@article {pmid41203044,
year = {2025},
author = {Jagwani, S and Musumeci, L and Flores, L and Mackenzie, GG and Amiji, MM},
title = {Strategic modulation of the gastrointestinal microbiome to enhance pancreatic cancer immunotherapy.},
journal = {Drug discovery today},
volume = {},
number = {},
pages = {104528},
doi = {10.1016/j.drudis.2025.104528},
pmid = {41203044},
issn = {1878-5832},
abstract = {Pancreatic cancer (PC) remains one of the most lethal malignancies, characterized by aggressive progression, late detection, and limited response to current therapies. Recent research has revealed that the gastrointestinal and intratumoral microbiomes are key modulators of immune regulation, metabolism, and epigenetic pathways, influencing tumor progression and therapeutic efficacy. This review summarizes the complex microbiome-PC interplay, emphasizing microbial modulation of inflammation, immunity, and treatment resistance. We also highlight microbiome-targeted strategies, such as probiotics, prebiotics, postbiotics, and fecal microbiota transplantation, along with advanced drug-delivery platforms - including nanoparticles, engineered bacteria, and stimuli-responsive systems - for precise microbiome modulation. Integrating microbiome science with immunotherapy, nanotechnology, and epigenetic reprogramming offers promising opportunities to improve outcomes in PC.},
}

@article {pmid41203008,
year = {2025},
author = {Wang, Y and Hernandez, E and Junejo, MH and Damsky, W},
title = {Granuloma Annulare Patients Treated with JAK Inhibitors Show Cutibacterium acnes Expansion: A clue to the Mechanism Underlying Acneiform Eruptions Seen with JAK Inhibitors.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.10.600},
pmid = {41203008},
issn = {1523-1747},
}

@article {pmid41203007,
year = {2025},
author = {Li, H and Wang, X and Zhang, X and Mu, H and Hao, R and Li, Y and Liu, Q and Chi, R and Zhai, D},
title = {Disrupted Microbiome-Metabolome Networks Underlie Gut Barrier and Immune Imbalance in Severe Fever with Thrombocytopenia Syndrome.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105586},
doi = {10.1016/j.micinf.2025.105586},
pmid = {41203007},
issn = {1769-714X},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening tick-borne viral infection with a high mortality rate and limited treatment options. While gastrointestinal symptoms are common, the contribution of gut microbiome disruption to disease progression remains unclear. Previous studies have noted taxonomic shifts in SFTS-associated microbiota, but their functional and metabolic consequences have not been systematically characterized. We conducted an integrated metagenomic and metabolomic analysis of fecal samples from 20 SFTS patients and 20 healthy controls. At the time of admission, patients with SFTS exhibited acute-stage infection, characterized by symptoms such as fever, thrombocytopenia, and gastrointestinal disturbances. Metagenomic sequencing was used to assess the microbial gene content, taxonomic composition, and functional potential. Untargeted metabolomics analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to profile fecal metabolites. The SFTS patients showed a significantly reduced microbial gene richness, alpha diversity, and compositional stability. Short-chain fatty acid (SCFA)-producing genera (e.g., Faecalibacterium and Roseburia) were depleted, while mucin-degrading and opportunistic taxa (e.g., Pseudomonas and Akkermansia) were enriched. Functionally, biosynthetic and homeostatic pathways were suppressed; while stress-adaptive, biofilm-forming, and virulence-associated pathways were elevated. Metabolomic profiling revealed depletion of anti-inflammatory metabolites (e.g., bile acids and curcumin sulfate) and enrichment of proinflammatory compounds (e.g., porphyrins and beta-tyvelose). Multi-omic correlation highlighted strong links between microbial disruption and altered metabolite production. In conclusion, SFTS is associated with significant alterations in the gut microbiome and its metabolic profile, which is characterized by the loss of beneficial microbial taxa and functions, alongside the emergence of virulence factors and stress-related signatures. These findings underscore the role of microbiome dysfunction in SFTS and suggest that microbiota-targeted strategies may offer supportive benefits, particularly in alleviating SFTS-associated gastrointestinal disturbances and secondary microbial imbalance.},
}

@article {pmid41202947,
year = {2025},
author = {Olsen, T and Elshorbagy, A and Johnson, JE and Nichenametla, SN and Dong, Z and Sambamurti, K and Richie, JP and Vinknes, KJ},
title = {Sulfur amino acids, metabolic health and beyond: Recent advances, translational implications, and future research considerations.},
journal = {Analytical biochemistry},
volume = {},
number = {},
pages = {116008},
doi = {10.1016/j.ab.2025.116008},
pmid = {41202947},
issn = {1096-0309},
abstract = {Dietary restriction of the sulfur amino acids methionine and cysteine (sulfur amino acid restriction [SAAR]) is a well-established paradigm for delaying disease onset and the aging process in several experimental models. In vivo, SAAR's anti-aging effects appear to be mediated by decreased growth hormone/insulin-like growth factor-1 (GH/IGF-1) signaling, along with improvement in insulin sensitivity and overall metabolic health. SAAR-fed animals also exhibit reduced regional and total adiposity, as well as oxidative stress and inflammation. Recent studies suggest that SAAR improves cognition, induces significant changes in gut microbiome composition, and that its benefits may depend on the age at which the intervention begins. In humans, observational studies have shown that higher plasma total cysteine levels are positively correlated with adiposity, insulin resistance, and an increased incidence of diabetes. Likewise, high dietary methionine and cysteine intake has been linked to increased risk of cardiovascular disease and diabetes-related mortality. Human dietary intervention studies have only been partly successful in translating the benefits of SAAR, and practical challenges for implementation remain to be addressed. This review summarizes recent advances in the SAAR field and discusses its translational potential for promoting metabolic health and reducing the risk of age-related diseases.},
}

@article {pmid41202881,
year = {2025},
author = {Hasan, MN and Wang, H and Luo, W and Du, Y and Xiong, L and Gu, L and Li, T},
title = {A Gly-β-muricholic acid and FGF15 combination therapy synergistically reduces "humanized" bile acid pool toxicity in cholestasis mice.},
journal = {Journal of lipid research},
volume = {},
number = {},
pages = {100936},
doi = {10.1016/j.jlr.2025.100936},
pmid = {41202881},
issn = {1539-7262},
abstract = {Hydrophobic bile acid-mediated hepatobiliary injury is a major driver of cholestasis progression. Most anti-cholestasis treatments being tested clinically are based on a single agent, which does not always sufficiently alleviate bile acid toxicity to slow disease progression. This study investigates a therapeutic strategy of combining glycine-conjugated β muricholic acid (Gly-βMCA) and fibroblast growth factor-15 (FGF15) to alleviate bile acid hepatobiliary toxicity in Cyp2c70 KO mice that lack endogenous muricholic acid (MCA) synthesis and have a "humanized" hydrophobic bile acid pool composition. The effects of the single and combination treatments on bile acid metabolism, liver injury, and gut microbiome were investigated in female Cyp2c70 KO mice with progressive cholangiopathy and portal fibrosis. While all three treatments significantly reduced biochemical and histologic features of liver injury, the Gly-βMCA and FGF15 combination achieved a remarkably higher reduction in both bile acid pool size and hydrophobicity than either single treatment. Mechanistically, this resulted from synergistically increased biliary hydrophilic MCA species derived from Gly-βMCA, inhibited intestine endogenous bile acid absorption by Gly-βMCA, and repressed cholesterol 7α-hydroxylase (CYP7A1) by FGF15, which counteracted the undesirable farnesoid x receptor (FXR) antagonism activity of Gly-βMCA. Furthermore, a hydrophobic bile acid pool in Cyp2c70 KO mice was associated with markedly reduced beneficial Lactobacillaceae family bacteria abundance, which was enriched by Gly-βMCA and the combination treatments. In conclusion, the Gly-βMCA and FGF15 combination shows enhanced efficacy in decreasing humanized bile acid pool size and hydrophobicity and holds potential as a therapeutic strategy to decrease bile acid burden in cholestasis.},
}

@article {pmid41202606,
year = {2025},
author = {Li, Y and Xiao, H and Liu, L and Jiang, F and Yu, E},
title = {Multi-omics reveals the mechanism of environmental concentration of microcystin-LR-induced muscle damage and nutrient loss and the role of gut-muscle axis in Nile tilapia.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119352},
doi = {10.1016/j.ecoenv.2025.119352},
pmid = {41202606},
issn = {1090-2414},
abstract = {Microcystin-LR (MC-LR), a prevalent and highly potent cyanobacterial toxin, is generated during the outbreaks of these blooms. Despite its prevalence, there is a scarcity of information regarding the chronic effects and underlying molecular mechanisms of MC-LR at environmentally relevant concentrations on muscular toxicity in fish. Hence, we assessed the muscular toxicity of chronic MC-LR exposure via histological and biochemical analyses and delved into the underpinning mechanisms via holistic multi-omics approaches of gut microbiome, serum metabolome, muscle transcriptome and metabolome in Nile tilapia. After 60 days of MC-LR exposure, 30 μg/L MC-LR exposure significantly triggered muscular toxicity, as illustrated by decreased nutrient value, reduced myofiber diameter and sarcomere length, and diffuse dissolution of myofibrils. Transcriptomic and metabolomic analyses of muscle revealed that MC-LR exposure altered antioxidant status, protein turnover, amino acid metabolism, nucleotide synthesis and breakdown, and lipid metabolism regulation, leading to oxidative stress, inflammation response, apoptosis, decreased protein deposition and inhibited myofiber growth of Nile tilapia. Furthermore, MC-LR exposure perturbed the intestinal microbiota composition and compromised the integrity of the intestinal barrier, resulting in increased toxicity-related metabolites such as lipopolysaccharide (LPS), phenol and phenylacetic acid entering the muscle through the bloodstream, promoting muscle injury. These results provided new insight into the underlying biomolecular mechanisms and potential roles of the gut-muscle axis in MC-LR-induced muscular toxicity in aquatic animals.},
}

@article {pmid41202528,
year = {2025},
author = {Hu, X and Wu, M and Zhao, B and Xu, T and Jia, Z and Zhao, X},
title = {Construction of a succession model for the microbiome in water from submerged corpses based on single-molecule real-time sequencing.},
journal = {Forensic science international. Genetics},
volume = {81},
number = {},
pages = {103378},
doi = {10.1016/j.fsigen.2025.103378},
pmid = {41202528},
issn = {1878-0326},
abstract = {Decomposition of corpses in aquatic environments is regulated by multiple factors, and traditional methods for estimating the postmortem submerged interval (PMSI) have clear limitations. To explore the microbial succession patterns in the water of submerged corpses and their potential application in PMSI estimation, this study submerged rat carcasses in both river water and tap water, collecting water samples on days 0, 2, 6, 9, 14, 20, 27, 40, 54, and 70 postmortem. The microbial succession dynamics in the water were analyzed using single-molecule real-time sequencing. The results indicated that, although the response patterns to decomposition differed between the two water sources, key microorganisms common to various decomposition stages were identified, suggesting their important role in the process. This study characterized the microbial community succession trajectory at the species level and identified several species with potential for PMSI indication. Based on this, we constructed a simple random forest prediction model. During the 70-day decomposition period, the mean absolute errors (MAE) of the river water model and the tap water model were 5.8745 days and 4.8599 days, respectively. This research elucidates the microbial community succession patterns induced by corpse submersion in water, constructs a methodological framework for PMSI estimation based on water microbiomes, and provides crucial support for the development of more versatile PMSI inference models.},
}

@article {pmid41202150,
year = {2025},
author = {Champagne-Jorgensen, K and Gommerman, JL},
title = {Two of a kind, one with MS: Gut microbes tip the balance.},
journal = {Science immunology},
volume = {10},
number = {113},
pages = {eaed4910},
doi = {10.1126/sciimmunol.aed4910},
pmid = {41202150},
issn = {2470-9468},
mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; Animals ; *Multiple Sclerosis/immunology/microbiology ; Mice ; Fecal Microbiota Transplantation ; },
abstract = {An MS twin study links ileal Lachnospiraceae to spontaneous CNS autoimmunity in mice receiving a human microbiome transplant.},
}

*Gastrointestinal Microbiome/immunology
Humans
Animals
*Multiple Sclerosis/immunology/microbiology
Mice
Fecal Microbiota Transplantation

@article {pmid41202107,
year = {2025},
author = {Pérez-Trejo, A and Aguirre-Macedo, ML and Banaszak, AT and García-Maldonado, JQ},
title = {Differentiation of the bacterial communities associated with Orbicella faveolata across different growth conditions and life-cycle stages.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335445},
doi = {10.1371/journal.pone.0335445},
pmid = {41202107},
issn = {1932-6203},
mesh = {Animals ; *Microbiota/genetics ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Anthozoa/microbiology/growth & development ; *Life Cycle Stages ; Phylogeny ; High-Throughput Nucleotide Sequencing ; },
abstract = {The coral microbiome can strongly influence coral health, development, and resilience. While larval settlement is fundamental for coral restoration efforts using assisted larval propagation, post-settlement survival remains a major challenge. The study of lab-bred Orbicella faveolata settlers (LBOFS) microbiome has been proposed due to its potential role in coral adaptation processes. However, there is limited information about LBOFS bacterial communities and comparisons between different growth conditions and life-cycle stages have not been conducted. Using 16S rRNA high-throughput sequencing, we analyzed the structure and composition of LBOFS-associated bacteria and compared them to those from outplanted LBOFS and wild settlers. We also compared the microbiomes of settlers to adult colonies. The LBOFS bacterial community was composed of 4224 ASVs with the Orders Kiloniellales, Rhodobacterales, Cytophagales, Cyanobacteriales, and Flavobacteriales being the most abundant across the samples, with a rare biosphere consisting of 44.6% relative abundance. A Principal Coordinates Analysis and a PERMANOVA indicated significantly different bacterial community structures based on settler growth conditions and life-cycle stage. Linear discriminant analysis Effect Size analysis identified specific taxa whose differential abundances contributed to the observed differences. For settler growth conditions, the differences were mainly due to the Order Cyanobacteriales for LBOFS, SAR202 clade for outplanted settlers, and Microtrichales for wild samples. Statistical analysis of functional prediction showed significant differences only in nitrogen fixation for LBOFS. For life-cycle stage, LEfSe revealed that the Orders Cytophagales and Cyanobacteriales exhibited the highest differential abundances in adults and settlers, respectively. Functional prediction revealed that nitrogen fixation and oxygenic photoautotrophy were more enriched in settlers, whereas nitrate reduction and anaerobic chemoheterotrophy were more enriched in adults. This study highlighted the bacterial taxa and predicted metabolic processes that could potentially contribute to coral settler functioning, providing a valuable baseline for future research to enhance their survival rates using probiotics.},
}

Animals
*Microbiota/genetics
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
*Anthozoa/microbiology/growth & development
*Life Cycle Stages
Phylogeny
High-Throughput Nucleotide Sequencing

@article {pmid41202104,
year = {2025},
author = {Huang, Y and Tang, T and Dai, X and Sun, F},
title = {Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations.},
journal = {PLoS computational biology},
volume = {21},
number = {11},
pages = {e1013691},
doi = {10.1371/journal.pcbi.1013691},
pmid = {41202104},
issn = {1553-7358},
abstract = {Understanding microbial interactions is fundamental for exploring population dynamics, particularly in microbial communities where interactions affect stability and host health. Generalized Lotka-Volterra (gLV) models have been widely used to investigate system dynamics but depend on absolute abundance data, which are often unavailable in microbiome studies. To address this limitation, we introduce an iterative Lotka-Volterra (iLV) model, a novel framework tailored for compositional data that leverages relative abundances and iterative refinements for parameter estimation. The iLV model features two key innovations: an adaptation of the gLV framework to compositional constraints and an iterative optimization strategy combining linear approximations with nonlinear refinements to enhance parameter estimation accuracy. Using simulations and real-world datasets, we demonstrate that iLV surpasses existing methodologies, such as the compositional LV (cLV) and the generalized LV (gLV) model, in recovering interaction coefficients and predicting species trajectories under varying noise levels and temporal resolutions. Applications to the lynx-hare predator-prey, Stylonychia pustula-P. caudatum mixed culture, and cheese microbial systems revealed consistency between predicted and observed relative abundances showcasing its accuracy and robustness. In summary, the iLV model bridges theoretical gLV models and practical compositional data analysis, offering a robust framework to infer microbial interactions and predict community dynamics using relative abundance data, with significant potential for advancing microbial research.},
}

@article {pmid41201920,
year = {2025},
author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ},
title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.},
journal = {Neoplasia (New York, N.Y.)},
volume = {70},
number = {},
pages = {101245},
doi = {10.1016/j.neo.2025.101245},
pmid = {41201920},
issn = {1476-5586},
mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; },
abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.},
}

*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology
Animals
*Gastrointestinal Microbiome
Mice
*Tumor Microenvironment/genetics
Humans
*Diet
*Gene Expression Regulation, Neoplastic
Disease Models, Animal
Age Factors
Male
*Aging

@article {pmid41201910,
year = {2025},
author = {Kulal, R and Touseef Khan, M and Bhaskarrao Borse, B and Peddha, MS},
title = {Effect of encapsulated spice oleoresins on chronic unpredictable mild stress-induced depression and gut microbiome modulation in mice model.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/1028415X.2025.2582520},
pmid = {41201910},
issn = {1476-8305},
abstract = {Depression affects millions globally, prompting the search for novel treatments. Natural compounds like spice oleoresins show promise due to their bioactive constituents. This study explores the use of Hydroxypropyl-beta-cyclodextrin (HPBCD) for nano-encapsulation to enhance the efficacy of pepper, turmeric, and chilli oleoresins in alleviating depression in a mice model. Chronic unpredictable mild stress (CUMS) was induced for 28 days, followed by administering nano-encapsulated oleoresins (25 mg/kg). Behavioural analyses revealed improved activity, while neurochemical studies showed increased serotonin and dopamine levels with reduced monoamine oxidase (MAO) activity. Western blot highlighted changes in BDNF, supported by histopathological evidence of neuroprotection. Biochemical assays indicated reduced oxidative stress, acetylcholinesterase activity, and enhanced catalase and superoxide dismutase levels. 16S rRNA sequencing revealed improved gut microbiota, with increased beneficial bacteria. Notably, nano-encapsulated chilli oleoresin exhibited the highest efficacy. These findings support the multi-targeted potential of nano-encapsulated spice oleoresins as complementary treatments for depression, addressing neurobiological and gut-related factors.},
}

@article {pmid41201906,
year = {2025},
author = {Gao, Y and Zhu, T and Zhang, Z and Hu, H and Wang, Q and Liu, H and Xiong, L},
title = {Characterization of a Cold-Active Xylanase from Paenibacillus sp. XP01, and Its Application in Hydrolyzing Alkali-Pretreated Corncob Residues.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08788},
pmid = {41201906},
issn = {1520-5118},
abstract = {Xylan, a key hemicellulose in agricultural byproducts, is significantly underutilized in biorefineries. The human gut microbiome, with its diverse enzymes, holds great potential for biocatalyst discovery. In this study, Paenibacillus sp. XP01, a xylan-degrading strain, was isolated from human feces. Genomic analysis identified a GH11 endo-β-1,4-xylanase, designated Xyn157, which exhibited a cold-active property. It retained 47% residual activity at 0 °C and 72% at 4 °C. It also exhibited catalytic activity against insoluble xylan in corncob. Enzymatic profiling confirmed its endoacting mode, with xylotriose as the minimum substrate and branched chains impairing efficiency. Xyn157 hydrolyzed alkali-pretreated corncob residues (ACR) to produce xylo-oligosaccharide (XOS), with a yield of 6.4% (w/w). In vitro fermentation of Xyn157-treated ACR, which produced hydrolysis products of ACR (CRH), significantly promoted the growth of beneficial bacteria (e.g., Bifidobacterium, Ligilactobacillus), suppressed pathogens (e.g., Enterobacter and Klebsiella), and boosted short-chain fatty acid (SCFA) production compared to the ACR group. These findings highlight Xyn157's potential to convert insoluble xylan in ACR into functional prebiotics, expanding its applications in waste-to-prebiotic bioprocessing.},
}

@article {pmid41201826,
year = {2025},
author = {Sorger, Z and Sengupta, P and Beier-Heuchert, K and Bautor, J and Parker, JE and Kemen, E and Doehlemann, G},
title = {GH25 lysozyme mediates tripartite interkingdom interactions and microbial competition on the plant leaf surface.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {45},
pages = {e2510124122},
doi = {10.1073/pnas.2510124122},
pmid = {41201826},
issn = {1091-6490},
support = {390686111//Deutsche Forschungsgemeinschaft (DFG)/ ; DECRyPT//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Arabidopsis/microbiology ; *Muramidase/metabolism/genetics ; *Plant Leaves/microbiology ; Plant Diseases/microbiology ; Microbiota ; Oomycetes ; },
abstract = {Microbial communities inhabiting plants have emerged as crucial factors in regulating plant health and defense against disease-causing pathogens. The yeast Moesziomyces bullatus ex. Albugo (MbA) on Arabidopsis produces a glycoside hydrolase 25 (GH25) protein that regulates the leaf microbiome by antagonizing the pathogenic oomycete Albugo laibachii. Applying MbA or GH25 rescued Arabidopsis thaliana shoot fresh weight under A. laibachii infection, highlighting their crop protection potential. Interaction assays revealed no antagonistic activity of GH25 against other plant pathogenic oomycetes or fungi besides A. laibachii. We identified a community of bacteria closely associated with A. laibachii. Three of these bacteria are inhibited by GH25 and one of them, Curtobacterium sp. could override the inhibition of A. laibachii by MbA. This points to a tripartite antagonism where Curtobacterium and A. laibachii protect each other from MbA. Moreover, Curtobacterium selectively inhibits other A. laibachii-associated bacteria not targeted by MbA but that themselves suppress A. laibachii. This study uncovers an interkingdom network where GH25 lysozyme shapes microbial interactions between yeast, oomycete, and associated bacteria.},
}

*Arabidopsis/microbiology
*Muramidase/metabolism/genetics
*Plant Leaves/microbiology
Plant Diseases/microbiology
Microbiota
Oomycetes

@article {pmid41201785,
year = {2025},
author = {Baker, SG and Morton, CO and Green, H},
title = {The impact of freezing temperatures on soft tissue and microbial decomposition using human and porcine remains: a pilot study.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
pmid = {41201785},
issn = {1556-2891},
abstract = {Environmental factors such as temperature, vertebrate and invertebrate activity and microbial succession patterns are important variables driving the decomposition process. However, the effects of low temperatures, specifically freezing on how a body decomposes are less understood. This pilot project aimed to determine the taphonomic effects of freezing on morphological changes during decomposition and the microbiome in an Australian context. Two human donors (one frozen, one non-frozen) and two frozen and two non-frozen Sus scrofa (pig) carcasses (n = 4) were allowed to decompose on the surface of woodlands for 12-weeks during summer 2017. Visual morphological changes were recorded, and microbial swabs were collected at regular intervals and analysed via real-time PCR to assess differences in bacterial community structure. Results indicated clear differences in decomposition patterns between frozen and non-frozen remains. Frozen remains were slow to enter 'early' decomposition but first to skeletonise. Microbial results suggest that patterns in community structure between bacteria may indicate if a body has been frozen at or around the time of death. This research suggests that quantifying the microbiome present during the fresh and early stages of decomposition and noting observations of an outside-in decomposition pattern may be a useful tool in identifying if remains have experienced extreme cold temperatures at the time of death. This knowledge could improve approaches to PMI estimation, particularly if the remains have experienced a freeze-thaw event after death.},
}

@article {pmid41201733,
year = {2025},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41201733},
issn = {1439-0973},
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}

@article {pmid41201719,
year = {2025},
author = {Gautam, P and Vishwakarma, RK and Nath, M and Nath, G and Pathak, A},
title = {Microbiota Dysbiosis in Amyotrophic Lateral Sclerosis: A Systematic Review of Human Studies.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {10},
pmid = {41201719},
issn = {1559-1182},
mesh = {*Amyotrophic Lateral Sclerosis/microbiology/complications ; Humans ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome/physiology ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron degeneration. Despite intensive research, its pathogenesis remains poorly understood. Recent insights suggest a pivotal role of the gut microbiota in modulating neuroinflammation and neurodegeneration via the gut-brain axis. This systematic review aims to synthesize clinical evidence on gut microbiota dysbiosis in ALS, exploring microbial and metabolic alterations and their associations with disease progression and severity. A comprehensive literature search was conducted across PubMed, Embase, Scopus, Web of Science, and other databases up to May 10, 2024, adhering to PRISMA 2020 guidelines. Eighteen eligible human studies were selected based on predefined inclusion criteria. Data on microbial diversity, taxonomic shifts, metabolite profiles, and clinical correlations were extracted and assessed using a modified Newcastle-Ottawa Scale. Most studies reported altered microbial diversity, reduced butyrate-producing bacteria (e.g., Faecalibacterium, Roseburia), and increased pro-inflammatory taxa (e.g., Escherichia coli, Bacteroides) in ALS. Integrated microbiome-metabolome analyses revealed disruptions in SCFAs, bile acids, and lipid metabolism, some correlating with ALSFRS-R scores and cognitive impairment. Although some studies showed minimal or no differences, the overall evidence supports a link between dysbiosis and ALS pathophysiology. Probiotic trials demonstrated limited efficacy, highlighting the need for targeted, patient-specific interventions. Gut microbiota dysbiosis is increasingly recognized as a contributor to ALS progression. However, methodological variability, small sample sizes, and limited longitudinal data restrict definitive conclusions. Future research should employ standardized, multi-omics approaches and larger cohorts to clarify causal links and develop microbiome-informed diagnostics and therapies for ALS.},
}

*Amyotrophic Lateral Sclerosis/microbiology/complications
Humans
*Dysbiosis/microbiology/complications
*Gastrointestinal Microbiome/physiology

@article {pmid41201258,
year = {2025},
author = {Zhang, Y and Wang, M and Sun, Y and Gao, H and Su, X},
title = {Function inference of million-scale microbiomes using multi-GPU acceleration.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0207225},
doi = {10.1128/spectrum.02072-25},
pmid = {41201258},
issn = {2165-0497},
abstract = {Amplicon sequencing enables taxonomic profiling of microbial communities but offers limited insight into their functional potential. Existing tools such as Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) infer functions through phylogenetic placement and ancestral state reconstruction; however, these methods are computationally intensive and inefficient for large-scale data sets. To address these challenges, we introduce microbiome graphics processing unit (GPU)-based function inference (MGFunc), an ultra-high-throughput framework for microbiome functional inference leveraging multi-GPU acceleration. MGFunc transforms functional prediction for amplicons into standardized matrix multiplication using a pre-constructed genomic content network. It further integrates split data loading, matrix partition, and dynamic scheduling across multiple GPUs, enabling scalable, batch-wise analysis of millions of samples under limited GPU memory and system random access memory (RAM). Compared to PICRUSt2, MGFunc achieves speedups of up to several hundred thousand times, completing the functional interpretation of one million samples within one minute by four GPUs on a single server. This work provides a highly efficient and low-latency solution for ultra-large microbiome data sets functional inference, paving the way for global-scale microbiome studies. The MGFunc software is freely accessible at https://github.com/qdu-bioinfo/MGFunc.IMPORTANCEUnderstanding what microbes do-their functions-is essential for studying health, disease, agriculture, and the environment. While cost-effective sequencing methods like 16S rRNA gene analysis are widely used, they do not directly reveal microbial functions. Existing tools that predict these functions from 16S data are often too slow for today's large studies involving hundreds of thousands of samples. In this work, we developed microbiome graphics processing unit (GPU)-based function inference (MGFunc), a new method that predicts microbial functions quickly and accurately by using GPUs and a streamlined mathematical approach. MGFunc can analyze over one million samples in under a minute, making it one of the fastest tools available. This enables researchers to study the functional potential of microbial communities on a truly global and population scale.},
}

@article {pmid41201243,
year = {2025},
author = {Nash, J and Tremble, K and Schadt, C and Cregger, MA and Bryan, C and Vilgalys, R},
title = {Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0028525},
doi = {10.1128/msystems.00285-25},
pmid = {41201243},
issn = {2379-5077},
abstract = {UNLABELLED: The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen (Populus tremuloides) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller "active core" subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere.

IMPORTANCE: Members of the rhizosphere exhibit dynamic patterns of activity and dormancy. This study stresses the need to focus on active microbial communities to detect temporal changes in plant microbiomes. Additionally, the metabolic activity of microbes should be considered a key determinant of core microbiome membership. Parallel patterns in active community dynamics between fungal and bacterial communities provide a potentially generalizable rule of microbial community temporal dynamics in plant rhizospheres.},
}

@article {pmid41201238,
year = {2025},
author = {Rees, NP and Conway, J and Dugan, B and Amir, SS and Parker, A and Carding, SR and Duggal, NA},
title = {Defining Microbiota-Derived Metabolite Butyrate as a Senomorphic: Therapeutic Potential in the Age-Related T Cell Senescence.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70257},
doi = {10.1111/acel.70257},
pmid = {41201238},
issn = {1474-9726},
abstract = {Advancing age is accompanied by an accumulation of senescent T cells that secrete pro-inflammatory senescence-associated secretory phenotype (SASP) molecules. Gut-microbiota-derived signals are increasingly recognised as immunomodulators. In the current study, we demonstrated that ageing and the accumulation of senescent T cells are accompanied by a reduction in microbial-derived short-chain fatty acids (SCFAs). Culturing aged T cells in the presence of butyrate suppresses the induction of a senescence phenotype and inhibits the secretion of pro-inflammatory SASP factors, such as IL6 and IL8. Administration of faecal supernatants from young mice rich in butyrate prevented in vivo accumulation of senescent spleen cells in aged mice. The molecular pathways governing butyrate's senomorphic potential include a reduced expression of DNA damage markers, lower mitochondrial ROS accumulation, and downregulation of mTOR activation, which negatively regulates the transcription factor NFκB. Our findings establish butyrate as a potent senomorphic agent and provide the evidence base for future microbiome restitution intervention trials using butyrate supplements for combating T cell senescence, ultimately reducing inflammation and combating age-related pathologies to extend lifelong health.},
}

@article {pmid41201223,
year = {2025},
author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q},
title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {37069},
doi = {10.31083/IJVNR37069},
pmid = {41201223},
issn = {0300-9831},
support = {2019YFF0301702//National Key R&D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration & dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; },
abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.

METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.

RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 ± 0.76 kg; LDG: -2.40 ± 0.67 kg), body fat percentage (HDG: -1.87 ± 0.69; LDG: -1.49 ± 0.45), cortisol (HDG: -6.79 ± 4.26 μg/dL; LDG: -4.5 ± 4.84 μg/dL), maximum power (HDG: 27.16 ± 9.77 W; LDG: 14.50 ± 9.43 W), maximal oxygen uptake (HDG: 8.78 ± 0.97; LDG: 6.90 ± 1.37), and half-court triangle run times (HDG: -0.48 ± 0.36 s; LDG: -0.25 ± 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 ± 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.

CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.},
}

Humans
Male
*Gastrointestinal Microbiome/drug effects
*Basketball/physiology
*Athletic Performance/physiology
Young Adult
*Dietary Fiber/administration & dosage
Adolescent
*Dietary Supplements
Adult
Body Composition
Athletes
Universities

@article {pmid41201222,
year = {2025},
author = {Zheng, Y and Gao, Z and Sun, L and Shi, J and Song, J and Ye, W},
title = {Calcium and Gastrointestinal Disorders: Mechanistic Insights and Therapeutic Interventions.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {39241},
doi = {10.31083/IJVNR39241},
pmid = {41201222},
issn = {0300-9831},
support = {ZA CACM 2024002//Clinical Research Project of the China Association of ChineseMedicine/ ; 2020SJZDXK13//Health Commission of Zhejiang Chinese Medical University Hangzhou Hospital of Traditional Chinese Medical/ ; },
mesh = {Humans ; *Gastrointestinal Diseases/drug therapy/therapy/metabolism/microbiology ; *Calcium/metabolism ; Gastrointestinal Microbiome ; Receptors, Calcium-Sensing/metabolism ; Dietary Supplements ; *Calcium, Dietary/administration & dosage ; Hypocalcemia ; },
abstract = {Calcium plays a central role in gastrointestinal (GI) physiology through regulating smooth muscle contractility, acid secretion, epithelial barrier integrity, and immune signaling. The dysregulation of calcium homeostasis has been increasingly implicated in the pathogenesis of GI disorders, including colorectal cancer, inflammatory bowel disease, peptic ulcer, and pancreatitis. Specifically, aberrant calcium-sensing receptor (CaSR) signaling has emerged as a critical molecular mechanism in colorectal tumorigenesis; meanwhile, calcium-mediated pathways influence gastric acid production and intestinal motility. This review critically evaluated recent advances in calcium signaling within the GI tract, highlighting the crosstalk involved with the gut microbiota and the roles of downstream effectors, including transient receptor potential vanilloid type 6 and store-operated calcium entry. This review also examined the therapeutic implications of calcium supplementation across various GI conditions, including bioavailability challenges under different disease states and nutrient interactions involving vitamin D and phosphate. Our review further addresses the role of calcium in mucosal immunity, the clinical relevance of hypocalcemia in GI diseases, and the potential of microbiome-guided nutritional interventions. However, despite growing mechanistic insights, considerable gaps remain in understanding host-microbiota-calcium interactions, genotype-specific responses to calcium, and long-term clinical outcomes. Thus, future research should clarify the dose-response relationships, stratify patient populations by CaSR polymorphisms and microbiome profiles, and establish precision strategies for calcium-based interventions in digestive health.},
}

Humans
*Gastrointestinal Diseases/drug therapy/therapy/metabolism/microbiology
*Calcium/metabolism
Gastrointestinal Microbiome
Receptors, Calcium-Sensing/metabolism
Dietary Supplements
*Calcium, Dietary/administration & dosage
Hypocalcemia

@article {pmid41200858,
year = {2025},
author = {Huang, Z and Brot, L and Fatouh, R and Bredon, M and Creusot, L and Lefèvre, A and Lamazière, A and Lefevre, JH and Emond, P and Planchais, J and Roux, X and Sokol, H and Rolhion, N},
title = {Saccharomyces boulardii CNCM I-745 mitigates antibiotic-induced gut microbiome functional alterations independently of the host.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2575924},
doi = {10.1080/19490976.2025.2575924},
pmid = {41200858},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Saccharomyces boulardii/physiology ; *Probiotics/pharmacology/administration & dosage ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Vancomycin/adverse effects ; Dysbiosis/chemically induced/microbiology ; Cytokines/metabolism ; Leukocytes, Mononuclear/drug effects/immunology ; Amoxicillin-Potassium Clavulanate Combination/adverse effects ; Intestinal Mucosa/microbiology/drug effects/immunology ; Bacteria/drug effects/genetics/classification/growth & development ; },
abstract = {The probiotic Saccharomyces boulardii CNCM I-745 (Sb) is widely prescribed to alleviate antibiotic-induced diarrhea, yet its mode of action, particularly its potential direct effects on the gut microbiome, remains incompletely defined. This study aimed to evaluate whether Sb can directly mitigate antibiotic-induced gut microbiota dysbiosis and influence downstream host immune response. Using both static (MiPro) and dynamic (SHIME[®]) in vitro gut microbiota models, we assessed the effects of Sb supplementation under antibiotic treatment with amoxicillin/clavulanic acid (AMC) or vancomycin (Van). Quantitative microbiome profiling integrated with targeted metabolomics showed that Sb helped stabilize bacterial biomass, partially preserved metabolic functions, and restored the production of immunoregulatory metabolites propionate and indole-3-propionic acid under AMC treatment. In addition, ex vivo exposure of primary human immune cells (PBMCs) and intestinal mucosal tissue to microbiota modulated by Sb led to a significant reduction in pro-inflammatory cytokine secretion compared to microbiota not supplemented with Sb. Collectively, these results support a beneficial role for S. boulardii CNCM I-745 in preserving directly gut microbiome function and supporting host immune homeostasis during antibiotic treatment, particularly under AMC exposure. Our findings advance the understanding of probiotic-antibiotic-gut microbiome interactions, thereby guiding future optimization of microbiome-targeted adjuvant therapies.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Saccharomyces boulardii/physiology
*Probiotics/pharmacology/administration & dosage
*Anti-Bacterial Agents/adverse effects/pharmacology
Vancomycin/adverse effects
Dysbiosis/chemically induced/microbiology
Cytokines/metabolism
Leukocytes, Mononuclear/drug effects/immunology
Amoxicillin-Potassium Clavulanate Combination/adverse effects
Intestinal Mucosa/microbiology/drug effects/immunology
Bacteria/drug effects/genetics/classification/growth & development

@article {pmid41200610,
year = {2025},
author = {Ur Rehman, M and Saeed, H and Omer, O and Tashfeen, S},
title = {Gut Microbiota-Directed Interventions in Type 2 Diabetes: A Systematic Review of Clinical Outcomes and Complication Risk.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e95045},
pmid = {41200610},
issn = {2168-8184},
abstract = {Type 2 diabetes mellitus is increasingly recognized as a disorder not only of glucose metabolism but also of gut microbial imbalance, with emerging evidence suggesting a bidirectional link between microbiome composition and metabolic dysfunction. Recent randomized controlled trials and dietary interventions highlight that specific microbial taxa, such as butyrate-producing bacteria and Akkermansia muciniphila, play crucial roles in regulating insulin sensitivity, lipid metabolism, and systemic inflammation. Modulation of the gut-metabolic axis through probiotics, prebiotics, dietary strategies, and pharmacological agents demonstrates promising effects on glycemic control, cardiometabolic risk reduction, and attenuation of diabetes-related complications, though results vary across populations and intervention types. The variability in outcomes underscores the importance of personalized approaches, where baseline microbiota signatures may dictate therapeutic response. Despite encouraging findings, many studies remain limited by short duration, small sample size, and heterogeneity in microbiome analysis methods. This review synthesizes current evidence, highlights mechanistic insights linking microbial shifts to metabolic benefits, and identifies gaps in the literature. By doing so, it emphasizes the potential of microbiome-directed therapies as adjunctive strategies in the prevention and management of type 2 diabetes and its complications.},
}

@article {pmid41200544,
year = {2025},
author = {Cheng, J and Gao, Y and Lv, H and Li, J and Sun, X and An, T and Liu, H and Wang, J and Zhang, H and Wang, H and Zou, S and Fan, Z and Chen, Y},
title = {LGG/LAC-MMT combination mitigates AFB1-induced liver and intestinal injury in mice based on intestinal microbiota modulation.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1654294},
pmid = {41200544},
issn = {2297-1769},
abstract = {AFB1 induces hepatotoxicity and enterotoxicity. Lactobacillus acidophilus (LAC) and Lactobacillus rhamnosus (LGG), both belonging to LAB, have strong binding affinity for AFB1. Montmorillonite (MMT) not only adsorbs AFB1 but also serves as a carrier for LAB, thereby enhancing their colonization ability and prolonging their survival. Despite the unclear effects of LGG/LAC-MMT combination on AFB1-induced tissue injury and intestinal microbiota disruption, this study aimed to determine whether it could effectively alleviate tissue damage from AFB1 exposure and enhance LAB colonization capacity in mouse intestines. Separately, LGG (2 × 10[9] cfu/mL) and LAC (2 × 10[9] cfu/mL) were combined with MMT (0.5 mg/kg), and the AFB1-intoxicated mice were gavaged with the mixtures for 4 weeks. Findings suggested that LGG, LAC, and MMT supplementation restored oxidative stress and inflammatory caused by AFB1 to some degree. Furthermore, they altered the intestinal microbiota structure, enhancing the colonization ability of LABs, thereby alleviating liver and intestinal injury. The combination of LGG/LAC-MMT was more effective, especially LAC-MMT. Overall, LGG/LAC-MMT exhibits a synergistic effect and can effectively ameliorate AFB1-induced tissue injury and intestinal microbiota disorder.},
}

@article {pmid41200416,
year = {2025},
author = {Shunmugavelu, K and Shakthi Chakravarthy, BG and Priya, S},
title = {Determination of Fusobacterium nucleatum levels in patients with periodontal disease and oral squamous cell carcinoma.},
journal = {GMS hygiene and infection control},
volume = {20},
number = {},
pages = {Doc60},
pmid = {41200416},
issn = {2196-5226},
abstract = {INTRODUCTION: Fusobacterium (F.) nucleatum, a Gram-negative anaerobic bacterium, has been implicated in both periodontal disease and oral squamous cell carcinoma (OSCC). This review aims to evaluate the levels of F. nucleatum in patients with periodontal disease and OSCC, exploring its potential role in the pathogenesis.

METHODS: A comprehensive literature search was conducted across multiple databases, identifying studies that measured F. nucleatum levels in periodontal disease and OSCC tissues.

RESULTS: A higher prevalence of F. nucleatum exists in both periodontal disease and OSCC tissues compared to healthy controls.

CONCLUSION: It appears that there is a link between infection with F. nucleatum and the development of these oral diseases. Further research is warranted to elucidate the mechanisms underlying this association and to explore potential therapeutic interventions targeting F. nucleatum.},
}

@article {pmid41200410,
year = {2025},
author = {Danjuma, FY and Dashen, MM and Ngene, AC and Egbere, OJ},
title = {Prevalence of bacterial vaginosis and its associated risk factors among women of reproductive age attending Jos University Teaching Hospital, Plateau State, Nigeria.},
journal = {GMS hygiene and infection control},
volume = {20},
number = {},
pages = {Doc51},
pmid = {41200410},
issn = {2196-5226},
abstract = {INTRODUCTION: Bacterial vaginosis (BV) remains the most common cause of abnormal vaginal discharge due to altered vaginal flora with decreased Lactobacillus spp. and increased anaerobic bacteria. The objectives of this study were to establish the prevalence of BV and its risk factors among women of reproductive age.

METHOD: This cross-sectional descriptive survey was conducted among 220 non-pregnant women of reproductive age attending Jos University Teaching Hospital (JUTH) in Plateau state, north central Nigeria, between August 2021 and January 2022, in which 110 women were asymptomatic, and 110 women were symptomatic. Self-administered questionnaires were used to identify the sociodemographic status and predisposing factors of the participants. Positive BV diagnosis was made using the Nugent scoring system and bacterial species were identified on selective media. A descriptive analysis was performed using the Chi-squared test at a 95% confidence interval to determine the prevalence of BV and its associated risk factors.

RESULTS: The overall BV prevalence was 33.6%. BV was higher in symptomatic women (39.1%) than in asymptomatic women (28.2%). No correlation was found between BV and demography, knowledge, or health behaviour, including age, education, marital status, number of children, occupation, income, alcohol, tobacco smoking, or sexual as well as hygienic behaviour (p≥0.05). A total of 328 bacterial isolates from 16 species were identified, with Enterococcus (E.) faecalis being the most prevalent species, accounting for 39.3% of the total isolates. Other species isolated include Staphylococcus (S.) saprophyticus (13.6%), S. epidermidis (13.0%), S. aureus (4.7%), Streptococcus (Sr.) agalactiae (5.9%), Klebsiella (K.) pneumoniae (4.1%), Proteus (P.) mirabilis (2.4%), and Pseudomonas (P.) aeruginosa (3.6%) in the symptomatic group. S. saprophyticus (10,7%), S. aureus (3.8%), K. pneumoniae (2.5%), and P. aeruginosa (1.9%) were isolated in the asymptomatic group. P. mirabilis was not detected. Lactobacillus spp. were present but not dominant, with an overall prevalence of 8.2%.

CONCLUSION: The observed diversity in vaginal microbiota, particularly the higher prevalence of E. faecalis in asymptomatic women, suggests the complexity of microbial interactions. The low prevalence of Lactobacillus spp. indicates a potential risk for infections, while the presence of potentially pathogenic bacteria such as S. saprophyticus and Streptococcus agalactiae underscores the need for further research. Overall, the understanding of the vaginal microbiome is crucial for developing effective healthcare interventions for managing BV.},
}

@article {pmid41200380,
year = {2025},
author = {Mojgani, N and Bagheri, M and Ashique, S and Hosseini, SH and Hussain, A and Moharrami, M and Zahmatkesh, A and Moradi, M},
title = {Probiotics and postbiotics: a promising prophylactic measure for American foulbrood and European foulbrood diseases of honey bees.},
journal = {Veterinary research forum : an international quarterly journal},
volume = {16},
number = {10},
pages = {545-555},
pmid = {41200380},
issn = {2008-8140},
abstract = {American foulbrood (AFB) and European foulbrood (EFB) diseases caused by Paenibacillus larvae and Meliscococcus plutonius are prevalent honeybee brood diseases that pose significant economic challenges to the apiculture industry globally. Antibiotic treatment has led to the emergence of antibiotic-resistant strains, encouraging the search for alternative and safe measures to effectively control these diseases. Honeybee gut microbiomes have proven effects on all spectra of honeybee health by enhancing resistance to several diseases via immune modulation and the production of different antimicrobial metabolites. The major part of the gut microbiota is identified as probiotic bacteria, which are live microorganisms that, when administered in adequate amounts, confer health benefits to the host. Probiotics have shown promising health benefits for honeybees. Honeybee gut probiotics provide protection via the production of different metabolites (postbiotics), such as hydrogen peroxide, vitamins, organic acids, free fatty acids, bacteriocins, neurotransmitters, secreted bio-surfactants, and reactive oxygen species. Vast numbers of these gut bacteria and their postbiotics have wide-spectrum antibacterial effects on AFB and EFB. This review highlights the significance of the honeybee gut microbial community, its probiotic potency, and the role of postbiotic metabolites as safe prophylactic measures for preventing AFB and EFB diseases in honeybees.},
}

@article {pmid41200350,
year = {2025},
author = {Mohammadzadeh, P and Samadi, N and Mohammadi, B},
title = {Revolutionizing oronasal fistula treatment in Felis silvestris: Integrating bioengineered solutions and microbiome insights for enhanced healing.},
journal = {Open veterinary journal},
volume = {15},
number = {9},
pages = {4775-4788},
pmid = {41200350},
issn = {2218-6050},
mesh = {Male ; Animals ; Cats ; Microbiota ; *Oral Fistula/veterinary/therapy ; Wound Healing ; Tissue Scaffolds ; Bioengineering ; Polyethylene Glycols ; },
abstract = {BACKGROUND: Oronasal fistulas (ONFs) present significant therapeutic challenges in veterinary medicine, particularly in patients with comorbidities, such as chronic kidney disease. This case report demonstrates an innovative bioengineered approach for ONF repair in Felis silvestris that combines autologous biomaterials with microbiome analysis.

CASE DESCRIPTION: A 15-year-old male European wildcat with a chronic traumatic ONF (11 × 8 mm) and concurrent International Renal Interest Society Stage 2 chronic kidney disease received a customized implant composed of autologous platelet-rich fibrin (PRF), bone marrow aspirate, and a 3D-printed polyethylene glycol diacrylate (PEGDA) scaffold. PEGDA was selected for its high biocompatibility and rapid photopolymerization. Healing was monitored via computed tomography imaging and 16S rRNA sequencing. The results demonstrated significant microbial dysbiosis post-injury (Shannon index: 5.2 ± 0.3 vs. 3.1 ± 0.4; p < 0.05), with opportunistic pathogen enrichment (Enterococcus faecalis: 0.5% → 12.8%). Antibiotics reduced the bacterial load by 99.9% (p < 0.001) but did not improve the closure rate (p = 0.89), underscoring the mechanical role of the scaffold.

CONCLUSION: The bioengineered implant facilitated complete mucosal integration and osteoconduction at the 10-month follow-up, demonstrating promise for complex ONF repair. However, the single-case design limits the generalizability.},
}

Male
Animals
Cats
Microbiota
*Oral Fistula/veterinary/therapy
Wound Healing
Tissue Scaffolds
Bioengineering
Polyethylene Glycols

@article {pmid41200191,
year = {2025},
author = {Qi, P and Gong, F and Leng, M and Wei, Z},
title = {Beneficial perspective on Staphylococcus epidermidis: a crucial species for skin homeostasis and pathogen defense.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1674392},
pmid = {41200191},
issn = {1664-3224},
mesh = {*Staphylococcus epidermidis/immunology/physiology ; Humans ; *Homeostasis ; *Skin/microbiology/immunology ; Biofilms/growth & development ; Animals ; Microbiota/immunology ; *Staphylococcal Infections/immunology/microbiology ; Host-Pathogen Interactions/immunology ; },
abstract = {Human skin harbors a diverse microbiome that shapes immune function, protects against pathogens, and sustains tissue homeostasis. Among its dominant members, Staphylococcus epidermidis-a coagulase-negative staphylococcus-was long considered primarily an opportunistic pathogen, especially in the context of biofilm formation and implant-associated infections. However, emerging evidence reframes S. epidermidis as an active commensal, capable of controlling inflammation, supporting antimicrobial defenses, and stabilizing the cutaneous barrier. These dual roles are largely determined by its extensive strain-level heterogeneity and dynamic colonization strategies. Here, we review current progress in understanding the ecological versatility of S. epidermidis, with particular focus on its potential benefits, its diversity and colonization dynamics, and the balance of costs and benefits associated with its presence on human skin.},
}

*Staphylococcus epidermidis/immunology/physiology
Humans
*Homeostasis
*Skin/microbiology/immunology
Biofilms/growth & development
Animals
Microbiota/immunology
*Staphylococcal Infections/immunology/microbiology
Host-Pathogen Interactions/immunology

@article {pmid41200143,
year = {2025},
author = {Toh, QY and Kang, YN and Chee, SY and Chiu, HH},
title = {Effects of probiotics on patients with Prader-Willi syndrome: a systematic review and meta-analysis of randomized controlled trials.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1583574},
pmid = {41200143},
issn = {2296-861X},
abstract = {BACKGROUND: Prader-Willi Syndrome (PWS) involves growth, obesity, and behavioral challenges; probiotics may improve symptoms through the gut-brain axis, aiding treatment. This meta-analysis aimed to assess the impact of probiotic supplementation on individuals with PWS in terms of probiotic abundance, psycho-social outcomes, behavioral issues, and adverse events.

METHODS: We systematically conducted searches across PubMed, the Cochrane Central Register of Controlled Trials, EMBASE, and the Web of Science. Our study included relevant randomized controlled trials (RCTs) published before February 2025. Two independent review authors evaluated study eligibility, extracted data, and assessed the risk of bias in the included studies. Data synthesis employed a random-effects model based on heterogeneity test results and was presented as the standardized mean difference (SMD) with a 95% confidence interval (CI).

RESULTS: A total of five RCTs were included. Probiotic supplementation led to a notable increase in the abundance of the Bifidobacterium genus (SMD 1.21; 95% CI, 0.02 to 2.39). Notably, 12 weeks of probiotics intake demonstrated a favorable trend on social engagement (SMD -0.68; 95% CI: -1.14 to -0.21; p = 0.004). In contrast, probiotics did not exhibit a significant influence on behavioural problems, and the safety of probiotics consumption was assured as there was no significant increase in gastrointestinal adverse events.

CONCLUSION: The validation of a probiotic treatment for PWS is currently an aspirational goal. Additional investigation is required to comprehensively comprehend the connection between PWS and the gut microbiome, as well as its potential ramifications for the disease phenotype.

PROSPERO, CRD42023416791.},
}

@article {pmid41199951,
year = {2025},
author = {Prasad, JS and Suman, A and Kumar, D and Sharma, P and Ramakrishnan, B and Aswini, K},
title = {Agroecology-based assembly and function of endophytic bacteria in seeds of Triticum aestivum.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699093},
pmid = {41199951},
issn = {1664-302X},
abstract = {The seed, a vital plant organ for its continuation, contains microbial endophytes that develop as part of the early plant microbiome and assist growing seedlings in various ways. In this study, bacterial endophytes from seeds of wheat cultivars grown under different agro-ecological conditions were genotypically and functionally analyzed. Despite environmental differences and cultivars adapted to distinct agroclimatic zones, the endophytic bacterial count ranged from 2.79 to 5.19 Log CFU/g. The dominant seed bacteria belonged to the phylum Firmicutes, with diverse members of the genus Bacillus. There were core and niche-specific bacteria among the different agroclimatic zones. The seed endophytic bacteria exhibited hydrolytic enzyme activities, mainly amylase, cellulase, and xylanase. The nitrogen fixation capacity ranged from 0.81 to 32.06 nmol ethylene h[-1] mg[-1] protein, while phosphate solubilisation ranged from 147 to 440 μg mL[-1]. Some seed endophytes from the North Western Plains Zone (NWPZ) showed strong antagonism toward Fusarium graminearum (52%), Bipolaris sorokiniana (35.9%), and Tilletia indica (43.4%). The green fluorescent protein (GFP)-tagged endophytic bacteria, when reintroduced to wheat seeds, were observed to colonize and migrate within germinating seedlings, Confirm their potential for internal establishment and movement within the host. These seed endophytic bacteria may offer notable benefits by colonizing root tissues during germination, thereby enhancing plant growth and yield.},
}

@article {pmid41199950,
year = {2025},
author = {Sang, Z and Zhang, Y and Kao, E and Zhu, T and Yang, J and Xu, ZZ and Huang, S and Teng, F and Wang, W},
title = {Decoding oral leukoplakia: microbiome dysbiosis and inflammatory dynamics unveiled in a rat model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1613165},
pmid = {41199950},
issn = {1664-302X},
abstract = {INTRODUCTION: Oral leukoplakia (OLK) is an oral precancerous lesion associated with oral microbiome dysbiosis and systemic inflammation. However, the longitudinal changes of the microbiome and its causal relationship with inflammation remain unclear, and traditional sequencing struggles to detect low-biomass samples.

METHODS: A 4-nitroquinoline-1-oxide (4-NQO)-induced rat OLK model was used. The oral microbiome was analyzed via 2bRAD-M sequencing; serum levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were measured. Additionally, functional pathway analysis of the microbiome and its correlation with inflammation were conducted.

RESULTS: In OLK, we observed significant shifts in the oral microbial diversity, marked by elevated abundances of Streptococcus, Glaesserella, and Pseudomonas aeruginosa. Moreover, shifts in the microbiota precede the manifestation of clinical symptoms of OLK. Functional pathway analysis highlighted enrichment in metabolism, quorum sensing, and cancer-associated microRNA pathways. Serum levels of inflammatory markers (TNF-α and IL-6) were significantly elevated in OLK and significantly correlated with specific bacterial taxa.

DISCUSSION: This study demonstrates the utility of 2bRAD-M sequencing in overcoming traditional metagenomic limitations, offering a high-resolution view of microbiome dynamics in low-biomass environments such as the oral mucosa. These findings establish the oral microbiota as candidate early biomarkers for OLK screening and prevention, opening avenues for precision diagnostics and targeted therapies to mitigate cancer risk associated with OLK.},
}

@article {pmid41199947,
year = {2025},
author = {Geng, Z and Yuan, L and See, D and Zhao, Y},
title = {Characterization of the integrated gut microbiota and metabolite profiles in osteoporosis patients with different traditional Chinese medicine syndromes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1663716},
pmid = {41199947},
issn = {1664-302X},
abstract = {INTRODUCTION: This study aims to investigate whether the Traditional Chinese Medicine (TCM) classification of osteoporosis corresponds to specific gut microbial and metabolic profiles, thereby providing a microbiological basis for TCM syndrome differentiation.

METHODS: Body composition was assessed using dual-energy X-ray absorptiometry in healthy elderly controls and osteoporosis patients categorized by TCM subtype. Gut microbiota composition and metabolite profiles were analyzed via 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively.

RESULTS: The gut microbiota dysbiosis index was significantly elevated in osteoporosis patients compared to healthy controls, with the highest levels observed in the spleen-kidney Yang deficiency subtype. Distinct microbial signatures were identified: Intestinibacter and Phascolarctobacterium were significantly enriched in kidney Yang deficiency osteoporosis, while Olsenella was markedly increased in spleen-kidney Yang deficiency osteoporosis. Correlation analyses revealed significant associations between these microbial markers and clinical parameters: Intestinibacter and Phascolarctobacterium abundances negatively correlated with bone mineral density at multiple skeletal sites, whereas Olsenella levels were negatively associated with appendicular skeletal muscle index. Importantly, microbial metabolic pathways differed between TCM subtypes, with kidney Yang deficiency associated with vitamin D metabolism and spleen-kidney Yang deficiency linked to lipid metabolism.

CONCLUSION: TCM classification captures meaningful biological heterogeneity in osteoporosis, reflected in distinct microbiome and metabolic signatures. These findings provide a microbiological basis for TCM syndrome differentiation and may inform personalized approaches to osteoporosis diagnosis and treatment.},
}

@article {pmid41199945,
year = {2025},
author = {Busi, SB},
title = {Editorial: Monitoring, modeling, and mitigation in terrestrial ecosystems: microbial response to climate change.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717735},
doi = {10.3389/fmicb.2025.1717735},
pmid = {41199945},
issn = {1664-302X},
}

@article {pmid41199864,
year = {2025},
author = {Wang, EM and Shremo Msdi, A and Quach, VN and Nguyen, SQ and Quach, E and Jo, J and Eubank, TA and Garey, KW and Rosario, N},
title = {Angiotensin converting enzyme inhibitors and angiotensin receptor blockers impact on the gut microbiome: a systematic review.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1685424},
pmid = {41199864},
issn = {1664-2392},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Animals ; *Angiotensin Receptor Antagonists/pharmacology ; Hypertension/drug therapy ; Blood Pressure/drug effects ; Renin-Angiotensin System/drug effects ; },
abstract = {BACKGROUND: Inhibition of the renin-angiotensin system (RAS) may influence gut microbial composition and blood pressure, yet current evidence remains limited. This review examines how angiotensin-converting enzyme inhibitors (ACEis) and angiotensin receptor blockers (ARBs) modify gut microbiome composition, function, and blood pressure regulation.

METHODS: We conducted a systematic search of MEDLINE and EMBASE from inception to September 2025 using terms including "human," "rat," "angiotensin converting enzyme inhibitor," "angiotensin receptor blocker," and "gut microbiome." Eligible studies were required to report changes in microbiome diversity, bacterial composition, or short-chain fatty acids (SCFAs) associated with ACEi/ARB treatment across animal or human models. Data extraction and risk of bias assessments were performed independently by multiple reviewers.

RESULTS: After deduplication, 642 retrieved articles were filtered and nine met inclusion criteria (eight in rodent models, one human study). ACEi/ARB administration in animals was associated with increased microbial diversity, restoration of intestinal oxygen balance, and enrichment of SCFA-producing anaerobic genera such as Bifidobacterium, Bacteroides, Blautia, and Akkermansia. In the human study, ACEi/ARB use did not significantly alter microbial diversity, but decreased populations of facultative aerobic pathogens including Staphylococcus and Enterobacterales. Functionally, prolonged RAS inhibition elevated levels of acetate, propionate, and butyrate, and enhanced gut barrier integrity while attenuating inflammatory signaling. The human study was found to have a moderate risk of bias.

CONCLUSIONS: ACEi and ARB therapies appear to reshape gut microbiome structure and metabolic function, promoting SCFA-producer expansion, improved gut barrier integrity, and modulation of microbial taxa linked to inflammation and hypertension. However, human data is limited, and further transitional research is needed to confirm these findings.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Angiotensin-Converting Enzyme Inhibitors/pharmacology
Animals
*Angiotensin Receptor Antagonists/pharmacology
Hypertension/drug therapy
Blood Pressure/drug effects
Renin-Angiotensin System/drug effects

@article {pmid41199641,
year = {2025},
author = {Postoeva, A and Krieger, E and Leontyeva, A and Kudryavtsev, AV and Galeeva, J and Fedorov, D and Kuzmichenko, P and Ilina, E and Govorun, V},
title = {Taxonomic diversity of fecal microbiota associated with different metabolic phenotypes in residents of Arkhangelsk, Northwestern Russia.},
journal = {Journal of biomedical research},
volume = {},
number = {},
pages = {1-17},
doi = {10.7555/JBR.39.20250258},
pmid = {41199641},
issn = {1674-8301},
abstract = {The study aimed to assess the taxonomic diversity and composition of gut microbiota in Arkhangelsk residents, Northwestern Russia, with varying metabolic statuses. A population-based cross-sectional "Know Your Heart" study (2015-2017, participants aged 35-69 years) included a health examination and gut microbiota analysis (n = 685). Participants were divided into four metabolic phenotypes: metabolically healthy non-obese (MHN), metabolically unhealthy non-obese (MUN), metabolically healthy obese (MHO), and metabolically unhealthy obese (MUO). Analyses were performed using RStudio software (v.4.2.0) with the vegan and phyloseq packages (v.1.42.0) for microbiota analysis. The sample was distributed across phenotypes as follows: MHN (47.6%), MUN (22.1%), MHO (10.4%), and MUO (19.9%). Beta-diversity analysis revealed significant differences in overall microbiome composition between MUO and MHN participants, while alpha-diversity did not differ significantly across phenotypes. The MHN group was characterized by a higher abundance of beneficial commensals such as Christensenellaceae R-7 group, Ruminococcaceae UCG-005, and Eubacterium xylanophilum group, which are taxa previously associated with metabolic health and longevity. In contrast, the MUO group showed an increased abundance of Streptococcus salivarius and Negativibacillus, taxa linked to gut dysbiosis and metabolic disorders. Blautia spp. emerged as a major hub in the microbiota of obese participants, consistent with its reported association with visceral fat. In conclusion, microbial composition was similar in obese participants despite metabolic dysfunction, whereas unidirectional taxonomic shifts were observed in those with metabolic dysfunction alone. The differences in the predominance of microbial taxa across metabolic phenotypes suggest that these taxa have a role in the development of metabolic disorders and obesity.},
}

@article {pmid41199396,
year = {2025},
author = {Liu, Q and Hu, D and Qiao, Y and Zai, X and Hao, X and Zong, Y and Zhang, D and Shi, X and Zhang, F and Li, P and Song, C},
title = {Phyllosphere microbes in foxtail millet primarily affect quality by modulating coloration and bitter compounds.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {229},
pmid = {41199396},
issn = {2049-2618},
support = {YDZJSX2022A041//The Development Fund of Central Government Guiding Local Science and Technology/ ; YDZJSX2024D046//The Development Fund of Central Government Guiding Local Science and Technology/ ; 2021YFD1900200//The National Key Research and Development Program of China/ ; },
mesh = {*Setaria Plant/microbiology/chemistry ; *Microbiota ; Taste ; Rhizosphere ; Pseudomonas/isolation & purification/metabolism/genetics/classification ; *Plant Leaves/microbiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; },
abstract = {BACKGROUND: Crop quality is influenced by crop-related factors such as varieties and metabolites, as well as by environmental conditions. Recent studies have shown the important role of rhizosphere microbes in determining crop quality and flavor, but the effects of phyllosphere (aboveground) microbes and metabolites remain unclear. Here, we examined the interaction between phyllosphere metabolites and the microbiome in three foxtail millet varieties with differing eating qualities: two high-eating-quality varieties (Yugu1, Jingu21) and one low-eating-quality variety (Daobaqi) in the field.

RESULTS: Thirteen metabolites were found to be depleted in the high-eating-quality varieties, four of which were identified as bitter compounds. These depleted metabolites were negatively correlated with the abundance of two microbial genera, Curtobacterium and Pseudomonas, enriched in the high-eating-quality foxtail millet panicles. Further analyses revealed that the abundance of these microbes was significantly associated with reduced bitterness and improved viscosity in the panicles. Additionally, synthetic microbial community experiments validated that these microbes enhanced foxtail millet quality by increasing the yellow coloration and reducing levels of bitter compounds.

CONCLUSIONS: In summary, the higher abundance of Curtobacterium and Pseudomonas in the panicles correlated with reduced bitter compounds and enhanced foxtail millet quality. This work provides new insights into the role of phyllosphere metabolites and microbiomes in determining crop quality.},
}

*Setaria Plant/microbiology/chemistry
*Microbiota
Taste
Rhizosphere
Pseudomonas/isolation & purification/metabolism/genetics/classification
*Plant Leaves/microbiology
Bacteria/classification/genetics/metabolism/isolation & purification

@article {pmid41199352,
year = {2025},
author = {Rahbar Saadat, Y and Barzegari, A and Saadatian, Z and Montazersaheb, S and Zununi Vahed, S},
title = {Gut microbiota and kidney aging: insights into current research.},
journal = {Nutrition & metabolism},
volume = {22},
number = {1},
pages = {133},
pmid = {41199352},
issn = {1743-7075},
abstract = {Aging induces structural and functional alterations in the kidneys, including changes in renal morphology and progressive decline in renal function. During aging, the gut microbiota undergoes profound shifts in composition and activity, transitioning from predominantly commensal to more pathogenic communities. Renal dysfunction further exacerbates this process by reducing toxin clearance and promoting the accumulation of uremic metabolites, which disrupt gut microbial balance. In turn, gut dysbiosis impairs kidney function, creating a self-perpetuating cycle of microbial imbalance and renal damage. Hence, breaking this vicious cycle of dysbiosis and kidney damage is important. This review sheds light on the bidirectional relationship between gut microbiota and kidney aging. It also highlights the potential of microbiota-targeted interventions to restore microbial balance and delay the onset of age-related issues.},
}

@article {pmid41199348,
year = {2025},
author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N},
title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {227},
pmid = {41199348},
issn = {2049-2618},
support = {ANR-11-DPBS-0001//Metagenopolis/ ; },
mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; },
abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.

RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3 min for taxonomic analysis and 10 min for strain-level analysis against the human microbial gene catalogue when processing 10 M paired reads - operating within a modest 5 GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.

CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.},
}

*Metagenomics/methods
Animals
Mice
Humans
*Microbiota/genetics
*Bacteria/genetics/classification
*Metagenome
*Gastrointestinal Microbiome/genetics
*Software
Computational Biology/methods

@article {pmid41199330,
year = {2025},
author = {Yin, L and Zhao, J and Zhou, Z and Zhang, J and Qu, X and Shi, J and Yin, F},
title = {Effects of prenatal bifidobacterium supplementation on the gut microbiome in preterm infants of preeclamptic mothers.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1237},
pmid = {41199330},
issn = {1479-5876},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; *Bifidobacterium/physiology ; *Infant, Premature ; *Pre-Eclampsia/microbiology ; Infant, Newborn ; *Dietary Supplements ; Adult ; *Mothers ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Male ; },
abstract = {BACKGROUND: This study examined the relationship between maternal preeclampsia (PE) and gut microbiota colonization in preterm infants and analyzed the effects of prenatal Bifidobacterium supplementation.

METHODS: This observational study included 45 preterm infants categorized according to their mothers' exposure status during pregnancy. Group A (healthy controls, n = 15) included infants born to healthy mothers who received no supplementation; Group B (PE+Bifidobacterium, n = 15) included infants whose mothers had PE and received Bifidobacterium supplementation as part of routine clinical management; and Group C (PE only, n = 15) included infants born to mothers with PE who did not receive Bifidobacterium supplementation. All enrolled infants were followed from birth for subsequent analyses. The initial postnatal fecal samples of the infants were collected and analyzed using 16S rRNA gene sequencing. Microbial diversity within the intestinal microbiota was evaluated using alpha diversity (within-sample) and beta diversity (between-sample) analyses. To identify taxon-specific differences among groups, we performed linear discriminant analysis effect size and differential abundance analysis, with statistical significance set at p < 0.05. The functional potential of the gut microbiota was inferred based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways via the PICRUSt2 algorithm.

RESULTS: Alpha diversity analysis revealed significantly greater microbial diversity in the fecal microbiota of preterm infants born to healthy mothers (Group A) than in those delivered by mothers with PE, regardless of prenatal Bifidobacterium exposure. Taxonomic profiling revealed distinct microbial community structures across groups: Group A exhibited significant enrichment of Bacteroides at all taxonomic levels, along with an elevated abundance of Clostridium at the class and order levels. Group B showed a markedly greater relative abundance of Actinobacteria at the phylum level and Rothia at the genus level, whereas Group C was dominated by Proteobacteria (phylum level) and Streptococcus (genus level). All intergroup differences were statistically significant following Benjamini‒Hochberg correction (q < 0.05). A functional analysis of the gut microbiota revealed 53 KEGG pathways with significant overall group differences (p < 0.05), among which 23 pathways were significantly different in at least two groups (q < 0.05). Notably, the activity of the LPS biosynthesis pathway was significantly upregulated in Group C compared with Group A (q = 0.001). Although LPS biosynthesis activity was reduced in Group B relative to Group C (q = 0.018), it remained elevated compared to Group A (q = 0.001), suggesting incomplete mitigation of endotoxin risk. Additionally, glycolytic activity was significantly impaired in Group C relative to Group A (q = 0.003) but was partially restored in Group B compared to Group C (q = 0.022).

CONCLUSIONS: Maternal PE impaired early-life gut microbiota establishment in preterm infants, manifesting in reduced microbial diversity, enrichment of pathogenic Proteobacteria and Streptococcus, and consequent functional dysbiosis characterized by elevated endotoxin biosynthesis potential and compromised energy metabolism. Although prenatal supplementation with Bifidobacterium partially restored the microbial compositional balance, promoting beneficial bacteria, reducing LPS synthesis activity, and partially improving glycolytic function, it failed to fully reverse endotoxin-related risks, indicating the need to develop more effective microbiota-targeted strategies to comprehensively optimize metabolic and immune homeostasis.},
}

Humans
Female
*Gastrointestinal Microbiome
Pregnancy
*Bifidobacterium/physiology
*Infant, Premature
*Pre-Eclampsia/microbiology
Infant, Newborn
*Dietary Supplements
Adult
*Mothers
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Male

@article {pmid41199168,
year = {2025},
author = {Guo, L and Pei, X and Tan, J and Sun, H and Jiang, S and Wei, H and Peng, J},
title = {Unraveling the role of bacteria with heritable versus non-heritable relative abundance in the gut on boar semen quality.},
journal = {Genetics, selection, evolution : GSE},
volume = {57},
number = {1},
pages = {66},
pmid = {41199168},
issn = {1297-9686},
support = {2022BBA0056//Hubei Technological Innovation Special Fund/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; CARS-35//Agriculture Research System of China/ ; },
mesh = {Animals ; Male ; Swine/microbiology ; *Gastrointestinal Microbiome/genetics ; *Semen Analysis/veterinary ; *Bacteria/classification/genetics/metabolism ; Fatty Acids, Volatile/metabolism ; Semen ; },
abstract = {BACKGROUND: The relative abundance of some bacteria in the gut of pigs is heritable, suggesting that host genetics may recursively influence boar semen quality by affecting the composition and function of gut microbiota. Therefore, it is essential to elucidate the specific contributions of heritable versus non-heritable gut microbiota to semen quality traits.

RESULTS: Our study aimed to identify heritable and non-heritable bacterial taxa at the genus level in the boar gut and to predict their functions and respective contributions to semen quality traits. At the genus level, 39 heritable and 91 non-heritable bacterial taxa were identified. Functional analysis revealed that predicted microbial functions in both groups were primarily enriched in carbohydrate, nucleotide, and amino acid metabolism. We further analyzed the average microbiability of heritable and non-heritable bacteria on short-chain fatty acids (SCFAs) and semen quality traits. The relative abundance of heritable bacteria was found to contribute more to SCFAs levels and semen quality than non-heritable bacteria. Mediation analysis revealed that SCFAs could mediate the influence of the relative abundance of heritable bacteria on host phenotypes, identifying 99 significant genus-SCFAs-semen quality trait mediation links.

CONCLUSIONS: Our findings underscore the substantial role of the relative abundance of heritable gut bacteria in shaping porcine semen quality through SCFAs mediation. These results highlight the potential of targeted microbiome interventions to enhance reproductive traits in pigs.},
}

Animals
Male
Swine/microbiology
*Gastrointestinal Microbiome/genetics
*Semen Analysis/veterinary
*Bacteria/classification/genetics/metabolism
Fatty Acids, Volatile/metabolism
Semen

@article {pmid41199152,
year = {2025},
author = {Han, X and Huang, H and Yu, X and Cha, M and Jian, J and Hu, X and Wu, Q},
title = {Letter to the Editor: The Oral Microbiome and Depression: An Emerging Medical Hypothesis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70143},
pmid = {41199152},
issn = {1601-0825},
support = {ZR2021QH283//Youth Project of Shandong Provincial Natural Science Foundation/ ; 202201060948//Shandong Provincial Medical and Health Technology Development Plan/ ; },
}

@article {pmid41198950,
year = {2025},
author = {Guendouzi, S and Ortega-Villaizan, AG and King, E and Benmati, M and Vicente-Carbajosa, J},
title = {Transcriptomic profiling of Arabidopsis Thaliana responses to Stutzerimonas stutzeri, chlorella vulgaris, and mixed consortium inoculation under salt stress.},
journal = {Plant molecular biology},
volume = {115},
number = {6},
pages = {125},
pmid = {41198950},
issn = {1573-5028},
support = {TED2021-1299998-l00//MCIN/AEI (Ministerio de Ciencia e Innovación / Agencia Estatal de Investigación, Spain)/ ; },
mesh = {*Arabidopsis/genetics/microbiology/physiology ; *Salt Stress/genetics ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; *Chlorella vulgaris/physiology ; *Transcriptome ; Arabidopsis Proteins/genetics/metabolism ; },
abstract = {Plants, constantly exposed to dynamic environmental conditions, encounter various abiotic stresses that significantly affect their growth and development. In response, plants initiate complex physiological and molecular adjustments, including altered gene expression. One of the most influential factors in mitigating stress impacts is the plant-microbe interaction. Among these, plant growth-promoting rhizobacteria (PGPR) are well-studied for their ability to enhance plant resilience. More recently, microalgae have emerged as potential members of the plant microbiome, although their roles remain comparatively underexplored. This study investigates the transcriptomic responses of Arabidopsis thaliana to inoculation with the PGPR strain Stutzerimonas stutzeri, the green microalgae Chlorella vulgaris, and a consortium of both microorganisms under salt stress conditions. Through RNA-seq analysis, we identified a set of core genes commonly regulated across all inoculation treatments, including SALT OVERLY SENSITIVE 3 (SOS3), the potassium channel AKT2, and CBL-INTERACTING PROTEIN KINASE 5 (CIPK5), suggesting a shared stress-mitigation mechanism. Additionally, we identified genes uniquely regulated in response to the S. stutzeri-C. vulgaris consortium. These included components of the ethylene signaling pathway (EIN3/EIL1), detoxification-associated genes such as β-GLUCOSIDASE (BGLU22), and transcription factors linked to stress response, notably NAC6 and MYB12. Together, these findings provide insight into the specific and overlapping transcriptomic changes induced by bacterial, algal, and combined inoculations, contributing to our understanding of plant-microbe interactions under salt stress.},
}

*Arabidopsis/genetics/microbiology/physiology
*Salt Stress/genetics
Gene Expression Regulation, Plant
Gene Expression Profiling
*Chlorella vulgaris/physiology
*Transcriptome
Arabidopsis Proteins/genetics/metabolism

@article {pmid41198897,
year = {2025},
author = {Wattanawongwan, W and Krasaesin, A and Khieota, T and Thongchotchat, V and Porntaveetus, T and Wiriyakijja, P},
title = {Effects of chlorhexidine and a polyherbal mouthwash on the oral microbiome and user satisfaction: a randomized controlled trial.},
journal = {Clinical oral investigations},
volume = {29},
number = {12},
pages = {555},
pmid = {41198897},
issn = {1436-3771},
mesh = {Humans ; *Mouthwashes/pharmacology/therapeutic use ; *Chlorhexidine/pharmacology/therapeutic use ; *Microbiota/drug effects ; Male ; Female ; Double-Blind Method ; Adult ; *Patient Satisfaction ; *Anti-Infective Agents, Local/pharmacology ; *Gingivitis/drug therapy/microbiology ; Middle Aged ; *Mouth/microbiology ; },
abstract = {OBJECTIVE: This study aimed to comparatively evaluate the effects of polyherbal, chlorhexidine (CHX), and normal saline (NCC) mouthwashes on oral microbiome composition, microbial metabolic pathways, and patient-reported outcomes, with the goal of assessing the potential of polyherbal mouthwash as a natural alternative to CHX for managing gingivitis, while aiming to minimize CHX-associated microbial dysbiosis.

METHODS: A randomized, double-blind trial was conducted among 27 patients with gingivitis, randomly assigned to polyherbal, CHX, or NCC mouthwash groups. Participants used the assigned mouthwash twice daily for 7 days. Saliva samples were analyzed via 16 S rRNA sequencing to assess microbial diversity (alpha and beta) and taxonomic composition. Differential taxa and pathways were identified using FDR-corrected Wilcoxon tests and log₂ fold-change analysis. Patient-reported outcomes were evaluated using numerical rating scales (NRS).

RESULTS: The polyherbal mouthwash demonstrated significantly higher patient acceptability than CHX and NCC, with superior scores in taste, smell, texture, moisture retention, overall satisfaction, and willingness for continued use (p < 0.05). While CHX exhibited strong antimicrobial activity, its alcohol-containing formulation markedly disrupted microbial diversity, increased potentially dysbiotic genera (Streptococcus, Porphyromonas), and altered 23 metabolic pathways associated with dysbiosis. In contrast, the polyherbal mouthwash-which also contained cetylpyridinium chloride (CPC)- selectively increased beneficial genera (Amnipila, Absconditabacteriales [SR1], Peptostreptococcus), preserved overall microbial diversity, and modulated only two pathways, notably upregulating L-isoleucine biosynthesis.

CONCLUSION: The polyherbal mouthwash represents a promising alternative to CHX, demonstrating selective microbial modulation, preservation of microbiome stability, and enhanced patient acceptability. These findings support its potential integration into routine oral healthcare as a microbiome-friendly and patient-acceptable solution. Further studies are warranted to evaluate CPC-free polyherbal formulations across larger and more diverse populations over extended durations.},
}

Humans
*Mouthwashes/pharmacology/therapeutic use
*Chlorhexidine/pharmacology/therapeutic use
*Microbiota/drug effects
Male
Female
Double-Blind Method
Adult
*Patient Satisfaction
*Anti-Infective Agents, Local/pharmacology
*Gingivitis/drug therapy/microbiology
Middle Aged
*Mouth/microbiology

@article {pmid41198867,
year = {2025},
author = {Boetto, C and Romero, VB and Henches, L and Frouin, A and Auvergne, A and Patin, E and Bredon, M and , and Kennedy, SP and Duffy, D and Quintana-Murci, L and Sokol, H and Aschard, H},
title = {The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1537},
pmid = {41198867},
issn = {2399-3642},
support = {ANR-20-CE15-0012-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Healthy Volunteers ; Young Adult ; *Environment ; },
abstract = {The gut microbiome is a complex ecosystem characterized not only by its marginal taxonomic composition but also by its emergent properties. Bacteria develop local interactions to form coherent functional communities, whose effects on health and diseases cannot be predicted from the behavior of individual members. Understanding the factors underlying variability in these communities may therefore provide critical insights on the biological links between the gut microbiome and human phenotypes. Here, we examined the effect of a range of host factors, including demographics, medical history, and dietary habits, on these communities in 938 healthy individuals using MANOCCA, a covariance-based approach developed to address existing limitations. Increased age and smoking were associated with a significant overall decrease in co-abundance, and conversely a higher body mass index was associated with increased co-abundance. At the taxon level, a core of 200 genera were systematically impacted in their co-abundance with other taxa, suggesting a central role in structuring the network. Finally, we demonstrate that our approach offers a powerful framework for prediction purposes, with taxa co-abundance being able to predict the age of participants with an accuracy three-fold higher than a model based on abundance only.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Adult
*Bacteria/classification/genetics/isolation & purification
Aged
Healthy Volunteers
Young Adult
*Environment

@article {pmid41198833,
year = {2025},
author = {Erdenetsetseg, B and Arakawa, K and Galipon, J and Undrakhbold, S and Fukuda, S and Boldgiv, B},
title = {Rhizospheric microbiomes differ between dormant and active Potaninia mongolica in the Gobi desert of Mongolia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38858},
pmid = {41198833},
issn = {2045-2322},
support = {ID No. R12205//Japan Society for the Promotion of Science/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; Desert Climate ; Mongolia ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Soil/chemistry ; Fungi/genetics/classification ; Plant Roots/microbiology ; },
abstract = {Rhizospheric microbiomes differ between active and dormant plants due to changes in root activity and exudate production, especially under environmental stress. In arid regions, native plants such as Potaninia mongolica Maxim enter dormancy to survive harsh conditions. However, rhizospheric microbial and chemical differences between active and dormant states of plants remain poorly described. This study investigated rhizospheric microbial communities and soil chemical changes in the case of active and dormant P.mongolica plants. Rhizospheric soil samples were collected, and soil texture and chemical variables were analyzed. High-throughput sequencing targeting the 16S rRNA and ITS regions was conducted to profile bacterial and fungal communities, respectively. Results showed that the dominant fungal phyla were Ascomycota and Basidiomycota, while Proteobacteria and Actinobacteria were the dominant bacterial phyla in both plant states. Although bacterial diversity did not differ significantly between active and dormant plants (p > 0.05, Welch's t-test), fungal diversity was significantly different. Among soil chemical variables, total nitrogen was notably elevated in the rhizosphere of dormant plants (mean = 7.93; SD = 5.91). These findings reveal differences in fungal community structure and nitrogen levels in the rhizosphere between active and dormant plant states. Understanding these interactions contributes to our knowledge of desert plant microbiome dynamics and may inform the use of microbial indicators or amendments to support vegetation restoration in arid environments.},
}

*Rhizosphere
*Soil Microbiology
*Microbiota
Desert Climate
Mongolia
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Soil/chemistry
Fungi/genetics/classification
Plant Roots/microbiology

@article {pmid41198730,
year = {2025},
author = {Garrigós, M and García-Ruiz, O and Enkvist, CR and García-López, MJ and Moreno-Indias, I and Ruiz-López, MJ and Veiga, J and Figuerola, J and Videvall, E and Martínez-de la Puente, J},
title = {Effects of avian Plasmodium exposure on the microbiota of Culex pipiens.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38898},
pmid = {41198730},
issn = {2045-2322},
support = {PRE2021-098544//Ministerio de Ciencia, Innovación y Universidades/ ; PU19/01925//Ministerio de Ciencia, Innovación y Universidades/ ; FJC2021-048057-I//Ministerio de Ciencia, Innovación y Universidades/ ; PID2020-118205GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; PTA2022-021854-I//Agencia Estatal de Investigación/ ; PID2020-118921RJ-100/AEI/10.13039/501100011033//Agencia Estatal de Investigación/ ; CPII21/00013//Instituto de Salud Carlos III/ ; 2023-05026//Swedish Research Council/ ; },
mesh = {Animals ; *Culex/microbiology/parasitology ; *Plasmodium/physiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Sparrows/parasitology ; Mosquito Vectors/microbiology/parasitology ; *Malaria, Avian/parasitology/transmission ; },
abstract = {Malaria parasites (Plasmodium spp.) are mosquito-borne parasites that infect humans and wildlife. Several studies support the role of mosquito microbiota as a major driver of Plasmodium transmission, although studies on wildlife malaria are typically neglected. Here, we used a 16S rRNA metabarcoding approach to assess whether the exposure to avian Plasmodium parasites affects the microbiota of their natural vector, Culex pipiens. Mosquitoes, captured in the field as larvae and grown in the laboratory, were allowed to feed on house sparrows (Passer domesticus) naturally infected with Plasmodium relictum (lineage SGS1) and uninfected birds. We analyzed the microbiota composition of the abdomens of individual mosquitoes and found 2,006 Amplicon Sequence Variants (ASVs). Culex pipiens' microbiota was dominated by bacteria of the genus Wolbachia, followed by the genera Stenotrophomonas and Faecalibacterium. We observed no difference in alpha nor beta diversity between mosquitoes that fed on Plasmodium-infected birds (exposed mosquitoes) and those that fed on uninfected birds (unexposed mosquitoes). However, exposed mosquitoes had a higher relative abundance of bacteria of the family Bacteroidaceae and the genus Bacteroides than the unexposed mosquitoes. Excluding the intracellular endosymbiont Wolbachia from the analyses, we obtained similar results, and also found a higher relative abundance of bacteria of the family Rikenellaceae in exposed mosquitoes. A pathway enrichment analysis based on KEGG annotations revealed that the bacterial community in exposed mosquitoes was enriched in pathways mainly related to biosynthesis and metabolism. Our results suggest that Cx. pipiens exposed to avian Plasmodium have slightly different microbiota composition, although further research is needed to establish the causality of these effects.},
}

Animals
*Culex/microbiology/parasitology
*Plasmodium/physiology
RNA, Ribosomal, 16S/genetics
*Microbiota
Sparrows/parasitology
Mosquito Vectors/microbiology/parasitology
*Malaria, Avian/parasitology/transmission

@article {pmid41198444,
year = {2025},
author = {Goryachok, M and Fairbanks-Mahnke, A and Fulte, S and Tamkin, E and McCarty, A and Larson, ED and Planet, PJ and Clark, SE},
title = {Functional CFTR may be required for Prevotella melaninogenica regulation of epithelial cell defense against Staphylococcus aureus.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.11.002},
pmid = {41198444},
issn = {1873-5010},
abstract = {BACKGROUND: Prevotella melaninogenica is enriched in the lungs of people with cystic fibrosis (pwCF), yet its functional impact on respiratory tract homeostasis remains incompletely understood. Prior studies identified immune modulatory effects following lung exposure to Prevotella, but the relevance of these findings for CF infections is unknown.

METHODS: The impact of P. melaninogenica on infection with the CF pathogen Staphylococcus aureus was evaluated using a mouse lung infection model and by measuring S. aureus adherence to human respiratory tract cystic fibrosis transmembrane conductance regulator (CFTR) mutant and isogenic wild-type (WT)-corrected CFBE41o- epithelial cells. Epithelial cytokine/chemokine secretion and RNA-sequencing were performed to compare P. melaninogenica-induced signaling programs in WT-corrected versus CFTR mutant cells.

RESULTS: P. melaninogenica significantly reduced S. aureus lung infection, associated with elevated S. aureus killing by lung neutrophils and impaired S. aureus adherence to epithelial cells. Live or killed P. melaninogenica were sufficient to mediate these effects, which were dependent on TLR2. P. melaninogenica impairment of S. aureus adherence required functional CFTR, as this effect was lost in CFTR mutant cells but restored by CFTR modulators. RNA-sequencing identified several antibacterial defense pathways selectively upregulated by P. melaninogenica in WT corrected epithelial cells, correlating with higher IL-8 and IL-6 cytokine production.

CONCLUSIONS: P. melaninogenica enhanced neutrophil and epithelial defense against S. aureus, but the benefits of epithelial cell regulation by P. melaninogenica were lost with CFTR dysfunction. CFTR modulators rescued P. melaninogenica responsiveness in epithelial cells, highlighting the potential for synergistic effects of host-microbiome interactions and CFTR targeted therapies.},
}

@article {pmid41198406,
year = {2025},
author = {Adame, MD and Segal, LN and Dickson, RP},
title = {The ensemble approach: integrating microbiome therapeutics into our treatment of pneumonia.},
journal = {The European respiratory journal},
volume = {66},
number = {5},
pages = {},
doi = {10.1183/13993003.01701-2025},
pmid = {41198406},
issn = {1399-3003},
}

@article {pmid41198034,
year = {2025},
author = {Dieter, L and Bowie, K and Luhung, I and Healy, HG and Roberts, SC and Mathew, T and Peaper, D and Martinello, RA and Gerstein, MB and Peccia, J},
title = {Aerosol-based Exposure to Opportunistic Pathogens Originating from Hospital Sink Drains.},
journal = {American journal of infection control},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajic.2025.10.030},
pmid = {41198034},
issn = {1527-3296},
abstract = {BACKGROUND: Hospital room sink drains contain biofilms that harbor opportunistic pathogens. Exposures to these pathogens may occur from aerosolization and droplet dispersion into patient rooms during sink use. This study characterizes aerosolization and droplet generation of sink drain opportunistic pathogens into operational hospital rooms.

METHODS: Sink drains, sink surfaces, water droplets, aerosols generated during sink use, and settled aerosols were sampled in patient rooms and analyzed via culture-, spectrometry- and genome-based approaches. Opportunistic pathogens were compared across samples via whole-genome sequencing and single-nucleotide polymorphism analysis. Biofilms and settled aerosols underwent 16S ribosomal deoxyribonucleic acid sequencing to assess impacts of sink drain biofilms into room bioaerosols.

RESULTS: Analyses suggested sink drain biofilm bacteria dispersed into hospital rooms. Opportunistic pathogens were identified in sink drains, droplets near sinks, and room aerosols. Stenotrophomonas maltophilia isolates from sink drain biofilm and droplets matched at the single-nucleotide level and microbial community analysis suggested general transmission of bacteria from sink drains into hospital rooms.

DISCUSSION: Viable opportunistic pathogens from sink drains were present in water droplets and aerosols within patient range, suggesting a potential exposure route.

CONCLUSIONS: Hospital sink drain biofilms contributed to the microbiome of hospital room surfaces and air, with microbes generally transmitted from sink drain sources to the room.},
}

@article {pmid41198001,
year = {2025},
author = {Gong, F and Liu, N and Miao, J and Wang, C and Lin, M and Luan, B and Chen, J and Chen, Y and Chen, X and Ge, F and Chen, W},
title = {Vitamin D regulation of gut microbiota-derived butyrate as a potential inhibitor of breast cancer proliferation.},
journal = {Gene},
volume = {},
number = {},
pages = {149872},
doi = {10.1016/j.gene.2025.149872},
pmid = {41198001},
issn = {1879-0038},
abstract = {Vitamin D is a fat-soluble vitamin implicated in the etiology, progression, and prognosis of breast cancer, yet its precise mechanisms of action remain elusive. We have integrated the latest insights from both basic and clinical research to find that in the human body, vitamin D is activated by hydroxylase to form the active form 1,25(OH)2D. 1,25(OH)2D may stimulate the abundance of butyrate-producing bacteria by upregulating their abundance, and butyrate can regulate the intestinal microenvironment and modulate the immune system to inhibit the proliferation of breast cancer. Notably, our investigations reveal a novel role of vitamin D in modulating the gut microbiome, particularly in stimulating the production of butyrate and other metabolites, which exhibit potent anti-proliferative effects on breast cancer cells. These findings open promising avenues for innovative clinical approaches in breast cancer therapy. This review delves into the intricate interplay between vitamin D, butyrate, and breast cancer, aiming to propose novel therapeutic strategies.},
}

@article {pmid41197947,
year = {2025},
author = {Zhou, Y and Li, J and Wang, D and Peng, L and Chen, K},
title = {Multimodal relationships and multifactorial associations between oral microecological and neurodegenerative diseases.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {110760},
doi = {10.1016/j.neuropharm.2025.110760},
pmid = {41197947},
issn = {1873-7064},
abstract = {Dysregulation of the oral microbiome can result in inflammation of the oral mucosa and is associated with the development and advancement of numerous local and systemic illnesses, including those triggered by viral infections. The review thoroughly examines how the IL-17/Th17 response contributes to both protective immunity and inflammation in the oral mucosa, as well as its role in the onset of neurodegenerative diseases. A theoretical structure is offered for the possible connections among immune cells and the bacteria in the mouth. Changes in the oral microbiome and its produced pro-inflammatory factors may serve as non-invasive biomarkers for the invasion of potential neurodegenerative pathogens, offering predictive and early warning value for the severity of neurodegenerative diseases. Studying the intricate connection between the oral microbiome and neurodegenerative diseases offers potential for innovative strategies in preventing and treating the advancement of such conditions. Additional investigation is needed to reveal the mechanisms behind this connection and offer important insights for upcoming clinical procedures.},
}

@article {pmid41197919,
year = {2025},
author = {Mohit, and Verma, S and Venkatesh, V and Nityanand, S},
title = {Immuno-Microbial Crosstalk in Aplastic Anemia: Role of Gut and Viral Triggers.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108158},
doi = {10.1016/j.micpath.2025.108158},
pmid = {41197919},
issn = {1096-1208},
abstract = {Aplastic anemia (AA) is a rare but life-threatening hematological disorder, manifested in bone marrow failure and pancytopenia, which occurs worldwide due to the preferential immune mediated destruction of hematopoietic stem and progenitor cells. Despite the autoimmune etiology of AA, recent findings emphasize the key role of microbial and viral factors in the pathogenesis of AA by driving the host immune dysregulation. We delve into the immune-microbial crosstalk that is relevant in AA pathogenesis to provide novel insights related to gut microbial ecology, microbial metabolites, viral infections mediated inflammation and cytotoxicity against bone marrow components. Additionally, providing the roadmap of current knowledge for immune-mediated bone marrow failure focusing on activated cytotoxic T cells, altered regulatory T cells and proinflammatory cytokines. Imbalanced immune activation via defects in gut barrier function which promotes pathogen-associated molecular patterns (PAMPs) signaling through Toll-like receptors (TLRs) and other innate sensors. Considering the role of viral trigger such as Parvovirus B19, Epstein-Barr and Hepatitis as inducers of dysregulated immunity and their ability to affect antigen presentation, T cell receptor repertoires, and interferon pathways. We also delineate the potential of targeting the gut-immune axis for personalized AA therapy, including potential microbiome-directed interventions, antiviral and anti-cytokine approaches, as promising complement lines for standard immunosuppression therapy in AA. This cited approach will provide the advanced and novel clinical paradigm for the interconnected immune-microbial signals in pathogenesis of AA which promotes the host immune surveillance and also lead to precision medicine in AA treatment.},
}

@article {pmid41197774,
year = {2025},
author = {Gholamipour-Shirazi, P and Gholamipour-Shirazi, A},
title = {Infant Gut Microbiota and Functional Foods: Opportunities for Early Health Intervention.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.10.032},
pmid = {41197774},
issn = {2405-4577},
abstract = {BACKGROUND & AIMS: The infant gut microbiome, established at birth, plays a critical role in immune, metabolic, and neurological development. Early-life exposures, including delivery mode and feeding practices, significantly influence microbial colonization. This review aims to evaluate how functional foods, including probiotics, prebiotics, synbiotics, and human milk oligosaccharides (HMOs), modulate the infant gut microbiota during this critical developmental window and their implications for long-term health.

METHODS: We synthesized findings from clinical trials, systematic reviews, and mechanistic studies exploring the role of functional food components in shaping infant microbiota composition and functionality. The review integrates insights from microbiology, immunology, and nutrition science, with emphasis on interventions during infancy.

RESULTS: Breastfeeding and HMOs promote Bifidobacterium dominance, linked to reduced risks of allergies, obesity, and inflammatory bowel disease. HMO-supplemented formulas approximate the microbial profiles of breastfed infants, and probiotics, such as Lactobacillus rhamnosus GG, reduce the incidence of atopic dermatitis. Synbiotics enhance gut health in preterm infants, thereby reducing morbidity. Despite the demonstrated benefits, challenges persist in probiotic stability, host-specific responses, and regulatory harmonization.

CONCLUSIONS: Functional foods offer a promising, evidence-based strategy to harness early microbial plasticity and promote resilience against chronic disease. Standardized formulations, longitudinal studies, and personalized approaches are needed to optimize their implementation in diverse infant populations.},
}

@article {pmid41197755,
year = {2025},
author = {Wang, XX and Liang, JJ and Duan, X and Chen, G},
title = {Microbial Metabolites for Cancer Immunotherapy: Current Evidence and Future Directions.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.10.005},
pmid = {41197755},
issn = {1096-3650},
abstract = {Immune checkpoint blockade (ICB) therapy has transformed cancer treatment by activating the body's immune defenses to combat malignancies, offering substantial therapeutic outcomes for patients with advanced cancers. However, its efficacy varies considerably across different tumor types and individual patients. Recent studies have identified the human microbiome as a pivotal regulator of host homeostasis and systemic immunity and also found that it is essential for regulating immunotherapy's efficacy. Beyond direct microbial-host interactions, microbiota-derived immunomodulatory products, including metabolites, extracellular vesicles, and polysaccharides, have been shown to profoundly influence tumorigenesis, disease progression, and therapeutic responses. These microbial-derived immunomodulatory products can reshape the tumor microenvironment (TME) and modulate tumor immunity. Notably, emerging therapeutic strategies targeting or utilizing microbial immunomodulators have demonstrated promising efficacy in both preclinical and clinical models. This review provides a comprehensive overview of current research on microbiota-derived immunomodulatory products in cancer immunotherapy, highlighting their mechanistic roles and potential as innovative adjuncts in future tumor treatment strategies.},
}

@article {pmid41197754,
year = {2025},
author = {Xia, F and Yi, Q and Xu, Z and Zhou, Z and Tang, H and Zhang, K and Yan, Y},
title = {Microbial Modulation as a Game Changer: Boosting Immunotherapy Efficacy in Breast Cancer.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.10.006},
pmid = {41197754},
issn = {1096-3650},
abstract = {Breast cancer is generally regarded as an immunologically cold tumor, characterized by limited T cell infiltration and poor responsiveness to immune checkpoint inhibitors. Increasing evidence suggests that the human microbiome, including both gut and tumor-associated microbial communities, serves as a critical regulator of systemic and local antitumor immunity, with potential to convert inert tumors into immune-responsive states. Gut microbiota influence systemic immune homeostasis through metabolites such as lipids, lactic acid, and trimethylamine N-oxide, which modulate T lymphocytes, dendritic cells, leukocytes, and stromal components. Tumor-resident microbiota further shape the tumor immune microenvironment by regulating CD4[+] and CD8[+] T cells, NKT cells, Tregs, and macrophages, thereby impacting the efficacy of immune checkpoint blockade. Emerging strategies to sensitize cold breast tumors through microbiome modulation include dietary phytochemicals, bariatric surgery induced microbial shifts, probiotics and postbiotics, polyvalent microbial antigen vaccines, and nanotechnology-based platforms. Clinical challenges remain, particularly interindividual microbial heterogeneity, safety and regulatory considerations, and the need for reliable microbial and immune biomarkers. This review summarizes current advances in microbiota-immune interactions in breast cancer and discusses opportunities for microbiome-targeted strategies to enhance immunotherapy outcomes.},
}

@article {pmid41197738,
year = {2025},
author = {Acevedo-Fontanez, LA and Sánchez-Feliciano, A and Ershadi, S and Reichenberg, J and Eichenfield, LF and Barbieri, JS},
title = {Periorificial Dermatitis: Pathophysiology, Diagnosis, and Management.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2025.10.138},
pmid = {41197738},
issn = {1097-6787},
abstract = {Periorificial dermatitis is a chronic papulopustular facial dermatitis. Despite being frequently encountered in clinical practice and associated with significant effects on quality of life, its etiology remains incompletely understood, and no therapies are specifically approved by the Food and Drug Administration for its treatment. In this review, the current mechanistic understandings of periorificial dermatitis pathogenesis are discussed including the role of inciting factors, skin barrier dysfunction, inflammation, and the microbiome. In addition, we review the diagnostic features of periorificial dermatitis and how to distinguish it from clinical mimickers. Finally, treatment is discussed including skincare, topical, and systemic therapies.},
}

@article {pmid41197619,
year = {2025},
author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM},
title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101218},
doi = {10.1016/j.crmeth.2025.101218},
pmid = {41197619},
issn = {2667-2375},
abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.},
}

@article {pmid41197616,
year = {2025},
author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X},
title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102431},
doi = {10.1016/j.xcrm.2025.102431},
pmid = {41197616},
issn = {2666-3791},
abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.},
}

@article {pmid41197352,
year = {2025},
author = {Jhetam, S and Shynkaruk, T and Hamaoka, T and Crowe, TG and Jeffery, A and Rogers, MB and Van Kessel, AG and Schwean-Lardner, K},
title = {Feeding leghorn chicks during simulated transport as an early feeding strategy and the benefits of a single spray probiotic application.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106024},
doi = {10.1016/j.psj.2025.106024},
pmid = {41197352},
issn = {1525-3171},
abstract = {This study examined early, interrupted, or no feeding, with (P) or without (N) a spray-on probiotic (Lactobacillus reuteri), on chick stress, growth, gastrointestinal tract (GIT) development, microbiota, and gene expression during and after simulated transport (ST; 24 Hz vibration, 25°C, uncontrolled humidity). Lohmann LSL-Lite chicks (n = 1520) underwent 24 h of ST (5 h post-hatch) with either 24, 16, 8, or 0 h of feed access (FA) during ST with P or N treatment (trt). Following ST, birds were housed in pens for 14 d (5 replications/trt). Body weight, blood chemistry and heterophil-to-lymphocyte (H/L) ratio, relative length, weight and histomorphology of the GIT, quantitative PCR for ileum expression of genes related to inflammation and gut-barrier function, and microbiome analysis were assessed. At d 7 and 14, P birds were heavier. On d 1 (post-ST), H/L ratios were higher in the P trt, possibly from immunostimulation. Blood pH was lowest, and ionized calcium was highest in the 8-h trt. Glucose was higher in the N trt, and more dehydration occurred in the 0- and 8-h trt. The 0-h trt had reduced small intestine length and weight, and jejunum weight was highest in the P trt on d1. On d 7, duodenum and ileum weight were lowest for 8 h and N, respectively. Histomorphology revealed interactions in the ileum and cecum, suggestive of P preventing delayed gut development with interrupted FA. On d 1, ileum IL-6 expression was greater for 0 compared to 24 h. The P trt had a lower microbiome diversity but may have improved gut development with interrupted FA and prevented dehydration in the 0- and 8-h trt. Interrupting FA after 8 h had more negative effects than 0-h FA. With 0-h FA during ST, GIT development was delayed and could have contributed to ileum inflammation. Early FA had a positive effect on leghorn chick health, gut development, and growth. One post-hatch spray application of P may improve chick well-being over long transport durations.},
}

@article {pmid41197206,
year = {2025},
author = {Li, Y and Gao, Y and Wang, L and Si, J},
title = {NK cell adaptation in the tumor microenvironment: Insights for NK cell-based immunotherapy.},
journal = {Cytokine & growth factor reviews},
volume = {86},
number = {},
pages = {181-198},
doi = {10.1016/j.cytogfr.2025.10.003},
pmid = {41197206},
issn = {1879-0305},
abstract = {Natural killer (NK) cells serve as critical first responders within the immune system, orchestrating antitumor responses by directly eliminating malignant cells and modulating broader immune functions. Their capacity to recognize stressed targets without MHC-restricted neoantigen presentation, together with a favorable safety profile, underpins growing enthusiasm for NK cell‑based therapeutics. Nonetheless, the clinical efficacy of NK-cell-based therapies in solid tumor has been hindered by tumor microenvironment (TME)-driven immunosuppression, metabolic competition, and cell-intrinsic exhaustion mechanisms. In this review, we outline the journey from the discovery of NK cells to their role as a breakthrough target in cancer immunotherapy. We then provide a comprehensive framework of NK cell biology, from homeostatic regulation to TME-driven epigenetic, transcriptional, and metabolic adaptations. Notably, we discuss recent investigations into NK cell subset heterogeneity and their interactions with tumor cells, immune cells and the gut microbiome. Finally, we critically evaluated clinical progress while highlighting the imperative for rationally designed, mechanism-based combinations that address tumor escape pathways. The review concludes with a forward-looking perspective on engineering solutions to unlock the full therapeutic potential of NK cells across solid tumors and hematologic malignancies.},
}

@article {pmid41196682,
year = {2025},
author = {Cao, L and Shi, X and Li, T and Zhu, H and Liu, Y and Pei, R and Chen, C and Xu, Q and Zhang, H and Raza, W and Logrieco, AF and Wang, G and Liu, D and Shen, Q},
title = {Fusaric acid detoxification mediates interspecies interactions for sustainable Fusarium wilt disease management.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116531},
doi = {10.1016/j.celrep.2025.116531},
pmid = {41196682},
issn = {2211-1247},
abstract = {Microbial biocontrol agents (BCAs) play a critical role in maintaining plant health by antagonizing pathogens. However, most research has focused on direct suppression mechanisms (e.g., antibiosis and competition), while the neutralization of mycotoxin for disease management remains unexplored. Here, we report that a fungal BCA, Trichoderma harzianum (Th), subverts Fusarium verticillioides (Fv) infection via a fusaric acid (FSA) detoxification process in maize. Salicylate hydroxylase was found to detoxify FSA into an almost non-toxic metabolite, 10OH-FSA. This mechanism not only neutralized the pathogenicity of Fv but also mediated interspecies interactions contributing to Fv suppression. Additionally, FSA detoxification exhibited broad applicability in controlling different Fusarium diseases in maize, tomato, and wheat. More profoundly, Th-induced FSA detoxification activity in the rhizosphere could stimulate the growth of other FSA detoxification-capable microbes, amplifying disease suppression through ecological cross-talk. These findings unveil an ecological tactic employed by BCAs to manage soil-borne Fusarium wilt disease.},
}

@article {pmid41196658,
year = {2025},
author = {Verna, G and De Santis, S and Islam, BN and Sommella, EM and Licastro, D and Zhang, L and De Almelda Celio, F and Miller, EN and Merciai, F and Caponigro, V and Xin, W and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F},
title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI196712},
pmid = {41196658},
issn = {1558-8238},
abstract = {Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors. In this report, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a missense mutation in the Muc2 gene. Upon rederivation from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice developed severe colitis and, notably, spontaneous CAC that progressively worsened over time. In contrast, CONV Winnie showed only mild colitis but no tumorigenesis. By comparison, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis and colon tumors, indicating an essential role for the gut microbiome in the development of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of the donor, only FMT from SPF Winnie donors resulted in CAC. Our studies present a relevant model of CAC, providing strong evidence that the microbiome plays a key role in its pathogenesis, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.},
}

@article {pmid41196474,
year = {2025},
author = {Song, H and Hosain, MM and Park, T},
title = {DeepIMB: Imputation of non-biological zero counts in microbiome data.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41196474},
issn = {2092-9293},
support = {NRF-2022R1A2C1092497//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: The high prevalence of non-biological zero counts, arising from low sequencing depth and sampling variation, presents a significant challenge in microbiome data analysis. These zeros can distort taxon abundance distributions and hinder the identification of true biological signals, complicating downstream analyses.

OBJECTIVE: To address the challenges of non-biological zeros in microbiome datasets, we propose DeepIMB, a deep learning-based imputation method for microbiome data, specifically designed to accurately identify and impute non-biological zero counts while preserving biological integrity.

METHODS: DeepIMB operates in two main phases. First, it identifies non-biological zeros using a gamma-normal mixture model applied to the normalized, log-transformed taxon count matrix. Second, it imputes these zeros with a deep neural network model that integrates diverse sources of information, including taxon abundances, sample covariates, and phylogenetic distances, thereby learning complex, nonlinear relationships within microbiome data.

RESULTS: By leveraging integrated information from multiple data types, DeepIMB accurately imputes non-biological zeros while preserving true biological signals. In our two simulation studies, DeepIMB outperformed existing imputation methods in terms of mean squared error, Pearson correlation coefficient, and Wasserstein distance.

CONCLUSION: DeepIMB effectively addresses the challenges posed by non-biological zeros in microbiome data. By improving the quality of the data and the reliability of downstream analyses, DeepIMB represents a significant advancement in microbiome research methodologies.},
}

@article {pmid41196415,
year = {2025},
author = {He, Y and Yang, T and Mi, J and He, S and Yang, Z and Lu, S and Yue, K and Huang, Y and Song, L and Xiao, Y and Ren, Z},
title = {B.uniformis IM01-derived IAA alleviates asthma via AhR/NLRP3 pathways in mice.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {388},
pmid = {41196415},
issn = {1420-9071},
support = {2023YFC0871200//the National Key R&D Program of China/ ; 33054//the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/ ; 29172//the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/ ; },
mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *Asthma/pathology/metabolism/immunology/drug therapy ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Indoleacetic Acids/metabolism/pharmacology ; Mice ; *Signal Transduction/drug effects ; Disease Models, Animal ; NF-kappa B/metabolism ; Mice, Inbred BALB C ; T-Lymphocytes, Regulatory/immunology ; Female ; Lung/pathology ; Interleukin-22 ; Tryptophan/metabolism ; Th2 Cells/immunology ; Interleukins/metabolism ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; },
abstract = {Symbiotic flora exhibits a strong association with the pathogenesis of allergic disorders. Certain Bacteroides species have demonstrated potential in ameliorating allergic conditions. However, the specific role of Bacteroides uniformis in allergic asthma and its underlying mechanisms remain incompletely understood. This study demonstrates that oral administration of B.uniformis IM01 significantly enhanced the production of indole-3-acetic acid (IAA), suppressed airway inflammatory cell airway infiltration and aberrant T helper 2 (Th2) immune responses, and improved the epithelial barrier function in a murine model of asthma. Mechanistically, B.uniformis IM01 upregulated tryptophan metabolism, elevating IAA levels in both colon and serum, which activated the aryl hydrocarbon receptor (AhR) and induced interleukin-22 (IL-22) production. Activated AhR may inhibit NF-κB/NLRP3 signaling pathway and facilitate the splenic differentiation of Foxp3[+] regulatory T cells (Tregs), thus attenuating lung barrier dysfunction and improving allergic asthma symptoms. In summary, our results revealed that B.uniformis IM01 upregulated production of IAA to activate AhR leading to inhibited NF-κB/NLRP3-mediated immune responses, and ameliorated allergic asthma through the gut-lung axis.},
}

Animals
*Receptors, Aryl Hydrocarbon/metabolism
*Asthma/pathology/metabolism/immunology/drug therapy
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
*Indoleacetic Acids/metabolism/pharmacology
Mice
*Signal Transduction/drug effects
Disease Models, Animal
NF-kappa B/metabolism
Mice, Inbred BALB C
T-Lymphocytes, Regulatory/immunology
Female
Lung/pathology
Interleukin-22
Tryptophan/metabolism
Th2 Cells/immunology
Interleukins/metabolism
*Basic Helix-Loop-Helix Transcription Factors/metabolism

@article {pmid41196286,
year = {2025},
author = {Ni, Z and Ye, D},
title = {The impact of gut microbiota modulation on responses to immune checkpoint inhibitors in cancer.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2025.02719},
pmid = {41196286},
issn = {1588-2640},
abstract = {The gut microbiota has emerged as a critical determinant of antitumor immunity and a potential modulator of responses to immune checkpoint inhibitors (ICIs). Although pre-clinical and clinical studies suggest that specific bacterial taxa may influence both efficacy and immune-related adverse events (irAEs). However, the magnitude and consistency of these associations remain unclear. A systematic search of PubMed, Embase, Web of Science, and the Cochrane Library was conducted through March 2025. Eligible studies evaluated baseline gut microbiota composition, fecal microbiota transplantation (FMT), probiotic/prebiotic interventions, or antibiotic exposure in cancer patients treated with ICIs. Pooled hazard ratios (HRs) for overall survival (OS) and progression-free survival (PFS), and odds ratios (ORs) for response rates and irAEs, were estimated using random-effects models. Across 38 studies involving 5,642 patients were included. Pooled analysis demonstrated that enrichment of Akkermansia muciniphila, Bifidobacterium longum and Faecalibacterium prausnitzii was significantly associated with improved OS (HR 0.62, 95% CI 0.51-0.76) and PFS (HR 0.69, 95% CI 0.55-0.83). Conversely, antibiotic exposure before or during ICI treatment was associated with worse OS (HR 1.84, 95% CI 1.45-2.34). Patients undergoing FMT from responders exhibited higher objective response rates (OR 2.91, 95% CI 1.48-5.73). Microbiota diversity indices were consistently higher in responders than in non-responders. Collectively, gut microbiota composition and its modulation significantly impact the therapeutic efficacy and toxicity profile of ICIs. These findings highlight the translational potential of microbiome-based biomarkers and interventions in optimizing immunotherapy.},
}

@article {pmid41196057,
year = {2025},
author = {Fait Kadlec, T and Ilett, EE and da Cunha-Bang, C and Sengeløv, H and Brieghel, C and Gulay, A and Rafiq, S and Ravn, HB and Zheng, C and Nielsen, RV and Sørensen, SS and Zargari Marandi, R and Niemann, CU},
title = {Explainable machine learning to identify chronic lymphocytic leukemia and medication use based on gut microbiome data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0094425},
doi = {10.1128/spectrum.00944-25},
pmid = {41196057},
issn = {2165-0497},
abstract = {Medication, particularly antibiotics, significantly alters gut microbiome composition, often reducing microbial diversity and affecting host health. Given that the gut microbiome may influence cancer progression, we integrated clinical, shotgun metagenomic, and medication data to assess microbiome composition across diseased and healthy cohorts, as well as the impact of medication on microbiome variation. The study cohorts included patients with chronic lymphocytic leukemia (CLL, n = 85), acute myeloid leukemia (AML, n = 61), myeloid dysplastic syndrome (MDS), and other severe hematological malignancies (n = 104); patients scheduled for elective cardiac surgery (n = 89); and kidney donors (n = 9), all collected as part of a consecutive microbiome sampling effort at Copenhagen University Hospital, Denmark; and healthy individuals (N = 59). First, our analyses revealed similarities in both diversity and composition between microbiomes of patients with CLL and patients prior to elective cardiac surgery, whereas patients with AML and MDS exhibited the least diverse and most distinct microbiomes. Second, when we quantified sources of microbiome variation, the combination of medication, disease, age, and sex accounted for 4% of variation between all cohorts and 10.4% of variation between CLL and pre-cardiac surgery patients only; the two cohorts selected for comparison due to their similar microbiomes. Notably, this left 90%-95% of the variation unexplained, emphasizing the need for better identification of the parts of the microbiome variation impacting health and disease. Third, using a machine learning approach, we validated and further refined the CLL-associated microbiome pattern from our previous studies. Overall, our data provide a foundation for further investigation into disease-specific microbial signatures and the potential interactions between medication, underlying disease, and the microbiome, with the ultimate goal to improve our understanding and clinical management of CLL.IMPORTANCEThis study reveals how disease and medication influence the gut microbiome in patients with chronic lymphocytic leukemia (CLL) when compared to other more severe hematological malignancies, a cohort of patients scheduled for elective cardiac surgery representing a severely diseased nonhematological cohort, and a cohort of healthy individuals. We found that patients with CLL and those scheduled for cardiac surgery had the most similar microbiome diversity and composition. Similarities across very different disease contexts suggest that disease status alone has limited impact. Consistently, across all cohorts, medication, disease, age, and sex together explained only less of microbiome variation, leaving 90%-95% unexplained. This underscores the important need for better identification of factors shaping the microbiome. In addition, we validated a previously published, machine learning-based CLL-associated microbiome signature, demonstrating the robustness of our previous findings differentiating the microbiome signature for CLL as compared to healthy individuals. The findings expand knowledge on how disease states and medical treatments shape gut microbiome composition and diversity, potentially leading to new ways of managing CLL and improving patient outcomes through microbiome signatures.},
}

@article {pmid41196055,
year = {2025},
author = {Plaza Oñate, F and Quinquis, B and Thirion, F and Gilles, M and Morabito, C and Valeille, K and Martin, R and Guidet, B and Kern, C and Pécastaings, S},
title = {Assessment of protocols for characterization of the human skin microbiome using shotgun metagenomics and comparative analysis with 16S metabarcoding.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173225},
doi = {10.1128/spectrum.01732-25},
pmid = {41196055},
issn = {2165-0497},
abstract = {The skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader taxonomic and functional insights but is challenging for low-biomass skin samples due to limited microbial DNA and high host contamination. In this study, we characterized the microbiome of the forehead and armpits in healthy individuals using shotgun metagenomics and assessed the strategies to improve sequencing success. We compared collection kits, DNA extraction protocols, and tested multiple displacement amplification (MDA). We found that sampling with D-Squame discs followed by an in-house DNA extraction protocol was the most effective combination to maximize DNA yields. MDA introduced significant compositional biases and is not recommended. Shotgun sequencing, without MDA, produced microbial compositions and diversity indices broadly consistent with 16S rRNA metabarcoding, although it showed discrepancies in the relative abundance of some genera. Consistent with prior studies, the armpit microbiome was dominated by Staphylococcus spp., whereas the forehead microbiome was dominated by Cutibacterium spp. Critically, shotgun sequencing provided additional insights into viral and eukaryotic microorganisms and revealed the functional potential of microbial communities, demonstrating its clear advantages over 16S rRNA metabarcoding for comprehensive skin microbiome research.IMPORTANCEWith growing evidence of the role of microorganisms in maintaining healthy skin, accurately characterizing the skin microbiome remains a significant challenge. In this study, we demonstrate that shotgun sequencing, carried out with adapted wet lab protocols, provides deep insights into the microbiome composition of specific areas, such as the forehead or the armpits. Notably, it enables the characterization of fungi and viruses while offering direct functional insights into microbial communities, providing a clear advantage over 16S ribosomal RNA gene sequencing. Our findings highlight the potential of shotgun metagenomics as a powerful tool for comprehensive skin microbiome analysis. They emphasize the importance of tailored protocols for low-biomass samples, improving the reliability of shotgun sequencing and paving the way for more robust clinical studies focused on the skin microbiome.},
}

@article {pmid41196050,
year = {2025},
author = {Lee, S and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Kim, H-L and Kang, S-H and Kim, H-N},
title = {Metagenome-assembled genomes reveal microbial signatures and metabolic pathways linked to coronary artery disease.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095425},
doi = {10.1128/msystems.00954-25},
pmid = {41196050},
issn = {2379-5077},
abstract = {Gut microbiota has emerged as a critical factor influencing cardiovascular disease (CVD) risk, particularly coronary artery disease (CAD) development. Using fecal metagenomic shotgun sequencing, we investigated gut microbiota signatures associated with CAD and provided strain-resolved insights through metagenome-assembled genome (MAG) reconstruction. We analyzed 14 patients with CAD and 28 propensity score-matched healthy controls. Differential abundance analysis identified 15 CAD-associated bacterial species. Members of the Lachnospiraceae family, previously associated with trimethylamine-N-oxide production, were significantly enriched in patients with CAD. Conversely, short-chain fatty acid-producing bacteria Slackia isoflavoniconvertens and Faecalibacterium prausnitzii were depleted, suggesting a potential contribution to gut-mediated inflammation and metabolic dysregulation. Metabolic pathway analysis revealed significant urea cycle and L-citrulline biosynthesis enrichment in CAD cases, with Alistipes and Coprococcus as key contributors. Among predicted metabolites, inosine, which is implicated in coronary artery relaxation, was elevated in patients with CAD, whereas C18:0e MAG and α-muricholate were depleted. A random forest model achieved a mean AUC of 0.89 for CAD classification, with improved performance when integrating microbial taxa and metabolites. CAD-derived MAGs showed metabolic signatures linked to inflammatory dysbiosis and cardiovascular dysfunction, such as enriched N2 fixation and sulfite reduction. Strain-resolved comparative genomic analysis of MAGs revealed distinctive functional characteristics between CAD-derived and control-derived strains of Akkermansia muciniphila and Megamonas fumiformis. F. prausnitzii MAG from the control group carried non-trimethylamine-producing gene, mtxB, suggesting its potential protective role in CAD pathophysiology. These findings provide insights into gut microbial alterations in CAD and highlight potential targets for microbiome-based therapeutic interventions to reduce CVD risk.IMPORTANCEGut microbiota plays a pivotal role in cardiovascular disease; however, its specific contribution to coronary artery disease (CAD) remains underexplored. This study identified distinct microbial signatures associated with CAD, including the enrichment of pro-inflammatory bacterial taxa and depletion of short-chain fatty acid-producing bacteria, which may contribute to systemic inflammation and metabolic dysregulation. Perturbations in key pathways, such as the urea cycle and glycolysis, suggest metabolic links between the gut microbiota and CAD. Additionally, the metagenome-assembled genome-based analysis revealed strain-resolved functional heterogeneity that shapes host-microbe interactions and may contribute to CAD pathophysiology. These findings provide novel insights into gut dysbiosis in CAD and highlight the potential of microbiome-targeted therapeutic strategies in precision medicine.},
}

@article {pmid41196042,
year = {2025},
author = {Lesani, M and Middleton, CE and Feng, T-Y and Urbán Arroyo, JC and Casarez, E and Ewald, SE and McCall, L-I},
title = {Spatially divergent metabolic impact of experimental toxoplasmosis: immunological and microbial correlates.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0112625},
doi = {10.1128/msystems.01126-25},
pmid = {41196042},
issn = {2379-5077},
abstract = {Maladaptive host metabolic responses to infection are emerging as major determinants of infectious disease pathogenesis. However, the factors regulating these metabolic changes within tissues remain poorly understood. In this study, we used toxoplasmosis, as a prototypical example of a disease regulated by strong type I immune responses, to assess the relative roles of current local parasite burden, local tissue inflammation, and the microbiome in shaping local tissue metabolism during acute and chronic infections. Toxoplasmosis is a zoonotic disease caused by the parasite Toxoplasma gondii. This protozoan infects the small intestine and then disseminates broadly in the acute stage of infection, before establishing chronic infection in the skeletal muscle, cardiac muscle, and brain. We compared metabolism in 11 sampling sites in C57BL/6 mice during the acute and chronic stages of T. gondii infection. Strikingly, major spatial mismatches were observed between metabolic perturbation and local parasite burden at the time of sample collection for both disease stages. By contrast, a stronger association with indicators of active type I immune responses was observed, indicating a tighter relationship between metabolic perturbation and local immunity than with local parasite burden. Loss of signaling through the IL1 receptor in IL1R knockout mice was associated with reduced metabolic impact of infection. In addition, we observed significant changes in microbiota composition with infection and candidate microbial origins for multiple metabolites impacted by infection. These findings highlight the metabolic consequences of toxoplasmosis across different organs and potential regulators.IMPORTANCEInflammation is a major driver of tissue perturbation. However, the signals driving these changes on a tissue-intrinsic and molecular level are poorly understood. This study evaluated tissue-specific metabolic perturbations across 11 sampling sites following systemic murine infection with the parasite Toxoplasma gondii. Results revealed relationships between differential metabolite enrichment and variables, including inflammatory signals, pathogen burden, and commensal microbial communities. These data will inform hypotheses about the signals driving specific metabolic adaptation in acute and chronic protozoan infection, with broader implications for infection and inflammation in general.},
}

@article {pmid41195911,
year = {2025},
author = {Pai, YC and Huang, CY and Lin, LY and Li, YH and Yu, LC},
title = {Infectious Carcinogens Derived from Intestinal Microflora: Mechanisms of Microbial Transitions from Eubionts to Pathobionts.},
journal = {Journal of physiological investigation},
volume = {},
number = {},
pages = {},
doi = {10.4103/ejpi.EJPI-D-25-00045},
pmid = {41195911},
issn = {2950-6344},
abstract = {A diverse community of microorganisms inhabits the gastrointestinal tract in a physiological state. While a symbiotic relationship exists between commensal bacteria and the healthy host, an imbalanced microbial population (dysbiosis) is associated with the development of colitis-associated colorectal cancers. The decline of beneficial microbes (eubionts) and the expansion of commensal-derived opportunistic pathogens (pathobionts) are widely recognized as key factors in the microbial etiology of various diseases. In particular, certain bacteria with emerging virulence elements are present in the gut microbiome and have been implicated as contributors to the development of colon cancer, such as Escherichia coli, Bacteroides fragilis, and Fusobacterium nucleatum. Bacterial virulent factors, including lipopolysaccharide, fimbriae and adhesins, and toxins, promote oncogenesis through direct or indirect mechanisms. These microbial products modify host cellular functions, resulting in DNA damage, increased epithelial proliferation, and intensified inflammation, all of which ultimately contribute to tumor formation. Although the existence of pathobionts is generally accepted nowadays, an open question remains regarding why bacteria shift from harmless commensals to disease-causing pathobionts. Accumulating evidence suggests that host epithelial functions influence the composition of the intestinal microbiota by regulating oxygen availability in the lumen, providing antimicrobial defense, activating innate immune responses, synthesizing mucin glycoproteins, and establishing a physical barrier through the organization of microvilli. This review examines the various aspects of mucosal drivers that shape microbiota and provides evidence that intraepithelial stress plays a significant role in configuring colitogenic and tumorigenic microflora. Understanding the mechanisms by which microbes transition from eubionts to pathobionts that promote cancer progression is crucial for developing bacterial precision medicine. Identifying the roles of intestinal pathobionts and the critical time point for host-microbe interactions in tumorigenesis could lead to the development of new strategies for prevention and therapy.},
}

@article {pmid41195700,
year = {2025},
author = {Crestani, E and Harb, H and Benamar, M and Kaddurah-Daouk, R and Phipatanakul, W and Chatila, TA},
title = {Metabolomic and immunological signatures of asthma severity in children.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {11},
pages = {e70242},
doi = {10.1111/pai.70242},
pmid = {41195700},
issn = {1399-3038},
support = {//National Institute of Allergy and Infectious Diseases/ ; /AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Asthma/immunology/metabolism/blood/diagnosis ; Child ; Female ; Male ; Severity of Illness Index ; *T-Lymphocytes, Regulatory/immunology/metabolism ; Metabolomics ; Child, Preschool ; Cytokines/blood ; Adolescent ; Growth Differentiation Factor 15/blood ; Biomarkers/blood ; Metabolome ; },
abstract = {BACKGROUND: Multiple risk factors for asthma severity have been identified by epidemiological studies. Yet, the pathophysiological mechanisms driving the severity of clinical asthma manifestations remain incompletely understood. In asthmatic children, Notch4 expression on circulating Treg cells and levels of circulating GDF15 have been shown to be increased as a function of disease severity, suggesting a contribution of Treg dysfunction to disease phenotype.

METHODS: 126 children with asthma (intermittent = 40; mild persistent = 43; moderate persistent = 29, and severe persistent = 14) and 83 non-asthmatic controls were recruited in the Allergy clinic at Boston Children's Hospital and from asthma cohorts. Untargeted metabolomic analysis and cytokine profiling were performed in plasma and results correlated with disease severity, Notch4 expression, and presence of other atopic comorbidities.

RESULTS: Children with moderate/severe asthma had higher levels of select lipids (triglycerides, ceramides) and carboxylic acids (lactic acid, aconitic acid) and lower levels of amino acids (sarcosine and arginine) and of IFNλ 2/3 compared to children with intermittent/mild asthma. Treg Notch4 expression and GDF15 levels, which increase with disease severity, correlated positively with lactic acid and xanthine levels and inversely with sarcosine and arginine. The concomitant presence of food allergy was associated with alterations in microbiome-related metabolites and allergic rhinitis with marked triglyceride dysregulation.

CONCLUSIONS: Untargeted metabolomic profiling identified both shared and unique pathways associated with known asthma severity contributors, Notch4 dysregulation and GDF15 elevation, suggesting that different mechanisms may both converge or independently contribute to determining clinical manifestations of asthma severity in asthmatic children.},
}

Humans
*Asthma/immunology/metabolism/blood/diagnosis
Child
Female
Male
Severity of Illness Index
*T-Lymphocytes, Regulatory/immunology/metabolism
Metabolomics
Child, Preschool
Cytokines/blood
Adolescent
Growth Differentiation Factor 15/blood
Biomarkers/blood
Metabolome

@article {pmid41195400,
year = {2025},
author = {Zhili, G and Jie, L and Peihao, Y},
title = {Macro- and metabolome-based characterization between gut microbiota and metabolites in patients with colorectal adenomas.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1628315},
pmid = {41195400},
issn = {1664-302X},
abstract = {OBJECTIVE: The gut microbiota has been recognized as a significant regulator in the development and progression of colorectal adenoma (CRA). However, few studies have investigated the presence and association of resident microbial species and metabolites in patients with CRA. Our aim was to analyze differences in gut microbiome composition and metabolites, as well as to evaluate their diagnostic potential for CRA.

METHODS: We conducted metagenomic and metabolomic analyses on fecal samples from 90 subjects, including 60 patients with CRA (CRA group) and 30 healthy subjects who served as normal controls (NC group). By integrating fecal metagenomic and metabolomic data, we identified gut microbiota-associated metabolites that showed significant abundance changes in CRA patients. Furthermore, we explored whether these metabolites and microbial species could distinguish CRA patients from healthy individuals.

RESULTS: 16S rRNA gene sequencing and untargeted metabolomics analysis revealed microbial changes that distinguished CRA patients from controls. Microbial population analysis showed that the CRA group formed distinct clusters from the controls, with significant β-diversity (PCA and PCoA analyses, p < 0.05). At the phylum level, the dominant taxa in terms of relative abundance included Firmicutes, Ascomycota, Mycobacteria, Actinobacteria, and Clostridia. Differential analysis of the gut flora based on species abundance revealed significant differences in taxonomic composition between healthy individuals and CRA patients. KEGG functional enrichment analysis indicated that the differential flora were primarily involved in metabolic pathways, including metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, amino acid biosynthesis, and cofactor biosynthesis. In this study, three microbial species-Fusobacterium mortiferum, Alistipes, and Bacteroides fragilis-were validated as discriminators between healthy individuals and CRA patients, with Alistipes showing higher classification efficacy. Metabolomic analysis revealed differences in tryptophan metabolism, protein degradation products, amides, and phenolic acid metabolites. KEGG enrichment results indicated that metabolic pathways were the most significantly enriched. Differential metabolites were mainly associated with the biosynthesis of plant secondary metabolites. Procrustes and Venn analyses were performed on functional entries of the two omics datasets, highlighting enriched pathways including Metabolic pathways, Glycerophospholipid metabolism, Sphingolipid metabolism, and Alpha-linolenic acid metabolism. A review of the literature confirmed that the differential flora and metabolites are associated with adenoma growth.

CONCLUSION: In this study, metagenomic and metabolomic analyses were conducted in subjects with CRA. The findings based on fecal metagenomic and metabolomic assays suggest that intestinal microecology is altered in CRA patients, leading to changes in gut cellular structure.},
}

@article {pmid41195399,
year = {2025},
author = {, },
title = {Correction: Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721706},
doi = {10.3389/fmicb.2025.1721706},
pmid = {41195399},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1652229.].},
}

@article {pmid41195394,
year = {2025},
author = {Sun, Q and Fei, S and Huang, S and Tan, R and Chen, H and Song, S and Wang, B},
title = {Wilt disease reshapes rhizosphere microbiota in small yellow ginger soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670956},
pmid = {41195394},
issn = {1664-302X},
abstract = {INTRODUCTION: Continuous cropping obstacles, particularly the prevalent ginger wilt disease (bacterial wilt), severely constrain the sustainable development of the small yellow ginger (Zingiber officinale Roscoe) industry in Rucheng County, China. However, the primary pathogen responsible for this disease in the local cultivar and the associated microbiome shifts within the rhizosphere remain unidentified. This study aimed to elucidate the distinctive rhizosphere microbial community changes induced by ginger wilt disease, identify the potential key pathogen responsible for this disease in Rucheng, and provide a scientific basis for overcoming continuous cropping obstacles in small yellow ginger cultivation.

METHODS: Soil samples were collected from an uncultivated plot and from the rhizosphere of healthy and wilted small yellow ginger plants. Microbial community structure and composition were analyzed using 16S rRNA gene high-throughput sequencing. Linear Discriminant Analysis (LDA) effect size (LEfSe) was employed to identify differential biomarkers, and functional prediction was performed using BugBase.

RESULTS: Ginger wilt disease significantly altered the rhizosphere soil bacterial community structure and composition: the relative abundance of Proteobacteria increased significantly, primarily due to the enrichment of the genus Ralstonia; conversely, the relative abundance of Acidobacteriota, Firmicutes, and Chloroflexi significantly decreased. Ginger wilt disease also significantly reduced the diversity of the rhizosphere soil bacterial community. LEfSe further confirmed Ralstonia as a diagnostic biomarker for ginger wilt disease. BugBase phenotypic prediction indicated that the microbiota enriched in the diseased ginger rhizosphere exhibited higher capabilities for oxidative stress resistance, pathogenic potential, and mobile element content, attributed to a functional consortium of multiple genera, such as Ralstonia as the dominant contributor alongside major contributors such as Rhodanobacter and Dokdonella.

DISCUSSION: Our findings highlight that the enrichment of Ralstonia is strongly associated with ginger wilt in Rucheng County and concomitant with profound changes in the rhizospheric microbiota of wilted ginger, involving alterations in both community structure and functional potential.},
}

@article {pmid41195389,
year = {2025},
author = {Li, J and Diao, L and Li, M and Huang, F and Sun, K},
title = {Unraveling the mysteries of the gut-kidney axis: the protective role of traditional Chinese medicine in chronic kidney disease.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1642377},
pmid = {41195389},
issn = {1664-302X},
abstract = {Chronic kidney disease (CKD) constitutes a globally progressive nephropathy orchestrating inexorable deterioration of renal architecture. The paradigmatic gut-kidney axis unveils sophisticated bidirectional interplay between enteric microbiome and renal homeostatic equilibrium. Dysbiotic perturbations catalyze aberrant accumulation of gut-derived uremic metabolites, attenuate intestinal epithelial fortification, and propagate subclinical inflammatory cascades, synergistically precipitating CKD trajectory acceleration. Contemporary therapeutic arsenals targeting this axis encompass probiotic reconstitution, prebiotic orchestration, synbiotic hybridization, precision nutritional calibration, and enteral sequestrants including AST-120. Traditional Chinese Medicine (TCM) paradigms deploy multifaceted strategies through meticulous microbiota choreography, mucosal barrier reinforcement, and renal fibrogenesis attenuation. Distinguished phytotherapeutics including Rhubarb (Rhei Radix et Rhizoma), Salvia miltiorrhiza, and Poria cocos, synergized with bioactive constituents curcumin and punicalagin, orchestrate nephroprotective virtuosity via intricate microbiome-metabolome networks. Sophisticated polyherbal architectures, exemplified by YQHG and YSHS, harmoniously fortify intestinal impermeability while nullifying uremic translocation. These revelations substantiate the transformative potential of integrative paradigms amalgamating TCM-based phytomedicine with microbiota-directed precision therapeutics for CKD stewardship.},
}

@article {pmid41195143,
year = {2025},
author = {Ducrocq, F and Hafidi, O and Grosjean, J and Hehn, A and Piutti, S},
title = {Influence of genotype and soil on specialized metabolites production and bacterial microbiota associated to wild hop (Humulus lupulus L.): an early-stage study.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1702956},
pmid = {41195143},
issn = {1664-462X},
abstract = {Hop (Humulus lupulus L.) is a dioecious climbing plant that is emblematic for the brewing industry because of its specialized metabolites. Many studies have focused on hop metabolism without considering the microbiota associated with hop tissues, although over the past decade, a paradigm shift has redefined plants as holobionts, with complex associations between the plant host and its associated microbial communities. In this study, we investigated the effects of three wild hop genotypes cultivated in two different agricultural soils under controlled conditions on specialized metabolite production and on bacterial community composition across different hop compartments (rhizosphere soil, roots, and leaves). Phytochemical analysis of leaf contents revealed distinct metabolic profiles across the six 'genotype×soil' interactions, driven by variations in the biosynthesis of prenylated chalcones, α- and β-type bitter acids, and their derivatives. PERMANOVA results demonstrated that both 'genotype' and 'soil' factors significantly influenced leaf metabolite composition, each explaining approximately 28% of the observed variance. However, the strongest effect was observed for the 'genotype×soil' interaction, which accounted for 66% of the variance. In parallel, soil type, hop genotype, and their interaction significantly shape hop-associated bacterial communities, with a predominant interaction effect in each compartment (rhizosphere soil, roots and leaves) (R[2] = 0.74, 0.74 and 0.32, respectively). Furthermore, Spearman microbiome-metabolome correlation analysis revealed that bacterial families were positively correlated with the biosynthesis of key metabolites, particularly bitter acids. Our findings further suggest that the hop-associated microbiota may contribute to metabolic biosynthesis, opening new perspectives for optimizing metabolite biosynthesis through microbiome manipulation.},
}

@article {pmid41195064,
year = {2025},
author = {Sun, W and Xue, N and Zhang, Q},
title = {Integrated multi-omics analysis reveals the mechanisms of naringin in ameliorating high-fat diet-induced metabolic dysfunction-associated steatotic liver disease.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1694191},
pmid = {41195064},
issn = {2296-861X},
abstract = {INTRODUCTION: Naringin (Nar), the predominant flavonoid in citrus fruits, shows therapeutic potential against metabolic dysfunction-associated steatotic liver disease (MASLD). However, its underlying mechanisms remain largely elusive.

METHODS: In this study, we investigated the efficacy and underlying mechanisms of Nar in a mouse model of high-fat diet (HFD)-induced MASLD using integrated analyses of network pharmacology, molecular docking, hepatic lipidomics, and gut microbiota.

RESULTS: Treatment with Nar markedly ameliorated MASLD phenotypes, as evidenced by reduced body and liver weights, lower hepatic triglycerides (TGs), and improved serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels. Network pharmacology analysis revealed that Nar targets associated with MASLD are primarily enriched in proteins such as SRC, AKT1, STAT3, FOS, ESR1, and NFKB1, which exert their effects through the PI3K-AKT signaling pathway. Molecular docking simulations further elucidated the interaction mechanisms. Lipidomic analysis revealed that Nar restored hepatic lipid homeostasis, significantly decreasing levels of TGs and diglycerides (DGs), with 20 differentially abundant lipid species identified as potential biomarkers. Additionally, Nar profoundly altered the gut microbial community, promoting the enrichment of beneficial genera including Oscillibacter, Allisonella, and Flavonifractor.

DISCUSSION: Our findings indicate that Nar prevents MASLD by harmonizing hepatic lipid metabolism and modulating the gut microbiome, providing a multifaceted mechanistic insight into its therapeutic potential.},
}

@article {pmid41194963,
year = {2025},
author = {Chen, L and Wang, F and Zhang, H and Qin, S and Sui, M and Ishigami, T},
title = {Lactulose for prevention of cardiovascular events after myocardial infarction: A retrospective cohort study.},
journal = {JRSM cardiovascular disease},
volume = {14},
number = {},
pages = {20480040251393767},
pmid = {41194963},
issn = {2048-0040},
abstract = {BACKGROUND: Acute myocardial infarction (AMI) remains a major cause of global mortality, with post-infarction cardiovascular events significantly contributing to poor outcomes. Emerging evidence suggests that gut microbiome dysbiosis may influence cardiovascular risk through increased intestinal permeability and systemic inflammation. Although lactulose-a prebiotic known to modulate gut microbiota-has shown beneficial effects in experimental models, its impact on major adverse cardiovascular events (MACEs) after AMI remains unclear.

METHODS: In this single-center retrospective cohort study, we analyzed 165 AMI patients hospitalized between 2016 and 2019. Participants were stratified by lactulose use during hospitalization. The primary outcome was in-hospital MACEs. Multivariable logistic regression was used. Secondary outcomes included pneumonia incidence and length of hospital stay.

RESULTS: After adjustment for confounders, lactulose use was independently associated with a reduced risk of MACEs (adjusted odds ratio (OR) 0.40, 95% confidence interval (CI) 0.16-0.95; p = 0.038). The overall incidence of MACEs was 18.2% in the lactulose group versus 30.0% in controls, though this difference was not statistically significant in unadjusted analysis (χ² = 2.41, p = 0.12), likely reflecting limited statistical power. No significant associations were observed for pneumonia (OR = 0.17, p = 0.09) or hospital stay duration (p = 0.60).

CONCLUSIONS: In this retrospective analysis, lactulose supplementation was associated with reduced in-hospital cardiovascular events following AMI. However, these preliminary findings require validation in larger prospective studies to establish causality and elucidate underlying gut-mediated mechanisms. If confirmed, lactulose may represent a simple and accessible adjunct therapy in post-infarction care.},
}

@article {pmid41194669,
year = {2025},
author = {Schleiss, MR},
title = {The urgent search for predictive biomarkers in the emerging era of universal congenital cytomegalovirus screening.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1938},
pages = {20240434},
pmid = {41194669},
issn = {1471-2970},
support = {/TR/NCATS NIH HHS/United States ; //NIH/ ; //CDC/ ; },
mesh = {Humans ; *Cytomegalovirus Infections/congenital/diagnosis/complications ; Biomarkers/analysis ; *Cytomegalovirus/physiology ; Infant, Newborn ; Developmental Disabilities/virology ; Pregnancy ; Female ; },
abstract = {In utero acquisition of cytomegalovirus (CMV) represents the most common infectious cause of paediatric developmental disability. With a global prevalence of approximately 0.7%, congenital CMV (cCMV) infection can produce wide-ranging injury to the developing fetal and neonatal central nervous system, leading to microcephaly, intracranial calcifications, neuronal migration defects and damage to the developing cochlea and retina. Clinical sequelae include cerebral palsy, seizure disorder, intellectual disabilities, developmental delay, autism spectrum disorders, sensorineural hearing loss (SNHL) and visual impairment. It has been generally believed that most cCMV infections are asymptomatic in nature, and are not associated with long-term neurodevelopmental impairment. This dogma, however, has been called into question in the context of several state and provincial universal cCMV screening programmes that have been implemented in recent years in the United States and Canada. Moreover, the full spectrum of neurodevelopmental sequelae amongst asymptomatic cCMV cases is just starting to be recognized. Host and/or viral factors that predict which asymptomatic infants will have sequelae, including SNHL, are unknown. This review summarizes the current state of the art with respect to the search for predictive biomarkers that can inform the prognosis of asymptomatic cCMV, and aid in decision-making about therapeutic intervention.This article is part of the discussion meeting issue 'The indirect effects of cytomegalovirus infection: mechanisms and consequences'.},
}

Humans
*Cytomegalovirus Infections/congenital/diagnosis/complications
Biomarkers/analysis
*Cytomegalovirus/physiology
Infant, Newborn
Developmental Disabilities/virology
Pregnancy
Female

@article {pmid41194539,
year = {2025},
author = {Rolhion, N and Sokol, H},
title = {Targeting the gut microbiome in inflammatory bowel disease: from concept to clinical reality.},
journal = {Intestinal research},
volume = {23},
number = {4},
pages = {396-404},
doi = {10.5217/ir.2025.00104},
pmid = {41194539},
issn = {1598-9100},
support = {ERC-2021-COG-101043802/ERC_/European Research Council/International ; //MSDAVENIR/ ; },
abstract = {The gut microbiota, a complex community of trillions of microorganisms inhabiting the human gastrointestinal tract, has emerged as a critical regulator of immune homeostasis and gastrointestinal health. In the context of inflammatory bowel disease (IBD), comprising primarily Crohn's disease and ulcerative colitis, disruptions to this microbial ecosystem-collectively termed dysbiosis-have been increasingly recognized as central to disease pathogenesis. Recent research has established that alterations in gut microbiota not only reflect disease states but may actively drive immune dysregulation, barrier dysfunction, and mucosal inflammation. This review synthesizes current knowledge on the role of the gut microbiota in IBD and evaluates the therapeutic landscape of microbiota-modulating strategies using selected examples. Fecal microbiota transplantation, while offering proof-of-concept validation, is hindered by standardization challenges and variable clinical outcomes. As a response, microbiome-based therapeutics have evolved toward defined live biotherapeutic products including bacterial consortia and single-strain products, postbiotics, and metabolite-centered approaches targeting specific pathways. Groundbreaking research into rationally designed synthetic microbiomes and next-generation probiotics is driving a paradigm shift in microbiota-based treatment for IBD from empirical to precision-guided interventions.},
}

@article {pmid41194479,
year = {2025},
author = {Das, S and Patel, M and Khandelwal, S and Rawat, R and Shukla, S and Kumari, AP and Singh, K and Kumar, A},
title = {From Mutations to Microbes: Investigating the Impact of the Gut Microbiome on Repeat Expansion Disorders.},
journal = {Journal of neurochemistry},
volume = {169},
number = {11},
pages = {e70278},
doi = {10.1111/jnc.70278},
pmid = {41194479},
issn = {1471-4159},
mesh = {*Gastrointestinal Microbiome/physiology/genetics ; Humans ; Animals ; *Mutation/genetics ; Dysbiosis/genetics ; *DNA Repeat Expansion/genetics ; },
abstract = {Repeat expansion disorders (REDs) are a diverse array of genetic disorders characterized by the expansion of specific DNA sequences. These expansions are frequently dynamic and are susceptible to further expansion across generations. They contribute to disease progression by leading symptoms to become more severe and manifest earlier in subsequent generations. Despite a substantial understanding of their molecular mechanisms, the exact etiology of REDs remains tricky. Emerging evidence indicates that gut microbiome dysbiosis significantly impacts REDs by regulating various biochemical pathways. Alterations in microbial diversity and composition have been observed across multiple REDs; however, a comprehensive understanding of the complete scenario remains a significant challenge. To elucidate these dynamic interactions, future research should utilize multifaceted approaches. This review focuses on the key modifications in the gut microbiome that contribute to the pathogenesis of REDs and discusses potential gut microbiome-targeted therapeutic strategies that could be effectively employed to treat these disorders.},
}

*Gastrointestinal Microbiome/physiology/genetics
Humans
Animals
*Mutation/genetics
Dysbiosis/genetics
*DNA Repeat Expansion/genetics

@article {pmid41194405,
year = {2025},
author = {Cheng, Z and Wang, X and Yu, J and Li, X and Tang, Q and Qu, C and Yang, D and Li, Y and Xia, Y and Guo, Y},
title = {Trigonelline Improves Metabolism and Cardiac Function of HFpEF Mice Via Gut Microbiome Alterations-Mediated AMPK Activation.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e13956},
doi = {10.1002/advs.202513956},
pmid = {41194405},
issn = {2198-3844},
support = {CYYY-BSHPYXM-202204//Postdoctoral Incubation Project of The First Affiliated Hospital of Chongqing Medical University/ ; CYYY-BSYJSCXXM-202306//Doctoral Innovation Project of The First Affiliated Hospital of Chongqing Medical University/ ; CSTB2022NSCQ-MSX0913//Natural Science foundation of Chongqing/ ; CSTB2022NSCQ-BHX0712//Natural Science foundation of Chongqing/ ; 2022CQBSHTBT003//Chongqing Postdoctoral Science Foundation/ ; KJQN202300480//Chongqing education committee/ ; WZSTC-20220133//Chongqing Wanzhou district/ ; 2022YJKYXM-039//Chongqing University Three Gorges Hospital & Chongqing Three Gorges Central Hospital/ ; W0168//Program for Youth Innovation in Future Medicine, Chongqing Medical University/ ; 2022M720601//China Postdoctoral Science Foundation/ ; 82200422//National Natural Science Foundation of China/ ; },
abstract = {Heart failure with preserved ejection fraction (HFpEF) is a prevalent end-manifestation of cardiovascular diseases currently lacking effective treatment. Using a high-fat diet and L-NAME-induced mouse model, untargeted metabolomic profiling is performed and trigonelline is identified as a markedly reduced metabolite in HFpEF hearts. Oral trigonelline supplementation alleviates metabolic syndromes, including obesity, insulin resistance, and hepatic injury, leading to improved cardiac function in HFpEF mice. AMPK inhibition blunts the protective effects of trigonelline despite trigonelline per se not activating AMPK directly. Gut microbiota is required in AMPK activation and consequent beneficial effects on HFpEF mice by trigonelline. Further investigations demonstrate that trigonelline significantly restores HFpEF mouse gut microbiome dysbiosis by decreasing Firmicutes and increasing Bacteroidetes. In conclusion, the studies demonstrate that trigonelline supplementation mitigates HFpEF-associated metabolic disorders and improves cardiac function via gut microbiome alterations-mediated AMPK activation. These findings suggest that trigonelline has therapeutic potential for HFpEF.},
}

@article {pmid41194195,
year = {2025},
author = {Cansado-Utrilla, C and Saldaña, MA and Golovko, G and Khanipov, K and Watson, RK and Wild, AL and Brettell, LE and Weaver, SC and Heinz, E and Hughes, GL},
title = {Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {116},
pmid = {41194195},
issn = {2524-4671},
abstract = {UNLABELLED: Mosquito microbiota abundance and composition are modulated by a variety of factors, including pathogen exposure. The microbiome can also influence pathogen infection of the host and thus harbours considerable potential to impact transmission of pathogens. As such, there is a growing interest in using particular bacterial members of the microbiota for novel vector-control strategies. However, before novel microbiota-based approaches can move towards translation, a more complete understanding of the interactions between mosquitoes, their microbiome, and the pathogens they transmit, is required to better appreciate how variation in the microbiome of field mosquitoes affects these interactions. To examine the impact of the mosquito background and the associated diversity of bacterial microbiota within distinct hosts, we exposed several laboratory-reared and field-collected Aedes aegypti mosquito lines to Zika virus (ZIKV) and examined their bacterial load and composition in response to pathogen exposure and viral infection success. Intriguingly, we show that ZIKV exposure and infection had distinct impacts on microbiome composition and density within different mosquito lines. In one laboratory-reared line ZIKV exposure and infection reduced the bacterial load, while conversely in another line load was increased by the virus. Distinct responses of the microbiome were also seen in mosquitoes collected from the field. Sampling site-specific differences in the microbiome of mosquitoes were observed as virus infection altered microbiome alpha and beta diversities in one cohort, while in mosquitoes from other sampling sites, viral progression through the mosquito had minimal effect on the microbiome. We also identified bacterial taxa correlating with either ZIKV infection or a lack of infection. These taxa are potential candidates for future follow-up studies disentangling functional mechanisms and directionality of interactions. Overall, our study highlights that interactions between mosquito, virus, and microbiota are variable and context dependent, and that tripartite interactions among distinct mosquito cohorts and their microbiomes are not universal.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00482-0.},
}

@article {pmid41194006,
year = {2025},
author = {Ivanova, A and Buzova, V},
title = {A novel enzymatic approach for a targeted fungal growth inhibition.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {719},
pmid = {41194006},
issn = {1471-2180},
support = {03-ZP23-087//SkyLab AG/ ; 03-ZP23-087//SkyLab AG/ ; },
mesh = {*Malassezia/drug effects/growth & development/genetics ; Humans ; *Antifungal Agents/pharmacology ; *Chitinases/pharmacology ; *Glycoside Hydrolases/pharmacology ; Dandruff/microbiology/drug therapy ; Microbial Sensitivity Tests ; Chitosan/metabolism ; Scalp/microbiology ; Dermatomycoses/microbiology/drug therapy ; Fibroblasts/drug effects ; Female ; Male ; Cell Line ; Adult ; Middle Aged ; },
abstract = {BACKGROUND: Dandruff represents a complex, multifactorial disorder characterized by impaired barrier function, altered lipid composition, and microbial imbalance. The principal pathogenic mechanism, however, involves excessive colonization by Malassezia species, notably M. furfur, M. restricta and M. globosa, on the scalp. Standard antifungal options often lead to undesirable effects, including itching and irritation, and may negatively impact the scalp microbiome. This study evaluates combination of chitinase and chitosanase, targeting fungal cell wall chitin and chitosan, as a promising targeted approach for scalp Malassezia spp.

METHODS: The in vitro antifungal activities of chitinase (100 U/g) and chitosanase (200 U/g) were evaluated against Malassezia furfur, Malassezia restricta, and Malassezia globosa at concentrations ranging from 0.125% to 5% w/w. Their efficacy was compared to that of conventional antifungal agents, including climbazole, piroctone olamine, selenium sulfide, zinc pyrithione, and propanediol caprylate. Cytotoxicity was assessed using fibroblast cell lines via MTT assay and fluorescence microscopy. A clinical study (n = 18) evaluated the impact of a solution containing 0.25% chitinase and 0.25% chitosanase on scalp M. furfur and M. restricta DNA and RNA levels using quantitative PCR (qPCR). A metagenomic analysis was conducted to assess the impact of enzymatic treatment on bacterial composition and diversity.

RESULTS: Individually, 0.25% chitinase and 0.25% chitosanase inhibited Malassezia spp. growth by 23.85% and 26.15%, respectively (p < 0.05). When combined at 0.25%, they achieved 98.38% inhibition (p < 0.05), with complete suppression observed at 0.5%. In a clinical study, a 3-hour scalp treatment with a solution containing 0.25% chitinase and 0.25% chitosanase followed by quantitative PCR of post-treatment samples demonstrated significant reductions in DNA and RNA levels of M. furfur and M. restricta. DNA content decreased 2.4- and 1.9-fold, and RNA levels declined 2.4- and 4.6-fold, respectively. Cytotoxicity was detected only at concentrations ≥ 7.6%, well above the effective antifungal doses. The metagenomic analysis demonstrated that a three-hour scalp treatment with chitinase - chitosanase solution increased alpha diversity (Chao1 index) and doubled the number of identifiable operational taxonomic units (OTUs).

CONCLUSIONS: The chitinase-chitosanase combination offers a promising targeted approach for scalp Malassezia spp. control without broad antimicrobial effects.},
}

*Malassezia/drug effects/growth & development/genetics
Humans
*Antifungal Agents/pharmacology
*Chitinases/pharmacology
*Glycoside Hydrolases/pharmacology
Dandruff/microbiology/drug therapy
Microbial Sensitivity Tests
Chitosan/metabolism
Scalp/microbiology
Dermatomycoses/microbiology/drug therapy
Fibroblasts/drug effects
Female
Male
Cell Line
Adult
Middle Aged

@article {pmid41193988,
year = {2025},
author = {Zhang, W and Xu, S and Bai, T and Aman, BO and Wang, Y and Li, S and Wang, J and Qin, Y and Wang, YY and Zheng, SJ},
title = {Banana genotype-associated microbiomes play an essential role in suppressing Fusarium wilt.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1513},
pmid = {41193988},
issn = {1471-2229},
support = {YNWR-QNBJ-2020-298//The Provincial Xingdian Talent Program "Young Talent" Project/ ; XDYC-QNRC-2022-0243//The Provincial Xingdian Talent Program "Young Talent" Project/ ; D23033//Funded in part by Seedqual Initiative of One CGIAR, and the International Atomic Energy Agency, under project "An Integrative Approach to Enhancing Disease Resistance Against Fusarium Wilt (Foc TR4) in Banana - Phase II/ ; D23033//Funded in part by Seedqual Initiative of One CGIAR, and the International Atomic Energy Agency, under project "An Integrative Approach to Enhancing Disease Resistance Against Fusarium Wilt (Foc TR4) in Banana - Phase II/ ; 202301AT070008//General Program of Yunnan Provincial Natural Science Foundation/ ; 202401BD070001-096//Yunnan Fundamental Research Projects/ ; NSFC32161143001//National Natural Science Foundation of China/ ; YNWR-YLXZ-2018-018//Yunling Scholar Programme of Yunnan Provincial Government/ ; },
abstract = {BACKGROUND: Fusarium wilt of banana (FWB) seriously threatens the banana industry’s sustainable development. Recent evidence indicates that FWB occurrence and development are not only regulated by host resistance genes, but are also significantly influenced by host microbiomes. However, the link between banana genotypes and genotype-associated microbiomes remains unclear.

RESULTS: In this study, we used the amplification sequencing method to characterize the bacterial and fungal communities in three root compartments (root peripheral, rhizosphere, and endosphere) of six banana genotypes with different levels of FWB resistance. Sequence analysis showed that the banana host’s resistance to FWB significantly correlated with its associated bacterial and fungal communities in the root peripheral and rhizosphere. The FWB highly resistant group (RG) have more stable cross-kingdom microbial networks than FWB moderately resistant group (MG) and susceptible group (SG). The relative abundance of potential beneficial microorganisms differs significantly between RG and SG in the root periphery and rhizosphere. Bacillus, Penicillium, and Trichoderma are enriched in the root periphery of RG, whereas Flavobacterium, Sphingobium, and Pseudomonas are enriched in the root periphery and rhizosphere of SG. Inoculation with the RG biomarker Penicillium sp., which showed high relative abundance in the root periphery, significantly reduced the FWB disease index in the susceptible banana genotypes Brazilian and Guijiao No.1 by 51.67% and 51.72%, respectively.

CONCLUSIONS: The outcome of this study provides solid data that banana genotype-linked, root-associated microbiomes can play a highly significant role in suppressing FWB. This provides a promising basis for microbiome-based interventions in FWB management.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07565-9.},
}

@article {pmid41193778,
year = {2025},
author = {Pirouzbakht, M and Hamzeh, S and Soleimani Samarkhazan, H},
title = {Beyond single biomarkers: multi-omics strategies to predict immunotherapy outcomes in blood cancers.},
journal = {Clinical and experimental medicine},
volume = {25},
number = {1},
pages = {355},
pmid = {41193778},
issn = {1591-9528},
mesh = {Humans ; *Immunotherapy/methods ; *Biomarkers, Tumor ; *Hematologic Neoplasms/therapy/genetics/immunology ; Genomics/methods ; Proteomics/methods ; Metabolomics/methods ; Treatment Outcome ; Multiomics ; },
abstract = {Immunotherapy has revolutionized hematologic cancer treatment, yet responses remain unpredictable due to primary resistance, relapse, and life-threatening toxicities. Conventional biomarkers fail to capture the complexity of tumor-immune interactions, necessitating integrative approaches. This review explores how multi-omics technologies, genomics, transcriptomics, proteomics, metabolomics, spatial omics, and microbiome profiling, decode the molecular drivers of immunotherapy efficacy and adverse events in hematologic malignancies. We highlight key advances: genomics reveals neoantigen landscapes and HLA diversity shaping checkpoint inhibitor responses; transcriptomics identifies T-cell exhaustion signatures predictive of CAR-T failure; metabolomics uncovers lactate-driven immunosuppression in AML; and spatial omics maps immune architectures linked to Hodgkin lymphoma outcomes. Supervised machine learning algorithms (e.g., random forest, support vector machines) integrate these layers to build predictive models for cytokine release syndrome (CRS) and resistance, while longitudinal ctDNA monitoring enables dynamic therapy adaptation. Emerging frontiers like CRISPR-based epitope editing, digital twins for in silico clinical trials, and non-coding RNA biomarkers further refine precision strategies. Despite challenges in data integration, tumor plasticity, and ethical frameworks, multi-omics is accelerating biomarker-driven trial designs (e.g., basket trials with omics stratification) and patient-centric tools (wearable sensors for real-time metabolite tracking). This review distinguishes itself by synthesizing these rapid technological advances not only to predict outcomes but also to chart a forward-looking roadmap for their clinical translation, offering a unique perspective on overcoming the current barriers to precision immuno-oncology. Together, these advances promise to transform immunotherapy from empirical to precision medicine, optimizing outcomes for leukemia, lymphoma, and myeloma patients.},
}

Humans
*Immunotherapy/methods
*Biomarkers, Tumor
*Hematologic Neoplasms/therapy/genetics/immunology
Genomics/methods
Proteomics/methods
Metabolomics/methods
Treatment Outcome
Multiomics

@article {pmid41193697,
year = {2025},
author = {Chica Cardenas, LA and Leonard, MM and Baldridge, MT and Handley, SA},
title = {Gut virome dynamics: from commensal to critical player in health and disease.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {41193697},
issn = {1759-5053},
abstract = {The gut virome is a complex ecosystem characterized by the interplay of diverse viral entities, predominantly bacteriophages and eukaryotic viruses. The gut virome has a critical role in human health by shaping microbial community profiles, modulating host immunity and influencing metabolic processes. Different viral metagenomics approaches have revealed the remarkable diversity of the gut virome, showing individual-specific patterns that evolve over time and adapt dynamically to environmental factors. Perturbations in this community are increasingly associated with chronic immune and inflammatory conditions, metabolic disorders and neurological conditions, highlighting its potential as a diagnostic biomarker and therapeutic target. The early-life gut virome is particularly influential in establishing lifelong health trajectories through its interactions with diet, immune pathways and others, thereby contributing to inflammatory and metabolic regulation. This Review synthesizes current knowledge of gut virome composition, dynamics and functional relevance, critically evaluating evidence distinguishing causal from correlative roles in disease pathogenesis. The interactions of the virome with other microbiome components and host immunity are examined, and emerging translational applications, including phage therapy and biomarker development, are discussed. Integrating these insights while acknowledging methodological challenges provides a comprehensive framework for understanding the complex roles of the gut virome in health and disease.},
}

@article {pmid41193636,
year = {2025},
author = {Hug, LA and Hatzenpichler, R and Moraru, C and Soares, AR and Meyer, F and Heyder, A and , and Probst, AJ},
title = {Author Correction: A roadmap for equitable reuse of public microbiome data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-025-02212-3},
pmid = {41193636},
issn = {2058-5276},
}

@article {pmid41193635,
year = {2025},
author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R},
title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41193635},
issn = {2058-5276},
support = {991222//Simons Foundation/ ; },
abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.},
}

@article {pmid41193561,
year = {2025},
author = {Chen, TY and Huang, WY and Liu, KH and Lin, S and Wu, HM},
title = {Circulating endotoxin is correlated with fatty acid binding protein 2 and leukocyte nuclear factor-κB activation in menopausal women.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38693},
pmid = {41193561},
issn = {2045-2322},
support = {111-CCH-IRP-086//Changhua Christian Hospital/ ; MOST 108-2314-B-371-004-MY3//National Science and Technology Council, Taiwan/ ; },
mesh = {Humans ; Female ; *Fatty Acid-Binding Proteins/blood/metabolism ; Middle Aged ; *Endotoxins/blood ; *Leukocytes/metabolism ; *NF-kappa B/metabolism ; *Menopause/blood ; Inflammation/blood ; Endotoxemia/blood ; Fasting/blood ; Glucose Tolerance Test ; Biomarkers/blood ; },
abstract = {Circulating endotoxin is mainly derived from gut microbiome and is frequently increased after meals. However, the interplay between endotoxemia and innate immune cells in systemic inflammation remains unclear. The aim was to investigate the role of endotoxemia in systemic inflammation, focusing on the immune responses in innate immune cells. Menopausal women (n = 174) were divided into 2 groups. Blood samples were collected from the participants of group 1 (n = 80), who fasted for at least 8 h, to analyze the correlation between endotoxin levels, fatty acid-binding protein 2 (FABP2), markers of systemic inflammation, and nuclear factor-κB (NF-κB) activation in leukocytes. The participants of group 2 (n = 94) fasted for at least 8 h and received oral glucose tolerance test (OGTT). Their fasting and post-OGTT blood samples were also collected to evaluate the impact of postprandial endotoxemia on the expression of NF-κB target genes in leucocytes. The study revealed that circulating endotoxin level was significantly associated with FABP2 level and NF-κB activation in leukocytes after fasting and within a 2 h-OGTT period. Variation in endotoxin levels (about 1 EU/ml) was sufficient to modulate NF-κB activation in leukocytes. These results provide clues for understanding the effects of postprandial endotoxemia on immune cell activation and inflammation induction. Our findings suggest that an increase in intestinal barrier permeability might be linked to endotoxemia-induced systemic inflammation in menopausal women.},
}

Humans
Female
*Fatty Acid-Binding Proteins/blood/metabolism
Middle Aged
*Endotoxins/blood
*Leukocytes/metabolism
*NF-kappa B/metabolism
*Menopause/blood
Inflammation/blood
Endotoxemia/blood
Fasting/blood
Glucose Tolerance Test
Biomarkers/blood

@article {pmid41193447,
year = {2025},
author = {Baskaran, N and V, M and S, S and Ranjan, J and Islam, A and Hussain, MS and Debnath, B and Ashique, S},
title = {Applications of Artificial Intelligence and Machine Learning in Microbiome and Colorectal Cancer Research: Diagnostic Advances, Prognostic Tools, and Forensic Implications.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128405592251004061813},
pmid = {41193447},
issn = {1873-4286},
abstract = {Artificial Intelligence (AI) and Machine Learning (ML) are rapidly transforming microbiome and colorectal cancer (CRC) research by enabling high-throughput data analysis and predictive modelling. This review highlights the current applications of AI/ML tools, such as Convolutional Neural Networks, Random Forest classifiers, and Support Vector Machines, in CRC diagnostics and microbiome profiling. It discusses how AI-integrated endoscopic and imaging systems improve polyp detection accuracy and reduce diagnostic delays. The manuscript also introduces the novel use of AI and microbial fingerprints in forensic science, including postmortem interval estimation and individual identification. Lastly, emerging trends in microbiotabased precision medicine and ethical considerations surrounding AI deployment are explored. These insights underscore AI/ML's potential in reshaping clinical diagnostics, prognostics, and forensic practices related to CRC. This review emphasizes the translational impact of AI/ML in CRC, from bench to bedside to the courtroom, highlighting both current challenges and future research directions.},
}

@article {pmid41192778,
year = {2025},
author = {Tabata, K and Ikarashi, N and Yoshida, R and Shinozaki, Y and Kato, Y and Kon, R and Iwasaki, Y and Yokoyama, K and Saito, R and Sakai, H and Hosoe, T},
title = {High-fat diet exacerbates atopic dermatitis through alterations in the gut microbiome.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110164},
doi = {10.1016/j.jnutbio.2025.110164},
pmid = {41192778},
issn = {1873-4847},
abstract = {Atopic dermatitis (AD) is a chronic, relapsing skin disorder characterized by pruritic eczema. In addition to genetic predispositions, environmental factors such as diet are thought to contribute to the exacerbation of AD. The aim of this study was to provide scientific evidence on how environmental factors, particularly a high-fat diet (HFD), influence the pathogenesis of AD. AD was induced in NC/Nga mice fed an HFD through the application of 2,4-dinitrochlorobenzene. In the AD-HFD group, the expression levels of inflammatory markers (Tnfa, Il1b, Ptgs2, and Nos2) and AD-related factors (Il4, Ccl17, and Tslp) in the skin were significantly elevated compared with those in the AD group (mice fed a normal diet). Alteration of gut microbiota was observed in the AD-HFD group, characterized by a reduction in the abundances of Bacteroides acidifaciens and Parabacteroides distasonis, bacteria involved in short-chain fatty acid (SCFA) production. Moreover, the levels of acetate, propionate, and butyrate in the cecal contents were significantly decreased in the AD-HFD group. Fecal microbiota transplantation experiments revealed that alterations in the gut microbiota were associated with the exacerbation of AD symptoms. Furthermore, the administration of acetate alleviated the increase in the expression of skin inflammation markers and AD-related factors and the overall exacerbation of AD-like symptoms induced by the HFD. HFD intake exacerbates AD-like symptoms, and this exacerbation is linked to alteration of gut microbiota and a decrease in SCFA levels. These results suggest that acetate and acetate-producing bacteria may serve as potential tools for the prevention and treatment of AD.},
}

@article {pmid41192743,
year = {2025},
author = {Ueyama, M and Ohue-Kitano, R and Kimura, I and Kimura, H},
title = {Association between Gut Actinobacteria and Obstructive Sleep Apnoea Severity in Japanese Adults.},
journal = {Respiratory medicine},
volume = {},
number = {},
pages = {108472},
doi = {10.1016/j.rmed.2025.108472},
pmid = {41192743},
issn = {1532-3064},
abstract = {BACKGROUND: Gut microbiota are known to mediate human health and are affected by physiological conditions, including hypoxia. Although studies involving animal models have shown that intermittent hypoxia alters gut microbiota, its effects in adult Japanese patients with obstructive sleep apnoea (OSA) remain unclear. We investigated the association between OSA severity and gut microbiota composition in Japanese adults with OSA.

METHODS: This cross-sectional study included 74 Japanese diagnosed with OSA via polysomnography. The average body mass index was 30.5 ± 3.8 kg/m[2] and the average 3% oxygen desaturation index (ODI) was 39.9 ± 20.0. No control group was included. Faecal samples were collected in a fasting period of >10 h. The association between 3% ODI and gut microbiota were analysed at the phylum, family and genus level.

RESULTS: At the phylum level, 3% ODI significantly positively correlated with Actinobacteria (r = 0.3151, p = 0.0126) and negatively correlated with Firmicutes (r = 0.3150, p = 0.0126). No significant correlations were found with Proteobacteria or Bacteroidetes. At the family level, 3% ODI significantly positively correlated with Bifidobacteriaceae in Actinobacteria (r = 0.2373, p = 0.0418). At genus level, Bifdobacterium was prominently increased compared with other group.

CONCLUSION: This study showed that the gut microbiome in Japanese with OSA showed an increase in Bifdobacterium. Although our cohort was biased towards moderate obesity and severe OSA severity, intermittent hypoxia might contribute to the change of gut microbiome. These findings suggest that increased Bifdobacterium may help maintain gut homeostasis under hypoxic stress, especially in Japanese.},
}

@article {pmid41188868,
year = {2025},
author = {Duan, S and Wang, Y and Zhan, S and Ye, Z and Luo, T and Zhou, Y and Xu, H and Huang, H},
title = {Engineered probiotics: a new era in treating inflammatory bowel disease.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1223},
pmid = {41188868},
issn = {1479-5876},
support = {82100124//National Natural Science Foundation of China/ ; 2024A1515220138//Basic and Applied Basic Research Foundation of Guangdong Province/ ; A2025164//Guangdong Medical Science and Technology Research Fund/ ; B2025093//Guangdong Medical Science and Technology Research Fund/ ; 2025A03J4148//Science and Technology Projects in Guangzhou/ ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic, relapsing condition that is often refractory to treatment. Data from the Global Burden of Disease Study (GBD) indicate that the incidence and disease burden of this condition continue to rise globally, posing a significant public health challenge. With advancements in synthetic biology, engineered probiotics constructed using gene-editing tools like CRISPR-Cas9 have offered a groundbreaking strategy for treating IBD. These engineered probiotics modulate the intestinal microenvironment with high precision through multiple mechanisms, including the targeted delivery of anti-inflammatory factors, scavenging of excess reactive oxygen species (ROS), restoration of barrier integrity, and regulation of microbial homeostasis. Preclinical studies indicate that, in terms of therapeutic precision and functionality, these probiotics may provide advantages over traditional medications. In addition, advances in delivery systems have improved acid resistance and targeted colonization at lesion sites. Engineered smart, responsive engineered probiotics can monitor inflammation in real-time and dynamically release therapeutic molecules. Their use in combination with conventional drugs can significantly improve mucosal healing. This study summarizes recent research progress of engineered probiotics in IBD diagnosis and treatment, aiming to provide insights into the application of microbiome-driven curative interventions in IBD.},
}

@article {pmid41192727,
year = {2025},
author = {Lai, J and Yang, B and Ju, P and Sun, Y and Sun, X and Cheng, W and Chen, J},
title = {Gut microbiota from adolescents with social anxiety disorder is associated with behavioral alterations and metabolic changes in the medial prefrontal cortex.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120597},
doi = {10.1016/j.jad.2025.120597},
pmid = {41192727},
issn = {1573-2517},
abstract = {BACKGROUND: Social anxiety disorder (SAD) is a prevalent and burdensome neuropsychiatric disorder characterised by pronounced and persistent fear and anxiety in social situations. While evidence links gut microbiota to neuropsychiatric disorders, its role in SAD remains poorly understood.

AIM: In this study, we aimed to investigate the potential involvement of gut microbiota in SAD pathophysiology through fecal microbiota transplantation.

METHOD: We collected demographic data and fecal samples from 40 first-episode, comorbidity-free, and drug-naive adolescent patients with SAD, along with 32 demographically matched healthy controls. Fecal samples underwent 16S rDNA amplicon sequencing and were pooled for transplantation into neonatal rats from postnatal day 1 through late adolescence. Recipient rats were evaluated with behavioral tests, microbiota detection, and non-targeted metabolomics of the medial prefrontal cortex.

RESULT: Patients with SAD displayed alterations in gut microbiota composition. Rats colonized with SAD-associated microbiota exhibited anxiety-like behaviors and reduced social novelty preference, alongside microbial profiles partially overlapping with those of patients. These behavioral changes were correlated with microbiota differences, and distinct metabolic alterations were detected in the medial prefrontal cortex of SAD-colonized rats.

CONCLUSION: Gut microbiota from adolescents with SAD is associated with behavioral and metabolic alterations in a rodent model, suggesting a potential role of the gut-brain axis in SAD. Further studies are warranted to establish causality and elucidate underlying mechanisms.},
}

@article {pmid41192697,
year = {2025},
author = {Forton, C and DeVries, J and Lou, M and Brundin, S and Cave, T and Anis, E and Madaj, Z and Isaguirre, C and Johnson, A and Sheldon, RD and Smart, L and Bohnert, KM and Kassien, J and Holzgen, O and Youssef, NA and Khan, T and Brundin, L},
title = {Gut microbiome-derived tryptophan metabolites predict relapse in alcohol use disorder.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106161},
doi = {10.1016/j.bbi.2025.106161},
pmid = {41192697},
issn = {1090-2139},
abstract = {Relapse is common in alcohol use disorder (AUD), a condition that affects nearly 11 % of adults in the US. Excessive alcohol consumption causes gut dysbiosis, which may in turn alter the production of bacterial-derived tryptophan metabolites. These metabolites impact the intestinal enteroendocrine environment and modulate neuroinflammation. This can ultimately affect behavior. However, the role of bacterial-derived tryptophan metabolites in AUD is not well-understood. Thus, in this study, we enrolled 40 patients admitted for severe AUD (26 males, 14 females) to investigate whether bacterial-derived indoles could predict AUD relapse. Upon enrollment, alcohol use as well as depression and anxiety symptoms were assessed. Peripheral blood samples were collected and analyzed for cytokines, bacterial-derived as well as endogenous tryptophan metabolites, and hematological factors. At three months after discharge, 25 patients completed follow-up and were re-assessed for clinical symptoms to identify AUD relapse. Ten patients relapsed and 15 patients were in early remission. Two bacterial tryptophan metabolites, indole-3-carboxaldehyde (IAld) and indole-3-acetic acid (IAA), significantly predicted relapse versus remission using logistic regression models (p = 0.019, SGPV = 0, and p = 0.035, SGPV = 0 respectively). These findings remained significant after adjustment for age, sex, BMI, and when additionally adjusting for nicotine use and depression severity. Moreover, higher IAld levels correlated with increased serotonin levels (Pearson's R; 0.592, p < 0.001) and fewer white blood cells (Pearson's R; -0.318, p < 0.05) in all 40 patients. Our data indicate significant interactions between microbiome-derived metabolites and host metabolism, and that IAld specifically may have a protective role in AUD, potentially through serotonin modulation.},
}

@article {pmid41192621,
year = {2025},
author = {Carpani, JM and Barta, JR and Guy, RA},
title = {Suppression/competition PCR: A novel method to minimize unwanted amplicons in metabarcoding, with applications to parasite detection in fecal samples.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107320},
doi = {10.1016/j.mimet.2025.107320},
pmid = {41192621},
issn = {1872-8359},
abstract = {Metabarcoding is widely used for detecting microorganisms in fecal samples, but its effectiveness is often limited by the co-amplification of abundant non-target DNA. In this study, a novel metabarcoding assay was developed to amplify a near-complete 18S rRNA gene fragment suitable for long-read nanopore sequencing, enhancing taxonomic resolution. The primers were optimized to maximize detection of parasitic taxa while minimizing off-target amplification of bacterial and archaeal sequences, thereby improving assay specificity. In this study, the 18S metabarcoding assay worked well on clinical fecal samples containing clinically relevant levels of parasites. However, analysis of ungulate fecal samples revealed that fungal and plant sequences vastly outnumbered other eukaryotic taxa in many samples, obscuring the detection of low-abundance protozoan and helminth parasites. To address this, Suppression/Competition PCR was developed, a novel method that selectively reduces amplification of unwanted DNA. This approach reduced fungal and plant reads by over 99 %, enabling sequences from other taxa to comprise an average of over 98 % of total reads as opposed to an initial 36 %. Utilizing this newly-developed metabarcoding assay in either the standard or Suppression/Competition configuration on fecal DNA extracts from a range of host species, parasites of interest such as Cryptosporidium sp., Cyclospora cayetanensis, Blastocystis sp., Entamoeba sp., Eimeria sp., Ancylostoma sp., and Toxocara sp. were detected, demonstrating its broad applicability.},
}

@article {pmid41192424,
year = {2025},
author = {Li, P and Sun, J and Geng, Y and Jiang, Y and Li, YZ and Zhang, Z},
title = {Assessment of enzyme diversity in the fermented food microbiome.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101430},
doi = {10.1016/j.cels.2025.101430},
pmid = {41192424},
issn = {2405-4720},
abstract = {Microbial bioactivity is essential for the flavor, appearance, quality, and safety of fermented foods. However, the diversity and distribution of enzymatic resources in fermentation remain poorly understood. This study explored 10,202 metagenome-assembled genomes from global fermented foods using machine learning, identifying over 5 million enzyme sequences grouped into 98,693 homologous clusters, representing over 3,000 enzyme types. Functional analysis revealed that 84.4% of these clusters were unannotated in current databases, with high novelty in terpenoid and polyketide metabolism enzymes. Peptide hydrolases exhibited broad environmental adaptability based on predicted optimal temperatures and pH, and niche breadth calculations indicated 31.3% of enzyme clusters displayed food-type specificity. Additionally, we developed a machine learning model to classify fermented food sources by enzyme clusters, highlighting key enzymes differentiating habitats. Our findings emphasize the untapped potential of fermented food environments for enzyme resource exploration, offering valuable insights into microbial functions for future food research. A record of this paper's transparent peer review process is included in the supplemental information.},
}