski, JC and Arabi, YM and Heels-Ansdell, D and Sligl, W and Kristof, AS and Duan, E and Dionne, JC and St-Arnaud, C and Reynolds, S and Khwaja, K and Cook, DJ and , },
title = {Frailty and the risk of ICU-acquired infections in a randomised trial: a protocol and statistical analysis plan.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e105227},
doi = {10.1136/bmjopen-2025-105227},
pmid = {41248372},
issn = {2044-6055},
mesh = {Humans ; *Frailty/complications ; *Intensive Care Units ; *Pneumonia, Ventilator-Associated/epidemiology/prevention & control ; *Cross Infection/epidemiology ; Length of Stay/statistics & numerical data ; Randomized Controlled Trials as Topic ; Risk Factors ; Aged ; Proportional Hazards Models ; Male ; Respiration, Artificial/adverse effects ; Female ; Research Design ; },
abstract = {INTRODUCTION: Dysregulated immunity may account for an increased risk of infection and other adverse outcomes among frail hospitalised persons. The primary objective of this study is to examine whether baseline frailty is associated with the risk of developing ventilator-associated pneumonia (VAP) or other intensive care unit (ICU)-acquired infections among invasively ventilated adults. Additional objectives are to examine the relationship between frailty and hospital length of stay, discharge to a long-term care facility and vital status. We hypothesise that persons with frailty compared with others would have an increased risk of VAP and other infections, a longer hospital stay, higher probability of discharge to a long-term care facility and higher mortality.

METHODS AND ANALYSIS: This is a preplanned secondary analysis of the PROSPECT trial (Probiotics to Prevent Severe Pneumonia and Endotracheal Colonization Trial) which enrolled patients across 44 ICUs in three countries. We will use Cox proportional hazards regression analysis to assess the association of frailty with the clinical outcomes of interest, adjusting for other baseline variables. Baseline demographic and descriptive outcome data will be reported using descriptive statistics. Regression results will be presented as adjusted HRs or ORs with 95% CIs for the associations of each independent variable with the primary, secondary and tertiary outcomes.

ETHICS AND DISSEMINATION: Participating hospital research ethics board approved the PROSPECT trial and data collection. The protocol for this study was approved by the Hamilton Integrated Research Ethics Board on 20 August 2015 (Project ID:19128). This study will identify whether frailty is associated with risk of VAP and other healthcare-associated infections in invasively ventilated patients, adjusted for other baseline factors. Results may be useful to patients, their caregivers, clinicians and the design of future research. Findings will be disseminated to investigators at a meeting of the Canadian Critical Care Trials Group. We will present study results at an international conference in the fields of critical care and infectious diseases, to coincide with or precede open-access peer-review publication. To aid knowledge dissemination, we will use a variety of formats. For example, for traditional and social media, we will create two different visual abstracts and infographics of our results suitable to share on clinician-facing and public-facing platforms.

TRIAL REGISTRATION NUMBER: NCT02462590.},
}

Humans
*Frailty/complications
*Intensive Care Units
*Pneumonia, Ventilator-Associated/epidemiology/prevention & control
*Cross Infection/epidemiology
Length of Stay/statistics & numerical data
Randomized Controlled Trials as Topic
Risk Factors
Aged
Proportional Hazards Models
Male
Respiration, Artificial/adverse effects
Female
Research Design

@article {pmid41248126,
year = {2025},
author = {Jefferson, J and Reigate, C and Giacomini, A and Rivero, MJ and Hitchings, M and Webster, TU and Wells, K},
title = {Triadic relationships between pasture exposure, gastrointestinal parasites, and hindgut microbiomes in grazing lambs.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0337086},
doi = {10.1371/journal.pone.0337086},
pmid = {41248126},
issn = {1932-6203},
mesh = {Animals ; Sheep/microbiology/parasitology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology/parasitology ; Bacteria/genetics/classification ; *Sheep Diseases/parasitology/microbiology ; Lolium ; },
abstract = {Livestock grazing in confined pastures often means grazing on a less diverse diet than under more natural conditions and increased exposure to gastrointestinal parasites prevailing in these pastures. However, how sward composition influences gut microbiome (GM) diversity and its relationship with parasite burden remains poorly understood. In this study, we analysed the faecal GM of weaned lambs grazing on two distinct sward types (perennial ryegrass and a mixed-species sward) over three consecutive months using 16S rRNA sequencing, in order to assess how microbial diversity and composition are related to environmental conditions and the gastrointestinal nematode (GIN) burden in naturally infected lambs. Sward type and sampling time explained some of the variation in GM alpha diversity and community composition (beta diversity), whereas individual lamb identity accounted for considerably more variation in microbial assemblages. Shifts in the relative abundance of bacterial genera such as Saccharofermentans, Anaerosporobacter, Butyrivibrio in relation to sward type and sampling time suggest mostly adaptive fluctuations in response to diet and pasture condition. Abundance shifts of Negativibacillus, and Candidatus Saccharimonas were also associated with GIN burden, which, in turn, was higher in lambs grazing on mixed swards compared to ryegrass. Our findings add to the growing understanding of how sheep microbiomes vary with pasture management and changes in parasite burden. We highlight that individual identity may shape gut microbiota, and that potential triadic interactions among gastrointestinal parasites, sward exposure, and the gut microbiome underscore the importance of considering host, parasite, and environmental factors collectively when evaluating microbiome dynamics in grazing livestock.},
}

Animals
Sheep/microbiology/parasitology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Feces/microbiology/parasitology
Bacteria/genetics/classification
*Sheep Diseases/parasitology/microbiology
Lolium

@article {pmid41247816,
year = {2025},
author = {Gao, Y and Wang, X and Wang, Q and Jiang, L and Wu, C and Guo, Y and Cui, N and Tang, H and Tang, L},
title = {Global impact of pelvic inflammatory diseases attributable to sexually transmitted infections in women of childbearing age: a comprehensive analysis based on GBD 2021 data and bibliometric analysis.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004066},
pmid = {41247816},
issn = {1743-9159},
abstract = {BACKGROUND: Pelvic inflammatory disease (PID), often caused by sexually transmitted infections (STIs), poses significant health threat to women of childbearing age (WCBA). This study assessed the global prevalence trends and research landscape of STIs-related PID.

METHODS: This study integrated GBD 2021 data and bibliometric analysis. Joinpoint regression calculated Average annual percentage change (AAPC) for age-standardized prevalence rate (ASPR) from 1990 to 2021. Decomposition analyses assessed the contributions of population growth, aging, and epidemiological changes to the prevalence trends for last 32 years. The Bayesian age-period-cohort (BAPC) model projected ASPR from 2022 to 2040, and the Nordpred model conducted a sensitivity analysis of the prediction results, which validated the findings' reliability. 1726 related publications were retrieved from the WOS Core Collection database. Bibliometric information was extracted with VOSviewer software for visualization.

RESULTS: In 2021, an estimated 1,009,957.64 cases of PID due to STIs occurred among WCBA globally, with chlamydial infection accounting for approximately 23%, gonococcal infection (4.98%), and other STIs (72.03%). From 1990 to 2021, the global ASPR of STIs-related PID increased by AAPC of 0.13%, with the largest increase observed among women in the 20-24 years age group. Regionally, the highest ASPR was observed in low SDI regions in 2021, while the fastest increase occurred in middle SDI regions over the last 32 years. Decomposition analyses highlighted the population growth as a key driver of global prevalence rise, accounting for 78.5 %. The global ASPR of STIs-related PID is projected to continue rising from 2022 to 2040. Bibliometric analysis showed stable research on STIs and PID, with an increased citation rate. The United States was the leading contributor. Research focused on chlamydia trachomatis, with recent studies exploring the vaginal microbiome, resistance and protective immunity.

CONCLUSIONS: This study performed an epidemiological assessment and bibliometric analysis of the PID attributable to STIs burden globally, informing policy-making and research directions.},
}

@article {pmid41247642,
year = {2025},
author = {Li, J and Hu, J and Yang, Y and Zhang, H and Liu, Y and Fang, Y and Qu, L and Lin, A and Luo, P and Jiang, A and Wang, L},
title = {Drug resistance in cancer: molecular mechanisms and emerging treatment strategies.},
journal = {Molecular biomedicine},
volume = {6},
number = {1},
pages = {111},
pmid = {41247642},
issn = {2662-8651},
support = {81772740//National Natural Science Foundation of China/ ; 82173345//National Natural Science Foundation of China/ ; 81972333//National Natural Science Foundation of China/ ; 82372883//National Natural Science Foundation of China/ ; 2022YFB4700904//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Drug Resistance, Neoplasm/genetics ; *Neoplasms/drug therapy/genetics/metabolism/pathology/therapy ; Tumor Microenvironment/drug effects ; Animals ; Immunotherapy ; Antineoplastic Agents/therapeutic use/pharmacology ; Epigenesis, Genetic ; },
abstract = {Therapeutic resistance remains a defining challenge in oncology, limiting the durability of current therapies and contributing to disease relapse and poor patient outcomes. This review systematically integrates recent progress in understanding the molecular, cellular, and ecological foundations of drug resistance across chemotherapy, targeted therapy, and immunotherapy. We delineate how genetic alterations, epigenetic reprogramming, post-translational modifications, and non-coding RNA networks cooperate with metabolic reprogramming and tumor microenvironment remodeling to sustain resistant phenotypes. The influence of the microbiome is highlighted as an emerging determinant of therapeutic response through immune modulation and metabolic cross-talk. By summarizing key regulatory circuits, We establishe a unified framework linking clonal evolution, metabolic adaptability, and tumor ecological dynamics. We further synthesizes novel therapeutic strategies that convert resistance mechanisms into therapeutic vulnerabilities, including synthetic lethality approaches, metabolic targeting, and disruption of stem cell and stromal niches. Advances in single-cell and spatial omics, liquid biopsy, and artificial intelligence are emphasized as transformative tools for early detection and real-time prediction of resistance evolution. This review also identifies major translational gaps in preclinical modeling and proposes precision oncology frameworks guided by evolutionary principles. By bridging mechanistic understanding with adaptive clinical design, this work provides an integrated roadmap for overcoming therapeutic resistance and achieving sustained, long-term cancer control.},
}

Humans
*Drug Resistance, Neoplasm/genetics
*Neoplasms/drug therapy/genetics/metabolism/pathology/therapy
Tumor Microenvironment/drug effects
Animals
Immunotherapy
Antineoplastic Agents/therapeutic use/pharmacology
Epigenesis, Genetic

@article {pmid41247431,
year = {2025},
author = {Dhungana, P and Dam, A and Kiang, TKL},
title = {Clinical Pharmacokinetic-Pharmacodynamic Relationships of Pharmacological Strategies for Attenuating p-Cresyl Sulfate in Patients with Kidney Disease.},
journal = {Clinical pharmacokinetics},
volume = {},
number = {},
pages = {},
pmid = {41247431},
issn = {1179-1926},
abstract = {p-Cresyl sulfate (pCS) is a highly toxic uremic compound that is produced from tyrosine and phenylalanine in the gut and primarily excreted renally. In patients with kidney dysfunction, the accumulation of pCS can lead to the worsening of kidney disease and manifestation of organ toxicities. Various pharmacological strategies have been proposed to reduce pCS in patients with chronic kidney disease (CKD), but systematic pharmacokinetic-pharmacodynamic assessments have not been conducted to our knowledge. The objectives of this scoping review were to comprehensively and critically summarize the available literature using a newly devised, pharmacokinetic-pharmacodynamic assessment method. We searched PubMed, Embase, and Scopus for primary research articles in patients with CKD and devised the following novel approach to systematically evaluate each study: (i) positive reduction or null reduction of pCS; (ii) dose dependency; (iii) time dependency; (iv) effects on free versus total pCS; and (v) relationships to diet regimens (e.g., protein intake), microbiome composition, blood biochemistry, and clinical outcomes (i.e., progression of renal disease measured by initiation of dialysis or renal transplant; cardiovascular outcomes such as incidence of myocardial infarction, heart failure, cardiovascular death; and changes in qualityof- life instruments). Fifty-nine studies were identified with a total of 2593 study participants (pre-dialysis CKD: n = 1060; CKD on dialysis: n = 1499; and post-transplant CKD: n = 34). The studies included AST-120 (n = 3), sevelamer (n = 9), sucroferric Noxyhydroxide (n = 1 [+ 1 overlapping with sevelamer]), prebiotics (n = 15), probiotics (n = 9), synbiotics (n = 13), antibiotics (n = 3), ketoanalogs (n=3), and curcumin (n = 3). Only AST-120 and synbiotics consistently demonstrated significant pCS reductions, and the percentage (%) reductions by AST-120 were 40.9-75.6% for free and 28.8-42.8% for total pCS; whereas the percentage reduction by synbiotics were 6.4-78.1% for total and 16.7% for free pCS, the latter only evident in a subgroup with antibiotic-free regimen. Although sevelamer was also associated with a pCS reduction, the percentage reduction was modest and only based on the total concentration. In contrast, the majority of sucroferric oxyhydroxide, prebiotics, probiotics, ketoanalogs, and curcumin studies did not demonstrate consistent pCS reductions. Furthermore, dose dependency was not established in the majority of studies, and although some temporal relationships were evident, the data were very limited. Only a few of the analyzed studies measured both bound and unbound forms of pCS, and inconsistencies have been reported in a few studies. In Ngeneral, it was also difficult to establish associations with outcomes in most studies because of limitations in experimental design, and in instances where potential pharmacokinetic-pharmacodynamic relationships were observed, they were generally weak and only with surrogate markers of commonly measured biochemistry, oxidative stress, lipid profiles, and inflammatory markers, with only a handful of studies capturing clinical outcomes. In conclusion, we have identified potential pharmacological interventions that may be further developed for the purpose of reducing pCS in patients with CKD.},
}

@article {pmid41247319,
year = {2025},
author = {Wang, Z and Guo, X and Zhang, H and Zheng, T and Liu, Y and Dai, L and Xie, Y and Shang, X and Zhang, L and Yang, L and Yuan, L and Hou, X},
title = {Rotation-driven changes in physicochemical properties modulate soil microbial diversity and community complexity in tobacco-woad soils.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0301624},
doi = {10.1128/spectrum.03016-24},
pmid = {41247319},
issn = {2165-0497},
abstract = {Continuous tobacco monocropping leads to soil degradation and yield reduction. To address this, we evaluated the effects of tobacco (Nicotiana tabacum L.)-woad (Isatis tinctoria L.) rotation (A2, A4) compared to tobacco monoculture (A1) and woad monoculture (A3) on soil health and crop quality over a multi-year period. Methods involved comparative analysis of soil nutrients, enzyme activities, microbial community structure, and crop chemical composition and economic value. Key results demonstrated that tobacco-woad rotation significantly improved soil fertility. The tobacco-woad rotation could increase the content of organic matter, alkaline available nitrogen, available phosphorus, and available potassium in the soil, which were increased by 1.44%, 17.96%, 4.61%, and 16.20%, respectively, compared to tobacco monoculture. Soil urease and catalase activities, particularly urease (increased by 2.31 times), were significantly enhanced during the tobacco pre-growth period under rotation. Soil microbial communities were significantly restructured under tobacco-woad rotation versus monocropping. Bacterial phyla Acidobacteria, Gemmatimonadota, and Methylomirabilota were enriched in tobacco-woad rotation (A2) relative to tobacco monoculture (A1), while Chloroflexi, Methylomirabilota, and Verrucomicrobiota increased in woad-tobacco rotation (A4) versus woad monoculture (A3). Fungal shifts featured decreased Ascomycota and Basidiomycota with increased Mortierellomycota in both rotations, alongside reduced Chytridiomycota in A4. Rotation enriched key bacterial genera (MND1, Nitrospira, Subgroup-10, and RB41) and fungal taxa (Mortierella, Saccharomyces, and Saitozyma). Crucially, rotation harmoniously improved the chemical composition of both tobacco and woad leaves, increasing reducing sugars, total sugars, nicotine, potassium, and the sugar ratio in tobacco. The proportion of high-quality tobacco leaves post-curing increased by 10.24% (A2), contributing to a significantly higher total crop production value. In conclusion, tobacco-woad rotation effectively alleviates soil degradation associated with continuous tobacco cropping by enhancing soil nutrient availability, boosting key enzyme activities, and optimizing the structure and interactions of the soil microbial community. These soil improvements collectively drive superior crop quality and economic returns, supporting their adoption as a sustainable agricultural practice.IMPORTANCE(i) The effects of rotation of tobacco with woad on the quality of tobacco production were clarified using physiological and biochemical analyses. (ii) The effects of rotating tobacco with woad on soil microorganisms were revealed by microbiome sequencing of tobacco soils. Tobacco-woad rotation significantly improved the relative abundance of soil-dominant bacteria and decreased the relative abundance of harmful fungi. (iii) An efficient cultivation model of tobacco and woad suitable for Shandong was established by combining soil microbiomics with tobacco plant growth and development. Rotation of tobacco to woad gave the best results.},
}