@article {pmid40859280,
year = {2025},
author = {Liu, M and Kochian, LV and Helgason, BL},
title = {The native soil microbiome is critical for early root-associated microbiota assembly and canola growth.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {112},
pmid = {40859280},
issn = {2524-6372},
support = {CARP.2019.24//Canola Agronomic Research Program/ ; RGPIN-2019-04158//Natural Sciences and Engineering Research Council of Canada/ ; },
}

@article {pmid40859157,
year = {2025},
author = {Gao, ZQ and Su, JW and Qin, Y and Ye, T and Cao, H and Yang, LH and Elsheikha, HM},
title = {Metagenomic analysis of vitamins B and K2 biosynthesis in chicken gut microbiota across laying periods.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {553},
pmid = {40859157},
issn = {1471-2180},
}

@article {pmid40858628,
year = {2025},
author = {Joshi, AA and Szafrański, SP and Steglich, M and Yang, I and Qu, T and Schaefer-Dreyer, P and Xiao, X and Behrens, W and Grischke, J and Häussler, S and Stiesch, M},
title = {Integrative microbiome- and metatranscriptome-based analyses reveal diagnostic biomarkers for peri-implantitis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {175},
pmid = {40858628},
issn = {2055-5008},
support = {SFB/TRR-298-SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy - EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR-298-SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR-298-SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR-298-SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy - EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Peri-implantitis is a severe biofilm-associated infection affecting millions worldwide. This cross-sectional study aimed to identify taxonomic and functional biomarkers that reliably indicate peri-implantitis by utilizing paired data from full length 16S rRNA gene amplicon sequencing (full-16S) and metatranscriptomics (RNAseq) in 48 biofilm samples from 32 patients. Both full-16S and RNAseq analyses revealed significant differences between healthy and peri-implantitis samples, with a shift toward anaerobic Gram-negative bacteria in peri-implantitis. Metatranscriptomics identified enzymatic activities and metabolic pathways associated with peri-implantitis and uncovered complex peri-implant biofilm ecology related to amino acid metabolism. Integrating taxonomic and functional data enhanced predictive accuracy (AUC = 0.85) and revealed diagnostic biomarkers including health-associated Streptococcus and Rothia species and peri-implantitis-associated enzymes (urocanate hydratase, tripeptide aminopeptidase, NADH:ubiquinone reductase, phosphoenolpyruvate carboxykinase and polyribonucleotide nucleotidyltransferase). Thus, biofilm profiling at taxonomic and functional levels provides highly predictive disease biomarkers, laying the foundation for novel diagnostic and personalized treatment approaches for peri-implant disease.},
}

@article {pmid40858623,
year = {2025},
author = {Marsaux, B and d'Hoker, W and Moens, F and Van Elst, D and Minnebo, Y and Marzorati, M and Van de Wiele, T},
title = {Candida albicans colonization in the human colon correlates with a reduction in acetate- and butyrate-producing bacteria, as simulated using the M-SHIME® model.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {176},
doi = {10.1038/s41522-025-00803-w},
pmid = {40858623},
issn = {2055-5008},
support = {812969//European Union's Horizon 2020/ ; },
abstract = {Candida albicans is a common gut commensal, typically restricted by the resident microbiota. However, microbiome disruption can enable its outgrowth, increasing the risk of life-threatening candidiasis. Restoring key protective microbes offer a therapeutic strategy, though their identification remains challenging. Using the M-SHIME® model simulating the human proximal colon, we investigated C. albicans-bacteriome interactions under eubiotic and dysbiotic conditions. We assessed how clindamycin, ciprofloxacin, and metronidazole modulate C. albicans colonization and evaluated associated microbial and metabolic shifts. The effects were antibiotic- and donor-specific: clindamycin facilitated colonization, ciprofloxacin had no impact, and metronidazole showed variable outcomes. Engraftment did not correlate with total bacterial concentration or α-diversity, but with the loss of specific taxa, notably Lachnospiraceae and Bifidobacterium. These correlations were supported functionally by reductions in acetate and butyrate, suggesting a metabolic mechanism of fungal suppression. This study highlights the role of dysbiosis in C. albicans outgrowth and supports targeted microbiome restoration strategies.},
}

@article {pmid40858622,
year = {2025},
author = {Valentino, V and Magliulo, R and Balivo, A and Krysmann, AM and Calvanese, CM and Esposito, A and Sequino, G and Genovese, A and Porcellato, D and Ercolini, D and De Filippis, F},
title = {Microbiome profiling of Grana Padano and Parmigiano Reggiano cheeses reveals cheese-specific biomarkers, psychobiotic potential, and bioprotective activities.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {177},
pmid = {40858622},
issn = {2055-5008},
support = {IR0000033//NextGenerationEU/ ; CN_00000033//NextGenerationEU/ ; P2022X8A9M//Ministero dell'Università e della Ricerca/ ; },
abstract = {Grana Padano (GP), Trentingrana (TG), and Parmigiano Reggiano (PR) are among the finest Italian Protected Designation of Origin (PDO) cheeses. GP, TG, and PR undergo extensive proteolysis during ripening, where the microbiome metabolizes amino acids, producing flavour and bioactive molecules. We explored the microbiome, volatilome, and metaproteome of PDO GP (n = 42), TG (n = 18), and PR (n = 60). Findings revealed diverse microbial communities enriched in proteolytic microbes, associated with cheese-specific processing technology. Correlations between lactic acid bacteria strains and specific volatile compounds were identified in PR. Importantly, we identified genes involved in the production of neuroactive molecules, suggesting potential connections between cheeses consumption and mental health, along with genes related to bacteriocin biosynthesis, possibly enhancing cheese safety, shelf life, and process sustainability. This study provides novel insights into the functional attributes of long-ripened cheeses microbiome, highlighting their potential as sources of psychobiotics and bioprotective strains.},
}

@article {pmid40858544,
year = {2025},
author = {Zou, X and Cao, H and Hong, L and Suo, L and Wang, C and Chang, K and Ni, Y and Liu, B and Cao, B},
title = {Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {272},
pmid = {40858544},
issn = {2059-3635},
abstract = {Respiratory microbial dysbiosis has been implicated in the occurrence and progression of community-acquired pneumonia (CAP). However, the dynamic variation in the respiratory microbiota and its interaction with the host response remain poorly understood. Here, we performed metagenomic analysis of respiratory and gut microbiota, along with blood transcriptomics, using longitudinally collected samples from 38 CAP patients. CAP patients presented disrupted sputum microbiota at the early, middle, and late stages of hospitalization. Microbial pathways involved in peptidoglycan biosynthesis and immune evasion, particularly contributed by the Streptococcus genus, were enriched in CAP patients. Additionally, several Streptococcus strains demonstrated correlation between respiratory and gut microbiota in CAP patients. By incorporating host response data, we revealed that Streptococcus oralis (SOR) was associated with host pathways involved in the innate immune response to infection, and this microbe‒host interaction was reproduced in a newly enrolled CAP cohort consisting of 22 patients with influenza infection. The host-SOR interaction was validated in a mouse model, where SOR demonstrated protective efficacy against influenza virus infection comparable to that of the well-established respiratory probiotic Lactobacillus rhamnosus GG. Preaspiration of SOR in mice significantly mitigated body weight loss, reduced lung inflammation, and lowered viral loads following influenza virus challenge. Host response profiling indicated that SOR priming activated a greater innate immune response at the early stage of infection and that this response resolved timely as the host began to recover. These findings suggest that respiratory commensals play an immune-protective role by inducing a timely innate immune response to prevent CAP progression.},
}

@article {pmid40858525,
year = {2025},
author = {Espinoza-Arrue, J and Arce, M and Endo, N and Hoare, A and Dutzan, N and Abusleme, L},
title = {Profiling the Bacterial Microbiome Across Peri-Implant Conditions.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70024},
pmid = {40858525},
issn = {1600-051X},
support = {1231728//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 1231350//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 1251739//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 2024-21240601//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 2022-21221003//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; DE031213-01/DE/NIDCR NIH HHS/United States ; /NH/NIH HHS/United States ; },
abstract = {AIM: To comprehensively characterise the bacterial microbiome in peri-implant health, peri-implant mucositis and peri-implantitis.

MATERIALS AND METHODS: A re-analysis of raw microbiome data was performed from 15 studies, which were finally selected based on the availability of 16S rRNA sequencing. Reads were pre-processed using mothur and classified using the HOMD database. A total of 522 samples were analysed to evaluate diversity estimates and bacterial relative abundance, identifying discriminant features via LEfSe, while predictions of functional potential were obtained using PICRUSt2. Bacterial co-occurrence networks were constructed, and dysbiosis was measured by employing the subgingival microbiome dysbiosis index.

RESULTS: Peri-implantitis showed higher bacterial diversity compared to health and greater microbial richness than peri-mucositis. Each clinical condition displayed a distinct community structure and bacterial co-occurrence networks. The representative species in peri-implant health were Rothia aeria, R. dentocariosa and Veillonella parvula_dispar. Peri-mucositis is characterised by Leptotrichia hongkongensis, L. wadei and Fusobacterium nucleatum subsp. polymorphum, while peri-implantitis is defined by Porphyromonas gingivalis, F. nucleatum subsp. vincentii and Tannerella forsythia. Peri-implantitis exhibited enrichment in predicted microbial pathogenesis pathways and greater bacterial dysbiosis.

CONCLUSIONS: These results provide deeper insights into the peri-implant microbiome, identifying key bacterial species, functional processes and interactions that may be crucial to inflammation and destruction during peri-implant diseases.},
}

@article {pmid40858176,
year = {2025},
author = {Thorat, P and Dass, RS},
title = {An overview of production, characterization, and bioactive potentials of Aspergillus exopolysaccharides.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {147102},
doi = {10.1016/j.ijbiomac.2025.147102},
pmid = {40858176},
issn = {1879-0003},
abstract = {Exopolysaccharides (EPS) produced by Aspergillus have attracted considerable scientific interest due to their complex structural, chemical, biological, and functional properties. This article summarizes the literature published between 2011 and 2024, during which scientists extensively explored the production, structural characterization, and biological activities of Aspergillus-derived EPS (Asp-EPS). Various factors influence Asp-EPS biosynthesis, including nutrient composition, pH, temperature, and aeration conditions. Advanced analytical techniques, such as gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and fourier-transform infrared spectroscopy (FTIR), have been used to analyze their monosaccharide composition, functional groups, glycosidic linkages, and degree of branching. Asp-EPS demonstrate a wide range of bio-functional activities, including antimicrobial, antioxidant, anti-tumor, anticoagulant, immunomodulatory, gut microbiome-modulating effect, emulsifying, and flocculating properties. However, only a limited number of Aspergillus spp. have been extensively studied for their EPS-producing capabilities. Further research into the genetic, metabolic, and rheological properties, with deeper investigation into the mechanisms underlying their biological activities, could support the development of tailored applications in diverse areas, including functional foods, pharmaceuticals, biomaterials, and environmental biotechnology.},
}

@article {pmid40858074,
year = {2025},
author = {Ruiz-Castilla, FJ and Barbudo-Lunar, M and Gutiérrez, MC and Michán, C and Martín, MÁ and Alhama, J},
title = {Storage of Alperujo influences composting performance: Insights into gaseous emissions and functional metagenomics.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127015},
doi = {10.1016/j.jenvman.2025.127015},
pmid = {40858074},
issn = {1095-8630},
abstract = {Alperujo (AL), the primary by-product of olive oil extraction, poses a significant environmental challenge in the Mediterranean region. Understanding the AL composting process is essential for controlled aerobic revalorisation to obtain a stable and good quality organic amendment with the minimum environmental impact. Our approach assumes that full-scale pond storage duration modifies the degree of hydrolytic fermentation of AL, affecting the subsequent stages of the composting process. In this work, AL raw materials for composting were stored for 3 or 6 months. Subsequently, during pilot-scale composting, the loss of organic matter (OM) not only induced key changes in the solid mass but also in gaseous emissions, which decreased along with the storage time. Consequently, the initial C/N ratio decreased from 25.76 to 22.24, and composting yields relative to the AL initially mixed with a bulking agent (3/1, wt./wt.) were 76.4 % and 41.7 %, respectively. Phenolic compounds were effectively degraded throughout the composting process under both initial conditions, enhancing the potential value of the final products. Metagenomic analysis revealed differences in the raw material bacteriome, variations that also became evident throughout composting. The thermophilic stage fostered the selection of a range of thermotolerant microorganisms, many of them with lignocellulosic activity, which is essential for the decomposition of OM. Then, at the final mesophilic phase, a significant increase in bacterial diversity and metabolic activity was observed. This study contributes to better understand the functional role of the microbiome in AL composting, particularly regarding the bacterial community dynamics and gaseous emissions to the atmosphere.},
}

@article {pmid40857842,
year = {2025},
author = {Zhou, X and Wang, H and Liu, M and Yan, F and Du, X and Yang, S and Zhao, A},
title = {Microbiome and metabolome changes in laying hens induced by dietary epsilon-polylysine.},
journal = {Poultry science},
volume = {104},
number = {11},
pages = {105708},
doi = {10.1016/j.psj.2025.105708},
pmid = {40857842},
issn = {1525-3171},
abstract = {Epsilon-polylysine (ε-PL) is a natural antimicrobial peptide that has been broadly applied in the food industry as a preservative. The effects of ε-PL on the intestinal microbiota, animal metabolism, and its potential as a "new feed additive" require further exploration. In this study, ninety Hy-Line Brown laying hens were randomly divided into three groups. Egg-laying performance, egg quality, and liver parameters were measured; expression of gut barrier, immunity, and ferroptosis related genes in each intestinal segment were detected; microbiome and metabolomic analyses were performed. The results demonstrated that dietary ε-PL supplementation significantly increased average egg weight and egg quality (P < 0.05). It also markedly, ε-PL supplementation significantly increased the villus height to crypt depth ratio in the duodenum and ileum (P < 0.01), significantly reduced the mRNA levels of interleukin-1 beta (IL-1β) and interleukin-6 (IL-6), and elevated the mRNA levels of interleukin-10 (IL-10) and tumor necrosis factor-alpha (TNF-α) in the intestine (P < 0.05). Moreover, ε-PL inhibited intestinal mucosal ferroptosis (P < 0.05) and mitigated severe fatty liver development, as evidenced by a significantly reduction in hepatic malondialdehyde (MDA) content (P < 0.01). Microbiota analysis revealed that ε-PL supplementation significantly increased the abundance of Lactobacillus and Saccharimonadales; while decreasing the abundance of Anaerotruncus and Slackia in the cecal microbiota. Additionally, ε-PL supplementation enhanced the amino acid metabolism, lipid metabolism, the digestive system, arginine biosynthesis, tryptophan metabolism, bile secretion, and steroid hormone biosynthesis in the intestine, which might contribute to improved egg quality and intestinal absorptive capacity, as well as the inhibition of fatty liver formation. In summary, dietary ε-PL supplementation exerts multiple beneficial effects in laying hens, including enhancing egg quality, alleviate inflammation, boosting antioxidant capacity, improving intestinal morphology, modulating gut microbiota, and protecting liver health.},
}

@article {pmid40857503,
year = {2025},
author = {Yue, Y and Mao, Y and Read, TD and Fedirko, V and Satten, GA and Chen, X and Zhan, X and Hu, YJ},
title = {Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency in testing differential abundance.},
journal = {Journal of the American Statistical Association},
volume = {},
number = {},
pages = {},
doi = {10.1080/01621459.2025.2516205},
pmid = {40857503},
issn = {0162-1459},
abstract = {The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Surprisingly, many microbiome studies have performed both experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, suggesting that an integrative analysis of both datasets could enhance the testing power for these signatures. However, differential experimental biases, partially overlapping samples, and uneven library sizes pose tremendous challenges when combining the two datasets. In this article, we introduce the first method of this kind, named Com-2seq, that combines the two datasets for testing differential abundance at the genus level as well as the community level while overcoming these difficulties. Our simulation studies demonstrate that Com-2seq substantially enhances statistical efficiency over analysis of a single dataset and outperforms two ad hoc approaches to integrative analysis. In analysis of real microbiome data, Com-2seq uncovered scientifically plausible findings, namely, the association of Butyrivibrio, Gemella and Ignavigranum with prediabetes status, which would have been missed by analyzing a single dataset. Butyrivibrio failed to reach the significance level in the analysis of each dataset despite showing a consistent trend; Gemella and Ignavigranum failed to produce adequate data in the 16S experiment.},
}

@article {pmid40857390,
year = {2025},
author = {Xia, JY and Komanduri, S and Keswani, RN and Rodrigues, TR and Sinha, J and Rengarajan, A and Tran, P and Hepler, C and Prindle, A and Aadam, AA},
title = {Integrating multi-omics in bile for biomarker discovery in cholangiocarcinoma.},
journal = {Hepatology communications},
volume = {9},
number = {9},
pages = {},
doi = {10.1097/HC9.0000000000000786},
pmid = {40857390},
issn = {2471-254X},
mesh = {Humans ; *Cholangiocarcinoma/diagnosis/metabolism/microbiology ; *Bile Duct Neoplasms/diagnosis/metabolism/microbiology ; *Bile/chemistry/microbiology/metabolism ; Metabolomics/methods ; Male ; Female ; Cholangiopancreatography, Endoscopic Retrograde ; *Biomarkers, Tumor/analysis ; Middle Aged ; Cholangitis, Sclerosing/complications ; Aged ; Sensitivity and Specificity ; Bile Acids and Salts/analysis ; Multiomics ; },
abstract = {BACKGROUND: Cholangiocarcinoma (CCA) is an aggressive cancer with a poor prognosis. Histopathology evaluation of brushings and biopsies obtained during endoscopic retrograde cholangiopancreatography (ERCP) currently remains the main method of diagnosis, which has limited sensitivity for malignancy detection. Our study aimed to identify human bile-derived biomarkers to improve CCA diagnosis. Bile samples were collected from patients during ERCP for primary sclerosing cholangitis, CCA, or benign biliary disease.

METHODS: Bile samples were collected from patients undergoing ERCP for biliary obstruction due to primary sclerosing cholangitis, newly identified malignant strictures concerning for CCA, or benign biliary disease. Using 16S sequencing, metabolomics, and bile acid quantification, we aimed to identify distinctive microbial and metabolite signatures associated with CCA.

RESULTS: Multi-omics analyses revealed distinct microbial and metabolite signatures associated with CCA. From these findings, we identified and validated microbial and metabolite markers capable of accurately detecting CCA with improved sensitivity and specificity for malignancy detection compared to current cytology-based methods.

CONCLUSIONS: These findings highlight the potential of multi-omics bile-based diagnostic panels to enhance endoscopic detection of biliary malignancies, offering a promising tool for evaluating indeterminate biliary strictures and advancing precision in ERCP diagnostics.},
}

Humans
*Cholangiocarcinoma/diagnosis/metabolism/microbiology
*Bile Duct Neoplasms/diagnosis/metabolism/microbiology
*Bile/chemistry/microbiology/metabolism
Metabolomics/methods
Male
Female
Cholangiopancreatography, Endoscopic Retrograde
*Biomarkers, Tumor/analysis
Middle Aged
Cholangitis, Sclerosing/complications
Aged
Sensitivity and Specificity
Bile Acids and Salts/analysis
Multiomics

@article {pmid40857311,
year = {2025},
author = {Xu, W and Jalomo-Khayrova, E and Gumerov, VM and Ross, PA and Köbel, TS and Schindler, D and Bange, G and Zhulin, IB and Sourjik, V},
title = {Specificities of chemosensory receptors in the human gut microbiota.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {35},
pages = {e2508950122},
doi = {10.1073/pnas.2508950122},
pmid = {40857311},
issn = {1091-6490},
support = {na//Max-Planck-Gesellschaft (MPG)/ ; LOEWE research cluster "Diffusible Signals"//Hessisches Ministerium für Wissenschaft und Kunst (Hessian Ministry for Science and Art)/ ; R35GM131760//HHS | National Institutes of Health (NIH)/ ; 464366151//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Ligands ; *Bacterial Proteins/metabolism/chemistry/genetics ; Chemotaxis ; Fatty Acids, Volatile/metabolism ; Uracil/metabolism ; },
abstract = {The human gut is rich in metabolites and harbors a complex microbial community, yet surprisingly little is known about the spectrum of chemical signals detected by the large variety of sensory receptors present in the gut microbiome. Here, we systematically mapped the ligand specificities of selected extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. Twenty-five metabolites from different chemical classes-including amino acids, nucleobase derivatives, amines, indole, and carboxylates-were identified as specific ligands for fifteen sensory domains from nine bacterial species, which represent all three major functional classes of transmembrane receptors: chemotaxis receptors, histidine kinases, and enzymatic sensors. We have further characterized the specificity and evolution of ligand binding to Cache superfamily sensors specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs). Structural and biochemical analysis of the dCache sensor of uracil and SCFAs revealed that its two different ligand types bind at distinct sensory modules. Overall, combining experimental identification with computational analyses, we were able to assign ligands to approximately half of the Cache-type chemotaxis receptors found in the eleven gut commensal genomes from our set, with carboxylic acids representing the largest ligand class. Among these, the most commonly found ligand specificities were for lactate and formate, indicating a particular importance of these metabolites in the human gut microbiota and consistent with their observed growth-promoting effects on selected bacterial commensals.},
}

Humans
*Gastrointestinal Microbiome/physiology
Ligands
*Bacterial Proteins/metabolism/chemistry/genetics
Chemotaxis
Fatty Acids, Volatile/metabolism
Uracil/metabolism

@article {pmid40856929,
year = {2025},
author = {Yan, C and Chen, Y and Tian, Y and Hu, S and Wang, H and Zhang, X and Chu, Q and Huang, S and Sun, W},
title = {The emerging role of microbiota in lung cancer: a new perspective on lung cancer development and treatment.},
journal = {Cellular oncology (Dordrecht, Netherlands)},
volume = {},
number = {},
pages = {},
pmid = {40856929},
issn = {2211-3436},
support = {Y-2023AZMETQN-0066//Beijing Xisike Clinical Oncology Research Foundation/ ; 62131009//National Natural Science Foundation of China/ ; },
abstract = {Lung cancer remains the leading cause of cancer-related mortality worldwide, with limited treatment efficacy and frequent resistance to conventional therapies. Recent advances have uncovered the critical influence of the human microbiota-complex communities of bacteria, viruses, fungi, and other microorganisms-on lung cancer pathogenesis and therapeutic responses. This review synthesizes current knowledge on the compositional and functional roles of microbiota across multiple body sites, including the gut, lung, tumor microenvironment, circulation, and oral cavity, highlighting their contributions to tumor initiation, progression, metastasis, and immune regulation. We emphasize the bidirectional communication between microbial metabolites and host immune pathways, particularly the gut-lung axis, which modulates systemic and local antitumor immunity. Importantly, microbiota composition has been linked to differential responses and toxicities in chemotherapy, radiotherapy, targeted therapy, and immune checkpoint blockade. Microbiota-targeted interventions, such as probiotics, fecal microbiota transplantation, and selective antibiotics, show promising potential to enhance treatment efficacy and mitigate adverse effects. However, challenges remain in clinical translation due to interindividual microbiome variability, mechanistic complexities, and limited longitudinal data. Future research integrating multi-omics, microbial functional profiling, and controlled clinical trials is essential to harness the microbiome as a precision medicine tool in lung cancer management. This review provides a comprehensive overview of the emerging role of microbiota in lung cancer development and therapy, offering new perspectives for innovative therapeutic strategies.},
}

@article {pmid40856922,
year = {2025},
author = {Durairaj, K and Gajendran, B and Manivel, G and Gnanam, H and Vasudevan, SA and Seenivasan, SN and Pandian, S and Shanmugarajan, S and Vily-Petit, J and Mariappan, KT and Swaminathan, K and Ramasamy, S and Gilles, M and Velmurugan, G},
title = {Exposure to chlorpyrifos pesticide at a realistic dose modulates gut microbiome and induces non-obese associated diabetes.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-025-36888-1},
pmid = {40856922},
issn = {1614-7499},
support = {6303-3//Indo-French Centre for the Promotion of Advanced Research/ ; },
abstract = {During the last decade, there has been a significant rise in the incidence of diabetes particularly, in Asian and African countries. Although obesity is an established risk factor for diabetes, more than 50% of diabetes patients in Asian and African countries are non-obese, which is in contrast to the Western population. The pathophysiology of non-obese diabetes remains largely unexplored, and recent studies have highlighted the possible role of endocrine-disrupting chemicals and gut microbiota in the prevalence of non-obese type 2 diabetes. Among the endocrine-disrupting chemicals, chlorpyrifos, a widely used organophosphate insecticide, has been associated with the prevalence of non-obese associated type 2 diabetes. However, experiments on animal models have shown that CPF-induces obesity and lipogenesis, contributing to insulin resistance. Notably, all these animal experiments were conducted at doses not equivalent to human exposure levels. Therefore, this study aimed to investigate the impact of chronic exposure of CPF at a realistic dose in mice. C57/Bl6 mice were treated with CPF at 0.02 mg/kg body weight daily, which is equivalent to the daily exposure of humans based on theoretical maximum daily intake. After 120 days of treatment, the chlorpyrifos-treated group showed a significant increase in fasting blood glucose levels with no changes in body weight in comparison with untreated controls. 16S rDNA sequencing and metabolomics analyses revealed the role of gut microbiota in chlorpyrifos-induced hyperglycemia in mice. CPF disrupted gut microbial balance, with depletion of beneficial taxa (Lactobacillus, Akkermansia, Blautia, Bifidobacterium and Faecalibaculum) and enrichment of pathobionts (Oscillospiraceae_uncultured, Helicobacter, Colidextrobacter, Desulfovibrioceae_uncultured and Alistipes). Overall, this is the first animal study demonstrating the impact of exposure to chlorpyrifos at a realistic dose equivalent to human exposure that correlates with the observations from the human epidemiological studies.},
}

@article {pmid40856866,
year = {2025},
author = {Mensi, M and Scotti, E and Marchetti, S and Sordillo, A and Garzetti, G and Calza, S and Buijs, MJ and Zaura, E and Brandt, BW},
title = {Clinical and microbiological effectiveness of limosilactobacillus reuteri in supportive periodontal therapy: randomized clinical trial.},
journal = {Clinical oral investigations},
volume = {29},
number = {9},
pages = {422},
pmid = {40856866},
issn = {1436-3771},
mesh = {Humans ; *Limosilactobacillus reuteri ; *Probiotics/therapeutic use ; Male ; Female ; Adult ; Treatment Outcome ; Middle Aged ; Periodontal Index ; *Periodontitis/therapy/microbiology ; Biofilms ; },
abstract = {OBJECTIVES: The purpose of the present randomized clinical trial was to evaluate the clinical and microbiological effects of Limosilactobacillus reuteri probiotic therapy as an adjunct to Guided Biofilm Therapy (GBT) during supportive periodontal therapy (SPT) of patients with a history of stage III or IV and grade B or C periodontitis and residual pockets.

MATERIALS AND METHODS: Forty-four systemically healthy patients were selected. Complete periodontal assessment was performed including Pocket Probing Depth (PPD), Bleeding on Probing (BOP), Presence of supragingival plaque (PI), Clinical Attachment Loss (CAL) and Recession (REC). Two sites per patient with PPD ≥ 6 mm or PPD of 5 mm with BOP were selected in two different quadrants as test sites. A session of full-mouth debridement was provided at baseline (T0), and patients were randomized to receive a 3-weeks treatment with lozenges containing probiotic or placebo. Periodontal parameters were taken at baseline (T0), 3 months (T2), and 6 months (T3). Microbiological samples from the test sites were taken at baseline (T0), 3 weeks (T1), 3 months (T2), and 6 months (T3).

RESULTS: Forty patients completed the study. Both groups showed a significant decrease in PPD, BOP, CAL, and number/percentage of residual pockets compared to baseline. However, no inter-group differences were noted. The test group showed a lower percentage of BOP at sites with plaque at T2 and T3. The microbiological analysis detected minimal proportion of L. reuteri in the periodontal pockets. No significant inter-group differences were detected in the red complex at any observation time. The subgingival microbial dysbiosis index (SMDI) revealed a decrease in dysbiosis from T0 to T1, followed by a slight increase in dysbiosis towards T3 for both groups. However, no significant differences were noted between the groups.

CONCLUSION: In our cohort of patients, 3 weeks of bi-daily supplementation with lozenges containing L. reuteri in conjunction with a session of SPT did not provide any additional reduction in PPD or number/percentage of residual pockets and did not have a long-lasting effect on the subgingival biofilm microbial composition. However, patients receiving the probiotic had less bleeding at sites with plaque.

CLINICAL RELEVANCE: Whilst L. reuteri cannot be recommended as a standard adjunctive therapy in SPT, it can be considered to reduce BOP levels in patients with poor plaque control.},
}

Humans
*Limosilactobacillus reuteri
*Probiotics/therapeutic use
Male
Female
Adult
Treatment Outcome
Middle Aged
Periodontal Index
*Periodontitis/therapy/microbiology
Biofilms

@article {pmid40856522,
year = {2025},
author = {Hafez-Ghoran, S and Taktaz, F and Sang, S},
title = {Whole grains are not equal: the role of fiber structure and phytochemicals in health.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo02603b},
pmid = {40856522},
issn = {2042-650X},
abstract = {Precision nutrition seeks to optimize human health by tailoring dietary interventions to individual genetic, metabolic, microbial, and lifestyle profiles. In this context, whole grains (WGs) serve as ideal candidates, as their diverse fiber structures and grain-specific phytochemicals interact dynamically with host physiology and the gut microbiome. This review examines six widely consumed WGs: wheat (Triticum aestivum L.), rye (Secale cereale L.), oats (Avena sativa L.), barley (Hordeum vulgare L.), brown rice (Oryza sativa L.), and corn (Zea mays L.), focusing on their distinct dietary fiber and bioactive compounds. WGs should not be viewed as uniform fiber sources. The quantity, structural complexity, solubility, viscosity, and fermentability of fibers vary among different WGs, contributing to the distinct health benefits of each grain. Moreover, while these grains offer general nutritional benefits, each grain contains unique secondary metabolites. Key examples include alkylresorcinols (ARs) in wheat and rye, avenanthramides (AVAs) in oats, hordatines in barley, γ-oryzanols (γ-OZs) and tricin in rice, and polyamine-conjugated hydroxycinnamates (PACH) in corn. These grain-specific phytochemicals exert diverse pharmacodynamic effects across metabolic, inflammatory, and oxidative pathways. For instance, hordatines shows effects on cardiovascular and glycemic regulation; ARs, γ-OZs, and tricin support lipid homeostasis and colorectal cancer mitigation; AVAs possess anti-inflammatory and microbiota-modulating properties; and PACH contribute to antioxidant capacity. Such functional specificity positions WGs as strategic components in individualized nutrition frameworks, holding promise for disease prevention and health optimization within the paradigm of precision nutrition.},
}

@article {pmid40856313,
year = {2025},
author = {Klier, K and Mehrjerd, A and Fässler, D and Franck, M and Weihs, A and Budde, K and Bahls, M and Frost, F and Henning, AK and Heinken, A and Völzke, H and Dörr, M and Nauck, M and Grabe, HJ and Friedrich, N and Hertel, J},
title = {Integrating population-based metabolomics with computational microbiome modelling identifies methanol as a urinary biomarker for protective diet-microbiome-host interactions.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00761e},
pmid = {40856313},
issn = {2042-650X},
abstract = {Background: Diet-microbiome interactions are core to human health, in particular through bacterial fibre degradation pathways. However, biomarkers reflective of these interactions are not well described. Methods: Using the population-based SHIP-START-0 cohort (n = 4017), we combined metabolome-wide screenings with elastic net machine learning models on 33 food items captured using a food frequency questionnaire (FFQ) and 43 targeted urine nuclear magnetic resonance (NMR) metabolites, identifying methanol as a marker of plant-derived food items. We utilised the independent SHIP-START-0 cohort for the replication of food-metabolite associations. Moreover, constraint-based microbiome community modelling using the Human Microbiome data (n = 149) was performed to predict and analyse the contribution of the microbiome to the human methanol pools through bacterial fibre degradation. Finally, we employed prospective survival analysis in the SHIP-START-0 cohort, testing urinary methanol on its predictive value for mortality. Results: Among 21 metabolites associated with 17 dietary FFQ variables after correction for multiple testing, urinary methanol emerged as the top hit for a range of plant-derived food items. In line with this, constraint-based community modelling demonstrated that gut microbiomes can produce methanol via pectin degradation with the genera Bacteroides (68.9%) and Faecalibacterium (20.6%) being primarily responsible. Moreover, microbial methanol production capacity was a marker of high microbiome diversity. Finally, prospective survival analysis in SHIP-START-0 revealed that higher urinary methanol is associated with lower all-cause mortality in fully adjusted Cox regressions. Conclusion: Integrating population-based metabolomics and computational microbiome modelling identified urinary methanol as a promising biomarker for protective diet-microbiome interactions linked to microbial pectin degradation.},
}

@article {pmid40856198,
year = {2025},
author = {Ammar, T and Abdelhedi, F and Keskes, LA and Triki, CC},
title = {Gut Microbiota Composition and Modulation in Developmental and Epileptic Encephalopathies.},
journal = {The European journal of neuroscience},
volume = {62},
number = {4},
pages = {e70234},
doi = {10.1111/ejn.70234},
pmid = {40856198},
issn = {1460-9568},
abstract = {The gut microbiota (GM) is a rapidly evolving field of research that is increasingly explored in the context of various diseases. The complex interactions between the host and microbial communities play a crucial role in health and well-being. It is now understood that the GM communicates with nearly every human organ, including the central nervous system (CNS), through the microbiome-gut-brain (MGB) axis. Furthermore, accumulating evidence suggests that pathological shifts in the GM may lead to various neurological disorders, including epilepsy. While the link between epilepsy and the MGB axis is increasingly recognized, studies investigating the impact of GM alterations in developmental and epileptic encephalopathies (DEEs) remain limited. This review highlights recent clinical and preclinical studies examining the impact of GM composition on DEEs, with a focus on infantile epileptic spasms syndrome (IESS) and Dravet syndrome (DS). Further investigation into the relationship between GM dysbiosis and the progression of DEEs is crucial for developing potential therapeutic strategies aimed at modulating the GM to alleviate seizures.},
}

@article {pmid40856172,
year = {2025},
author = {de-Dios, T and Bonucci, B and Barbieri, R and Kushniarevich, A and D'Atanasio, E and Dittmar, JM and Cessford, C and Solnik, A and Robb, JE and Warinner, C and Oras, E and Scheib, CL},
title = {Bone adhered sediments as a source of target and environmental DNA and proteins.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf202},
pmid = {40856172},
issn = {1537-1719},
abstract = {In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from sediments adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material usually discarded, as it is sediments adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual.},
}

@article {pmid40855336,
year = {2025},
author = {Haro-Moreno, JM and Roda-Garcia, JJ and Molina-Pardines, C and López-Pérez, M},
title = {The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {110},
pmid = {40855336},
issn = {2524-6372},
support = {PRE2021-098122//Ministerio de Ciencia e Innovación/ ; PID2023-150293NB-I00//Ministerio de Economía y Competitividad/ ; },
abstract = {BACKGROUND: Intraspecific genetic diversity is fundamental to understanding microbial adaptation, evolution, and contributions to ecosystem stability. However, traditional short-read metagenomics often underrepresents this diversity, particularly structural variants (SVs), due to assembly limitations in complex natural populations. To overcome these constraints, we employed third-generation (long-read) metagenomics to investigate the eco-evolutionary role of SVs in microbial and viral marine populations. Our analysis focused on the cellular metagenome fraction (0.22–5 μm size range) across distinct ecological niches within the photic zone of the marine water column.

RESULTS: Insertions and deletions emerged as the predominant SVs in the marine microbiome, occurring at similar frequencies across genomes. These SVs were not only found within the core genome but also in the flexible genome, serving as a source of genetic variability within genomic islands. Insertions were significantly larger, reaching more than 2 Kb, in streamlined microbes such as Pelagibacter (SAR11 clade) or the archaeon Nitrosopumilus. In contrast, SVs in viral populations were smaller and more uniform in size (~ 430 bp). Functionally, SVs were enriched in genes linked to nutrient uptake, amino acid metabolism, and regulatory networks due to the presence of non-coding RNAs. These SVs often encompassed entire genes or operons, acting as an important reservoir of niche-specific diversity that supports the emergence of ecological lineages better adapted to environmental gradients, such as rhodopsin-containing subpopulations in shallower waters. In viruses, SV-driven genetic plasticity facilitated host range adaptation and the evolution of mechanisms modulating host metabolism. We identified long-term genetically stable populations of cyanophages and pelagiphages, wherein SVs represented the primary source of genomic diversification. Notably, certain subpopulations of pelagimyophages carry SVs encoding a pstS gene, which enhances host phosphate uptake and increases viral replication efficiency—a beneficial adaptation in phosphate-depleted environments such as the oligotrophic Mediterranean Sea.

CONCLUSIONS: By capturing SVs directly from natural populations, this study provides new insights into microbial evolution, phage-host interactions, and the broader implications of genomic plasticity for ecosystem resilience in marine environments. Furthermore, these results highlight the transformative potential of third-generation sequencing to unveil previously hidden layers of microbial and viral diversity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00773-8.},
}

@article {pmid40855911,
year = {2025},
author = {Wei, L and Wu, H and Wen, L and Chen, M and Cui, B and Wang, X and Wu, T and Cheng, Y},
title = {Rice protein peptides alleviate lipid accumulation via modulating liver metabolism and remodeling the gut microbiota in HFD-induced mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01536g},
pmid = {40855911},
issn = {2042-650X},
abstract = {Hyperlipidemia is a significant risk factor for lipid metabolism disorder and gut health impairment. Rice protein peptides (RPs) have emerged as promising interventions for hyperlipidemia management, owing to their safety profile, bioavailability, and cost-effectiveness. However, comprehensive investigations into their anti-hyperlipidemic effects and underlying mechanisms remain insufficiently explored. This study aimed to investigate the efficacy of RPs in alleviating hyperlipidemia and hepatic lipid accumulation by lipidomic and microbiome analyses. Results revealed that RP administration significantly ameliorated lipid metabolism disorders by reducing fat accumulation, normalizing blood lipid levels, and inhibiting lipase activity. Additionally, RPs exhibited hepatoprotective effects by increasing antioxidant enzyme activity and decreasing pro-inflammatory cytokines. Lipidomic analysis further revealed that RPs altered lipid metabolic patterns, identifying 10 differentially regulated lipid species that may serve as potential biomarkers for hyperlipidemia. Furthermore, RP supplements significantly regulated the mRNA levels of gene expression (HMGR, SREBP2, CYP7A1, LDLR, PPARα, PPARγ, FAS, and ACS) involved in hepatic lipid metabolism. Metagenomic analysis demonstrated that RPs reversed gut microbiota dysbiosis by reducing the Firmicutes/Bacteroidetes ratio and increasing the abundance of beneficial genera such as Akkermansia, Muribaculaceae, Clostridia_UCG-014, and Blautia. Furthermore, RP intervention significantly elevated fecal short-chain fatty acid (SCFA) content, particularly butyrate, isobutyrate, and isovalerate, suggesting a link between microbial modulation and metabolic improvement. These findings suggested RPs as an effective strategy for improving lipid metabolism and the gut microbiota composition, offering a promising dietary intervention for hyperlipidemia management.},
}

@article {pmid40855409,
year = {2025},
author = {Graeber, E and Tysha, A and Nisar, A and Wind, D and Mendling, W and Finzer, P and Dilthey, A},
title = {Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {544},
pmid = {40855409},
issn = {1471-2180},
abstract = {BACKGROUND: The vaginal microbiome plays an important role in female health; it is associated with reproductive success, susceptibility to sexually transmitted infections, and, importantly, the most prevalent vaginal condition in reproduction-age women, bacterial vaginosis (BV). Traditionally, 16S rRNA gene sequencing-based approaches have been used to characterize the composition of vaginal microbiomes, but shallow shotgun metagenomic sequencing (SMS) approaches, in particular when implemented with the Oxford Nanopore Technologies, have important potential advantages with respect to cost effectiveness, speed of data generation, and the availability of flexible multiplexing schemes.

RESULTS: Based on a study cohort of n = 52 women, of which 23 were diagnosed with BV, we evaluated the applicability of Nanopore-based SMS for the characterization of vaginal microbiomes in direct comparison to Illumina 16S-based sequencing. We observed perfect agreement between the two approaches with respect to detecting the dominance of individual samples by either Lactobacilli, vaginosis-associated, or other taxa; very high concordance (92%) with respect to community state type (CST) classification; and a high degree of concordance with respect to the overall clustering structures of the sequenced microbiomes. Comparing the inferred abundances of individual species in individual samples, we observed significant differences (Wilcoxon signed-rank test p < 0.05) between the two approaches for 12 of the 20 species most abundant in our cohort, indicating differences in the fine-scale characterization of vaginal microbiomes. Higher overall abundance of Gardnerella vaginalis, associated with an increased number of CST IV detections, in the Nanopore shallow SMS data indicated potentially increased sensitivity of this approach to dysbiotic states of the vaginal microbiome. Nanopore shallow SMS also enabled the methylation-based quantification of different human cell types in the characterized samples as well as the detection of non-prokaryotic species, including Lactobacillus phage and Candida albicans in study participants with microscopically detected Candida. One important potential limitation of the evaluated Nanopore-based SMS approach was marked variation in sequencing yields.

CONCLUSION: Our study demonstrated the successful application and potential advantages of Nanopore-based shallow SMS for the characterization of vaginal microbiomes and paves the way for its application in larger-scale research or diagnostic settings.},
}

@article {pmid40855353,
year = {2025},
author = {Mousa, AA and Zhang, H and Duan, H and Zhang, J and Mao, S},
title = {Correction: Metagenomic analysis reveals rumen microbiome enrichment and functional genes adjustment in carbohydrate metabolism induced by different sorting behavior in mid-lactation dairy cows.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {90},
pmid = {40855353},
issn = {2524-4671},
}

@article {pmid40854905,
year = {2025},
author = {Szczerbiak, P and Szydlowski, LM and Wydmański, W and Renfrew, PD and Leman, JK and Kosciolek, T},
title = {Large protein databases reveal structural complementarity and functional locality.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7925},
pmid = {40854905},
issn = {2041-1723},
support = {2023/05/Y/NZ2/00080//Narodowe Centrum Nauki (National Science Centre)/ ; 2023/05/Y/NZ2/00080//Narodowe Centrum Nauki (National Science Centre)/ ; 857533//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; MEiN/2023/DIR/3796//Ministerstwo Nauki i Szkolnictwa Wyższego (Ministry of Science and Higher Education)/ ; PN/01/0195/2022//Ministerstwo Nauki i Szkolnictwa Wyższego (Ministry of Science and Higher Education)/ ; },
abstract = {Recent breakthroughs in protein structure prediction have led to a surge in high-quality 3D models, highlighting the need for efficient computational solutions. In our work, we examine the structural clusters from the AlphaFold Protein Structure Database (AFDB), a high-quality subset of ESMAtlas, and the Microbiome Immunity Project (MIP). We create a single cohesive low-dimensional representation of the resulting protein space. We show that, while each database occupies distinct regions, they collectively exhibit significant overlap in their functional profiles. High-level biological functions tend to cluster in particular regions, revealing a shared functional landscape despite the diverse sources of data. By creating a representation of protein structure space, localizing functional annotations within this space, and providing an open-access web-server for exploration, this work offers insights for future research concerning protein sequence-structure-function relationships, enabling biological questions to be asked about taxonomic assignments, environmental factors, or functional specificity. This approach is generalizable, thus enabling further discovery beyond findings presented here.},
}

@article {pmid40854874,
year = {2025},
author = {Kaelin, EA and Mitchell, C and Soria, J and La Rosa, A and Ticona, E and Coombs, RW and Frenkel, LM and Bull, ME and Lim, ES},
title = {Longitudinal cervicovaginal bacteriome and virome alterations associate with discordant shedding and ART duration in women living with HIV in Peru.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7904},
pmid = {40854874},
issn = {2041-1723},
support = {R00DK107923//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Despite successful suppression of plasma HIV replication by antiretroviral therapy (ART), some women living with HIV (WLHIV) can still experience genital HIV shedding (discordant shedding). Female genital tract (FGT) bacterial and viral microbiome (bacteriome and virome) community dynamics during long-term ART in WLHIV are poorly understood but might contribute to discordant HIV shedding, as the bacteriome and virome are known to influence FGT health. Here, using metagenomic next-generation sequencing, we characterize the bacteriome and virome in 125 cervicovaginal specimens collected over two years from 31 WLHIV in Lima, Peru, and show that FGT bacteriome instability is associated with discordant HIV shedding, while longitudinal changes in FGT virome composition are associated with ART duration. Intrapersonal bacteriome variation is higher in discordant HIV shedders compared to non-shedders. Cervicovaginal virome composition changes over time, particularly in non-shedders. Specifically, anellovirus relative abundance is inversely associated with ART duration and CD4 counts. Our results suggest that discordant HIV shedding is linked with FGT bacteriome instability, and immune recovery during ART influences FGT virome composition.},
}

@article {pmid40854688,
year = {2025},
author = {Miyauchi, E and Taida, T and Uchiyama, K and Nakanishi, Y and Kato, T and Koido, S and Sasaki, N and Ohkusa, T and Sato, N and Ohno, H},
title = {Smoking affects gut immune system of patients with inflammatory bowel diseases by modulating metabolomic profiles and mucosal microbiota.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-334922},
pmid = {40854688},
issn = {1468-3288},
abstract = {BACKGROUND: The aetiology and pathogenesis of IBD are intricate, involving genetic and environmental factors. Notably, cigarette smoking has contrasting effects, being detrimental to Crohn's disease (CD) and beneficial to UC. However, the mechanisms underlying these opposite effects remain unclear.

OBJECTIVE: This study aimed to elucidate the precise mechanisms by which smoking influences IBD pathogenesis, by focusing on the roles of microbiota and metabolomics.

DESIGN: We analysed the microbiota composition of saliva, faeces and the colonic mucosa, and the faecal metabolite profile of patients with IBD and healthy participants. The effects of smoking-associated bacteria on the gut immune system and colitis were evaluated using gnotobiotic mice and murine models of UC and CD.

RESULTS: People with UC who smoke showed increased concentrations of short-chain fatty acids and aromatic compounds in the faeces compared with the people who quit smoking. The analysis of the mucosal microbiota revealed that smoking is associated with the increased oral bacteria in the colonic mucosa. Monocolonisation of germ-free mice with Streptococcus mitis, one of the oral bacteria ectopically increased in the colonic mucosa, induced interferon (IFN)-γ-producing T cells in the colon. S. mitis also attenuated inflammation in a murine model of UC but exacerbated it in a CD model.

CONCLUSION: We demonstrated that smoking affects the gut immune system by modulating mucosal microbiota. Our findings provide insights into how smoking can have beneficial or detrimental effects on UC or CD, respectively, and may shed light on the reasons why individuals with UC who quit smoking experience disease exacerbation.},
}

@article {pmid40854667,
year = {2025},
author = {Anbarasu, S and Kacha, S and Ramaiah, S and Anbarasu, A},
title = {In-silico investigation reveals microbial metabolic biomarkers and their regulatory roles in hormone sensitive cancers.},
journal = {Journal, genetic engineering & biotechnology},
volume = {23},
number = {3},
pages = {100549},
doi = {10.1016/j.jgeb.2025.100549},
pmid = {40854667},
issn = {2090-5920},
abstract = {Cancer burden has become a global concern, specifically with hormone-sensitive cancers (HSC). Among the various factors influencing the progress and treatment of cancers, the human microbiota plays a vital role. The current analysis explores the role of microbial metabolites in various regulatory pathways associated with cancer biomarkers and finds the common microbial metabolites associated with HSCs. AR, ESR1, and TP53 in breast cancer; ERBB2, MAPK21, and TP53 in ovarian cancer; AKT1, EGFR, and ERBB2 in endometrial cancer and AR, MYC, and RB1 in prostate cancer were identified as important genes in HSC development. The associated metabolites of these genes were contributing to various regulatory pathways. The metabolites hydrogen peroxide, adenosine triphosphate, adenosine diphosphate, guanosine diphosphate, and guanosine triphosphate produced by microbes within the humans were found to be involved in nucleotide and amino acid metabolism pathways. The purine and pyrimidine metabolism pathways, glyoxylate, and dicarboxylate metabolism pathway, arginine and proline pathway, and glycine, serine, and threonine pathways were found common and significantly enriched between human and microbial metabolites showing close association between the microbial metabolites and the HSCs. The microbes belonging to Bacteroidetes, Proteobacteria, and Firmicutes phylum were found to be significantly associated with HSCs. The expression analysis and the similar pathways enriched between the correlated genes and hub genes validated the significance of the metabolites which can be used as potential biomarkers. Thus, the metabolic biomarkers can help in early diagnosis, targeted therapy based on the microbiome, and in prevention of cancer.},
}

@article {pmid40854660,
year = {2025},
author = {Lahnsteiner, F and Dünser, A},
title = {A simplified, one step technique for disinfection of non-hardened rainbow trout eggs with tosylchloramide (Chloramine T) and peroxide (Wofasteril) compounds and the effects on bacterial load and microbiome composition in comparison to iodophore disinfection.},
journal = {Journal, genetic engineering & biotechnology},
volume = {23},
number = {3},
pages = {100541},
doi = {10.1016/j.jgeb.2025.100541},
pmid = {40854660},
issn = {2090-5920},
abstract = {Disinfection of the interior of non-hardened eggs with iodophors (Buffodine®) is an established hygienic practice in salmonid aquaculture to prevent pathogen transmission from the broodstock fish to their offspring. As iodophors inhibit sperm motility, fertilization is first performed in a 0.75 % NaCl solution, followed by egg disinfection in a second step after fertilization is complete. Although this two-step egg disinfection procedure is simple to perform under laboratory conditions, it presents challenges for fish farms using mass stripping. The process involves two highly time-sensitive steps, requiring precise execution, as any errors can lead to fertilization failure or ineffective disinfection. A more practical approach would be to simplify disinfection into a single-step procedure. The present study demonstrates that non-hardened rainbow trout eggs can be fertilized and disinfected simultaneously using a one-step method with tosylchloramide (100 mg/l Chloramine T®) or peroxide (100 µl Wofasteril®) compounds in 0.75 % NaCl for 40 min. This procedure is feasible as the applied concentrations of Chloramine T and Wofasteril have only low impact on sperm motility. The one-step methods do also not negatively impact embryo and early larval development. Non-hardened rainbow trout egg disinfection methods with Chloramine T and Wofasteril were as effective as the conventional Buffodine method in reducing total bacterial load of eggs at 3 h post-fertilization (hpf), the point at which water hardening is complete. Reanalysis of total bacterial load after 22 days of development (embryo stage at the onset of eye pigmentation) proved Chloramine T more effective than Wofasteril and Buffodine. Microbiome composition differed significantly across developmental stages and disinfection treatments. Notable variations were observed between non-disinfected controls and eggs treated with Buffodine, Chloramine T, or Wofasteril, in persistent bacterial communities, stage-specific bacteria, and bacteria colonizing the chorion during embryogenesis. Buffodine treatment increased bacterial diversity, while Chloramine T and Wofasteril led to reduced diversity compared to the control. These findings are discussed in the context of microbiome stability and resilience, key factors for long-term fish health. In summary, the simplified one-step disinfection protocol offers practical advantages in reducing time-sensitive handling steps and improving efficiency in large-scale aquaculture operations. Moreover, it is environmentally preferable as both Wofasteril and Chloramine T are used at lower concentrations than Buffodine and degrade rapidly in water, leaving no harmful residues.},
}

@article {pmid40854654,
year = {2025},
author = {Gelaye, Y and Li, J and Luo, H},
title = {Exploring the role of Peanut (Arachis hypogaea L.) root architecture in enhancing adaptation to climate change for sustainable agriculture and resilient crop production: A review.},
journal = {Journal, genetic engineering & biotechnology},
volume = {23},
number = {3},
pages = {100535},
doi = {10.1016/j.jgeb.2025.100535},
pmid = {40854654},
issn = {2090-5920},
abstract = {Peanut (Arachis hypogaea L.) cultivation is increasingly vulnerable to climate change, with drought and heat stress emerging as major constraints to productivity and food security. This review explores the critical role of root architecture in enhancing peanut adaptation to environmental stressors, and evaluates current strategies and future directions for improving root traits through genetic, physiological, and agronomic approaches. Efficient root systems, characterized by deeper rooting and optimized xylem design, significantly improve water and nutrient acquisition under drought conditions. Key regulators such as abscisic acid (ABA), strigolactones, and specific root-related genes modulate root development and stress responses. Root exudates further enhance soil root interactions, while the peanut root microbiome contributes to nutrient cycling and resilience. Biotechnological tools, including quantitative trait loci (QTL) mapping and CRISPR/Cas-based genome editing, are being harnessed to manipulate root traits at the molecular level. Agronomic practices like mulching and cover cropping synergize with genetic improvements by enhancing soil structure and moisture retention. Strengthening peanut root architecture through the integration of modern breeding, biotechnological advances, and sustainable soil management offers a promising path toward climate-resilient peanut production. Future research should prioritize the convergence of these approaches, alongside microbiome exploration, to secure yield stability and food security in a changing climate.},
}

@article {pmid40854639,
year = {2025},
author = {Silvederio, GXL and Javellana, TF and Genciana, ABN and Fontanilla, MAG and Traifalgar, RFM and Huervana, FH and Del Castillo, CS},
title = {Gut microbiome composition and diversity of wild-caught and hatchery-bred milkfish (Chanos chanos) fry.},
journal = {Journal, genetic engineering & biotechnology},
volume = {23},
number = {3},
pages = {100520},
doi = {10.1016/j.jgeb.2025.100520},
pmid = {40854639},
issn = {2090-5920},
abstract = {Milkfish is the most produced finfish in the Philippines, with approximately 75 % of its fry sourced from hatcheries. Despite numerous studies on gut microbiota of wild and cultured fish species, the diversity and functional roles of the milkfish fry gut microbiome remain poorly understood. This study presents the first gut microbiome profiles of wild and hatchery-bred milkfish fry using 16S rRNA amplicon analysis. A total of 437 OTUs were recovered and significant differences in gut bacterial communities among fry from different sources was observed, indicating that habitat is a key determinant of gut microbiome diversity. The core gut microbiota analysis identified Vibrionaceae and Roseobacteraceae as the most common and abundant bacterial families across fry sources. However, Paenibacillaceae and Bacillaceae under Phylum Bacillota were dominant in wild fry sources, particularly Hamtic and Kirayan, whereas families belonging to Phyla Cyanobacteriota, and Thermodesulfobacteria were more prevalent in Dumagas and Kirayan hatchery fry sources. Functional predictions of the gut bacterial microbiome revealed 26 differentially abundant pathways between wild-caught and hatchery-bred fry, including those related to metabolism, organismal systems, cellular processes, environmental and genetic information processing. These findings highlight significant variations in gut microbiome composition, diversity, and functional potential across different sources of wild-caught and hatchery-bred fry. Understanding these source-specific microbial communities could provide insight into the development of interventions that can improve gut health and enhance milkfish hatchery practices. It can also generate information on ideal fry selection across local milkfish sources that will enhance larval productivity and survival in the succeeding nursery and grow-out culture stages.},
}

@article {pmid40854282,
year = {2025},
author = {Lv, X and Zhou, H and Yang, J and Hao, J and Zhong, Z and Feng, K and Xing, D},
title = {Simultaneous denitrification and phosphorus removal in MBfR with methane as the sole carbon source.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127107},
doi = {10.1016/j.jenvman.2025.127107},
pmid = {40854282},
issn = {1095-8630},
abstract = {Aerobic methane oxidation coupled to denitrification (AME-D) employed in membrane biofilm reactor (MBfR) is a promising strategy to reduce methane emission and enhance denitrification in wastewater treatment. However, focusing on enhancing nitrogen removal efficiency during AME-D has consistently overlooked the changes in phosphorus (P), and the underlying microbiome assembly mechanisms remain unclear. In this study, the MBfR was established to simultaneously enhance methane oxidation, denitrification, and P removal by the AME-D process under seasonal temperatures. The system achieved 72% of nitrate removal efficiency at 30 °C, while the P removal efficiency improved with the decrease of seasonal temperatures and stabilized at 86-99%. Microbiome analysis indicated that aerobic methanotrophs (Methylobacter), denitrifiers (Caenimonas), and denitrifying phosphorus-accumulating organisms (Gemmatimonas) were enriched in MBfR, facilitating the integrated removal of nitrogen and phosphorus alongside methane oxidation. The neutral community model (NCM) analysis revealed that microbiome assembly in MBfRs was driven by deterministic selection. Moreover, more network connectivity of the microbiome in MBfR biofilm suggested that membrane module enhanced the diversity and stability of microbiome. Our findings highlight the potential of AME-D with MBfRs as a robust and resilient platform for integrated greenhouse gas reduction and nutrient removal, offering practical implications for energy-efficient wastewater treatment.},
}

@article {pmid40854125,
year = {2025},
author = {Gause, H and Johnson, AD},
title = {Shared metabolism between a bacterial and fungal species that reside in the human gut.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {35},
pages = {e2504785122},
doi = {10.1073/pnas.2504785122},
pmid = {40854125},
issn = {1091-6490},
support = {R01AI049187//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; RO1AI55O80//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {The fungal species Candida albicans and the bacterium Enterococcus faecalis are members of the human gut microbiome. To explore the range of interactions between these two species, we utilized dual RNA-sequencing to transcriptionally profile both C. albicans and E. faecalis during coculture (compared with monoculture controls) under two conditions: 1) an in vitro setting that mimics certain features of the gut environment and 2) a gnotobiotic mouse gut model. RNA-seq analysis revealed a large number of gene expression changes induced by one species in the presence of the other. More specifically, both species highly upregulate citrate-metabolizing genes during coculture: C. albicans upregulates CIT1 (citrate synthase) which produces citrate, while E. faecalis upregulates its cit operon, which breaks down citrate. In vitro analysis showed directly that citrate cross-feeding (production of citrate by C. albicans and breakdown by E. faecalis) enhances growth of E. faecalis. A main byproduct of citrate metabolism in E. faecalis is formate, a short chain fatty acid toxic to fungi. Our RNA profiling revealed that C. albicans upregulates three formate dehydrogenases (FDHs) during coculture; we show that the FDH genes confer a growth advantage to C. albicans when E. faecalis (or simply formate) is present. These findings reveal a metabolically driven cycle between C. albicans and E. faecalis in the mouse gut and in vitro, where cross-feeding of citrate and detoxification of formate facilitates the growth of both species when they are cultured together.},
}

@article {pmid40853338,
year = {2025},
author = {Zeissig, S and Frost, F and Haller, D and Stallmach, A and Vehreschild, MJGT and Schneider, KM},
title = {The Role of the Intestinal Microbiome in Inflammation and Cancer.},
journal = {Deutsches Arzteblatt international},
volume = {},
number = {Forthcoming},
pages = {},
doi = {10.3238/arztebl.m2025.0142},
pmid = {40853338},
issn = {1866-0452},
abstract = {BACKGROUND: Changes in the microbiome have been described in many diseases and are thought to play a role in their pathogenesis and progression. In this article, we approach the topic critically and discuss the areas in which the development of microbiome-based clinical applications may soon be expected.

METHODS: We selectively review the literature on disease-associated microbiome signatures and therapeutic modulation of the microbiome. We discuss clinical studies as well as relevant preclinical studies that reveal causal relationships between the microbiome and disease.

RESULTS: The intestinal microbiome undergoes dynamic regulation by lifestyle factors such as the diet. Particularly in inflammatory and malignant neoplastic diseases, changes in the microbiome have been identified that contribute to the progression of disease in animal models. Studies have also shown that the response to systemic antitumor therapy is regulated by the microbiota. In view of this, initial clinical trials have been conducted that document the efficacy of fecal microbiome transfer and of selective approaches to microbiome modulation in the treatment of several inflammatory and malignant diseases.

CONCLUSION: Evidence from animal models and initial clinical studies indicates that therapeutic modulation of the microbiome can be of benefit to patients suffering from a number of inflammatory and malignant diseases. The further translation of research of this kind into clinical applications will require the validation of these data in controlled trials and the development of targeted approaches to microbiome modulation.},
}

@article {pmid40853088,
year = {2025},
author = {Ellegaard-Jensen, L and Carvalho, PN and Anwar, MZ and Schostag, MD and Bester, K and Jacobsen, CS},
title = {Concurrent stimulation of diflufenican biodegradation and changes in the active microbiome in gravel revealed by Total RNA.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0016425},
doi = {10.1128/spectrum.00164-25},
pmid = {40853088},
issn = {2165-0497},
abstract = {The use of slowly degraded pesticides poses a particular problem when these are applied to urban areas such as gravel paths. The urban gravel provides an environment very different from agricultural soils; i.e., it is both lower in carbon and microbial activity. We, therefore, endeavored to stimulate the degradation of the pesticide diflufenican added to urban gravel microcosms amended with dry alfalfa to increase microbial activity. In the present study, alfalfa addition significantly increased the formation of diflufenican's primary metabolite, 2-[3-(trifluoromethyl)phenoxy]nicotinic acid (AE-B), indicating stimulated biotransformation. The concurrent changes of the active microbial communities within the gravel were explored using shotgun metatranscriptomic sequencing of ribosomal RNA and messenger RNA. Although bacterial taxa remained dominant (87.0%-98.5% relative abundance), the alfalfa treatment led to a 4-5-fold increase in eukaryotic groups, including fungi and microbial grazers. Several microbial taxa potentially involved in the degradation of complex carbon compounds and aromatic pollutants-including Bacteroidetes, Verrucomicrobia, Sordariomycetes, Mortierellales, Tremellales, Sphingopyxis, and Phenylobacterium-increased in relative abundance following alfalfa amendment. Functional gene profiling revealed elevated expression of genes related to microbial activity and biomass production. Genes with potential roles in the breakdown of complex carbon structures (e.g., xylanases/chitin deacetylases) and in the transformation of aromatic compounds (e.g., ring-cleaving dioxygenases) were revealed. We conclude that complex carbon amendments can enhance the microbial activity, promoting the biotransformation of diflufenican in urban gravel environments. These findings provide new insights into the interactions between microbial community dynamics, gene expression profiles, and pesticide biotransformation in non-agricultural matrices.IMPORTANCEPesticides used on urban areas, e.g., gravel paths, are likely to have different effects and fates than when these are used on agricultural soils. Hence, studies into the degradation of pesticides applied to urban matrices are needed. We have previously shown that metabolites of the persistent pesticide diflufenican are even more persistent in urban soils, and it has also previously been shown that these metabolites leach from gravel surfaces. The reasons behind this are that the urban gravel provides an environment very different from agricultural soils; i.e., it is both lower in carbon and microbial activity. In the present study, we, therefore, endeavored to stimulate the degradation of the pesticide diflufenican added to urban gravel microcosms amended with dry alfalfa to increase microbial activity, concurrently studying the changes in the active microbiome by Total RNA-metatranscriptomics.},
}

@article {pmid40853021,
year = {2025},
author = {Zhu, Z and Zhang, C and Liao, Z and Guan, J and Xie, X and Li, Z and Lin, B and Chen, H and Zhuang, Z and Meng, S and Zou, Y and Li, W and Luo, M and Dai, D},
title = {Draft genome sequence of Parabacteroides distasonis SZCHProba001, isolated from feces of a 6-year-old boy.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0042225},
doi = {10.1128/mra.00422-25},
pmid = {40853021},
issn = {2576-098X},
abstract = {Parabacteroides distasonis is a prevalent human gut bacterium. Here, we report the draft genome of P. distasonis SZCHProba001 isolated from a 6-year-old boy's feces. The 5.03 Mb assembly (102 contigs) contains 4,099 predicted proteins and 76 RNAs. This resource aids research into P. distasonis' role in pediatric gut health.},
}

@article {pmid40853000,
year = {2025},
author = {Timsina, R and Gora, RA and Ferguson, DJ},
title = {Proteomic and metabolomic analysis reveals new insights into quaternary amine metabolism in Citrobacter amalonaticus CJ25.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0042125},
doi = {10.1128/msphere.00421-25},
pmid = {40853000},
issn = {2379-5042},
abstract = {Gut microbiota and human physiology are closely linked, and our microbiota can influence disease through immunological and metabolic activity. Quaternary amines, such as choline and carnitine, are abundant in the human gut and are found in red meat, beef, eggs, seafood, wheat, and beets. Canonically, choline and carnitine are broken down into the pro-atherogenic metabolite, trimethylamine (TMA), by various microbes in the human gut. A glycyl radical enzyme, CutC, is involved in the breakdown of choline to TMA. Carnitine is broken down to TMA via a gamma-butyrobetaine intermediate. TMA from the human gut increases levels of TMA N-oxide in blood and promotes atherosclerosis. Citrobacter amalonaticus CJ25, a gut strain isolated and characterized in our lab, has been shown to grow on choline or carnitine as the sole carbon-energy source without generating TMA. Because the genome lacks canonical enzymes involved in the degradation of choline and no TMA was produced in both choline and carnitine growth conditions, we analyzed the choline and carnitine metabolism using a combined metabolomic and proteomic approach. CJ25 metabolizes choline and carnitine into glycine betaine (GB) via pathways involving novel enzyme homologs, as indicated by proteomic analysis. The proteomics showed putative dehydrogenases that could be oxidizing choline and carnitine to GB. These non-atherogenic pathways involving novel enzyme homologs that we identify in CJ25 may also exist in other gut microbiota, which could amplify the effects of these pathways significantly, possibly reducing the risk of atherosclerotic cardiovascular disease in individuals harboring these microbiota.IMPORTANCEThe human gut microbiome has been shown to contribute to atherosclerotic cardiovascular disease with adverse health effects throughout the world. Gut microbes canonically metabolize quaternary amines into proatherogenic TMA. In this study, a gut bacterium, CJ25, metabolizes choline and carnitine to a non-atherogenic product, glycine betaine, potentially using novel dehydrogenase homologs for their oxidation. Notably, the ability of CJ25 to metabolize choline and carnitine in a non-atherogenic manner establishes its potential as a beneficial human gut bacterium. Additionally, enzymes identified in CJ25 for choline and carnitine breakdown may be present in other gut microbes, which could amplify the effects of these pathways and reduce the risk of atherosclerotic cardiovascular disease more universally.},
}

@article {pmid40852997,
year = {2025},
author = {Velte, JM and Mudiyanselage, S and Hofmann, OF and Lee, STM and Huguet-Tapia, J and Miranda, M and Martins, SJ},
title = {Interactions between native soil microbiome and a synthetic microbial community reveals bacteria with persistent traits.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0092125},
doi = {10.1128/msystems.00921-25},
pmid = {40852997},
issn = {2379-5077},
abstract = {Synthetic microbial communities (SynComs) are curated microbial groups that can be designed to optimize microbial functions, such as enhancing plant growth or disease resistance. Attaining SynCom stability in the presence of native soil communities remains a key challenge. This study investigated the survival, persistence, and chemical interactions of a SynCom with a native soil microbial community using a transwell system that spatially constrains bacteria while permitting chemical interactions. The SynCom, composed of six compatible Pseudomonas species identified through whole-genome sequencing, was analyzed for antagonistic interactions with native microbes over time and assessed using biomass and viability measurements. Over time, the SynCom exhibited reduced growth in the presence of native soil microbes compared to the SynCom not exposed to the native microbes. Flow cytometry analysis showed an 81% reduction of live cells for the persistent strain in the presence of native microbes and a 78% and 99% increase in dead and unstained cells, respectively. Compared to a non-persistent strain, one persistent SynCom strain showed lower metabolic utilization across five key compound classes: polymers, carboxylic acids, amino acids, amines, and phenols when exposed to the native soil microbes. These findings underscore the importance of understanding complex SynCom-environment interactions to enhance SynCom stability and optimize in situ applications.IMPORTANCESynComs are an emerging technology that can augment plant health. Still, their application in situ depends on deciphering the complex interactions between SynCom microbes and native microbial communities. This study provides insight into several Pseudomonas strains displaying persistent characteristics. Understanding the persistent traits of these bacteria is a vital advancement in SynCom technology and an important next step toward implementing SynComs in agricultural systems.},
}

@article {pmid40852720,
year = {2025},
author = {Kumar, M and Yip, L and Wang, F and Marty, SE and Fathman, CG},
title = {Autoimmune disease: genetic susceptibility, environmental triggers, and immune dysregulation. Where can we develop therapies?.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1626082},
pmid = {40852720},
issn = {1664-3224},
mesh = {Humans ; *Autoimmune Diseases/genetics/therapy/etiology/immunology ; *Genetic Predisposition to Disease ; Animals ; Gene-Environment Interaction ; Genome-Wide Association Study ; Environmental Exposure/adverse effects ; },
abstract = {Autoimmune diseases are a diverse group of chronic disorders characterized by inappropriate immune responses against self-antigens, resulting in persistent inflammation and tissue destruction. Affecting an estimated 7-10% of the global population, these conditions include both systemic and organ-specific entities such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), type 1 diabetes (T1D), and multiple sclerosis (MS). Despite their clinical heterogeneity, autoimmune diseases share a common etiologic framework involving the convergence of genetic predisposition, environmental exposures, and immune dysregulation. Genome-wide association studies (GWAS) have identified hundreds of risk loci, most notably within the major histocompatibility complex (MHC), and highlighted the role of non-HLA genes regulating cytokine signaling, antigen presentation, and T cell tolerance. The majority of disease-associated variants lie in non-coding regulatory elements, suggesting that transcriptional dysregulation plays a central role in disease susceptibility. Yet, genetics alone does not determine disease onset-environmental factors such as infections, diet, microbiome alterations, and hormonal influences critically shape immune responses and may trigger disease in genetically susceptible individuals. Additionally, epigenetic modifications further compound these effects, creating lasting changes in gene expression and immune cell function. At the core of autoimmune pathogenesis lies immune dysregulation, particularly failure of peripheral tolerance maintained by regulatory T cells (Tregs). While Treg frequencies may appear normal in patients, emerging data indicate intrinsic signaling defects-especially impaired IL-2 receptor (IL-2R) signal durability-compromise Treg suppressive function. This dysfunction is linked to aberrant degradation of key IL-2R second messengers, including phosphorylated JAK1 and DEPTOR, due to diminished expression of GRAIL, an E3 ligase that inhibits cullin RING ligase activation. This review integrates recent insights across genetic factors, environmental triggers, and immune dysregulation to build a comprehensive understanding of autoimmune disease pathogenesis. We propose a novel therapeutic strategy targeting IL-2R signaling using Neddylation Activating Enzyme inhibitors (NAEis) conjugated to IL-2 or anti-CD25 antibodies. This approach selectively restores Treg function and immune tolerance without inducing systemic immunosuppression. By focusing on immune restoration rather than suppression, This therapy could provide an off the shelf therapy for many different autoimmune diseases.},
}

Humans
*Autoimmune Diseases/genetics/therapy/etiology/immunology
*Genetic Predisposition to Disease
Animals
Gene-Environment Interaction
Genome-Wide Association Study
Environmental Exposure/adverse effects

@article {pmid40852708,
year = {2025},
author = {Shen, L and Zhao, Y and Liu, S and Li, S and Li, Q and Tung, TH and Shen, B},
title = {Changes in the Subdoligranulum genus in patients with autoimmune disease: a systematic review and meta-analysis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1619160},
pmid = {40852708},
issn = {1664-3224},
mesh = {Humans ; *Autoimmune Diseases/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; Biomarkers ; },
abstract = {BACKGROUND: Autoimmune diseases have different pathogenic mechanisms but share underlying patterns of gut microbiome perturbation and intestinal barrier dysfunction. Recent evidence suggests that an arthritogenic strain of Subdoligranulum causes a local inflammatory response in the gut. Therefore, the aim of this review was to systematically summarize the relationships between Subdoligranulum and multiple autoimmune diseases.

OBJECTIVE: To evaluate the changes of Subdoligranulum in different autoimmune diseases.

METHODS: Four databases, including PubMed, Cochrane, Web of Science, and Embase, were searched up to June 17, 2025, to identify studies that detected Subdoligranulum in autoimmune diseases. A meta-analysis was conducted to compare the differences in Subdoligranulum between healthy people and patients with autoimmune diseases, and the changes in these bacteria under different treatments were compared for similar diseases. The relationships between Subdoligranulum and inflammation-related biomarkers were also analyzed.

STUDY SELECTION: We included articles that addressed both autoimmune diseases without intervention and the detection of Subdoligranulum in feces, and we presented a description of changes in bacteria in patients and healthy controls.

QUALITY ASSESSMENT: We used the Newcastle-Ottawa Scale (NOS) to independently assess the methodological quality of the case-control studies. The Journal of Biomedical Informatics (JBI) critical appraisal checklists were utilized to assess the quality and risk of bias in cross-sectional studies.

RESULTS: Twelve studies were included. These studies were conducted in four different countries and included a total of 1,792 participants (patients with autoimmune disease and healthy controls). Our meta-analysis results indicate that, compared with healthy controls, most patients with autoimmune diseases included in the study had lower levels of Subdoligranulum (p = 0.027). In addition, it was found that bacteria were associated with several inflammation-related biomarkers. For example, bacterial levels were positively correlated with C-reactive protein (CRP), lipopolysaccharide (LPS)-binding protein (LBP), and Treg cells. However, the levels were negatively correlated with IL-8. These relationships may underlie both the occurrence and development of autoimmune diseases.

CONCLUSION: The abundance of Subdoligranulum in patients with organ-specific autoimmune diseases was decreased, whereas no consistent findings were observed for systemic autoimmune diseases.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42024543767, identifier CRD42024543767.},
}

Humans
*Autoimmune Diseases/microbiology/immunology
*Gastrointestinal Microbiome/immunology
Biomarkers

@article {pmid40852612,
year = {2025},
author = {Hao, M and Xu, H and Li, M and Jiao, D},
title = {The role and challenges of intratumoral microbiota in colorectal cancer immunotherapy.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1634703},
pmid = {40852612},
issn = {1663-9812},
abstract = {Colorectal cancer (CRC) is the third most common malignant tumor globally, and its development is closely related to interactions between the host and microbes. Recent studies have shown that the diversity of intratumoral microbiota significantly influences CRC progression and responses to immune therapy. This influence occurs through mechanisms such as immune microenvironment regulation, metabolic reprogramming, and epigenetic modifications. However, there is still a lack of systematic analysis regarding the diversity of intratumoral microbiota in CRC and its immune regulatory mechanisms, particularly in the metabolic and immune regulation. This article presents a systematic review of the compositional characteristics of intratumoral microbiota in CRC, the associated immune regulatory mechanisms, and their roles in chemotherapy and immunotherapy. It also discusses challenges like standardizing microbiome detection methods and the ethics of clinical translation, while proposing a strategy for integrating multi-omics using artificial intelligence. This article provides a theoretical basis for developing personalized treatment regimens that target the microbiota.},
}

@article {pmid40852190,
year = {2025},
author = {Chen, J and Peng, H and Shao, Y and Wu, Z},
title = {The impact of altered gut microbiota and lipid metabolism on the progression of endometrial cancer in overweight populations.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1610534},
pmid = {40852190},
issn = {1664-2392},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/physiology ; *Endometrial Neoplasms/metabolism/microbiology/pathology ; *Overweight/complications/metabolism/microbiology ; *Lipid Metabolism/physiology ; Middle Aged ; Disease Progression ; Adult ; Case-Control Studies ; Aged ; },
abstract = {BACKGROUND: Endometrial cancer (EC) is one of the common malignant tumors among women, and in recent years, the role of gut microbiota in tumorigenesis has been increasingly gaining attention.Existing research has shown that the gut microbiome, establishes axis connections with multiple extra-intestinal organs. However, whether gut microbes affect the process of endometrial carcinogenesis through metabolic pathways and the specific mechanisms by which they promote the development of EC remain unclear. This study aims to explore the impact of overweight-mediated gut microbiota on the initiation or progression of EC and to assess its relationship with metabolites, thereby providing new insights for early diagnosis and treatment.

METHODS: In this study, we analyzed gut microbiota differences among normal-weight, overweight EC patients, and healthy controls using 16S rRNA sequencing. Liquid chromatography-mass spectrometry (LC-MS) and KEGG analysis identified group-specific metabolites and pathways, while Spearman correlation analysis revealed associations between microbiota and metabolites.

RESULTS: This study revealed that in the ECMO group, the genus Megamonas exhibited the highest abundance and significant intergroup differences (H=13.46, P<0.05). Additionally, the Bacillota/Bacteroidota ratio (B/B ratio) gradually increased in the CN, ECMN, ECMO group. LEfSe analysis identified Megamonas and Amedibacillus as potential biomarkers for the ECMO group. Serum metabolomics of overweight EC patients highlighted lipid metabolism-related metabolites with the most specific expression. KEGG enrichment analysis of differential metabolites highlighted that the Glycerophospholipid metabolism and Purine metabolism pathways were notably significant in both the ECMN and ECMO groups.

CONCLUSION: The study found significantly elevated abundance of Megamonas in the gut microbiota of overweight EC patients, which may promote EC progression by degrading inositol to enhance lipid absorption. This reveals the role of gut microbiota in EC pathogenesis through lipid metabolism regulation, providing a theoretical basis for microbiota-based diagnostic and therapeutic strategies.},
}

Humans
Female
*Gastrointestinal Microbiome/physiology
*Endometrial Neoplasms/metabolism/microbiology/pathology
*Overweight/complications/metabolism/microbiology
*Lipid Metabolism/physiology
Middle Aged
Disease Progression
Adult
Case-Control Studies
Aged

@article {pmid40852127,
year = {2025},
author = {Noël-Romas, L and Fehr, K and Khakisahneh, S and Azad, MB},
title = {Milk matters: seeding gut ecosystems and shaping microbiota rivalries.},
journal = {Microbiome research reports},
volume = {4},
number = {2},
pages = {17},
pmid = {40852127},
issn = {2771-5965},
abstract = {Maternal milk contains its own diverse microbiome, which has been hypothesized to colonize the infant gut during breastfeeding; however, the dynamics of this process are not well understood, particularly among very-low-birth-weight (VLBW) infants. A recent study published in Cell Reports Medicine by Shama et al. identifies novel dose-dependent relationships between maternal milk microbiota and infant gut microbiota in a cohort of VLBW infants and further explores the potential impact of infant feeding practices and antibiotic use on these microbial colonization dynamics.},
}

@article {pmid40852125,
year = {2025},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {Early-life gut microbiome development and its potential long-term impact on health outcomes.},
journal = {Microbiome research reports},
volume = {4},
number = {2},
pages = {20},
pmid = {40852125},
issn = {2771-5965},
abstract = {The initial gut colonization of the infant plays a pivotal role in shaping the immune system, developing the intestinal tract, and influencing host metabolism, all of which are strongly influenced by several determinants, such as gestational age at birth, mode of delivery, neonatal feeding practices, early-life stress (ELS), and exposure to perinatal antibiotics. However, resulting gut microbiome (GM) dysbiosis may alter this developmental programming, leading to long-term adverse health outcomes. This narrative review synthesizes current knowledge on early-life GM development and its long-term impact on health. Specifically, it addresses how early-life GM dysbiosis may affect the trajectory of physiological processes, predisposing individuals to conditions such as allergic diseases, metabolic disorders, type 1 diabetes, inflammatory bowel disorders, and atherosclerotic cardiovascular diseases. In addition, it examines the influence of probiotic and prebiotic supplementation during pregnancy and early life in shaping infant GM composition, as well as the impact of ELS-induced GM dysbiosis on mental health. Recent research suggests that the early-life microbiota initiates long-lasting effects, and inadequate or insufficient microbial exposure triggers inflammatory responses associated with several physiological conditions. Although several studies have reported a connection between ELS and the GM during both prenatal and postnatal periods, a unified microbiome signature linked to either prenatal or postnatal stress remains to be fully elucidated. Thus, future studies are needed to establish causality and determine whether modifiable factors affecting the GM could be targeted to improve gut health, especially in children exposed to contextual stress or adverse conditions.},
}

@article {pmid40852124,
year = {2025},
author = {Douglas S Stuehler, and Hunter, WB and Qureshi, JA and Cano, LM},
title = {Transcriptomic characterization of Wolbachia endosymbiont from Leuronota fagarae (Hemiptera: Psylloidae).},
journal = {Microbiome research reports},
volume = {4},
number = {2},
pages = {19},
pmid = {40852124},
issn = {2771-5965},
abstract = {Aim: Wolbachia species are among the most abundant intracellular endosymbionts of insects worldwide. The extensive distribution of Gram-negative Wolbachia among insects highlights their evolutionary success and close relationship with many insect host species. This study aimed to characterize a novel Wolbachia strain from the Wild Lime Psyllid, Leuronota fagarae (L. fagarae), to understand its evolutionary relationship with Wolbachia from psyllid pests like Diaphorina citri, the vector of Huanglongbing (HLB). Methods: Wild-caught L. fagarae colonies from Florida, USA, were maintained on Zanthoxylum fagara. RNA was extracted from the salivary glands, heads, and whole bodies of male and female adult L. fagarae. Four cDNA libraries were sequenced using short read technology and de novo transcriptome assembly was performed. Multilocus sequence typing (MLST) of nine conserved loci and wsp gene analysis classified the strain's phylogeny, while sequence mapping and functional annotation provided insight into host-microbe interactions. Results: The new Wolbachia strain, designated Wolbachia endosymbiont of Leuronota fagarae (wLfag-FL), was assigned to supergroup B, showing relation to Wolbachia strains of other related psyllids. Transcriptome analysis identified 1,359 Wolbachia transcripts with 465 assigned functions encompassing metabolic and secretion system pathways. Ankyrin domain proteins and a partial bacterioferritin sequence were detected, suggesting nutritional provisioning roles. Conclusion: The characterization of wLfag-FL expands the known Wolbachia host range and informs HLB-related pest biology. Its phylogenetic placement and transcript annotations offer insights into symbiotic interactions, potentially guiding environmentally safe pest control strategies targeting psyllid fitness and pathogen transmission.},
}

@article {pmid40852123,
year = {2025},
author = {Linehan, K and Healy, K and Hurley, E and O'Shea, CA and Ryan, CA and Ross, RP and Stanton, C and Dempsey, EM},
title = {Perinatal factors influencing the earliest establishment of the infant microbiome.},
journal = {Microbiome research reports},
volume = {4},
number = {2},
pages = {24},
pmid = {40852123},
issn = {2771-5965},
abstract = {Background: While extensive research exists on the human microbiome, a number of outstanding questions remain regarding the infant microbiome in the initial stages of life. This study aimed to determine the timing of very early microbial colonization in humans, assess the contribution of maternal microbial sources to their offspring and examine the effects of perinatal factors such as delivery mode, gestational age, and feeding practices on the maternal and infant microbiota in early life. Methods: Using a cohort of 18 healthy mother-infant dyads, maternal saliva (within 24 h postpartum), vaginal (1 h prepartum), and placental (1 h postpartum) samples were collected. From their corresponding infants, saliva (within 24 h postpartum) and meconium (within 96 h postpartum) samples were collected. 16S rRNA amplicon sequencing was utilized to assess the taxonomic and inferred functional compositions of the bacterial communities from both mothers and infants. Results: Our results consolidate and corroborate recent findings addressing the existence of a meconium microbiome and the absence of a placental microbiome. We show that significant sharing of microbiota, primarily Streptococcus and Veillonella species, between the maternal oral cavity and the infant oral cavity occurs in early life. Perinatal factors such as vaginal delivery and exclusive breastfeeding were strongly associated with enhanced microbial richness and diversity in infants. Conclusions: This study provides information on the relationship between health and delivery factors and the first establishment of the infant microbiota. These findings could offer valuable guidance to clinicians and mothers in optimizing the infant microbiota toward health during infancy and later life.},
}

@article {pmid40852122,
year = {2025},
author = {Wang, S and Healy, D and Patangia, D and Uniacke-Lowe, S and Kamilari, E and Kozak, IM and Yang, B and Dempsey, EM and Stanton, C and Ross, RP},
title = {Assessment of absolute abundance in mother-infant gut microbiome using marine-sourced bacterial DNA spike-in and comparison with conventional quantification methods.},
journal = {Microbiome research reports},
volume = {4},
number = {2},
pages = {23},
pmid = {40852122},
issn = {2771-5965},
abstract = {Aim: To evaluate the effectiveness of marine-sourced bacterial DNA spike-in quantification for determining absolute microbial abundance in the gut microbiome of mother-infant pairs and to compare this method with conventional quantification techniques. Methods: We conducted a pilot study involving six mother-infant pairs, applying a DNA spike-in quantification method using bacterial DNA from Pseudoalteromonas sp. APC 3896 and Planococcus sp. APC 3900, isolated from deep-sea fish. We compared our approach with established absolute quantification methods - flow cytometry, total DNA measurement, quantitative PCR (qPCR), and culture-based plate count - to evaluate microbial load and taxonomic composition across mother-infant samples. Results: Our spike-in method accurately estimated microbial loads, producing results consistent with qPCR and total DNA quantification. We observed that mothers exhibited higher total bacterial loads than infants by approximately half a log, while the abundance of Bifidobacterium was comparable in both groups. The spike-in method revealed significant differences in taxonomic composition, highlighting the impact of absolute quantification on microbiome analysis outcomes. Importantly, the method did not alter alpha diversity measures but slightly affected beta diversity analysis, reflecting more precise inter-group differences. Conclusion: Marine-sourced bacterial DNA spike-in offers a reliable, scalable, and accurate approach for absolute microbiome quantification. This method enhances microbiome analysis by addressing biases inherent in relative abundance measures, providing a deeper understanding of microbial dynamics in mother-infant gut microbiomes.},
}

@article {pmid40852120,
year = {2025},
author = {Mulet Margalef, N and Martín Abad, B and Martínez-Balibrea, E and Manzano Mozo, JL and Borgognone, A and Obón-Santacana, M},
title = {Microbiome as a predictive biomarker in locally advanced rectal cancer.},
journal = {Microbiome research reports},
volume = {4},
number = {2},
pages = {18},
pmid = {40852120},
issn = {2771-5965},
abstract = {The incidence of locally advanced rectal cancer (LARC) among young people is rising alarmingly. In recent years, new protocols have been introduced for the management of LARC, some of which are associated with the risk of significant toxicity. Despite these advancements, robust predictive biomarkers for LARC have yet to be established. The microbiome has emerged as a potential biomarker due to its interaction with tumor multiomics. This article provides a critical overview of the current evidence on the microbiome and LARC, including its relationship with the immune system and epigenomics, and also highlights both the current limitations and future perspectives in the field.},
}

@article {pmid40851996,
year = {2025},
author = {Nebieridze, A and Abu-Bakr, A and Nazir, A and Ghosson, A and Minova, A and Uwishema, O},
title = {Microbiome and cardiovascular health unexplored frontiers in precision cardiology: a narrative review.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {7},
pages = {4255-4261},
pmid = {40851996},
issn = {2049-0801},
abstract = {BACKGROUND AND PURPOSE: Gut microbiota has a symbiotic relationship with their host. It is known that the gut microbiome has the potential to affect the host and vice versa. Cardiovascular disease and its comorbidities are the leading cause of death worldwide. Patients with various heart conditions have been observed to have a different composition of the gut microbiome. It has been postulated that the gut microbiome and its derivatives exert various effects on the cardiovascular system, termed the gut-heart axis. In this study, we aim to explore how the gut microbiome and the active metabolites produced by these microorganisms affect patient cardiovascular health. Additionally, we will discuss how gut microbiota can become a target for the new era of precision cardiology.

METHODS: Data were collected through the online databases PubMed, Google Scholar, Ovid MEDLINE, and ScienceDirect. Articles regarding cardiovascular health and pathology as well as its overlap with gut microbiome and health were used.

RESULTS: Emerging evidence suggests that gut microbiome has a significant influence on cardiovascular disease through its metabolites, such as trimethylamine N-oxide and short-chain fatty acids, which impact cholesterol metabolism, systemic inflammation, and plaque stability. Targeting said derivatives has proven to provide beneficial results for patients suffering from cardiovascular disease.

CONCLUSIONS: Finding reported here highlights the importance of microbiome in cardiovascular disease and health and suggest that microbiome-based interventions hold promise for prevention and treatment of cardiovascular disease. More research needs to be conducted to study more concrete effects of specific microorganisms on cardiovascular health. Multicenter, longitudinal studies with a large sample size will provide the best evidence for clinically significant findings. Using precision cardiology, to target the gut microbiome and its derivatives, with medications like antibiotics, and nonpharmacologic interventions like lifestyle modification and fecal transplantation can positively influence cardiovascular health and help with the effective management of ongoing diseases.},
}

@article {pmid40851867,
year = {2025},
author = {Chen, G and Zhao, X and Yang, B and Gu, H},
title = {Peri-implant diseases triggered by oral microdysbiosis: pathogenesis and precision intervention strategies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1639095},
pmid = {40851867},
issn = {1664-302X},
abstract = {Peri-implant disease is a chronic infection-induced inflammation condition affecting tissues around dental implants, categorized into peri-implant mucositis and peri-implantitis. Oral microbial dysbiosis plays an important role in this disease. Currently, researchers face three challenges in establishing the pathogenic link between peri-implant disease and microdysbiosis: (1) elucidating the underlying molecular mechanisms; (2) Clarifying causal links between host and microbiome; and (3) Identifying secondary microbial changes during disease progression. In this review, we systematically classify dysbiosis from a conceptual perspective and outline the immunological associations within each category. We further elaborate on the causes of bacterial dysbiosis and analyze its potential implications for clinical treatment strategies. At the molecular level, understanding the origins, intrinsic and environmental regulatory mechanisms, and downstream effects may be conducive to develop microbiome targeted therapies. This research direction is of great significance for promoting precision medicine in peri-implant disease.},
}

@article {pmid40851859,
year = {2025},
author = {Li, Y and Xie, X and Yu, Y and Hua, S and Zhang, Z and Zhao, Z and Gao, H and Zhang, C and Huang, M},
title = {Cross-matrix multi-omics profiling identifies host-microbe interactions and diagnostic signatures in bovine subclinical mastitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1613949},
pmid = {40851859},
issn = {1664-302X},
abstract = {Subclinical mastitis (SCM) is a widespread but frequently undetected condition in dairy cows, leading to reduced milk quality and compromised animal health. This study utilizes an integrated multi-omics strategy encompassing metabolomics and microbiome analyses to investigate the systemic effects of SCM across four biological matrices: blood, milk, feces, and rumen fluid. Our findings reveal significant alterations in hematological and biochemical parameters, with key biomarkers such as digalacturonic acid and N-ε-methyl-L-lysine indicating systemic metabolic and immune dysregulation. Metabolomic profiling uncovered distinct disease-related metabolic patterns, while 16S rRNA sequencing revealed substantial microbial shifts, particularly involving Succinivibrio and Methanobrevibacter, which are implicated in carbohydrate fermentation and methanogenesis. Noteworthy correlations between specific metabolites (e.g., ropinirole, arachidonic acid) and microbial genera (e.g., Succinivibrionaceae UCG-001, Alistipes) highlight the complex host-microbiome-metabolite interplay associated with SCM. These findings provide new insights into the pathophysiology of SCM and identify candidate biomarkers for early detection. The integrative multi-omics approach adopted in this study offers a valuable framework for developing innovative diagnostic and therapeutic strategies to enhance dairy cow health and productivity.},
}

@article {pmid40851803,
year = {2025},
author = {Da Silva, AS and Anwar, S and Park, S and Park, S and Goodfellow, L and Sergaki, C},
title = {The untapped potential of vaginal microbiome diagnostics for improving women's health.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1595182},
pmid = {40851803},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota ; *Women's Health ; },
abstract = {Microbiome research has expanded rapidly over the past 15 years; however, the primary focus has been on the gut microbiome. Although understudied, the vaginal microbiome holds significant potential to improve women's health. In this paper, we describe the current clinical diagnostic techniques utilised in women's health and examine their drawbacks and limitations. We also discuss emerging diagnostic technologies based on microbiome analysis that could enable greater precision in diagnosis and personalised treatment. We additionally emphasise the need for standardisation in microbiome analysis and strengthening the knowledge base to enable advancements in accurate diagnosis, ultimately improving patient outcomes. This article aims to highlight opportunities in the field that can transform women's health outcomes and outline the necessary actions to realise these opportunities, thereby enhancing women's lives.},
}

Humans
Female
*Vagina/microbiology
*Microbiota
*Women's Health

@article {pmid40851781,
year = {2025},
author = {Knufinke, M and Lebbing, M and Mesnage, R},
title = {Case Report: Sustained weight loss and glycemic control from repeated long-term fasting in type 2 diabetes.},
journal = {Frontiers in clinical diabetes and healthcare},
volume = {6},
number = {},
pages = {1572245},
pmid = {40851781},
issn = {2673-6616},
abstract = {Type 2 diabetes mellitus (T2DM) is a common metabolic disorder typically managed with medication; however, fasting has recently attracted attention for its potential benefits in glycemic control, weight management, and even potential remission. This case report examines the effects of repeated long-term fasting on weight reduction, glycemic control, and medication requirements in a 57-year-old man with T2DM. The patient, who had a history of inadequate glycemic control despite conventional treatment, opted for repeated long-term fasting under medical supervision. He completed several fasts ranging from 11 to 20 days each, with each fasting period followed by a gradual reintroduction of food via a hypocaloric lactovegetarian diet (800-1,800 kcal) over 4 to 16 days. The intervention resulted in sustained weight loss and improved blood sugar control. Notably, clinically meaningful improvements occurred in fasting blood glucose levels, which necessitated adjustments in his antidiabetic medications. Enhanced insulin sensitivity was evidenced by decreased HbA1c levels and a reduced dependence on hypoglycemic agents. Additionally, post-fasting evaluations indicated improvements in inflammatory markers and a reduction in fatty liver disease. In summary, repeated long-term fasting in this patient was associated with sustained weight loss, improved glycemic control, and reduced medication requirements, thereby enhancing the overall management of T2DM. Further research, including randomized controlled trials, is needed to better understand the long-term safety and effectiveness of this intervention.},
}

@article {pmid40851518,
year = {2025},
author = {Kontogiannis, DS and Romanos, LT and Tzvetanova, ID and Voulgaris, GL and Falagas, ME},
title = {Antibiotics and non-traditional antimicrobial agents for carbapenem-resistant Acinetobacter baumannii in Phase 1, 2, and 3 clinical trials.},
journal = {Expert opinion on investigational drugs},
volume = {},
number = {},
pages = {},
doi = {10.1080/13543784.2025.2552846},
pmid = {40851518},
issn = {1744-7658},
abstract = {INTRODUCTION: Carbapenem-resistant Acinetobacter baumannii (CRAB) infections have become common in healthcare settings worldwide, yet current therapeutic options are limited. A pipeline of new antibiotics and non-traditional antimicrobial agents is being developed to address the urgent need for efficacious therapeutic options for patients with CRAB infections.

AREAS COVERED: At the time of this writing, 13 traditional antibiotics are in clinical development for CRAB infections, some with a novel mechanism of action. Specifically, 9 antibiotics are in Phase 1 (R-327, xeruborbactam/QPX-7728, upleganan/SPR-206, MRX-8, QPX-9003, zifanocycline/KBP-7072, apramycin/EBL-1003, zosurabalpin/RG-6006, and ANT-3310), two in Phase 2 (BV-100, OMN-6), and two in Phase 3 (zidebactam/WCK-5222, funobactam/XNW-4107) clinical trials. Additionally, there are six non-traditional antimicrobial agents in Phase 1 or 2 clinical trials for treating CRAB infections. In particular, two monoclonal antibodies (TRL-1068, CMTX-101), a phage therapy (Phagebank), an immune-modulating agent (recombinant human plasma gelsolin/Rhu-pGSN), a microbiome-modulating agent (SER-155), and an engineered cationic antibiotic peptide (PLG-0206).

EXPERT OPINION: Several agents with promising characteristics against CRAB infections are in clinical development (Phases 1, 2, and 3). The urgent need for therapeutic options against CRAB infections necessitates optimizing efforts and time for introducing successfully studied agents into clinical practice.},
}

@article {pmid40851476,
year = {2025},
author = {Li, MY and Wu, XQ and Lee, TKW},
title = {Harnessing the Microbiome: Unveiling the Influence of the Gut Microbiota on Hepatobiliary Cancer Therapeutic Strategies.},
journal = {Clinical and molecular hepatology},
volume = {},
number = {},
pages = {},
doi = {10.3350/cmh.2025.0476},
pmid = {40851476},
issn = {2287-285X},
abstract = {The gut microbiota significantly influences hepatobiliary cancer therapeutics. Growing evidence indicates that shifts in the gut microbial ecosystem are hallmarks of hepatocellular carcinoma and cholangiocarcinoma, strongly correlating with tumor development, therapeutic resistance, and patient survival. The composition of gut microbiota has emerged as a biomarker associated with treatment outcomes across various modalities, including chemotherapy, radiotherapy, targeted therapy, and immunotherapy. Beneficial bacterial communities enhance antitumor immunity, while pathogenic taxa are linked to reduced therapeutic efficacy. Multi-omics analyses have identified microbial metabolite signatures, such as short-chain fatty acids and bile acids, as potential targets for boosting antitumor responses. This review highlights the transformative potential of leveraging the gut microbiota to enhance precision oncology in hepatobiliary cancer. Future directions should prioritize personalized microbiota modulation approaches, combinatorial therapies targeting gut-liver axis crosstalk, and large-scale validation of microbial biomarkers across diverse populations.},
}

@article {pmid40851218,
year = {2025},
author = {Li, C and Gao, B and Xiao, H and Shi, W and Lu, H and Miao, G and Tu, X and Tang, Y and Shen, H},
title = {Mapping Nutrition and Tuberculosis Research: Insights From Bibliometric Perspective.},
journal = {Clinical and experimental pharmacology & physiology},
volume = {52},
number = {10},
pages = {e70069},
doi = {10.1111/1440-1681.70069},
pmid = {40851218},
issn = {1440-1681},
support = {//National Natural Science Foundation (No. 81573150), the Shanghai Sailing Program (No. 24YF2758300), the Shanghai Youth Program of Public Health Research (No. 2024GKQ26), the Natural Science Research Project of Shanghai Jiading District (No. JDKW-2024-0013), the Project of Third Affiliated Hospital of Naval Medical University (No. 2025QN09); and the Military Key Discipline Construction Projects of China (HL21JD1206)./ ; },
mesh = {Humans ; *Bibliometrics ; *Biomedical Research ; *Tuberculosis/epidemiology/metabolism ; },
abstract = {BACKGROUND: Malnutrition and tuberculosis form a mutually reinforcing vicious cycle. While nutritional interventions are crucial for TB management, the knowledge structure and research frontiers remain insufficiently characterised.

OBJECTIVE: To systematically analyse the structure, trajectory and frontiers of research in the nutrition-tuberculosis field using bibliometric methods.

METHODS: Relevant literature published since 2007 was retrieved from the Web of Science Core Collection database. CiteSpace was employed to perform multidimensional analyses, including co-occurrence, cluster timeline visualisation and burst detection for keywords, citations and authors, thereby constructing knowledge maps and identifying key nodes through network centrality metrics.

RESULTS: A total of 4502 bibliographic records were analysed. Key findings include: (1) Vitamin D occupies a central position (frequency 326, centrality 70), bridging basic immune mechanisms and clinical applications; (2) research paradigms evolved from molecular mechanism exploration (2007-2012), through clinical translation validation (2011-2019), to systems biology integration (2019-2025); (3) gut microbiota (burst strength 11.73) and (fatty) acids emerged as frontiers; (4) diabetes-tuberculosis comorbidity revealed the complexity of metabolic-immune interaction networks and (5) high citation frequency of WHO reports indicates a pressing need for translating research into policy.

CONCLUSIONS: Nutrition-tuberculosis research is shifting from single-nutrient studies towards integrated 'nutrition-microbiome-metabolism-immunity' networks. Vitamin D remains central, but future priorities should focus on precision interventions, multi-omics integration and translation from mechanism to practice, especially for high-risk groups.},
}

Humans
*Bibliometrics
*Biomedical Research
*Tuberculosis/epidemiology/metabolism

@article {pmid40847308,
year = {2025},
author = {Wan, S and Li, M and Li, W and Ren, Y and Wu, Y and Luo, Q and Gong, W},
title = {Development and validation of a multimodal model integrating gut microbiota and metabolite for identifying sarcopenia in patients with MASLD: a study from two centers in China.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {129},
pmid = {40847308},
issn = {1475-2891},
support = {82401448//National Natural Science Foundation of China/ ; 2021A1515110799//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20240813145414019//Shenzhen Science and Technology Program/ ; NSZD2024015//Shenzhen Nanshan District Science and Technology Plan Funding Program/ ; },
abstract = {BACKGROUND AND AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common chronic liver disease worldwide, and identifying sarcopenia is critical since it is correlated with poor prognosis. Little is known about mechanistic alterations in the pathogenesis of this condition. This study aimed to explore the alterations in the gut microbiome and metabolome in patients with sarcopenia and develop a predictive model.

METHODS: We performed shotgun metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling of fecal samples from the discovery cohort (70 patients without sarcopenia, 30 with sarcopenia). A microbiota-metabolite score (MM score) was developed using LASSO regression to identify key microbiome and metabolite features associated with sarcopenia. A multimodal prediction model incorporating the MM score and clinical parameters was then developed and validated in an independent cohort of 50 patients.

RESULTS: Patients with sarcopenia exhibited altered gut microbiota and metabolomic profiles, with significantly elevated Enterococcus faecium and Bacteroides vulgatus species, and elevated bile acids. Integration of the MM score with clinical variables (age, BMI, AST, presence of diabetes) resulted in a multimodal model with an AUC of 0.911, outperforming existing models including FIB-4 (AUC 0.765), NFS (AUC 0.724), and using only MM score alone (AUC 0.818). In a prospective validation cohort, the multimodal model demonstrated superior diagnostic performance (AUC 0.897), with significant improvements in clinical utility as evidenced by calibration curves and decision curve analysis.

CONCLUSIONS: This study developed a novel multimodal model combining gut microbiome, metabolomics, and clinical data for accurate prediction of sarcopenia, offering a promising approach for early identification of high-risk MASLD patients with sarcopenia.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12937-025-01198-2.},
}

@article {pmid40841599,
year = {2025},
author = {Li, C and Cheng, Z and Sun, X and Yang, J and Chen, N and Yang, K and Wang, M},
title = {Partial replacement of corn silage with sorghum-sudangrass silage improves growth performance and rumen function in Hu sheep via microbial and metabolic modulation.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {527},
pmid = {40841599},
issn = {1471-2180},
support = {2023YFD1301705//14th Five Year Plan Key Research and Development Program/ ; 2023YFD1301705//14th Five Year Plan Key Research and Development Program/ ; NCG202232//the Key Program of State Key Laboratory of Sheep Genetic Improvement and Healthy Production/ ; },
abstract = {BACKGROUND: The rumen hosts a diverse microbial community and serves as a natural bioreactor that efficiently utilizes plant biomass. To explore the potential of sorghum-sudangrass silage (SS) as an alternative to whole-plant corn silage (WS), this study evaluated the growth performance, rumen microbiota, serum metabolome, and rumen fermentation characteristics of Hu sheep. The aim was to assess the feasibility of SS as a feed resource and to identify specific rumen bacteria that interact with host metabolism.

RESULTS: Feeding Hu sheep a diet containing 50% WS and 50% SS (T1 group) improved both growth performance and rumen fermentation compared to a diet of 100% WS (T0 group). In contrast, replacing WS entirely with SS (T2 group) did not affect growth performance. Microbiome analysis revealed that SS inclusion increased the relative abundance of beneficial bacteria. In particular, the T1 group showed an enrichment of Sphingomonas, while the T2 group had higher levels of Bacillus, Enterococcus, and Ruminobacter. Metabolomic analysis indicated that both T1 and T2 diets enhanced purine metabolism.

CONCLUSION: Partial replacement (50%) of WS with SS improves rumen microbial composition, promotes purine metabolism, enhances rumen fermentation, and supports better growth performance in Hu sheep. These findings demonstrate that SS is a promising alternative to WS for enhancing growth and rumen function in ruminants.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04211-0.},
}

@article {pmid40851072,
year = {2025},
author = {Zhang, L and Wang, S and Wong, MCS and Mok, CKP and Ching, JYL and Mak, JWY and Chen, C and Huo, B and Yan, S and Cheung, CP and Chiu, EOL and Fung, EYT and Cheong, PK and Chan, FKL and Ng, SC},
title = {The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {171},
pmid = {40851072},
issn = {2055-5008},
support = {COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; NCI202346//New Cornerstone Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Aged ; *Synbiotics/administration & dosage ; SARS-CoV-2/immunology ; Female ; Male ; *COVID-19/prevention & control/immunology ; *COVID-19 Vaccines/immunology/administration & dosage ; Feces/microbiology ; Bifidobacterium ; *Immunogenicity, Vaccine ; *Diabetes Mellitus/immunology/microbiology ; Vaccination ; BNT162 Vaccine/immunology ; Middle Aged ; Antibodies, Viral/blood ; },
abstract = {The study aims to tackle the seed and soil microbiome and mechanisms that contribute to the effect of synbiotics in enhancing immunogenicity after SARS-CoV-2 vaccination in elderly and diabetic patients. Among 369 subjects who received 3 months of SIM01, a gut microbiota-derived synbiotic formula of three Bifidobacterium strains (B. adolescentis, B. bididum, and B. longum) or a placebo after the SARS-CoV-2 vaccines (mRNA vaccine BNT162b2 (Pfizer-BioNTech) or the inactivated vaccine Sinovac-CoronaVac), we performed metagenomic sequencing in stool samples of 280 vaccinees collected at baseline and 3-month postvaccination and metabonomic sequencing in 276 vaccinees collected at baseline and 1-month postvaccination. The open niche of autochthonous gut microbiota (lower levels of Bifidobacterium and decreased functional potential for carbohydrate metabolism) was associated with enhancing SIM01-contained species. The enrichment of three bifidobacterial species after 3 months of SIM01 intervention (BABBBL_fc) was positively correlated with the level of neutralizing antibodies to the BNT162b2 vaccine at 6-month postvaccination. The fold change of benzoic acid was positively correlated with BABBBL_fc in the BNT162b2 vaccinees, which was also implicated with SARS-CoV-2 surrogate virus neutralization test (sVNT)% levels at 1-month postvaccination. Importantly, SIM01 strain engraftment assessed by StrainPhlAn (A metagenomic strain-level population genomics tool) was associated with a higher fold change of three bifidobacterial species and could be predicted based on the baseline gut microbiome. Therefore, the resident gut microbiome affected the SIM01 engraftment, which was associated with the immunogenicity of SARS-CoV-2 BNT162b2 vaccines.},
}

Humans
*Gastrointestinal Microbiome/immunology
Aged
*Synbiotics/administration & dosage
SARS-CoV-2/immunology
Female
Male
*COVID-19/prevention & control/immunology
*COVID-19 Vaccines/immunology/administration & dosage
Feces/microbiology
Bifidobacterium
*Immunogenicity, Vaccine
*Diabetes Mellitus/immunology/microbiology
Vaccination
BNT162 Vaccine/immunology
Middle Aged
Antibodies, Viral/blood

@article {pmid40851038,
year = {2025},
author = {Binyamin, D and Turjeman, S and Asulin, N and Schweitzer, R and Koren, O},
title = {The microbiome is associated with obesity-related metabolome signature in the process of aging.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {173},
pmid = {40851038},
issn = {2055-5008},
support = {Adams Fellowships program//Israel Academy of Sciences and Humanities/ ; },
mesh = {Animals ; Mice ; *Aging/metabolism ; Female ; *Metabolome ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Obesity/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Germ-Free Life ; Lipid Metabolism ; },
abstract = {Aging involves changes in the gut microbiome impacting health and longevity; however, the roles of specific microbial metabolites remain understudied. Here, we examine the microbial contribution to the metabolic profile in aged mice. Fecal samples were collected from female Swiss-Webster mice raised conventionally (Conv) or germ free (GF), at 8 weeks (young) and 18 (aged) months of age, and the microbiome and metabolome were characterized. Significant differences were observed in bacterial composition and its predicted functional activity between young and aged mice. Interestingly, we found more age-related differences in metabolite abundances among Conv mice than GF mice, highlighting the contribution of the microbiome to aging. Moreover, microbiome-associated metabolites, predominantly lipids, were higher in aged mice, with linoleic acid metabolism enriched in this group. Our study underscores a microbiome-dependent component to age-related metabolic changes in mice, particularly in lipid-associated pathways, and contributes to the growing body of literature linking gut microbiota to host metabolism in aging.},
}

Animals
Mice
*Aging/metabolism
Female
*Metabolome
*Gastrointestinal Microbiome
Feces/microbiology
*Obesity/microbiology/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Germ-Free Life
Lipid Metabolism

@article {pmid40851026,
year = {2025},
author = {Yan, F and Chen, S and Xia, X and Fan, Y and Yu, S and Zhang, X and Chen, X},
title = {Microbiome characteristics associated with lymph node metastasis in laryngeal squamous cell carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31123},
pmid = {40851026},
issn = {2045-2322},
support = {2022FY100800//Science & Technology Fundamental Resources Investigation Program/ ; 2021-I2M-1-023, 2023-I2M-C&T-B-005//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 2022-PUMCH-B-094//National High Level Hospital Clinical Research Funding/ ; },
mesh = {Humans ; *Lymphatic Metastasis/pathology ; *Microbiota ; *Laryngeal Neoplasms/microbiology/pathology ; Male ; Female ; Middle Aged ; *Carcinoma, Squamous Cell/microbiology/pathology ; Aged ; Lymph Nodes/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Squamous Cell Carcinoma of Head and Neck/microbiology/pathology ; },
abstract = {Lymph node (LN) metastasis is a key prognostic factor in laryngeal squamous cell carcinoma (LSCC). Emerging evidence implicates the role of the microbiome in cancer progression. This study aimed to investigate the microbial features associated with lymph node metastasis in LSCC and their potential for patient stratification. Using 16 S rRNA gene sequencing, we characterized the microbiome of tumor tissues, adjacent normal tissues, lymph nodes, and oral rinses from 108 LSCC patients, including 36 with (LN+) and 72 without (LN-) cervical LN metastasis. Microbial functional potential was predicted using PICRUSt2. Based on repeated stratified 3 cross-validation, random forest models were used to identify metastasis-associated genera. Significant microbial differences were observed between LN + and LN- tumor tissues, with Ralstonia enriched in LN + tumors and Fusobacterium more abundant in LN- cases. All genera detected in lymph nodes were also found in tumor tissues. Functional predictions revealed enrichment of lipid biosynthesis, energy metabolism, and cell wall synthesis pathways in LN + patients, particularly in tumor and oral rinse samples, with low intra-group variability. Classifiers based on tumor, lymph node, and oral microbiota demonstrated the ability to distinguish LN + from LN- patients. The lymph node-derived classifier achieved an accuracy of 84.31% (95% confidence interval [CI]: 81.76% - 86.85%), followed by the tumor-based model (AUC = 84.11%, 95% CI: 81.75% - 86.46%) and oral rinse classifier (AUC = 79.88%, 95% CI: 77.09% - 83.11%). A tumor-specific 17 genera panel showed a discriminative efficacy of 84.11% (95% CI: 81.75% - 86.46%) in tumor tissues. These findings suggest that microbiome alterations may be associated with lymph node metastasis in LSCC. In addition, the oral microbiome showed potential as a non-invasive tool for occult lymph node metastasis detection. However, these results are preliminary and require validation in larger, independent cohorts.},
}

Humans
*Lymphatic Metastasis/pathology
*Microbiota
*Laryngeal Neoplasms/microbiology/pathology
Male
Female
Middle Aged
*Carcinoma, Squamous Cell/microbiology/pathology
Aged
Lymph Nodes/microbiology/pathology
RNA, Ribosomal, 16S/genetics
*Squamous Cell Carcinoma of Head and Neck/microbiology/pathology

@article {pmid40851019,
year = {2025},
author = {El-Maradny, YA and Abouakkada, AS and Abbass, AAG and Abaza, AF and El-Fakharany, EM},
title = {Prebiotic properties and antioxidant effect of crude extracts and polysaccharides from Agaricus bisporus and Pleurotus ostreatus mushrooms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31113},
pmid = {40851019},
issn = {2045-2322},
mesh = {*Agaricus/chemistry ; *Pleurotus/chemistry ; *Prebiotics ; *Antioxidants/pharmacology/chemistry ; *Polysaccharides/pharmacology/chemistry ; *Complex Mixtures/pharmacology/chemistry ; Probiotics ; Lactobacillus acidophilus ; },
abstract = {Modifying the gut microbiome, also known as bacteriotherapy, is a key strategy that uses probiotics, prebiotics, or synbiotics to reduce inflammation and fight infection and colonization by pathogenic bacteria. Various food sources, particularly those rich in Lactobacillus species, are well-recognized for their probiotic properties. Edible mushrooms are rich with their nutrient-dense composition, including carbohydrates, proteins, fibers, minerals, vitamins, and lipids, which stand out as a promising bio-source for several biological uses. In this study, four probiotic strains were isolated and identified from food samples: Lactobacillus acidophilus (L. acidophilus), L. pentosus, L. plantarum, and L. paracasei. Then the prebiotic and antioxidant properties of crude and polysaccharide extracts were assessed from two edible mushrooms, Agaricus bisporus (brown) and Pleurotus ostreatus (oyster). Using the phenol-sulfuric acid method, the ethanol extract of P. ostreatus exhibited the highest yields of total carbohydrates and reducing sugars (6.14 and 3.15 mg/mL, respectively). Among the mushroom extracts, the polysaccharide from A. bisporus demonstrated the strongest radical scavenging activity (93.73%), with a half-maximal effective concentration (EC50) of 0.19 mg/mL, measured using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging method. The prebiotic properties of the mushroom extracts were evaluated by their ability to promote probiotic growth and inhibit pathogenic bacteria. The polysaccharide extracts from A. bisporus and P. ostreatus significantly stimulated the growth of L. paracasei (1.99 and 2.04 nm, respectively). Additionally, the cell-free supernatant from L. acidophilus cultured with the A. bisporus polysaccharide extract exhibited the highest antimicrobial activity, producing a 36.33 mm inhibition zone against the pathogen L. monocytogenes. These findings demonstrate that polysaccharides from A. bisporus and P. ostreatus are promising candidates for functional food development. These extracts offer a multifaceted approach to promoting gut health and reducing oxidative stress through selectively stimulating beneficial Lactobacillus species while inhibiting the growth of pathogens and exerting significant antioxidant effects.},
}

*Agaricus/chemistry
*Pleurotus/chemistry
*Prebiotics
*Antioxidants/pharmacology/chemistry
*Polysaccharides/pharmacology/chemistry
*Complex Mixtures/pharmacology/chemistry
Probiotics
Lactobacillus acidophilus

@article {pmid40850975,
year = {2025},
author = {Yeo, LF and Lee, AWY and Tee, PYE and Chin, JSF and Lee, BKB and Lim, J and Teo, SH and Pan, JW},
title = {Characterization of intra-tumoral microbiota from transcriptomic sequencing of Asian breast cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31147},
pmid = {40850975},
issn = {2045-2322},
mesh = {Humans ; *Breast Neoplasms/microbiology/genetics/pathology/immunology ; Female ; *Microbiota/genetics ; *Transcriptome ; Middle Aged ; Tumor Microenvironment/genetics/immunology ; Malaysia ; Asian People/genetics ; Gene Expression Profiling ; Adult ; Aged ; },
abstract = {The human microbiome has garnered significant interest in recent years as an important driver of human health and disease. Likewise, it has been suggested that the intra-tumoral microbiome may be associated with specific features of cancer such as tumour progression and metastasis. However, additional research is needed to validate these findings in diverse populations. In this study, we characterized the intra-tumoral microbiota of 883 Malaysian breast cancer patients using transcriptomic data from bulk tumours and investigated their association with clinical variables and immune scores. We found that the tumour microbiome was not associated with breast cancer molecular subtype, cancer stage, tumour grade, or patient age, but was weakly associated with immune scores. We also found that the tumour microbiome was associated with immune scores in our cohort using random forest models, suggesting the possibility of an interaction between the tumour microbiome and the tumour immune microenvironment in Asian breast cancer.},
}

Humans
*Breast Neoplasms/microbiology/genetics/pathology/immunology
Female
*Microbiota/genetics
*Transcriptome
Middle Aged
Tumor Microenvironment/genetics/immunology
Malaysia
Asian People/genetics
Gene Expression Profiling
Adult
Aged

@article {pmid40850684,
year = {2025},
author = {Lei, G and Han, Z and Wang, X and Malacrinò, A and Kang, T and Zhang, D and Zhang, J and Zhang, Z and Wu, H},
title = {Synthetic microbial communities rescues strawberry from soil-borne disease by enhancing soil functional microbial abundance and multifunctionality.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.08.040},
pmid = {40850684},
issn = {2090-1224},
abstract = {INTRODUCTION: Synthetic microbial communities (SynCom) contribute to mitigating soil-borne crop diseases while enhancing both crop quality and yield. However, relatively little research has been done on the intricate regulatory mechanisms of SynCom on the suppression of soil-borne diseases.

OBJECTIVES: We aimed to elucidate the dynamic regulatory mechanisms and legacy effects of a SynCom on the composition of soil functional microorganisms, soil multifunctionality and crucial functions, and the suppression of soil-borne diseases.

METHODS: We conducted an extensive series of experiments to assess the effect of a SynCom on the changes in the rhizosphere functional microorganisms and soil functions (e.g., multifunctionality, functionality of C, N, and P cycling) across six successive generations of strawberry in consecutive monoculture soils by employing amplicon metagenomics and transcriptome sequencing.

RESULTS: Our results showed that the SynCom increased the aboveground fresh biomass of strawberry by 31-70.3% and the fruit biomass by 171.39-280.71%, and decreased the Fusarium oxysporum abundance by 17.91-49.51% compared to the consecutive monoculture. The SynCom significantly enhanced the soil C cycling and P cycling function, and soil multifunctionality (SMF). SynCom treatment significantly increased the Shannon diversity index and relative abundances of potentially beneficial bacteria and consumer protistan communities, while exerted a significant inhibitory effect on the Shannon diversity index and relative abundances of fungal pathogen. SEM result showed that SynCom significantly affected SMF by influencing soil nutrients, the abundance and diversity of functional microbial community. Our result also showed that the SynCom established the positive legacy effects on the abundance of rhizosphere soil beneficial bacteria, strawberry biomass and plant disease resistance-associated pathways (phenylpropanoid biosynthesis pathway, alpha-linolenic acid metabolism pathway), and negative effect on the abundance of pathogenic F. oxysporum under the 7th generation of strawberry cropping.

CONCLUSION: Collectively, our study demonstrated the effectiveness of employing SynCom in mitigating soil-borne Fusarium oxysporum diseases by enhancing soil functional microbial abundance and soil multifunctionality.},
}

@article {pmid40850681,
year = {2025},
author = {Wei, Z and Gao, G and He, Q and Kwok, LY and Sun, Z},
title = {The gut-tumor connection: the role of microbiota in cancer progression and treatment strategies.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.08.038},
pmid = {40850681},
issn = {2090-1224},
abstract = {BACKGROUND: The tumor microenvironment (TME) has become a critical focus in the diagnosis and treatment of cancer. The involvement of the microbiome in tumor initiation and progression underscores its potential as a promising biomarker and therapeutic target. Furthermore, microorganisms in the gut and other ecological niches play pivotal roles in shaping cancer immune surveillance and modulating responses to immunotherapy, acting as key mediators connecting gut health to cancer progression. Thus, investigating the intricate interplay between the TME and gut microbiota could offer valuable insights to advance personalized cancer therapies.

AIM OF REVIEW: This comprehensive review explores the complex interactions between the gut microbiota, tumor-associated microbiota, and TME, examining their origins, diversity, connections, and therapeutic implications. We investigate the potential for gut microbiota to translocate to tumors, where they may directly impact the TME and influence cancer progression. We compile the current knowledge on the diversity of intratumoral microbiota across various cancer types and its effects on cellular, immune, and spatial heterogeneity within the TME. Furthermore, we assess the efficacy of various methods for characterizing and identifying intratumoral microbiome, emphasizing their importance in understanding their composition and function in the TME. We also explore the therapeutic potential of modulating the gut microbiota, highlighting strategies such as dietary interventions, fecal microbiota transplantation, probiotics, prebiotics, and synthetic biology approaches. We then address the challenges and future directions in this emerging field, emphasizing the need for standardized protocols, advanced sequencing technologies, and refined animal models to enhance our understanding of microbiota-cancer interactions. In conclusion, the gut microbiota represents a promising therapeutic target for cancer treatment. Harnessing the power of gut microbial modulation could lead to novel combinatorial strategies that improve clinical outcomes for cancer patients. Nevertheless, further research is essential to surmount existing challenges and translate these insights into impactful, personalized cancer therapies.},
}

@article {pmid40850636,
year = {2025},
author = {Płoszka, Z and Nowak, KH and Tischer, M and Michalik, A and Kolasa, MR and Łukasik, P},
title = {Dissecting multitrophic interactions: The relationships among Entomophthora, their dipteran hosts, and associated bacteria.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108425},
doi = {10.1016/j.jip.2025.108425},
pmid = {40850636},
issn = {1096-0805},
abstract = {Interactions with microorganisms across the parasite-mutualist continuum shape the biology of insects at all levels - from individual traits to populations to communities. However, the understanding of pathogens infecting non-model insect species in natural ecosystems, or their interactions with other insect-associated microorganisms, is fragmentary. Here, we tested a conceptually novel approach - the simultaneous sequencing of insect, fungal, and bacterial marker gene amplicons - as a means of dissecting interactions among entomopathogenic fungi in the genus Entomophthora and their dipteran hosts in South Greenland. We aimed to describe the taxonomic diversity of Entomophthora, their dipteran hosts, and the bacterial diversity within a set of field-collected dead insects exhibiting signs of Entomophthora infection. Across nine collected dipteran species, we identified multiple Entomophthora genotypes, with strong but not perfect patterns of host-specificity across the five targeted marker regions. Additionally, we found consistent differences in bacterial community composition among fungus-killed fly species and sampling sites. Our results substantially expand the knowledge of Entomopthora diversity and host associations while providing the very first insights into associated bacteria and their potential roles. We also conclude that multi-target amplicon sequencing can be a powerful tool for addressing broad questions about biological interactions in diverse natural communities.},
}

@article {pmid40850628,
year = {2025},
author = {Horrocks, V and Hind, CK and Sutton, JM and Tribe, RM and Mason, AJ},
title = {Metabolism of Lactobacillus and Gardnerella vaginalis in vaginal defined media.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {102991},
doi = {10.1016/j.anaerobe.2025.102991},
pmid = {40850628},
issn = {1095-8274},
abstract = {OBJECTIVES: This study evaluates how well a vaginal defined medium (VDM) replicates the in vivo metabolic behaviour of key vaginal microbiota members - Lactobacillus crispatus, L. jensenii, and diverse Gardnerella vaginalis isolates - compared to brain heart infusion (BHI) medium.

METHODS: We used [1]H NMR spectroscopy to characterise metabolic profiles during in vitro growth of Lactobacillus and Gardnerella species in VDM and BHI. Differences in metabolite production, growth, acidification, and carbohydrate utilisation were assessed.

RESULTS: Both L. crispatus and L. jensenii grow well in VDM, produce substantially more lactate than in BHI, and acidify the culture more strongly - better reflecting the low pH environment of Lactobacillus-dominant vaginal microbiota. In contrast, G. vaginalis grows less robustly in VDM than in BHI, though key metabolic traits such as the Bifidobacterium shunt and mixed acid fermentation (evidenced by formate production) are preserved. Notably, neither genus consume available glucose, yet still ferment carbohydrates, suggesting a metabolic preference for glycogen over glucose. Evidence of glucose release further indicates glycogen breakdown in culture.

CONCLUSIONS: VDM more accurately models the metabolic activity and environmental effects of vaginal Lactobacillus species than BHI, particularly in terms of acidification and lactate production. Although G. vaginalis growth is limited in VDM, its characteristic metabolic pathways remain evident. These findings underscore the value of VDM in modelling key metabolic features of the vaginal microbiota, especially under conditions where Lactobacillus dominate or Gardnerella is prevalent.},
}

@article {pmid40850579,
year = {2025},
author = {Chen, P and Yu, K and Yang, K and Zhang, D and Li, P and He, Y},
title = {Indole-3-acetic acid-mediated root exudates as potential inhibitors of antibiotic resistance genes in the rhizosphere microbiome: Mechanistic insights into microbial community assembly and resistome dissemination.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133191},
doi = {10.1016/j.biortech.2025.133191},
pmid = {40850579},
issn = {1873-2976},
abstract = {Although the threat of antibiotic resistance genes (ARGs) in agriculture to human health has raised concerns, there is still a lack of effective and environmentally friendly measures to mitigate antibiotic resistance. Indole-3-acetic acid (IAA) and root exudates are environmentally friendly natural substances. However, the development of technologies harnessing their potential to suppress agricultural ARGs remains unexplored. Here, IAA-mediated key root exudates, N-acetylserotonin and N-methyltryptamine, were found to effectively reduce ARGs in rhizosphere soil. They affected microbial community assembly and further shaped ARGs profiles. Additionally, they inhibited antibiotic-resistant bacteria, potentially suppressing the vertical transfer of ARGs. More importantly, N-acetylserotonin and N-methyltryptamine inhibited ARGs conjugative transfer through suppressing pili assembly and homologous recombination. Overall, IAA-mediated root exudates reduce ARGs in rhizosphere soil by influencing microbial community assembly and inhibiting ARGs transfer. This study provides inspiration for the development of technologies related to plant auxins and root exudates to reduce ARGs in agriculture.},
}

@article {pmid40850461,
year = {2025},
author = {Wang, H and Lim, JJ and Gu, H and Xia, Z and Cui, JY},
title = {Cadmium-induced gut dysbiosis precedes the onset of hippocampus-dependent learning and memory deficits in mice.},
journal = {Toxicology},
volume = {},
number = {},
pages = {154265},
doi = {10.1016/j.tox.2025.154265},
pmid = {40850461},
issn = {1879-3185},
abstract = {Cadmium (Cd) is a heavy metal recognized as a neurotoxicant, but the detailed mechanisms contributing to its neurotoxicity remain to be fully elucidated. The gut-brain axis-a bidirectional communication pathway between the gut microbiome and the central nervous system-has been implicated in various neurological disorders. Since Cd targets the gut microbiome, it is important to investigate whether this axis contributes to Cd-induced neurotoxicity. In this study, adult male mice were exposed to environmentally relevant levels of Cd (3mg/L) via drinking water for nine weeks. Cognitive function was assessed throughout the exposure period, and fecal samples were collected biweekly to track changes in the gut microbiome. We found that Cd exposure caused gut dysbiosis before the onset of cognitive deficits, with specific bacterial species correlating with impaired cognition. RNA sequencing revealed alterations in the expression of genes involved in cognition and neuroinflammation in the hippocampus. Additionally, Cd exposure reduced the expression of genes related to intestinal barrier integrity, increased levels of inflammatory cytokines, and altered the levels of neuroactive microbial metabolites. These findings suggest a critical role for the gut-brain axis in mediating Cd neurotoxicity and highlight the gut microbiome as a potential target for therapeutic strategies to prevent or mitigate Cd-induced cognitive decline.},
}

@article {pmid40850390,
year = {2025},
author = {Pang, Y and Thomas, ZO and Ayanruoh, LD and Enriquez, GH and Chrisman, LP and Hooper, MJ and Stagaman, E and McCool, M and Achmar No Advanced Degree, D and Rahman No Advanced Degree, S and Seed, PC and Budunova, IV and Green, SJ and Guitart, J and Burns, MB and Zhou, XA},
title = {Skin microbiota differs between Black and White patients with cutaneous T-cell lymphoma.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2025.08.049},
pmid = {40850390},
issn = {1097-6787},
}

@article {pmid40850168,
year = {2025},
author = {Tomassini, L and Goracci, V and Onofri, M and Gambelunghe, C and Fedeli, P and Vanni, N and Guarino, M and Scendoni, R and Lancia, M},
title = {Microbial succession after death: genomic and culture-based insights from external sampling sites in forensic science.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {78},
number = {},
pages = {102685},
doi = {10.1016/j.legalmed.2025.102685},
pmid = {40850168},
issn = {1873-4162},
abstract = {BACKGROUND: Post-mortem microbial communities (microbiota and microbiome) have emerged as promising tools for forensic investigations, particularly in estimating the post-mortem interval (PMI). However, experimental variability in sampling protocols, analytical methods, and reporting standards has limited the comparability and reproducibility of findings across studies.

METHODS: A systematic review was conducted in accordance with PRISMA guidelines to evaluate the current literature on human post-mortem microbiota and microbiome. Inclusion criteria focused on studies that examined microbial communities in human cadavers using culture-based techniques, next-generation sequencing (NGS), or both. Data were extracted regarding sample types, microbial targets, analytical methods, decomposition stages, insect activity, and study objectives.

RESULTS: A total of 24 studies were included, revealing substantial heterogeneity in methodological approaches. NGS techniques dominated recent literature, targeting bacterial 16S rRNA gene sequences to characterize microbial succession during decomposition. While some studies have shown promising correlations between microbial taxa and PMI, the inconsistent use of controls and variable decomposition conditions impeded cross-study comparisons. Culture-based approaches were generally limited to early investigations and provided narrower taxonomic resolution.

CONCLUSIONS: Despite encouraging results, the forensic application of post-mortem microbiome and microbiota remains hindered by methodological inconsistencies and a lack of standardization. Establishing unified protocols and adopting interdisciplinary approaches will be essential for validating microbial signatures as reliable forensic tools.},
}

@article {pmid40850119,
year = {2025},
author = {Ellwood, KM and Kramer, AE and Dutta, A},
title = {Age-driven changes in the layer hen reproductive microbiome are associated with lay performance.},
journal = {Poultry science},
volume = {104},
number = {11},
pages = {105703},
doi = {10.1016/j.psj.2025.105703},
pmid = {40850119},
issn = {1525-3171},
abstract = {Eggs are a globally important food source and integral to optimal poultry production. Understanding the microbial ecology of the hen reproductive tract is essential for improving both food safety and reproductive efficiency. While the oviduct has been shown to harbor a continuous microbial community, this study is the first to demonstrate the presence of microbiota on the hen ovary surface, suggesting that the ovary is an extension of the oviductal microbial continuum. In this study, the ovarian and oviductal microbiomes of white-leghorn hens from mid-lay (high laying) and post-lay (lower laying) cohorts were analyzed. Using 16S rRNA sequencing, we identified significant shifts in reproductive tract microbiota between 9- and 18-month-old hens, coinciding with changes in lay performance. Several differentially abundant genera, including Acinetobacter, Ligilactobacillus, Bacillus, and Akkermansia, are known to modulate steroid hormone metabolism, with age-related abundance changes suggesting potential effects on hormone-driven reproductive processes. Other genera such as Ruminococcus_torques_group, Mucispirillum, and Fusobacterium-not traditionally associated with reproductive hormone pathways-may influence laying efficiency through their roles in mucin degradation, immune modulation, and inflammation. Notably, Turicibacter, newly identified on the ovary, increased with age and negatively correlated with lay performance, raising questions about its role in bile acid metabolism and stress response within the hen reproductive tract. Collectively, these findings highlight the ovary as an active microbial niche influenced by age and suggest that both hormone-associated and mucosal-interactive microbes contribute to lay dynamics. This work opens new avenues for probiotic strategies targeting key genera to support hen fertility and egg production across the productive lifespan.},
}

@article {pmid40850001,
year = {2025},
author = {Huang, X and Hu, L and Sun, W and Shao, Z and Ma, W and Yuan, Q and Liu, J and Wu, D and Cheng, L and Li, H},
title = {Integrative analysis of gut microbiome and serum metabolomics explores the therapeutic mechanism of tongfeng qingxiao prescription in treating gouty arthritis.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {266},
number = {},
pages = {117121},
doi = {10.1016/j.jpba.2025.117121},
pmid = {40850001},
issn = {1873-264X},
abstract = {Gouty arthritis (GA), a metabolic inflammatory disorder, shows increasing global prevalence, especially in China. Conventional GA treatments often cause adverse reactions, necessitating alternative therapies. Tongfeng Qingxiao Prescription (TFQXP) demonstrates clinical efficacy in GA, though its mechanisms remain unclear. This research explored TFQXP's effects in GA rats using gut microbiome and serum metabolomics analyses. Sprague-Dawley rats (n = 36) were randomly divided into six groups: control, model, TFQXP low-dose, medium-dose, high-dose, and positive groups. GA was induced in all groups except the control group and confirmed via gait analysis and infrared thermal imaging. Inflammation was assessed by measuring ankle joint edema. Histopathology evaluated colon and ankle joint tissues, while transmission electron microscopy examined intestinal epithelium. Mucin 2 expression was analyzed via immunohistochemistry. Synovial TLRs/MyD88/NF-κB pathway components were evaluated using western blotting and qRT-PCR. Gut microbiota structure was assessed via 16S rDNA sequencing, while serum metabolites were analyzed using non-targeted metabolomics. Multi-omics correlation analyses explored gut microbiota-serum metabolite relationships. TFQXP appears to mitigate GA-induced synovial and cartilage damage by suppressing the TLRs/MyD88/NF-κB signaling pathway, resulting in downregulation of pro-inflammatory mediators. Furthermore, TFQXP promoted intestinal barrier repair, alleviated dysbiosis, and ameliorated metabolic pathway dysregulation. Thus, TFQXP may exert therapeutic effects on GA by modulating the "gut-joint" axis.},
}

@article {pmid40849910,
year = {2025},
author = {Weis, AM and Bauer, KM and Tang, WW and Stephen-Victor, E and Bell, R and Brown, DG and Ekiz, HA and Tran, V and Klag, KA and Swanson, EA and Barrios, L and Harwood, M and Hill, JH and Ost, KS and Gigic, B and Schneider, M and Ose, J and Hardikar, S and Toriola, AT and Shibata, D and Li, CI and Figueiredo, JC and Byrd, DA and Siegel, EM and Arnolds, K and Lozupone, C and Ulrich, CM and O'Connell, RM and Stephens, WZ and Round, JL},
title = {A capsular polysaccharide from a healthy human microbiota member activates a Lag-3-NK cell axis to restrain colon cancer and augment immunotherapy.},
journal = {Cell reports},
volume = {44},
number = {9},
pages = {116172},
doi = {10.1016/j.celrep.2025.116172},
pmid = {40849910},
issn = {2211-1247},
abstract = {Colorectal cancer (CRC) is increasing globally, making identification of preventative measures necessary. Transplantation of the microbiota from CRC and non-CRC patients into mice demonstrates that non-diseased individuals possess organisms that reduce tumor formation and highlights Bacteriodes uniformis as protective. B. uniformis is reduced in humans with CRC, and proactive treatment with B. uniformis slows tumor growth in mice. Natural killer (NK) cells, but not T cells, are required for B. uniformis-mediated protection. CRC is recalcitrant to immunotherapies; however, addition of B. uniformis restores response to α-CTLA-4 treatment in an NK cell-dependent manner. We report that high Lag-3 expression is associated with greater survival in CRC patients and that B. uniformis-mediated protection is reliant on Lag-3 in innate cells. Induction of NK cell activity and reduced tumor growth is dependent on a specific B. uniformis capsular polysaccharide. Thus, healthy individuals possess tumor suppressor microbes that prevent cancer development and can be harnessed therapeutically.},
}

@article {pmid40849761,
year = {2025},
author = {Mahima, and Mazumder, A and Pentela, B},
title = {Future Directions in Anxiolytic Therapy: A Comprehensive Review of Novel Targets and Strategies.},
journal = {Current neurovascular research},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115672026394052250808075022},
pmid = {40849761},
issn = {1875-5739},
abstract = {BACKGROUND: With 301 million cases worldwide, anxiety disorders represent a serious public health concern. Many people endure ongoing distress while receiving several treatments because of the drawbacks of traditional therapy, such as adverse effects, dependence, and inconsistent efficacy. This emphasizes the absolute need for novel treatment approaches.

OBJECTIVE: This review examines emerging pharmacological and non-pharmacological strategies for anxiety disorders, assessing existing and developing therapeutic options while examining the drawbacks of conventional therapies.

METHODS: A comprehensive literature review was carried out using the NIH, PubMed, and Google Scholar databases. Studies from 2020-2025 were given priority in the inclusion criteria, with a few supporting references from earlier years. Personalized medicine, combination therapy, non-pharmacological interventions, and novel anxiolytic targets, etc., were among the keywords used.

RESULTS: Conventional therapies, including benzodiazepines, SSRIs, and SNRIs, are still the major choices, but they have significant disadvantages. The protein kinase pathway, endocannabinoid and orexin systems, NK1R antagonists, and microbiome modulation are examples of emerging targets. Emerging strategies that show preliminary promise include digital therapeutics, gene therapy, optogenetics, personalized medicine, combination therapy, herbal therapy, and peptide-based medicines (e.g., NPY, NPS, oxytocin analogs, CRF, vasopressin, and melanocortin receptor antagonist). Several of these approaches modulate key neural circuits, such as the involvement of the amygdala-prefrontal cortex axis, via the HPA axis, and biomarker-informed personalization, among others; yet many remain in early-phase or preclinical investigation. However, limited comparative data exist between these novel strategies and standard therapies, underlining the need for rigorous head-to-head evaluations.

CONCLUSION: Advances in molecular neuroscience and precision medicine offer potential alternatives to conventional treatments. However, most emerging therapies require further clinical validation, large-scale trials, and translational refinement before they can be integrated into realworld decision-making for anxiety disorders.},
}

@article {pmid40849659,
year = {2025},
author = {Wang, H and Niu, X and Jin, Z and Zhang, S and Fan, R and Xiao, H and Hu, SS},
title = {Immunotherapy resistance in non-small cell lung cancer: from mechanisms to therapeutic opportunities.},
journal = {Journal of experimental & clinical cancer research : CR},
volume = {44},
number = {1},
pages = {250},
pmid = {40849659},
issn = {1756-9966},
support = {2024ZZ2027//Shanghai Municipal Health Commission Medical New Technology Research and Transformation Seed Program/ ; YG2025LC10//Fundamental Research Funds for the Central Universities of Interdisciplinary Program of Shanghai Jiao Tong University/ ; TMSK-2024-116//Translational Medicine National Major Science and Technology Infrastructure/ ; GWVI-11.2-XD40//Shanghai Municipal Medical and Health Outstanding Academic Leader Program/ ; 2024ZY01013//Guiding grants from the Central Government for Supporting the Development of the Local Science and Technology/ ; 2024ZY01013//Guiding grants from the Central Government for Supporting the Development of the Local Science and Technology/ ; 2024ZY01013//Guiding grants from the Central Government for Supporting the Development of the Local Science and Technology/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology/pathology/drug therapy ; *Immunotherapy/methods ; *Lung Neoplasms/immunology/therapy/pathology/drug therapy ; *Drug Resistance, Neoplasm ; Tumor Microenvironment ; Animals ; },
abstract = {This review provides a comprehensive synthesis of current knowledge on immunotherapy resistance in non-small cell lung cancer (NSCLC), a disease that accounts for approximately 85% of all lung cancer cases and remains the leading cause of cancer-related death worldwide. Although immune checkpoint inhibitors (ICIs) have significantly improved survival for a subset of patients with advanced NSCLC, over 70% of cases ultimately exhibit primary or acquired resistance, underscoring the urgent need to understand the underlying mechanisms. The review categorizes resistance into tumor-intrinsic and tumor-extrinsic processes and provides an in-depth mechanistic analysis of how factors such as tumor antigen loss, impaired antigen presentation, cGAS-STING pathway dysregulation, metabolic reprogramming in tumor microenvironment (TME), immune cell exhaustion, and microbiomes collectively contribute to immune escape. In parallel, the influence of the lung and gut microbiome on shaping immunotherapy responses is discussed, with emphasis on microbial dysbiosis, immunosuppressive metabolite production, and TME remodeling. Therapeutic strategies to overcome resistance are also discussed, including combination approaches involving chemotherapy, radiotherapy, and antiangiogenic agents, as well as epigenetic modulators (HDAC and BET inhibitors). Moreover, the review explores bispecific antibodies, antibody-drug conjugates, and small-molecule agents that enhance T cell function or disrupt immunosuppressive signaling networks. By integrating insights from preclinical models and clinical trials, the review underscores the necessity of biomarker-guided patient stratification, combination immunotherapy approaches, and interventions that restore tumor immunogenicity. It concludes that a multipronged therapeutic strategy, one that addresses both immune evasion and TME-induced suppression, holds the greatest promise for improving response durability and advancing personalized immunotherapy for NSCLC.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/therapy/immunology/pathology/drug therapy
*Immunotherapy/methods
*Lung Neoplasms/immunology/therapy/pathology/drug therapy
*Drug Resistance, Neoplasm
Tumor Microenvironment
Animals

@article {pmid40849632,
year = {2025},
author = {Jang, S and Lee, EJ and Park, S and Lim, H and Ahn, B and Huh, Y and Koh, H and Park, YR},
title = {Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {189},
pmid = {40849632},
issn = {2049-2618},
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory bowel disease involving complex relationships between the gut microbiome and host immune system. However, the spatial relationships between tissue-resident bacteria and host cells in CD pathogenesis remain poorly understood. We developed a spatial host-microbiome profiling approach to simultaneously detect host transcriptomics and bacterial species at high taxonomic resolution in pediatric ileal CD tissues.

RESULTS: In this prospective case-control study, we analyzed 14 terminal ileal tissue samples from six pediatric patients with ileal CD and two controls. Spatial host-microbiome sequencing, combined spatial transcriptomics and in-situ polyadenylation, and bulk shotgun metagenome sequencing were performed. We developed a comprehensive bioinformatics pipeline to identify bacterial species and analyze host-microbiome interactions at cellular resolution, resulting in 13,876 analyzed cells. Our approach revealed increased bacterial abundance in CD tissues compared with controls. The extent of bacterial infiltration at diagnosis correlated with disease prognosis and severity of endoscopic findings. We identified 16 potentially beneficial and nine pathogenic microbiome members in ileal CD, including several newly discovered risk-modulating bacterial species. Cell-type-specific host gene expression analysis revealed transcriptome alterations related to bacterial defense mechanisms in the presence of various bacterial species.

CONCLUSIONS: Our spatial host-microbiome profiling approach enables simultaneous species-level identification of bacteria and host transcriptomics. It reveals the intricate interactions between host cells and bacteria, providing cellular-level insights into CD pathogenesis. Our approach offers a powerful tool for investigating host-microbiome interactions in various microbiome-associated diseases to direct new strategies for microbiome-based therapeutics and prognostic markers. Video Abstract.},
}

@article {pmid40849417,
year = {2025},
author = {Chen, D and Sun, L and Wan, L and Chen, Z and Peng, L and Peng, J and Ouyang, R and Long, X and Du, K and Dong, X and Wu, X and Xiao, X and He, R and Qiu, R and Tang, B and Jiang, H},
title = {Alterations of the skin microbiome in multiple system atrophy: a pilot study.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {257},
pmid = {40849417},
issn = {2373-8057},
support = {2024JJ6493//Natural Science Foundation of Hunan Province/ ; 2024JJ6638//Natural Science Foundation of Hunan Province/ ; 2024JJ3050//Natural Science Foundation of Hunan Province/ ; 82301628//National Natural Science Foundation of China/ ; 82371272//National Natural Science Foundation of China/ ; 82401496//National Natural Science Foundation of China/ ; 82171254//National Natural Science Foundation of China/ ; 2022RC1027//Science and Technology Innovation Program of Hunan Province/ ; GZB20230870//Postdoctoral Fellowship Program of CPSF/ ; 2024M753690//China Postdoctoral Science Foundation/ ; 2021YFA0805200//National Key Research and Development Program of China/ ; R2023047//Major Scientific Research Project for High-level Health Talent in Hunan Province/ ; 2023SK2084//Furong Lab Research Project/ ; 2023QYJC010//Central South University Research Program of Advanced Interdisciplinary Study/ ; },
abstract = {Multiple system atrophy (MSA) alters skin physiology, potentially impacting skin microbiota. This pilot study investigated whether skin microbiota differs in MSA and whether these differences relate to disease severity. Using 16S rRNA sequencing of cervical and axillary sites in MSA, Parkinson's disease, and controls, we identified distinct microbial patterns among groups. These patterns allowed cohort classification and showed strong associations with clinical symptoms, suggesting disease-related microbial alterations in MSA.},
}

@article {pmid40849229,
year = {2025},
author = {Tanabe, N and Matsumoto, H},
title = {From mucus plugging to airway dilatation in chronic airway diseases: A perspective on the contribution of the airway microbiome and inflammation.},
journal = {Allergology international : official journal of the Japanese Society of Allergology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alit.2025.07.003},
pmid = {40849229},
issn = {1440-1592},
abstract = {Airway mucus plugs are the main pathological and computed tomography (CT) findings that affect clinical outcomes in patients with asthma, chronic obstructive pulmonary disease (COPD), and asthma-COPD overlap. Despite the introduction of biologics targeting type 2 inflammation, mucus plug removal remains challenging and understanding its pathogenesis is critical for improved management. In eosinophilic airways, elevated MUC5AC and eosinophil-derived molecules (galectin-10 and extracellular traps) cause highly viscoelastic plugs detectable as high-density regions on ultra-high-resolution CT. In neutrophilic airways, where phylum Proteobacteria and genus Haemophilus are predominant, excessive neutrophil elastase impairs mucociliary clearance, induces neutrophil extracellular traps (NETs), and promotes mucus overproduction. Since mucus plugs could be reservoirs for bacterial colonization, an altered airway microbiome and airway inflammation may be associated with mucus plugging. Phylum Firmicutes and genus Streptococcus are positively and genus Fusobacterium is negatively associated with mucus plugging in severe eosinophilic inflammation. Anaerobic commensals produce short-chain fatty acids, which suppress eosinophilic inflammation. In moderate eosinophilic inflammation, anaerobic commensals may be replaced by pathogenic bacteria of the phylum Proteobacteria and genus Haemophilus, which triggers severe neutrophilic inflammation and exacerbates mucus plugging. Finally, in eosinophilic inflammation, mucus plugs containing aggregated eosinophils may induce mechanical dilation of the airways. In contrast, the presence of mucus plugs in a neutrophilic milieu may reflect severe inflammation characterized by excessive neutrophil extracellular traps and degenerative tissue remodeling, which is consistent with the pathological features of bronchiectasis. This review provides clues regarding how inflammation and microbiome alterations interact with mucus plugging in chronic airway disease.},
}

@article {pmid40849086,
year = {2025},
author = {Gattuso, JJ and Kong, G and Bezcioglu, B and Lu, D and Ekwudo, M and Wilson, C and Gubert, C and Hannan, AJ and Renoir, T},
title = {Chronic psilocybin administration increases sociability and alters the gut microbiome in male wild-type mice but not in a preclinical model of obsessive-compulsive disorder.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {110648},
doi = {10.1016/j.neuropharm.2025.110648},
pmid = {40849086},
issn = {1873-7064},
abstract = {Psilocybin, a serotonergic compound that produces psychedelic effects primarily through activation of the 5-HT2A receptor, has shown promise in treating neuropsychiatric conditions, including obsessive-compulsive disorder (OCD). However, the effects of chronic psilocybin administration on gut function, microbiota, and behavioural phenotypes remain understudied. The present study investigated the impact of chronic psilocybin (0.1 mg/kg and 1 mg/kg, oral gavage) on gut and behavioural measures in wild-type (WT) and SAPAP3 knockout (KO) mice, a model of OCD-like phenotypes. We present novel evidence that SAPAP3 KO mice exhibit social deficits, and that chronic psilocybin increases sociability in male WT mice. Although no therapeutic effects were observed at either dose on anxiety-, compulsive-, or depressive-like behaviour, chronic psilocybin also did not induce psychosis-like behaviours. A dose-dependent effect of psilocybin was observed on gut motility. While chronic administration did not significantly affect overall gut microbiome diversity, reductions in Lactobacillus murinus, Lactobacillus animalis and Alistipes dispar were observed in male WT, but not female, mice. Integrative analysis revealed that a microbial cluster, comprising Lactobacillus and Alistipes species, correlated with locomotion, head twitch response and gut motility, effectively differentiating psilocybin-treated mice from vehicle controls. This suggests a potential host-microbiome feedback mechanism regulating host serotonin signalling, linked to central and peripheral 5-HT2A receptor activation. Additionally, separate microbial clusters were associated with startle response and sociability, indicating that psilocybin may engage distinct neural pathways to mediate these behaviours. These findings highlight the importance of considering the microbiome and sex in future psychedelic research and open new avenues for exploring the microbiota-gut-brain axis as a target for future therapeutic strategies.},
}

@article {pmid40848905,
year = {2025},
author = {Yang, J and Shi, J and Xu, W and Mu, J and Chang, Y and Zhang, X and Wang, X},
title = {Effects of Modified Xuanbai Chengqi Decoction Against Secondary Streptococcus pneumoniae Infection Following Influenza Virus Infection: A Multi-Omics Analysis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120458},
doi = {10.1016/j.jep.2025.120458},
pmid = {40848905},
issn = {1872-7573},
abstract = {The Modified Xuanbai Chengqi Decoction (XBCQ), derived from the classical formula "Xuanbai Chengqi Decoction," is a traditional Chinese herbal preparation. Traditional Chinese Medicine (TCM) is crucial for influenza management. Our previous studies have demonstrated the therapeutic effects of XBCQ on pulmonary and intestinal injuries induced by influenza A virus (IAV)/Streptococcus pneumoniae (SPN) co-infection, although the underlying gut-lung axis mechanisms remain to be further elucidated.

AIM OF THE STUDY: We hypothesize that XBCQ ameliorates secondary SPN infection by modulating the gut-lung axis through microbiota-metabolite-immune interactions, and we will evaluate its protective effects and mechanistic basis against IAV-induced secondary SPN infection through integrated multi-omics analyses (gut microbiota and metabolomics).

MATERIALS AND METHODS: Chemical profiling of XBCQ was performed using ultra-high-performance liquid chromatography coupled with quadrupole-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap-HRMS). A sequential infection model was established by intranasal inoculation of IAV followed by SPN to mimic post-influenza secondary bacterial infection. Therapeutic efficacy was validated through quantification of viral/bacterial loads, histopathological analysis, inflammatory cytokines, and intestinal tight junction (TJ) proteins, demonstrating XBCQ's protective effects on both pulmonary and colonic tissues. 16s RNA sequencing and metabonomics were used to evaluate the mechanism of XBCQ intervention in secondary bacterial infection after influenza.

RESULTS: UHPLC-Q-Orbitrap-HRMS analysis identified 60 bioactive components in XBCQ, including sucrose, adenosine, guanosine, and mulberroside A. XBCQ reduced SPN burden by 81.9%, restored gut microbiota balance, and modulated host metabolic profiles. Correlation analysis revealed that the microbiota altered by XBCQ was significantly associated with pharmacodynamic indicators and metabolites, further confirming the reliability of these findings.

CONCLUSIONS: XBCQ prevents SPN superinfection following IAV infection by modulating the microbiota-gut-lung axis. These findings provide a potential scientific basis for the clinical application of XBCQ, offering prospective guidance for preventing bacterial pneumonia during influenza seasons.},
}

@article {pmid40848874,
year = {2025},
author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Petersen, AM and Holzknecht, BJ and Westh, H and Rosenberg, J},
title = {A prospective cohort study of the rectal microbiome in patients with suspected appendicitis.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102675},
doi = {10.1016/j.clinre.2025.102675},
pmid = {40848874},
issn = {2210-741X},
abstract = {PURPOSE: Diagnosing appendicitis is difficult. An infectious origin has been proposed, therefore signals from the microbiome could be a potential diagnostic measure. The aim was to evaluate the diagnostic potential of the rectal microbiome in patients with suspected appendicitis.

METHODS: We included adult Danish patients with suspected appendicitis undergoing appendectomy in a prospective, observational cohort study. Patients were first grouped as patients with and without appendicitis according to histopathological findings, and second, as having uncomplicated or complicated appendicitis according to the surgical report. Rectal swabs were analysed with shotgun metagenomics. The outcomes were alpha diversity, beta diversity, and differential abundance of bacteria.

RESULTS: Rectal swabs from 220 patients were analysed: 49 patients without appendicitis, 111 patients with uncomplicated and 60 patients with complicated appendicitis, respectively. Across all groups, both the alpha and beta diversity were similar. The relative abundance of bacterial genera and species was also similar across all groups. Thus, the three groups of patients had similar rectal microbiomes.

CONCLUSION: The rectal microbiome in adult patients with suspected appendicitis was similar and does not seem to have the potential to be used to diagnose neither appendicitis nor the severity of appendicitis preoperatively.

TRIAL REGISTRATION: NCT03349814 (clinicaltrials.gov).},
}

@article {pmid40848571,
year = {2025},
author = {Sang, S and Jiang, H and Gan, J and Ke, C},
title = {Microbial community dynamics across salinity gradients in coastal aquifers: Linking hydrogeochemical variability to prokaryotic diversity in a seawater-intruded aquifer of the Pearl River Delta, China.},
journal = {Marine environmental research},
volume = {211},
number = {},
pages = {107471},
doi = {10.1016/j.marenvres.2025.107471},
pmid = {40848571},
issn = {1879-0291},
abstract = {Coastal groundwater salinization driven by seawater intrusion creates dynamic salt-freshwater interfaces with steep biogeochemical gradients. While hydrological changes during seawater intrusion are well characterized, the linkage between hydrogeochemical variability and microbial community structure remains poorly resolved. Here, an integrated approach coupling V4-region 16S rRNA amplicon sequencing (Illumina) with geochemical profiling was employed to decipher prokaryotic diversity dynamics and environmental determinants in a Quaternary aquifer undergoing salinization, Pearl River Delta, China. Proteobacteria dominated bacterial communities across salinity gradients, whereas archaeal assemblages shifted from Thaumarchaeota-dominated freshwater zones to Methanobacteriota-enriched brackish/saline groundwater. High-salinity zones harbored anaerobic functional taxa, including sulfate-reducing Desulfovibrio and methanogenic Methanococcus, confirming active sulfate reduction and methanogenesis in the aquifer-processes critical to carbon and sulfur cycling in coastal groundwater systems. Microbial α-diversity correlated positively with salinity (total dissolved solids, TDS >1 g/L), despite non-linear community shifts along the intrusion path. Vector-based redundancy analysis identified TDS and total nitrogen (TN) as primary drivers of microbial assemblage restructuring (p < 0.01). Our results established salinity as a master regulator of groundwater microbiome composition and function, with direct implications for predicting biogeochemical feedbacks (e.g., methane emissions, sulfide mobilization) in coastal aquifers under climate-driven seawater intrusion. This mechanistic understanding of microbe-environment interactions supports optimized management of contaminated coastal groundwater resources facing salinization threats.},
}

@article {pmid40848430,
year = {2025},
author = {Vaithilingam, P and Seetharaman, B and Achudhan, AB and Mudgal, G and Vasantharekha, R},
title = {Chronic exposure to food additives: Monosodium glutamate and tartrazine dysregulate gut-brain axis in zebrafish model.},
journal = {The Science of the total environment},
volume = {998},
number = {},
pages = {180295},
doi = {10.1016/j.scitotenv.2025.180295},
pmid = {40848430},
issn = {1879-1026},
abstract = {The commonly used food additives to enhance color and flavor are Monosodium glutamate and Tartrazine. The effects of both were investigated on chronic exposure of over 30 days to adult zebrafish, in four groups: control, tartazine (31,844 ppm), monosodium glutamate (10.9 × 10[3] ppm), and a combined exposure group (monosodium glutamate+tartazine = 5450 ppm + 15,922 ppm), with 10 fish per group in triplicates. Neurobehavioral tests, acetylcholinesterase (AChE) activity, metabolic enzyme assays, and quantification of serotonin and cortisol levels were performed. DNA was extracted from zebrafish gut samples for gut microbiota analysis. Zebrafish exposed to monosodium glutamate and tartazine showed a statistically significant reduction in social interaction, mirror biting, and preference for familiar and novel objects. The combined exposure group showed increased anxiety, spent more time in light zones, and increased transition movements. Tartazine exposure elevated AChE activity and serotonin levels, and monosodium glutamate exposure increased cortisol. Disruptions in cortisol and serotonin levels, with increased AChE activity, were linked to stress, mood swings, memory deficits, and cognitive impairment. Gut microbiota analysis revealed a higher abundance of Actinobacteria, and increased Enterobacter indicates inflammation in the gut of treatment groups. Chronic consumption of monosodium glutamate and tartazine may disrupt metabolic processes, induce obesity, and impair cognitive functions, indicating potential health risks associated with these additives.},
}

@article {pmid40848419,
year = {2025},
author = {Jeong, SH and Jung, J and Park, YJ and Lee, SJ and Lee, SJ},
title = {The Influence of polycyclic aromatic hydrocarbons exposure on the gut microbiome composition and inflammatory responses.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118910},
doi = {10.1016/j.ecoenv.2025.118910},
pmid = {40848419},
issn = {1090-2414},
abstract = {Particulate matter (PM) is recognized as a contributor to various gastrointestinal diseases, including inflammatory bowel disease. However, the specific impact of polycyclic aromatic hydrocarbons (PAHs), a major component of PM, on microbial community dynamics and immune regulation remains unexplored. In this study, we investigated the effects of PAHs on the inflammatory response of mouse intestinal tissues and microbiota composition using PAHs extracted from PM10 (PM10_PAHs). With increasing duration of exposure to PM10_PAHs, damage to the colonic mucosa and lung tissues was aggravated and the secretion of inflammatory cytokines increased. The composition of the gut microbiota was also significantly altered, with a decrease in Firmicutes and an increase in Bacteroidetes at the phylum level, along with an increase in Lactobacillus, Clostridium, and Romboutsia at the genus level. Notably, despite the cessation of PM10_PAHs administration and the recovery of gut microbial diversity, the microbiota composition and inflammatory cytokine levels did not return to pre-exposure conditions. These results suggest that exposure to PM can have lasting adverse health effects, such as inflammation induced by its main component, PAHs.},
}

@article {pmid40848192,
year = {2025},
author = {Parker, G and Russo, N},
title = {Antibiomania: An update.},
journal = {Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists},
volume = {},
number = {},
pages = {10398562251370946},
doi = {10.1177/10398562251370946},
pmid = {40848192},
issn = {1440-1665},
abstract = {BackgroundAntibiomania, whereby an antibiotic induces a manic/hypomanic episode in those with or without a pre-existing bipolar condition, is a little-known phenomenon, diagnostically elusive, may be more prevalent than recognised and thus warrants the current overview.MethodRepresentative studies and clinical observations are noted.ResultsSeveral mechanistic issues are considered but with a weighting to the antibiotic causing gut dysbiosis and so activating gut-brain axis pathways that may induce manic/hypomanic episodes.ConclusionFuture studies should seek to determine the prevalence of antibiomania and whether differing antibiotics effect differential risks, while clinicians identifying such a potential linkage in a patient who has developed a first episode or recurrence of a manic/hypomanic episode should consider nuanced pre-emptive and management strategies in such instances.},
}

@article {pmid40848105,
year = {2025},
author = {Proskynitopoulos, PJ and Woltemate, S and Rhein, M and Böke, I and Molks, J and Schröder, S and Schneider, HU and Bleich, S and Frieling, H and Geffers, R and Glahn, A and Vital, M},
title = {The effect of alcohol withdrawal therapy on gut microbiota in alcohol use disorder and its link to inflammation and craving.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70128},
pmid = {40848105},
issn = {2993-7175},
support = {//Hetzler Foundation for Addiction Research and Prevention/ ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) is linked to changes in the function and composition of the human gut microbiome (GM). The GM affects inflammation by producing anti-inflammatory molecules such as short-chain fatty acids (SCFA), in particular butyrate, which are linked to appetite regulation, a mechanism involved in alcohol craving. This study investigates changes in GM composition and functional capacity to produce SCFA during alcohol withdrawal and their link to inflammation and craving.

METHODS: Sixty-three patients (mean age 48, SD = 12) with AUD were enrolled. We collected stool (n = 63) and blood (n = 48) during the first 48 h (timepoint A) of withdrawal therapy and between Days 10-14 (timepoint B). Microbiota were analyzed using shotgun metagenomics along with bacterial load determinations. TNF-α, IL-6, IL-8, and IL-10 were measured in plasma.

RESULTS: Bacterial diversity (species richness, Shannon Index) did not change significantly throughout withdrawal, while overall bacterial load increased. Abundances of several taxa changed, and the overall community composition during withdrawal was approaching those of healthy controls; the potential to synthesize butyrate, a key SCFA, increased. However, it remained at lower levels compared with controls. Both diversity parameters correlated with cell concentrations and the butyrate pathway at baseline. The latter was negatively associated with IL-6 at baseline. IL-8 and IL-10 levels decreased significantly during withdrawal, as did craving, which was linked to abundance alterations of six species and IL-8.

CONCLUSIONS: Alcohol withdrawal affected GM composition and increased concentration of the butyrate pathway along with overall bacterial load. Changes in bacterial composition and the butyrate production capacity demonstrate a shift toward healthier microbiota during withdrawal therapy. Changes in some species and IL-8 were linked to alcohol craving, replicating findings of previous studies. Our study adds new findings helping to understand the microbiome-gut-brain axis.},
}

@article {pmid40848087,
year = {2025},
author = {Shamsuzzaman, M and Dahal, RH and Choi, YJ and Kim, S and Kim, J},
title = {Segatella intestinalis sp. nov., and Parabacteroides caeci sp. nov., novel potential probiotics from the human gut microbiome.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {136},
pmid = {40848087},
issn = {1572-9699},
mesh = {Humans ; Phylogeny ; *Gastrointestinal Microbiome ; *Probiotics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Bacteroidetes/classification/isolation & purification/genetics/physiology ; Fatty Acids/analysis ; Base Composition ; DNA, Bacterial/genetics ; Republic of Korea ; Bacterial Typing Techniques ; },
abstract = {Two bacterial strains, B2-R-102[T] and W1-Q-101[T], were isolated from the feces of a healthy Korean individual. These strains were Gram-stain negative, anaerobic, and non-motile, growing optimally between 20 and 40 °C and at pH 5.5-8.0. Importantly, they survived at pH 2.0 and tolerated 0.3% bile salts and pepsin after a 4 h exposure. The strains demonstrated in vitro antioxidant activity, inhibiting DPPH radicals by 48.12 ± 1.45 and 70.80 ± 12.8%, respectively. Furthermore, they inhibited α-amylase activity by 46.52 ± 4.42 to 60.84 ± 2.20%, compared to 74.82 ± 0.76% inhibition by sitagliptin. In vitro, anti-inflammatory assays revealed 57.77 ± 3.15 to 62.39 ± 2.23% inhibition of albumin protein denaturation, comparable to aspirin 72 ± 2.39% inhibition. The abundant cellular fatty acids were C15:0, C16:0, iso-C15:0, C18:1ω9c, anteiso-C15:0 and iso-C17:0 3-OH. Neither strain exhibited haemolytic activity, and genomic analysis revealed no acquired antibiotic resistance or virulence genes. Phylogenetic analysis showed that B2-R-102[T] and W1-Q-101[T] belonged to the genera Segatella and Parabacteroides, with 96.9 and 97.7% 16S rRNA gene sequence similarities to Segatella copri CB7[T] and Parabacteroides goldsteinii DSM 19448[T], respectively. Furthermore, biosynthetic gene cluster analysis revealed the potential for antimicrobial thiopeptides, lanthipeptides, and non-ribosomal peptides (NRPs). In silico average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the thresholds to distinguish novel species. Based on phenotypic, genomic, and phylogenetic analysis, we propose the names Segatella intestinalis sp. nov. (type strain B2-R-102[T] = CGMCC 1.17963[T] = KCTC 25417[T]) and Parabacteroides caeci sp. nov. (type strain W1-Q-101[T] = KCTC 25456[T] = CGMCC 1.17991[T]).},
}

Humans
Phylogeny
*Gastrointestinal Microbiome
*Probiotics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Bacteroidetes/classification/isolation & purification/genetics/physiology
Fatty Acids/analysis
Base Composition
DNA, Bacterial/genetics
Republic of Korea
Bacterial Typing Techniques

@article {pmid40847749,
year = {2025},
author = {Mu, C and Rho, JM and Shearer, J},
title = {The Interplay between the Gut and Ketogenic Diets in Health and Disease.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04249},
doi = {10.1002/advs.202504249},
pmid = {40847749},
issn = {2198-3844},
support = {RGPIN-2018-04238//Natural Sciences and Engineering Research Council of Canada (JS)/ ; },
abstract = {The gut plays a central role in translating dietary signals into systemic health effects, making it a key mediator of the ketogenic diet (KD), a high fat, low carbohydrate regimen. This review synthesizes current knowledge on the interaction between the KD and the gut, emphasizing gut-mediated mechanisms as an interface between dietary interventions and systemic health outcomes, spanning gastrointestinal to neurological health. Topics address gut physiology (gut digestion and absorption, epithelial nutrient sensing, gut motility), intestinal immunity (covering innate, adaptive, and antiviral responses), and extracellular to intracellular processes (i.e. mitochondrial function, stem cell fate, and intestinal circadian rhythm). Special focus is given to the gut microbiome, including both bacterial and fungal communities and how the KD modulates them in conditions such as epilepsy, obesity, traumatic brain injury, and multiple sclerosis. Innovative methods for tailoring the KD, including the use of alternative formulations, ketone esters, and microbiome-focused interventions such as prebiotics and probiotics are examined. Strategies to maximize the diet's benefits while reducing potential side effects are considered. Together, these insights herein offer a comprehensive framework for understanding the interactions between the KD and the gut, a prerequisite for optimizing the overall health benefits of metabolism-based treatments.},
}

@article {pmid40847462,
year = {2025},
author = {Ma, H and Wang, M and Feng, Y and Zhang, W and Wang, W and Xie, Y and Kong, G and Feng, J and Wang, P and Wang, Q and Huang, X},
title = {Microbial profile of the appendix niche in acute appendicitis: a novel sampling approach.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70105},
pmid = {40847462},
issn = {2211-5463},
support = {GSWSKY2020-50//Gansu Provincial Health Commission, Provincial Health Industry Research Project/ ; 20240050058//Lanzhou University Student Innovation and Entrepreneurship Action Plan Project/ ; CY2023-QN-B17//Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University in 2023/ ; },
abstract = {Relatively little is known about the microbial variations within the human appendix niche. To overcome this knowledge gap, we employed endoscopic retrograde appendicitis treatment (ERAT) technology to collect microbial samples from the appendix lumen, followed by shotgun metagenomic sequencing on participants with acute appendicitis without antibiotic treatment. Compared to the cecum and terminal ileum, the appendix had a higher abundance at the genus level of Sphingobium, Leptotrichia and Oribacterium, as well as a significant increase in species-level abundance of oral bacteria, including Streptococcus sanguinis, Streptococcus australis, Streptococcus sp. A12, Leptotrichia sp. oral taxon 215, Veillonella dispar, Veillonella infantium and Oribacterium sinus. Pearson correlation analysis showed that bacterial species abundant in the appendix, such as Acinetobacter johnsonii, Sphingobium yanoikuyae and Agrobacterium tumefaciens, had negative correlations with the top five most abundant Gene Ontology (GO) categories (molecular function, biological process and cellular component). Conversely, species underrepresented in the appendix, including Mogibacterium diversum, Streptococcus sanguinis, Megasphaera micronuciformis and Actinomyces graevenitzii, had significant positive correlations with these GO categories. Our results show that ERAT technology can be used to improve sampling and microbiome profiling in the appendix. Furthermore, this in-depth microbial characterization could inform clinicians during antibiotic prescription. However, further large sample size studies are required to validate these results.},
}

@article {pmid40847238,
year = {2025},
author = {Zugman, M and Jaime-Casas, S and Zang, PD and Shah, K and Nguyen, CB},
title = {Immunotherapy in Renal Cell Carcinoma.},
journal = {Cancer treatment and research},
volume = {129},
number = {},
pages = {293-308},
pmid = {40847238},
issn = {0927-3042},
mesh = {Humans ; *Carcinoma, Renal Cell/therapy/immunology/drug therapy ; *Kidney Neoplasms/therapy/immunology/drug therapy/pathology ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {There have been tremendous advancements in immunotherapy approaches for patients with renal cell carcinoma (RCC) from the initial interleukin-2 era to the current immune checkpoint inhibitor (ICI) combinations. Several ICI-based therapies have greatly improved outcomes for patients with RCC with the potential for durable responses for a subset of patients. In this chapter, we review the data of key frontline ICI-based combinations for RCC in the metastatic setting and recent data on adjuvant immunotherapy. We also discuss recent data on the role of immunotherapy rechallenge following prior ICI treatment as well as emerging novel immunotherapy strategies with chimeric antigen receptor (CAR) T and gut microbiome interventions. Lastly, we highlight a multidisciplinary team-based approach for patients with RCC treated with ICI including management of immune-related adverse events as well as potential role of cytoreductive nephrectomy in an evolving treatment landscape.},
}

Humans
*Carcinoma, Renal Cell/therapy/immunology/drug therapy
*Kidney Neoplasms/therapy/immunology/drug therapy/pathology
*Immunotherapy/methods
*Immune Checkpoint Inhibitors/therapeutic use

@article {pmid40847229,
year = {2025},
author = {Duesberg, M and LeVee, A and Chang, H and Tsai, K and Crossman, B and Tadi, M and Xu, S and Wheeler, D and Kang, I},
title = {Breast Cancer Immunotherapy: A Team Science Approach.},
journal = {Cancer treatment and research},
volume = {129},
number = {},
pages = {67-82},
pmid = {40847229},
issn = {0927-3042},
mesh = {Humans ; Female ; *Immunotherapy/methods ; *Breast Neoplasms/therapy/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Triple Negative Breast Neoplasms/immunology/therapy/drug therapy ; },
abstract = {Immunotherapy has reshaped the treatment landscape of several malignancies, including breast cancer. While historically considered less immunogenic, breast cancer-particularly the triple-negative subtype (TNBC)-has demonstrated responsiveness to immune checkpoint inhibitors (ICIs). TNBC is characterized by higher tumor mutational burden, elevated PD-L1 expression, and increased tumor-infiltrating lymphocytes, making it a leading focus of immunotherapy development. In metastatic TNBC with PD-L1 expression, trials such as KEYNOTE-355 have shown improvements in progression-free and overall survival with the addition of the ICI, pembrolizumab to chemotherapy, leading to regulatory approval. In early-stage TNBC, KEYNOTE-522 established a neoadjuvant chemotherapy plus ICI as the standard of care for stage II and III tumors. This was based on improved pathologic complete response and event-free survival in this pivotal clinical trial regardless of PD-L1 expression. ICIs in other subtypes, such as HER2-positive and hormone receptor-positive/HER2-negative disease, remain under active investigation. Ongoing studies are also exploring novel strategies including dual immune checkpoint blockade, cellular therapies (e.g., CAR-T, TILs), cancer vaccines, and rational combinations with targeted agents and antibody-drug conjugates (ADCs). Biomarkers such as PD-L1, tumor mutational burden, immune gene signatures, and the gut microbiome are being evaluated to refine patient selection and predict response. Additionally, effective management of immune-related toxicities is critical, particularly in curative-intent settings. As the role of immunotherapy expands, a multidisciplinary, biomarker-driven approach will be essential to optimize outcomes and broaden its applicability across breast cancer subtypes.},
}

Humans
Female
*Immunotherapy/methods
*Breast Neoplasms/therapy/immunology
*Immune Checkpoint Inhibitors/therapeutic use
*Triple Negative Breast Neoplasms/immunology/therapy/drug therapy

@article {pmid40847065,
year = {2025},
author = {Al Masri, MT and Ali, AS and Vijayan, R and Muzaffar, SB and Al-Deeb, MA},
title = {Microbiome variation between male and female Hyalomma dromedarii ticks from camels in the UAE.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30990},
pmid = {40847065},
issn = {2045-2322},
support = {G00003718//United Arab Emirates University/ ; G00003718//United Arab Emirates University/ ; },
abstract = {Hyalomma dromedarii, a predominant camel tick species in the Arabian Peninsula, plays a significant role in pathogen transmission, yet its sex-specific microbiome composition remains poorly understood. This study analyzed the bacterial communities of male and female H. dromedarii ticks collected from camels across three locations in the United Arab Emirates: Al Khazna, Al Ja'ae, and Al Jabeeb. High throughput 16S rRNA gene sequencing revealed a total of 432,495 reads clustering into 848 operational taxonomic units, encompassing 20 phyla and 261 genera. Male ticks consistently exhibited higher microbial diversity and genus richness compared to females. Notably, Francisella dominated the female microbiome, accounting for over 90% of sequences in Al Ja'ae and Al Jabeeb, while males displayed a more balanced microbial profile, with genera such as Corynebacterium, Staphylococcus, and Trueperella being prevalent. Pearson's correlation and principal coordinate analyses (PCoA) indicated distinct sex-based microbial associations and clustering patterns. These findings underscore sex-associated disparities in the microbiome of H. dromedarii, suggesting potential implications for tick physiology and vector competence within the One Health framework.},
}

@article {pmid40847054,
year = {2025},
author = {Wagner, KS and Salasc, F and Marten, SM and Roth, O},
title = {Paternal microbiota manipulation influences offspring microbial colonization and development in a sex role-reversed pipefish.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30911},
pmid = {40847054},
issn = {2045-2322},
abstract = {Microbes are acquired through vertical and environmental horizontal transmission. Vertical transmission is directly linked to reproductive success and entails early transmission, facilitating coexistence of host and microbes over generations. The multiple potentially interacting routes of vertical transmission are challenging to be disentangled in conventional sex-role species, as they are mostly intermingled on the maternal side, i.e., through egg production, pregnancy, birth and postnatal care. The evolution of male pregnancy in syngnathids (pipefishes and seahorses) offers an opportunity to separate vertical microbial provisioning through the egg (maternal) from provisioning through pregnancy (paternal). We experimentally evaluated the existence and role of paternal vertical microbiota provisioning through male pregnancy on offspring development and microbial colonization. Male pipefish were exposed to antibiotics, and subsequently recolonized with bacteria of paternal, maternal, and environmental origin (spike treatment). After pregnancy, the microbiota of developing offspring was characterized using 16 S rRNA sequencing of the V3-V4 region. Paternal antibiotic and spike treatments influenced the microbial composition of the brood pouch and offspring microbiome development. Paternal spike treatment shortened pregnancy duration and enhanced offspring survival, underlining its beneficial effect for early life stages. Expanding on how distinct vertical microbial transmission routes shape the offspring microbiome will foster our understanding of holobiont function in health and disease.},
}

@article {pmid40846900,
year = {2025},
author = {Karta, J and Meyers, M and Rodriguez, F and Koncina, E and Gilson, C and Klein, E and Gabola, M and Benzarti, M and Pérez Escriva, P and Molina Tijeras, JA and Correia Tavares Bernardino, C and Ponath, F and Carpentier, A and Pujabet, MA and Schmoetten, M and Tsenkova, M and Saoud, P and Gaigneaux, A and Ternes, D and Alonso, L and Zügel, N and Willemssen, E and Koppes, P and Léonard, D and Casanova, LP and Haan, S and Mittelbronn, M and Meiser, J and Pozdeev, VI and Vogel, J and Nuciforo, PG and Wilmes, P and Letellier, E},
title = {Fusobacterium nucleatum interacts with cancer-associated fibroblasts to promote colorectal cancer.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40846900},
issn = {1460-2075},
support = {CORE/C16/BM/11282028//Fonds National de la Recherche Luxembourg (FNR)/ ; CORE/C20/BM/14591557//Fonds National de la Recherche Luxembourg (FNR)/ ; CORE/C15/BM/10404093//Fonds National de la Recherche Luxembourg (FNR)/ ; PoC/18/12554295//Fonds National de la Recherche Luxembourg (FNR)/ ; AFR 17103240//Fonds National de la Recherche Luxembourg (FNR)/ ; CORE/C21/BM/15718879//Fonds National de la Recherche Luxembourg (FNR)/ ; PRIDE17/11823097//Fonds National de la Recherche Luxembourg (FNR)/ ; FNR matched funding scheme,MFP20/15251414/MelCol PFP//Fonds National de la Recherche Luxembourg (FNR)/ ; PRIDE21/16763386//Fonds National de la Recherche Luxembourg (FNR)/ ; Internal Research Project at the University of Luxembourg,MiDiCa//Université du Luxembourg (University of Luxembourg)/ ; Télévie,7.4565.21 and 7.6603.02//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; Télévie,7.4560.22//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; Télévie,7.4552.23//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; Fondation du Pélican de Mie and Pierre Hippert-Faber//Fondation de Luxembourg/ ; SFB 1583/1,Project number: 492620490,Subproject A09//Deutsche Forschungsgemeinschaft (DFG)/ ; C17937/A29070/CRUK_/Cancer Research UK/United Kingdom ; PI20/00889//Fondo de Investigaciones Sanitarias (FIS)/ ; MMADRILEÑA/PREMI/2020CCAA_NUCIFORO//Instituto de Salud Carlos III (ISCIII) and Fundación Mutua Madrileña/ ; P500PB_214405/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {Gut microbial species contribute to colorectal cancer (CRC) by interacting with tumor or immune cells, however if CRC-associated bacteria engage with stromal components of the tumor microenvironment remains unclear. Here, we report interaction between the CRC-associated bacterium Fusobacterium nucleatum and cancer-associated fibroblasts (CAFs), and show that F. nucleatum is present in the stromal compartment in murine CRC models in vivo and can attach to and invade CAFs. F. nucleatum-exposed CAFs exhibit a pronounced inflammatory-CAF (iCAF) phenotype, marked by elevated expression of established iCAF markers, secretion of pro-inflammatory cytokines such as CXCL1, IL-6 and IL-8, generation of reactive oxygen species (ROS), and an increased metabolic activity. In co-culture experiments, the interaction of cancer cells with F. nucleatum-stimulated CAFs enhances invasion, a finding further validated in vivo. Altogether, our results point to a role for the tumor microbiome in CRC progression by remodeling the tumor microenvironment through its influence on cancer-associated fibroblasts, suggesting novel therapeutic strategies for targeting CRC.},
}

@article {pmid40846880,
year = {2025},
author = {Kotrbová, L and Grabicová, K and Švecová, H and Staňová, AV and Petrlíková, M and Grabic, R and Kodešová, R and Chroňáková, A},
title = {The effect of WWTP products amendments on Phaseolus vulgaris rhizosphere and its ability to inactivate clarithromycin.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30950},
pmid = {40846880},
issn = {2045-2322},
support = {QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; 063/2023/P//Grantová agentura Jihočeské univerzity v Českých Budějovicích/ ; },
mesh = {*Rhizosphere ; *Phaseolus/microbiology/drug effects/growth & development ; *Clarithromycin/pharmacology/metabolism ; Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Wastewater/chemistry ; Phylogeny ; Microbiota/drug effects ; },
abstract = {With increasing efforts to reuse wastewater treatment plant (WWTP) products in agriculture, assessing their impact on soil-plant systems is crucial, while the effects of accompanying antibiotic residues on soil microbial communities have not yet been adequately studied. This study focuses on clarithromycin (CLR), highly present in wastewater, and investigates the CLR-degradation potential of plant-associated microorganisms. Phaseolus vulgaris plants were grown in raised beds filled with Haplic Cambisol and amended with or without WWTP products (treated wastewater, biosolid, or composted biosolid), as a source of CLR residues. The rhizosphere microbiomes after biosolid amendments was significantly enriched by Pseudomonadaceae as assessed by 16S rRNA metagenomics and cultures enriched by CLR revealed dominance of Proteobacteria. However, no degradation of CLR by microbial consortia or enrichment cultures was observed, suggesting the multiplication of CLR-resistant bacteria with other resistance mechanisms. Cultivation-based approach combined with antibiotic modulation assays and subsequent LC-MS analysis confirmed the complete CLR removal by seven phylogenetic groups of actinomycetes in vitro. The proportion of isolates indicated that the rhizosphere is a natural reservoir for CLR-inactivating microorganisms; however, the amendment of soils with WWTP products can significantly increase their abundance and diversity.},
}

*Rhizosphere
*Phaseolus/microbiology/drug effects/growth & development
*Clarithromycin/pharmacology/metabolism
Soil Microbiology
*Anti-Bacterial Agents/pharmacology
RNA, Ribosomal, 16S/genetics
*Wastewater/chemistry
Phylogeny
Microbiota/drug effects

@article {pmid40846855,
year = {2025},
author = {Zhang, M and Wang, X and Yao, H and Shen, Y and Teng, Y and Garber, PA and Pan, H and Li, M},
title = {Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {169},
pmid = {40846855},
issn = {2055-5008},
support = {32330015, 31821001//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Diet ; *Colobinae/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; },
abstract = {The effects of seasonal fluctuations in food availability on gut microbiome composition, diversity, and function present significant challenges to animals with hard-to-digest diets. Here, we investigate seasonal variation the gut microbiome of wild golden snub-nosed monkeys (Rhinopithecus roxellana), a foregut fermenting primate, using metagenomics and metatranscriptomics data. We reconstructed 578 metagenome-assembled genomes (MAGs), 76.5% of which did not have exact matches in reference databases, highlighting the novelty of their gut microbiota. The gut microbiome of wild golden snub-nosed monkeys exhibited high diversity and enrichment in plant secondary compound metabolism during summer, while in winter it was enriched with enzymes that function in lichen polysaccharide degradation and Lachnospiraceae, which is important for energy balance. Captive monkeys on a consistent diet showed minimal seasonal variation in gut microbiome composition. Habitat changes also affected golden snub-nosed monkey microbiota community assembly and carbon cycling pathways. These findings underscore the gut microbiome's plasticity in meeting host dietary needs under varying environmental conditions.},
}

Animals
*Seasons
*Gastrointestinal Microbiome
*Diet
*Colobinae/microbiology
Metagenomics
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology

@article {pmid40846748,
year = {2025},
author = {Ge, Y and Liu, L and Wu, L and Liu, X and Hao, Y and Wang, S and Xiong, Y and Yang, Z and Zhang, Z and Li, Q and Li, B and Wu, J and Ren, G and Jiang, Q},
title = {Impaired nutrient absorption, reduced bone mass and alterations in the gut microbiome contribute to postnatal growth retardation in a mouse model of MWS.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30890},
pmid = {40846748},
issn = {2045-2322},
support = {JCYJ-2023-04//Research Foundation of Capital Institute of Pediatrics/ ; CXYJ-2021-05//Research Foundation of Capital Institute of Pediatrics/ ; 82400215//National Natural Science Foundation of China/ ; 82370522, 82070532//National Natural Science Foundation of China/ ; PX2022054//Beijing Municipal Administration of Hospitals Incubating Program/ ; PX2020054//Beijing Municipal Administration of Hospitals Incubating Program/ ; 2021RU015//Research Unit of Minimally Invasive Pediatric Surgery on Diagnosis and Treatment, Chinese Academy of Medical Sciences/ ; CIP2024-0040//Beijing Finance Bureau/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Disease Models, Animal ; Zinc Finger E-box Binding Homeobox 2/genetics/metabolism ; Dysbiosis ; Haploinsufficiency ; Bone and Bones/pathology ; *Intestinal Absorption ; *Nutrients/metabolism ; *Hirschsprung Disease/microbiology/genetics/metabolism/pathology ; Bone Density ; Male ; *Growth Disorders ; },
abstract = {Mowat‒Wilson syndrome (MWS), a rare genetic disorder caused by heterozygous loss-of-function mutations in ZEB2, is characterised by significant growth retardation with unclear mechanisms. In this study, we developed a Zeb2 haploinsufficient (Zeb2[+/-]) mouse model that recapitulates key features of MWS, including reduced body weight, impaired intestinal development and skeletal hypoplasia. RNA sequencing revealed significant downregulation of nutrient digestion and absorption pathways in the duodenum of Zeb2[+/-] mice, which was associated with reduced body fat and bone mass loss. Additionally, Zeb2[+/-] mice presented severe gut microbiota dysbiosis, as indicated by the depletion of beneficial Actinobacteria and Bifidobacterium and increases in the abundances of the proinflammatory Proteobacteria and Rikenella. These microbial shifts correlated with impaired intestinal development and key growth indicators. Our findings delineate a pathological cascade wherein Zeb2 haploinsufficiency disrupts nutrient absorption and bone homeostasis, while concomitant dysbiosis likely exacerbates intestinal dysfunction, collectively driving growth retardation. The model we developed can provide a platform for exploring therapeutic interventions targeting nutritional support and microbiome modulation in MWS.},
}

Animals
*Gastrointestinal Microbiome
Mice
Disease Models, Animal
Zinc Finger E-box Binding Homeobox 2/genetics/metabolism
Dysbiosis
Haploinsufficiency
Bone and Bones/pathology
*Intestinal Absorption
*Nutrients/metabolism
*Hirschsprung Disease/microbiology/genetics/metabolism/pathology
Bone Density
Male
*Growth Disorders

@article {pmid40846688,
year = {2025},
author = {Ding, SQ and Lei, Y and Zhao, ZM and Li, XY and Lang, JX and Zhang, JK and Li, YS and Zhang, CD and Dai, DQ},
title = {Crosstalk Between Microbiome and Ferroptosis in Diseases: From Mechanism to Therapy.},
journal = {Comprehensive Physiology},
volume = {15},
number = {4},
pages = {e70042},
doi = {10.1002/cph4.70042},
pmid = {40846688},
issn = {2040-4603},
support = {81972322//National Natural Science Foundation of China/ ; JYTMS20230108//Scientific Study Project for Institutes of Higher Learning, Ministry of Education, Liaoning Province/ ; RXXM202302//Young Backbone Talents of China Medical University/ ; 2023-MS-163//Liaoning Provincial Natural Science Foundation/ ; },
mesh = {*Ferroptosis/physiology ; Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Iron/metabolism ; Dysbiosis/metabolism ; Reactive Oxygen Species/metabolism ; *Microbiota/physiology ; Lipid Peroxidation ; },
abstract = {The human microbiome is a unique organ and maintains host immunomodulation and nutrient metabolism. Structural and functional microbiome alterations are commonly known as dysbiosis, which is strongly associated with disease progression. Ferroptosis is a novel iron-dependent cell death mode characterized by intracellular iron accumulation, increased reactive oxygen species (ROS), and lipid peroxidation (LPO). Importantly, the complex crosstalk between the microbiome and ferroptosis in disease has attracted considerable research attention. The microbiome influences ferroptosis by regulating host iron homeostasis, mitochondrial metabolism, and LPO, among many other pathways. Thus, the in-depth analysis of microbiome-ferroptosis crosstalk and associated mechanisms could provide new strategies to treat human diseases. Therefore, understanding this crosstalk is critical. Here, we systematically explore the associations between gut microbiome and ferroptosis across multiple diseases. We show that the oral microbiome also influences disease progression by regulating ferroptosis. Furthermore, we provide a potential for certain disease therapies by targeting the crosstalk between the microbiome and ferroptosis.},
}

*Ferroptosis/physiology
Humans
*Gastrointestinal Microbiome/physiology
Animals
Iron/metabolism
Dysbiosis/metabolism
Reactive Oxygen Species/metabolism
*Microbiota/physiology
Lipid Peroxidation

@article {pmid40846661,
year = {2025},
author = {Qin, Q and Zhu, Y and Yang, L and Guo, R and Song, L and Wang, D and Li, W},
title = {Oral microbiome between patients with non-obstructive and obstructive hypertrophic cardiomyopathy.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {40846661},
issn = {2542-5641},
abstract = {BACKGROUND: The profile and clinical significance of the oral microbiome in patients with non-obstructive hypertrophic cardiomyopathy (noHCM) and obstructive hypertrophic cardiomyopathy (oHCM) remain unexplored. The objective of this study was to evaluate the difference of oral microbiome between noHCM and oHCM patients.

METHODS: This cross-sectional study enrolled 18 noHCM patients and 26 oHCM patients from Fuwai Hospital, Chinese Academy of Medical Sciences between 2020 and 2021. Clinical and periodontal evaluations were conducted, and subgingival plaque samples were collected. Metagenomic sequencing and subsequent microbial composition and functional analyses were performed.

RESULTS: Compared to oHCM patients, those with noHCM had higher systolic blood pressure (138.1 ± 18.8 mmHg vs. 124.2 ± 13.8 mmHg, P = 0.007), a larger body circumference (neck circumference: 39.2 ± 4.0 cm vs. 35.1 ± 3.7 cm, P = 0.001; waist circumference: 99.7 ± 10.5 cm vs. 92.2 ± 10.8 cm, P = 0.027; hip circumference: 102.5 ± 5.6 cm vs. 97.5 ± 9.1 cm, P = 0.030), a greater left ventricular end-diastolic diameter (46.6 ± 4.9 mm vs. 43.1 ± 4.9 mm, P = 0.026), and a lower left ventricular ejection fraction (64.1 ± 5.7 % vs. 68.5 ± 7.8%, P = 0.048). While overall biodiversity and general microbial composition were similar between the noHCM and oHCM groups, ten taxa displayed significant differences at the genus and species levels, with Porphyromonas gingivalis showing the highest abundance and greater enrichment in noHCM (relative abundance: 7.79535 vs. 4.87697, P = 0.043). Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis identified ten distinct pathways, with pathways related to energy and amino acid metabolism being enriched in oHCM patients, and those associated with genetic information processing less abundant in the oHCM group. Metabolic potential analysis revealed ten significantly altered metabolites primarily associated with amino sugar and nucleotide sugar metabolism, porphyrin metabolism, pentose and glucuronate interconversion, and lysine degradation.

CONCLUSIONS: The higher abundance of Porphyromonas gingivalis, which is known to impact cardiovascular health, in noHCM patients may partially account for clinical differences between the groups. Pathway enrichment and metabolic potential analyses suggest microbial functional shifts between noHCM and oHCM patients, potentially reflecting inherent metabolic changes in HCM.},
}