@article {pmid40275044,
year = {2025},
author = {Guo, Y and Tang, G and Wang, Z and Chu, Q and Zhang, X and Xu, X and Fan, Y},
title = {Characterization of the gut microbiota in different immunological responses among PLWH.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14311},
pmid = {40275044},
issn = {2045-2322},
support = {CZWJ2022B002//Project of Chuzhou Health Commission/ ; IMMDL20220001//Inflammation and Immune Mediated Diseases Laboratory of Anhui Province Open Project/ ; JKS2022003//Research Funds of Center for Big Data and Population Health of IHM/ ; },
abstract = {Despite gut microbial dysbiosis has been demonstrated in people living with HIV (PLWH), the association between gut microbial and inflammatory cytokines in PLWH with different immunoreaction to antiretroviral therapy (ART) is poorly understood. The purpose of this study is to explore between gut microbial and inflammatory cytokines in PLWH with different immunoreaction. 68 PLWH and 27 healthy controls(HCs) in Anhui Province were recruited from December 2021 to March 2022, including 35 immunological responders (IRs) (CD4[+]T-cell count ≥ 350 cells/µL) and 33 immunological non-responders (INRs) (CD4[+]T-cell count < 350 cells/µL) without comorbidities. Blood and stool samples were collected from all participants. Blood was used to detect microbial translocation biomarkers and inflammatory cytokines. Luminex Multifactor Detection Technology was performed to quantify plasma microbial translocation biomarkers and inflammation cytokines. Bacterial 16S rDNA sequencing was performed on stool samples. Microbiome sequencing revealed that the relative abundances of Fusobacteria, Actinobacteria, Verrucomicrobiaceae Acidaminococcaceae, Fusobacteriaceae and Megasphaera were greater, whereas Verrucomicrobia, Ruminococcaceae, Megamonas, Faecalibacterium, Roseburia and Dialister were more depleted in the HIV groups than those in the HCs (all P < 0.05). In the INRs group, the relative abundances of Actinomycetales, Micrococcaceae, Actinomyces, Intestinibacter, Rothia were greater (all P < 0.05), whereas Sutterellaceae, Parabacteroides, Veillonella, Butyricimonas resulted less abundant than in the IRs (all P < 0.05). TNF-ɑ are negatively correlated with the abundances of Dialiste (P = 0.022). CD54 are negatively correlated with Dialister and Subdoligranulum (P = 0.011). Recent and baseline CD4[+]T cells counts are directly proportional to Butyricimonas and Parabacteroides, while are inversely proportional with Veillonella and Rothia (all P < 0.05). Dysbiosis of the gut microbial might be one of the factors leading to the different immunoreaction and therapeutic effects of ART.},
}

@article {pmid40274773,
year = {2025},
author = {Kolland, D and Kuhlmann, M and de Almeida, GP and Köhler, A and Arifovic, A and von Strempel, A and Pourjam, M and Bolsega, S and Wurmser, C and Steiger, K and Basic, M and Neuhaus, K and Schmidt-Weber, CB and Stecher, B and Zehn, D and Ohnmacht, C},
title = {A specific microbial consortium enhances Th1 immunity, improves LCMV viral clearance but aggravates LCMV disease pathology in mice.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3902},
pmid = {40274773},
issn = {2041-1723},
support = {395357507 CRC1371 P07, P14, Z01 and Z02//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 716718//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Anti-viral immunity can vary tremendously from individual to individual but mechanistic understanding is still scarce. Here, we show that a defined, low complex bacterial community (OMM[12]) but not the general absence of microbes in germ-free mice leads to a more potent immune response compared to the microbiome of specific-pathogen-free (SPF) mice after a systemic viral infection with LCMV Clone-13. Consequently, gnotobiotic mice colonized with OMM[12] have more severe LCMV-induced disease pathology but also enhance viral clearance in the intestinal tract. Mechanistically, single-cell RNA sequencing analysis of adoptively transferred virus-specific T helper cells and endogenous T helper cells in the intestinal tract reveal a stronger pro-inflammatory Th1 profile and a more vigorous expansion in OMM[12] than SPF mice. Altogether, our work highlights the causative function of the intestinal microbiome for shaping adaptive anti-viral immunity with implications for vaccination strategies and anti-cancer treatment regimens.},
}

@article {pmid40274681,
year = {2025},
author = {Dhurandhar, Y and Tomar, S and Das, A and Prajapati, JL and Singh, AP and Bodake, SH and Namdeo, KP},
title = {Chronic inflammation in obesity and neurodegenerative diseases: exploring the link in disease onset and progression.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {424},
pmid = {40274681},
issn = {1573-4978},
abstract = {Obesity, a worldwide health emergency, is defined by excessive fat accumulation and significantly impacts metabolic health. In addition to its recognized association with cardiovascular disease, diabetes, and other metabolic illnesses, recent studies have revealed the connection between obesity and neurodegeneration. The main reason for this link is inflammation caused by the growth of fat tissue, which activates harmful processes that affect how the brain works. Fat tissue, particularly the fat around the organs, produces various substances that cause inflammation, such as cytokines (TNF-α, IL-6), adipokines (leptin, resistin), and free fatty acids. These chemicals cause low-grade, persistent systemic inflammation, which is becoming more widely acknowledged as a major factor in peripheral metabolic dysfunction and pathology of the central nervous system (CNS). Inflammatory signals in the brain cause neuroinflammatory reactions that harm neuronal structures, change neuroplasticity, and disrupt synaptic function. When obesity-related inflammation is present, the brain's resident immune cells, known as microglia, become hyperactivated, which can lead to the production of neurotoxic chemicals, which can cause neuronal death. This neuroinflammation exacerbates the negative effects of obesity on brain health and is linked to cognitive decline, Alzheimer's disease, and other neurodegenerative disorders. Moreover, the blood-brain barrier (BBB) exhibits increased permeability during inflammatory states, facilitating the infiltration of peripheral immune cells and cytokines into the brain, hence exacerbating neurodegeneration. Adipose tissue is a source of chronic inflammatory mediators, which are examined in this review along with the molecular pathways that connect inflammation brought on by obesity to neurodegeneration. Additionally, it addresses various anti-inflammatory treatment approaches, including lifestyle modifications, anti-inflammatory medications, and gut microbiota modulation, to lessen the metabolic and neurological effects of obesity. Recognizing the link between obesity and inflammation opens up new opportunities for early intervention and the development of targeted treatments to prevent or alleviate neurodegenerative disorders.},
}

@article {pmid40274492,
year = {2025},
author = {Singh, BK and Jiang, G and Wei, Z and Sáez-Sandino, T and Gao, M and Liu, H and Xiong, C},
title = {Plant pathogens, microbiomes, and soil health.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.03.013},
pmid = {40274492},
issn = {1878-4380},
abstract = {Healthy soil is vital for ecosystem sustainability and global food security. However, anthropogenic activities that promote intensive agriculture, landscape and biodiversity homogenization, and climate change disrupt soil health. The soil microbiome is a critical component of healthy soils, and increasing evidence suggests that soils with low diversity or homogenized microbial systems are more susceptible to soil pathogen invasion, but the extent and mechanisms that increase the threat of pathogen invasion (i.e., increase in prevalence of existing species and introduction of new species) remain unclear. This article aims to fill this knowledge gap by synthesizing the literature and providing novel insights for the scientific community and policy advisors. We also present the current and future global distribution of some dominant soil-borne pathogens. We argue that an improved understanding of the interplay between the soil microbiome, soil health, host, and pathogen distribution, and their responses to environmental changes is urgently needed to ensure the future of productive farms, safe food, sustainable environments, and holistic global well-being.},
}

@article {pmid40274457,
year = {2025},
author = {Liu, ZQ and Ciudad, MT and McGaha, TL},
title = {New insights into tryptophan metabolism in cancer.},
journal = {Trends in cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.trecan.2025.03.008},
pmid = {40274457},
issn = {2405-8025},
abstract = {Tryptophan (Trp) is an essential amino acid and key intermediate in a range of biological processes. Early studies identified altered Trp utilization in cancer cells favoring cancer survival and growth. Seminal findings linking Trp metabolism and suppression of immunity led to an explosion of interest ultimately culminating in clinical trials targeting these pathways in melanoma. The failure of these trials led to a clinical retreat in this approach; however, recent insights into the complex interplay of the various Trp circuits and between tumor cells, immune cells, and the microbiota have shown that reconsideration of Trp metabolism is needed. Here, we discuss recent developments in our understanding of Trp metabolism and apparent contradictions in the field. We also discuss adaptations that occur when Trp pathways are manipulated, which may impact therapy responses.},
}

@article {pmid40274155,
year = {2025},
author = {Yang, H and Lei, C and Li, D and Ma, L and Zhang, N and Lang, Y and Wu, L and Wang, M and Tian, H and Li, C},
title = {An integrated fecal microbiome and metabolomics in type 2 diabetes mellitus rats reveal mechanism of action of Moringa oleifera Lamarck seeds polysaccharides to alleviate diabetes.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {143437},
doi = {10.1016/j.ijbiomac.2025.143437},
pmid = {40274155},
issn = {1879-0003},
abstract = {Moringa oleifera Lamarck seeds (MOS) have been traditionally used in folk medicine and documented for their potential to alleviate type 2 diabetes symptoms, but the potential mechanisms are still unknown. The purpose of this article is to investigate the effects of MSAP (alkali-extracted polysaccharide from MOS) on diabetic rats by assessing its impact on the gut microbiome, diabetes-related biochemical markers, and fecal metabolomics. The results demonstrated that the fasting blood glucose, glucose tolerance, insulin tolerance, insulin level and lipopolysaccharides (LPS) level in the rats treated with MSAP were all improved. Specifically, MSAP was found to modulate the composition and diversity of the gut microbiota, increasing the ratio of Firmicutes/Bacteroidetes, which enhanced the quantity of probiotic Lactobacillus and butyrate-producing bacteria, such as Roseburia, thereby reinforcing the intestinal epithelial barrier. Furthermore, fecal metabolomics indicates that MSAP actively regulates pathways closely associated with diabetes, including sphingolipid metabolism, amino acid synthesis and catabolism, retrograde endogenous cannabinoid signaling, and the modulation of TRP channels by inflammatory mediators. By integrating microbiome and metabolomics data, this study elucidated the mechanisms through which MSAP alleviates diabetes. In conclusion, the findings suggest that polysaccharides from MOS hold potential as a medicinal and edible homologous food for diabetes management.},
}

@article {pmid40274034,
year = {2025},
author = {Chi, L and Niu, H and Niu, Y and Yao, R and Shi, D and Lu, B and Pang, Z},
title = {Trigonella foenum-graecum L. ameliorates metabolism-associated fatty liver disease in type 2 diabetic mice: a multi-omics mechanism analysis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119862},
doi = {10.1016/j.jep.2025.119862},
pmid = {40274034},
issn = {1872-7573},
abstract = {Trigonella foenum-graecum L. (HLB), a widely recognized traditional Chinese medicine, has been historically used for the treatment of diabetes mellitus and its complications. However, the efficacy and mechanism of HLB in the treatment of type 2 diabetes mellitus (T2DM) combined with metabolic-associated fatty liver disease (MAFLD) remain poorly understood AIM OF THE STUDY: To investigate the therapeutic effects of HLB on T2DM combined with MAFLD in mice and elucidate its underlying mechanisms MATERIALS AND METHODS: The indices of glucose and lipid metabolism, along with oxidative stress markers, were measured using commercially available assay kits. Histopathological analyses of liver and colon tissues were conducted. Additionally, the mRNA expression levels of genes related to fatty acid metabolism, inflammatory factors, and intestinal tight junction proteins were quantified using reverse transcription polymerase chain reaction (RT-PCR). Microbiome, metabolomic, and transcriptomic analyses were employed to evaluate gut microbiota composition, metabolic profiles, and liver differential genes, respectively.

RESULTS: After a 4-week treatment period, HLB effectively ameliorated abnormalities of glucose-lipid metabolism, hepatic oxidative stress, and inflammatory responses. Furthermore, HLB modulated hepatic function and intestinal damage. Through comprehensive multi-omics analysis, the observed improvements were attributed to the remodeling of the gut microbiota and its metabolic alterations, including an increased abundance of beneficial bacteria, regulation of bile acid metabolism CONCLUSIONS: These findings not only provide a theoretical foundation for the broader application of HLB in traditional Chinese medicine but also offer novel insights into the potential pharmacological mechanisms underlying HLB's efficacy in T2DM and MAFLD treatment.},
}

@article {pmid40273900,
year = {2025},
author = {Zhou, L and Li, T and Zheng, Q and Xu, J and Xu, C and Zhang, B and Wang, Z and Wang, J},
title = {Research progress and future opportunities of pediatric cow milk protein allergy: a bibliometric overview and evidence mapping.},
journal = {International archives of allergy and immunology},
volume = {},
number = {},
pages = {1-22},
doi = {10.1159/000545367},
pmid = {40273900},
issn = {1423-0097},
abstract = {INTRODUCTION: This study employs bibliometric methods to reveal research trends, hot topics, and development trajectories in the field of cow milk protein allergy (CMPA) in children.

METHODS: We retrieved and downloaded literature on CMPA in children from the Web of Science Core Collection database on the basis of specific search strategies and screening criteria. Using VOSviewer software, we analyzed the collaboration networks among countries, institutions, and authors, as well as the co-occurrence of keywords. We utilized Biblioshiny software to analyze highly cited papers and research trend topics and to construct thematic maps.

RESULTS: We included 1,128 articles related to pediatric CMPA for analysis. The results show that since 2014, the number of research papers on CMPA has increased. The United States, Italy, and China are the countries with the greatest number of publications, with the United States occupying a central position in the collaboration network. The Icahn School of Medicine at Mount Sinai ranks first in terms of research output. Professor Hugh A. Sampson is the most influential author in this field. The main research areas include clinical manifestations, molecular mechanisms, immune regulation, and immunotherapy for CMPA. Emerging research hotspots in recent years include the gut microbiome, the development of dairy substitutes, and the application of sandwich enzyme-linked immunosorbent assay (sELISA) technology in milk protein detection.

CONCLUSION: Through bibliometric analysis, this study revealed the research trends and hotspots in the field of CMPA in children. Future research should further strengthen international cooperation to promote in-depth research and effective management of CMPA.},
}

@article {pmid40273881,
year = {2025},
author = {Campbell, DE and Mehr, S and Moscatelli, OG and Anderson, RP and Tye-Din, JA},
title = {Immune therapies in coeliac disease and food allergies: Advances, challenges, and opportunities.},
journal = {Seminars in immunology},
volume = {78},
number = {},
pages = {101960},
doi = {10.1016/j.smim.2025.101960},
pmid = {40273881},
issn = {1096-3618},
abstract = {Coeliac disease and food allergy management primarily relies on the strict avoidance of dietary antigens. This approach is challenging to maintain in real-world settings and in food allergy carries the risk of life-threatening anaphylaxis. Despite their distinct pathogenesis, both disorders are driven by maladaptive responses to dietary proteins, creating opportunities for shared treatment strategies. In food allergy, desensitisation therapies such as oral, sublingual, and epicutaneous immunotherapy are well-established, complemented by biologics like omalizumab and dupilumab. However, the induction of sustained tolerance remains challenging. In contrast, therapeutic advancements for coeliac disease are still in their early stages. Current efforts focus on gluten detoxification or modification, immune blockade or modulation, tolerogenic approaches, and barrier restoration. Emerging therapies, including JAK and BTK inhibitors and microbiome-targeted interventions, support further targeted treatment options for both conditions. Biomarkers tracking gluten-specific T cells have emerged as valuable tools for immunomonitoring and symptom assessment in coeliac disease, although standardisation of patient-reported outcome measures and gluten challenge protocols is still needed. Food allergy trials are reliant on double-blind placebo-controlled food challenges to measure allergen reactivity, but these are time-consuming, carry risks, and underscore the need for surrogate biomarkers. The successful development of immune-targeted therapies will require building an immune toolset to optimally assess systemic responses to antigens in both conditions. Clinically, this could lead to better outcomes for patients who might otherwise remain undiagnosed or untreated due to the absence of significant enteropathy or allergen-specific symptoms.},
}

@article {pmid40273556,
year = {2025},
author = {Van Pee, T and Engelen, L and De Boevre, M and Derrien, M and Hogervorst, J and Pero-Gascon, R and Plusquin, M and Poma, G and Vich I Vila, A and Covaci, A and Vanhaecke, L and De Saeger, S and Raes, J and Nawrot, TS},
title = {Sex differences in the association between long-term ambient particulate air pollution and the intestinal microbiome composition of children.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109457},
doi = {10.1016/j.envint.2025.109457},
pmid = {40273556},
issn = {1873-6750},
abstract = {The intestinal microbiome is essential for gastrointestinal and overall health, yet its response to air pollution in children remains underexplored. In a study involving 412 young children from the ENVIRONAGE cohort, stool samples were analysed via Illumina Miseq sequencing to assess microbiome alpha diversity (observed richness, species evenness, and Shannon diversity) and composition. Exposure to previous year particulate air pollution (black carbon, PM2.5, coarse PM, and PM10) was modeled using high-resolution spatial-temporal interpolation models. Multiple linear regression models were adjusted for a priori selected covariables and stratified by sex. Furthermore, we performed a differential relative abundance analysis at family and genus level, while accounting for the same covariables. Statistically significant effect modification by sex was apparent for several intestinal alpha diversity indices and air pollutants. In boys, we observed negative associations between particulate air pollution exposure and intestinal microbiome richness (estimates ranging from -5.55 to -9.06 per interquartile range (IQR) increase in particulate air pollution exposure) and Shannon diversity (estimates ranging from -0.058 to -0.095 per IQR increase). Differently, in girls non-significant positive associations were observed with species evenness (estimates ranging from 0.019 to 0.020 per IQR increase) and Shannon diversity (estimate 0.065 per IQR increase in black carbon). After multiple testing correction, we reported several bacterial families and genera (Streptococcaceae, Clostridiales Incertae Sedis XIII, Coriobacteriaceae, Streptococcus, and Paraprevotella) to be oppositely associated with particulate air pollution exposure in boys and girls. Our findings show a sex-dependent association between particulate air pollution exposure and intestinal microbiome composition, highlighting boys as potentially more vulnerable to diversity loss associated with childhood exposure to particulate pollution.},
}

@article {pmid40273425,
year = {2025},
author = {Bonacolta, AM and Weiler, BA and Grimes, CJ and Trznadel, M and Vermeij, MJA and Keeling, PJ and Del Campo, J},
title = {Fireworms are a reservoir and potential vector for coral-infecting apicomplexans.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf078},
pmid = {40273425},
issn = {1751-7370},
abstract = {Corals (Cnidaria; Anthozoa) play critical roles as habitat-forming species with a wide range, from warm shallow-water tropical coral reefs to cold-water ecosystems. They also represent a complex ecosystem as intricate holobionts made up of microbes from all domains of the Tree of Life that can play significant roles in host health and fitness. The corallicolids are a clade of apicomplexans that infect a wide variety of anthozoans worldwide and can influence the thermal tolerance of habitat-forming corals. Despite their potentially important impacts on reef ecosystems, much of the basic biology and ecology of corallicolids remains unclear. Apicomplexans often have a closed life cycle, with minimal environmental exposure and sometimes multiple hosts. Corallicolids have only been documented in anthozoan hosts, with no known secondary/reservoir hosts or vectors. Here, we show that abundant corallicolid sequences are recovered from bearded fireworms (Hermodice carunculata) in tropical reef habitats off Curaçao and that they are distinct from corallicolids infecting the corals on which the fireworms were feeding at the time of their collection. These data are consistent with a fireworm-specific corallicolid infection, not merely a byproduct of the worms feeding on infected corals. Furthermore, we suggest that H. carunculata is potentially a vector moving corallicolids among coral hosts through its feces. These findings not only expand our understanding of the ecological interactions within coral reef ecosystems but also highlight the potential role of host-associated parasites in shaping the resilience of reef habitats.},
}

@article {pmid40273394,
year = {2025},
author = {Chen, CC and Chiu, JY and Tan, AH and Toh, TS and Lim, SY and Tan, EK and Pettersson, S and Hsu, CC and Liou, JM and Wu, MS and Hsu, CL and Lin, CH},
title = {Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism.},
journal = {Neurology},
volume = {104},
number = {10},
pages = {e213592},
doi = {10.1212/WNL.0000000000213592},
pmid = {40273394},
issn = {1526-632X},
abstract = {BACKGROUND AND OBJECTIVES: Coffee intake is linked to a reduced risk of Parkinson disease (PD), but whether this effect is mediated by gut microbiota and metabolomic changes remains unclear. This study examines PD-associated metabolomic shifts, caffeine metabolism, and their connection to gut microbiome alterations in a multicenter study.

METHODS: We conducted an untargeted serum metabolomic assay using liquid chromatography with high-resolution mass spectrometry on an exploratory cohort recruited from National Taiwan University Hospital (NTUH). A targeted metabolomic assay focusing on caffeine and its 12 downstream metabolites was conducted and validated in an independent cohort from University Malaya Medical Centre (UMMC). In the exploratory cohort, the association of each caffeine metabolite with gut microbiota changes was investigated by metagenomic shotgun sequencing. A clustering-based approach was used to correlate microbiome changes with plasma caffeine metabolite level and clinical severity. Body mass index, antiparkinsonism medication use, and dietary habits (including coffee and tea intake) were recorded.

RESULTS: Sixty-three patients with PD and 54 controls from NTUH formed the exploratory cohort while 36 patients with PD and 20 controls from UMMC served as an validation cohort to replicate the plasma caffeine findings. A total of 5,158 metabolites were detected from untargeted metabolomic analysis, with 3,131 having high confidence for analysis. Compared with controls, the abundance of 56 metabolites was significantly higher and that of 7 metabolites was significantly lower (adjusted p < 0.05 and log2 fold change >1) in patients with PD. Caffeine metabolism was significantly lower in patients with PD (p = 0.0013), and serum levels of caffeine and its metabolites negatively correlated with motor severity (p < 0.01). Targeted metabolomic analysis confirmed reduced levels of caffeine and its metabolites, including theophylline, paraxanthine, 1,7-dimethyluric acid, and 5-acetylamino-6-amino-3-methyluracil, in patients with PD; these findings were replicated in the validation cohort (p < 0.05). A clustering approach found that 56 microbiome species enriched in patients with PD negatively correlated with caffeine and its metabolites paraxanthine and theophylline (both p < 0.05), notably Clostridium sp000435655, Acetatifactor sp900066565, Oliverpabstia intestinalis, and Ruminiclostridium siraeum.

DISCUSSION: This study identifies PD-related changes in microbial-caffeine metabolism compared with controls. Our findings offer insights for future functional research on caffeine-microbiome interactions in PD.},
}

@article {pmid40272913,
year = {2025},
author = {Bohm, MS and Joseph, SC and Sipe, LM and Kim, M and Leathem, CT and Mims, TS and Willis, NB and Tanveer, UA and Elasy, JH and Grey, EW and Pye, ME and Mustafa, ZT and Harper, BA and McGrath, LG and Daria, D and Landvoigt Schmitt, B and Myers, JA and Pantoja Newman, P and Pence, BD and Van der Merwe, M and Davis, MJ and Pierre, JF and Makowski, L},
title = {The gut microbiome enhances breast cancer immunotherapy following bariatric surgery.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.187683},
pmid = {40272913},
issn = {2379-3708},
abstract = {Bariatric surgery is associated with improved breast cancer (BC) outcomes, including greater immunotherapy effectiveness in a pre-clinical BC model. A potential mechanism of bariatric surgery-associated protection is the gut microbiota. Here, we demonstrate the dependency of improved immunotherapy response on the post-bariatric surgery gut microbiome via fecal microbial transplant (FMT). Response to αPD-1 immunotherapy was significantly improved following FMT from formerly obese bariatric surgery-treated mice. When stool from post-bariatric surgery patients was transplanted into recipient mice and compared to the patients' pre-surgery transplants, post-surgery microbes significantly reduced tumor burden and doubled immunotherapy effectiveness. Microbes impact tumor burden through microbially derived metabolites, including branched chain amino acids (BCAA). Circulating BCAAs correlated significantly with natural killer T (NKT) cell content in the tumor microenvironment in donor mice after bariatric surgery and FMT recipients of donor cecal content after bariatric surgery compared to obese controls. BCAA supplementation replicated improved αPD-1 effectiveness in two BC models, supporting the role of BCAAs in increased immunotherapy effectiveness after bariatric surgery. Ex vivo exposure increased primary NKT cell expression of anti-tumor cytokines, demonstrating direct activation of NKT cells by BCAAs. Together, findings suggest that reinvigorating anti-tumor immunity may depend upon bariatric surgery-associated microbially derived metabolites, namely BCAAs.},
}

@article {pmid40272597,
year = {2025},
author = {Thim-Uam, A and Chantawichitwong, P and Phuengmaung, P and Kaewduangduen, W and Saisorn, W and Kumpunya, S and Pisitkun, T and Pisitkun, P and Leelahavanichkul, A},
title = {Accelerating and protective effects toward cancer growth in cGAS and FcgRIIb deficient mice, respectively, an impact of macrophage polarization.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {74},
number = {1},
pages = {69},
pmid = {40272597},
issn = {1420-908X},
support = {RGNS 65-137//the Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innovation/ ; RGNS 65-137//the Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innovation/ ; Fundamental Fund 2024, Grant No. 229/2567//the University of Phayao and Thailand Science Research and Innovation Fund/ ; Grant No. MS251001//the School of Medical Sciences, University of Phayao/ ; },
mesh = {Animals ; *Macrophages/immunology ; *Nucleotidyltransferases/genetics ; *Receptors, IgG/genetics/deficiency ; Mice, Knockout ; *Colonic Neoplasms/pathology/immunology ; Cytokines/blood ; Cell Line, Tumor ; Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Male ; Feces/microbiology ; },
abstract = {BACKGROUND: Due to the possible influence of inflammation and gut microbiota in cancers.

METHODS: Fc gamma receptor IIb deficient (FcGRIIb-/-) and cyclic GMP-AMP synthase deficient (cGAS-/-) mice, the model with hyperinflammation and hypo-inflammation, respectively, were subcutaneously injected with MC38 cells (a murine colon cancer cell line).

RESULTS: As such, the tumor burdens were most prominent in cGAS-/- mice, while FcGRIIb-/- mice demonstrated the least tumor sizes compared with wild-type (WT). Intra-tumoral mononuclear cells of FcGRIIb-/- (hematoxylin and eosin staining) were more prominent than other groups with the most dominant CD86-positive cells (mostly M1 proinflammatory macrophages) and the least CD206-positive cells (mostly M2 anti-inflammatory macrophages). While fecal microbiome analysis demonstrated a subtle difference among mouse strains with tumors at 24 days post-cancer injection, serum cytokines (TNF-α, IL-6, IL-1α, IFN-β, IFN-γ, IL-23, IL-12p70, GM-CSF, IL-27, and IL-17A) (fluorescence-encoded bead multiplex assay) and the expansion of immune cells in the spleens of FcGRIIb-/- mice (flow cytometry) were more prominent than others. With bone marrow-derived macrophages, prominent M1 (LPS) and M2 polarization (IL4 and cancer supernatant) in FcGRIIb-/- and cGAS-/- macrophages, respectively, were demonstrated using polymerase chain reaction and flow cytometry. The most prominent tumoricidal activity (percentage of F4/80-negative flexible780 viable dye-positive cells using flow cytometry) of LPS-stimulated FcGRIIb-/- macrophages compared with other groups supported dominant pro-inflammatory characteristics of FcGRIIb-/- macrophages.

CONCLUSIONS: In conclusion, the protective and promoting effects of FcGRIIb-/- and cGAS-/- mice, respectively, against cancers are partly related to macrophage functions with a subtle correlation to fecal microbiota, and FcGRIIb inhibitors and cGAS enhancers might be helpful for cancer adjuvant treatment.},
}

Animals
*Macrophages/immunology
*Nucleotidyltransferases/genetics
*Receptors, IgG/genetics/deficiency
Mice, Knockout
*Colonic Neoplasms/pathology/immunology
Cytokines/blood
Cell Line, Tumor
Gastrointestinal Microbiome
Mice
Mice, Inbred C57BL
Male
Feces/microbiology

@article {pmid40272208,
year = {2025},
author = {Chen, Z and Wang, P and Zhao, S and Sun, Y and Liu, Y and Chen, S and Chen, W and Zhao, G and Wei, G and Chen, C},
title = {Functionalized Silica Nanoparticles Mitigate Salt Stress in Soybean: Comprehensive Insights of Physiological, Metabolomic, and Microbiome Responses.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00194},
pmid = {40272208},
issn = {1520-5118},
abstract = {Silica nanoparticles (SiO2 NPs) have potential for mitigating salt stress in crops; however, the effects of surface modifications in enhancing their effectiveness remain unclear. This study investigated the effects of pristine and functionalized SiO2 NPs (SiO2-NH2 and SiO2-COOH) on soybean growth, root metabolism, and microbiome dynamics under 200 mM NaCl stress. All SiO2 NPs treatments significantly reduced Na[+]/K[+], with SiO2-COOH NPs showing the greatest efficacy, reducing by 46.6%. Enhanced salt tolerance correlated with altered root metabolism, including increased l-tyrosine, uridine, and indole-3-acetamide levels and enrichment of stress-response pathways. Furthermore, SiO2-COOH NPs enhanced microbial diversity, increasing the abundance of beneficial genera Variovorax and Pseudomonas in the endosphere, and Haliangium and Arthrobacter in the rhizosphere. Microbe-metabolite correlations suggest that altered root exudation under functionalized SiO2 NPs treatments selectively recruits beneficial bacteria, enhancing salt tolerance. These findings highlight the potential of functionalized SiO2 NPs, particularly SiO2-COOH, as nanoenabled biostimulants for sustainable agriculture.},
}

@article {pmid40272187,
year = {2025},
author = {Zhang, G and He, Y and Yang, W and Liu, Z and Lin, Z and Zhang, T and He, X and Xia, H and Huo, M and Yao, H and Zhao, G and Wu, Y and Kong, G},
title = {Integrated microbiology and metabolomics analysis reveal the fermentation process and the flavor development in cigar tobacco leaf.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0102924},
doi = {10.1128/spectrum.01029-24},
pmid = {40272187},
issn = {2165-0497},
abstract = {UNLABELLED: The purpose of this study was to elucidate how the microbiota affects the metabolic state and characteristic flavor development of cigar tobacco leaves (CTL) in the fermentation process through microbial metabolism and co-metabolism with the host. The results showed that core bacterial communities in the fermentation process were Cyanobacteria, Pseudomonas, and Staphylococcus, and Aspergillus, Penicillium, and Inocybe were the most metabolically active fungi. Pseudomonas fulva, Staphylococcus nepalensis, Bacillus subtilis, Stenotrophomonas rhizophila, Alternaria alternata, and Aspergillus cristatus could degrade carbon and nitrogen compounds, such as protein, starch, lignin, and nicotine. There were 12 common non-volatile metabolites and three common volatile metabolites in DH, LC, PE, and YX before and after fermentation, of which menatetrenone, solanidine, γ-glutamylphenylalanine, carotol, and phenol, 4-(1,1,3,3-tetramethylbutyl) were significantly different before and after fermentation. The synthesis and degradation metabolism of various amino acids, alkaloids, and flavonoids are the key metabolic pathways of characteristic flavor development during CTL fermentation. Co-occurrence and interaction patterns showed that seven bacteria and 12 fungi were strictly linearly positively or negatively correlated with 72 and 55 volatile compounds, respectively. In conclusion, this study preliminarily confirmed that CTL fermentation is a microbially mediated carbon-nitrogen coupling metabolism. The carbohydrates in tobacco leaves were largely decomposed and consumed, providing energy sources for microorganisms and the carbon skeleton required for cell construction. The nitrogen-containing macromolecular compounds were degraded to form volatile compounds or flavor precursors with typical flavor.

IMPORTANCE: The development of the metabolic state and characteristic flavor of cigar tobacco during fermentation is the key to process control. Innovative discoveries in the development of the metabolic state and characteristic flavor of cigar tobacco during fermentation are the key to process control. Innovative discoveries of core functional microorganisms and key metabolites were made during fermentation, suggesting potential pathways for carbon and nitrogen metabolisms. We demonstrate for the first time that cigar tobacco leaf fermentation is a microbially mediated carbon-nitrogen coupling metabolism. Many carbohydrates in tobacco leaves are decomposed and consumed to provide energy source and carbon skeleton for the construction of microbial cells, and nitrogen-containing macromolecular compounds are degraded to form volatile compounds or flavor precursors with typical flavors.},
}

@article {pmid40272147,
year = {2025},
author = {Dai, X and Cao, Y and Li, L and Gao, Y-X and Wang, J-X and Liu, Y-J and Ma, T-T and Zheng, J-M and Zhan, P-P and Shen, Z-Y},
title = {Gut microbiome and metabolome profiles in renal allograft rejection from multiomics integration.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0162624},
doi = {10.1128/msystems.01626-24},
pmid = {40272147},
issn = {2379-5077},
abstract = {UNLABELLED: The gut microbiome and metabolome play crucial roles in renal allograft rejection progression. Integrated multiomics analyses may provide a comprehensive understanding of specific underlying mechanisms, which remain elusive. This study aimed to identify new approaches for clinical renal allograft rejection diagnosis and treatment. Thirty-five patients were divided into three groups: the rejection (n = 16), dysfunction (n = 7), and control (n = 12) groups. Metagenomic sequencing and nontargeted metabolomics were used to analyze stool and plasma samples. Significant microbiota, metabolites, and signaling pathways were identified. LASSO regression was used to construct a diagnostic model, and its diagnostic value was assessed via receiver operating characteristic curves. The microbiota composition and the related genes in the rejection group significantly differed from that in the dysfunction and control groups at the phylum, genus, and species levels (P < 0.001). The core species in the rejection group networks were Escherichia coli and Ruminococcus gnavus, while core species in the dysfunction group networks were Faecalibacterium prausnitzii and Bacteroides ovatus. The balance of specific microbial species was associated with kidney function in rejection patients. Spearman analysis revealed that specific differential species like Agathobaculum butyriciproducens and Gemmiger qucibialis were closely linked to the levels of serum 4-pyridoxic acid, 4-acetamidobutanoate, and fecal tryptamine from specific differential pathways. Finally, we constructed four clinical models to distinguish the rejection and dysfunction groups, and the model had excellent diagnostic performance. Altered gut microbiota may contribute to changes in metabolic pathway activity and metabolite abundance in rejection and dysfunction patients, which are strongly correlated with host immunological rejection. The diagnostic model, developed based on the gut microbiota and metabolites, has high clinical value for diagnosing renal rejection.

IMPORTANCE: This study aimed to screen new markers for non-invasive diagnosis by the gut microbiome and metabolome analysis, providing new insights into rejection mechanisms and identifying new approaches for clinical renal allograft rejection diagnosis.},
}

@article {pmid40272094,
year = {2025},
author = {Li, X and Zhang, Z and Xie, J and Cao, B and Wang, X and Yu, Y and Su, J},
title = {A Smart Injectable Hydrogel with Dual Responsivity to Arginine Gingipain A and Reactive Oxygen Species for Multifunctional Therapy of Periodontitis.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2408034},
doi = {10.1002/smll.202408034},
pmid = {40272094},
issn = {1613-6829},
support = {82071159//National Natural Science Foundation of China/ ; 82170913//National Natural Science Foundation of China/ ; 22120240368//Independent Original Basic Research Foundation of Tongji University/ ; },
abstract = {Distinct clinical phenotypes of periodontitis are associated with specific microbiome profiles and diverse inflammatory conditions. Current drug delivery systems face challenges in precisely modulating this dynamic microenvironment. Effective inhibition of bone resorption can only be achieved through a strategic response to bacterial infections and inflammation within the periodontal pocket, followed by prompt treatment tailored to disease severity. In this study, tannic acid (TA) is loaded into hollow mesoporous silica nanoparticles (HMSNs) that are functionalized with positively charged polyarginines (R8) and negatively charged human serum albumin (HSA). These HMSNs-R8@TA-HSA (HRT) nanoparticles are then encapsulated within an injectable Nap-Gly-Phe-Phe-Tyr-OH (NapGFFY) hydrogel (NHRT). The intermediate linker R8 can interact with both arginine gingipain A (RgpA) and reactive oxygen species (ROS), which serve as markers of bacterial infections and inflammation, respectively. HSA, arginine, TA, and nitric oxide are differentially released from the hydrogel in response to varying concentrations of RgpA and ROS, demonstrating excellent antibacterial, antioxidant, and anti-inflammatory properties. This smart RgpA/ROS dual-responsive and injectable hydrogel with multifunctional therapy provides new prospects for the management of periodontitis.},
}

@article {pmid40272000,
year = {2025},
author = {Pincus, K and Kearns, PJ and Williams, K and Woodhams, DC},
title = {Nutrient enrichment alters the microbiome and increases chytrid load in the American bullfrog Lithobates catesbeianus.},
journal = {Diseases of aquatic organisms},
volume = {162},
number = {},
pages = {27-34},
doi = {10.3354/dao03846},
pmid = {40272000},
issn = {0177-5103},
mesh = {Animals ; *Rana catesbeiana/microbiology ; *Microbiota/drug effects ; *Batrachochytrium/physiology ; *Nutrients ; *Mycoses/veterinary/microbiology ; Bacteria/classification/drug effects ; Skin/microbiology ; },
abstract = {Agricultural practices have a profound impact on watershed dynamics, water quality, and the well-being of aquatic life. One major concern is agricultural pollution, particularly the excess of nutrients, which can elevate disease risks in various host-pathogen relationships. However, the exact mechanisms driving this effect remain uncertain. Elevated nutrient levels are believed to significantly influence populations of aquatic environmental bacteria, potentially reshaping the microbiomes of aquatic organisms and affecting their vulnerability to disease. Despite this, the impact of nutrient enrichment on host microbiomes as a link to diseases in aquatic organisms has been largely overlooked. In this study, we investigated the impact of nutrient enrichment on the skin-associated microbial communities of the American bullfrog Lithobates catesbeianus. We observed a significant shift in bacterial richness and community composition in nutrient-enriched ponds compared with reference ponds. Although the proportion of the community inhibitory towards Batrachochytrium dendrobatidis (Bd) did not change significantly, Bd loads were markedly higher in nutrient-enriched ponds. Nutrient enrichment significantly altered carbon utilization patterns as measured by Biolog EcoPlates, and antibiotic resistance was prevalent across all ponds and samples, with resistance to trimethoprim, sulfamethazine, and chloramphenicol significantly higher in nutrient-enriched ponds. Our findings indicate that nutrient enrichment affects the structure and function of skin-associated microbial communities in American bullfrogs, influencing both Bd load and antibiotic resistance.},
}

Animals
*Rana catesbeiana/microbiology
*Microbiota/drug effects
*Batrachochytrium/physiology
*Nutrients
*Mycoses/veterinary/microbiology
Bacteria/classification/drug effects
Skin/microbiology

@article {pmid40271800,
year = {2025},
author = {Huang, F and Dai, Q and Ma, Q and Zheng, K and Wu, Y and Sun, D and Yu, Z and Liu, Y and Jiang, W and Yan, X},
title = {Skipjack Tuna (Katsuwonus pelamis) Dark Muscle Hydrolysate Ameliorates Hyperuricemia in Mice via Regulating Gut Microbiota and Serum Metabolism.},
journal = {Journal of food science},
volume = {90},
number = {4},
pages = {e70232},
doi = {10.1111/1750-3841.70232},
pmid = {40271800},
issn = {1750-3841},
support = {//the National Key R&D Program of China (2020YFD0900900)/ ; //Zhejiang Provincial Natural Science Foundation of China (LTGN23C200013)/ ; //the Dinghai Science and Technology Project (2022C31007)./ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Hyperuricemia/drug therapy/metabolism/chemically induced/diet therapy ; Mice ; *Tuna/metabolism ; Uric Acid/blood ; Male ; Liver/metabolism ; Xanthine Oxidase/metabolism/blood ; *Protein Hydrolysates/pharmacology ; Disease Models, Animal ; Kidney/drug effects ; },
abstract = {Peptides have emerged as promising agents for ameliorating hyperuricemia (HUA), a condition that poses significant risks to human health. This study evaluated the HUA-alleviating potential of skipjack tuna dark muscle hydrolysate (STDH) in a mouse model of HUA induced by potassium oxonate (PO) and hypoxanthine (Hx). The results demonstrated elevated serum uric acid (SUA) levels, increased xanthine oxidase (XOD) activity in the serum and liver, and kidney and intestinal damage in HUA mice. Although the standard drug allopurinol (AP) effectively reduced SUA levels and lowered XOD activity in the serum and liver, it exacerbated kidney damage and caused significant weight loss. In contrast, STDH intervention not only significantly lowered SUA, serum creatinine (SCr), and blood urea nitrogen (BUN) levels but also inhibited XOD activity in serum and liver. Notably, STDH ameliorated renal and intestinal morphological damage, as evidenced by hematoxylin-eosin (HE) staining. Gut microbiome analysis further revealed that STDH normalized the HUA-associated elevation of the Bacteroidetes/Firmicutes ratio. Untargeted metabolomics identified STDH's regulatory effects on glycine, serine, and threonine metabolism; arginine and proline metabolism; and glycerophospholipid metabolism, with glutamine implicated as a key player in HUA pathogenesis. These findings demonstrate that STDH effectively alleviates HUA while avoiding adverse effects associated with conventional therapy, positioning it as a safe and cost-effective functional food candidate for HUA management.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Hyperuricemia/drug therapy/metabolism/chemically induced/diet therapy
Mice
*Tuna/metabolism
Uric Acid/blood
Male
Liver/metabolism
Xanthine Oxidase/metabolism/blood
*Protein Hydrolysates/pharmacology
Disease Models, Animal
Kidney/drug effects

@article {pmid40271508,
year = {2025},
author = {Singlitico, A and Grassa, D and Kaplan, R and Smimmo, A and Maccauro, G and Vitiello, R},
title = {The hidden connection between gut microbiota and periprosthetic joint infections: a scoping review.},
journal = {Journal of bone and joint infection},
volume = {10},
number = {2},
pages = {85-92},
doi = {10.5194/jbji-10-85-2025},
pmid = {40271508},
issn = {2206-3552},
abstract = {Background: Periprosthetic joint infections (PJIs) pose a significant challenge in orthopedic surgery, and emerging evidence suggests that the gut microbiome may play a crucial role in their development and management. Despite the rarity of these infections, the continuous increase in prosthetic joint arthroplasties has made understanding how to prevent them more pressing. A stronger comprehension of the disruption of the gut microbiome and how this can lead to more of these infections and other pre-surgical risks may be crucial in preventing them. Objective: This article aims to provide a stronger understanding of the topic through the analysis of different pieces of already existing literature to help draw new conclusions and raise potential questions that need answering. Methods: A comprehensive search strategy without filters was employed, and multiple papers were thoroughly analyzed, understood, and compiled into this paper. Conclusions: Despite the limitations of some of the analyzed studies and finite evidence, this paper suggests that there could be a connection between periprosthetic joint infections and a compromised gut microbiome. However, further research is required to draw a definitive conclusion.},
}

@article {pmid40271433,
year = {2025},
author = {Overton, E and Emelyanova, A and Bunik, VI},
title = {Thiamine, gastrointestinal beriberi and acetylcholine signaling.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1541054},
doi = {10.3389/fnut.2025.1541054},
pmid = {40271433},
issn = {2296-861X},
abstract = {Research has highlighted numerous detrimental consequences of thiamine deficiency on digestive function. These range from impaired gastric and intestinal motility to aberrant changes in pancreatic exocrine function, gastric acidity and disturbances in gut barrier integrity and inflammation. Thiamine and its pharmacological forms, as a primary or adjunctive therapy, have been shown to improve symptoms such as nausea, constipation, dysphagia and intestinal dysmotility, in both humans and animals. This review aims to explore molecular mechanisms underlying the therapeutic action of thiamine in gastrointestinal dysfunction. Our analysis demonstrates that thiamine insufficiency restricted to the gastrointestinal system, i.e., lacking well-known symptoms of dry and wet beriberi, may arise through (i) a disbalance between the nutrient influx and efflux in the gastrointestinal system due to increased demands of thiamine by the organism; (ii) direct exposure of the gastrointestinal system to oral drugs and gut microbiome, targeting thiamine-dependent metabolism in the gastrointestinal system in the first line; (iii) the involvement of thiamine in acetylcholine (ACh) signaling and cholinergic activity in the enteric nervous system and non-neuronal cells of the gut and pancreas, employing both the coenzyme and non-coenzyme actions of thiamine. The coenzyme action relies on the requirement of the thiamine coenzyme form - thiamine diphosphate - for the production of energy and acetylcholine (ACh). The non-coenzyme action involves participation of thiamine and/or derivatives, including thiamine triphosphate, in the regulation of ACh synaptic function, consistent with the early data on thiamine as a co-mediator of ACh in neuromuscular synapses, and in allosteric action on metabolic enzymes. By examining the available evidence with a focus on the gastrointestinal system, we deepen the understanding of thiamine's contribution to overall gastrointestinal health, highlighting important implications of thiamine-dependent mechanisms in functional gastrointestinal disorders.},
}

@article {pmid40271314,
year = {2025},
author = {Patki, A and Kar, S and Patel, N and Ingale, K and Bansal, K and Durga, P},
title = {Expert Opinion: Place in Therapy of Probiotics in Infertility and Recurrent Implantation Failure.},
journal = {Cureus},
volume = {17},
number = {3},
pages = {e81067},
doi = {10.7759/cureus.81067},
pmid = {40271314},
issn = {2168-8184},
abstract = {Infertility is a widespread medical condition, affecting a notable percentage of couples globally, with a rising prevalence in India. While assisted reproductive technologies (ART) provide hope, recurrent implantation failure (RIF) continues to challenge approximately one in 10 couples undergoing in-vitro fertilization (IVF). This expert opinion document intends to highlight the promise of probiotics, particularly from Lactobacillus, as a therapeutic approach for improving fertility and treating RIF. In India, on June 29-30, 2024, a physical expert meeting was organized involving 14 specialists from gynecology, obstetrics, and fertility fields. The role of probiotics in reproductive health was discussed in the meeting with an emphasis on infertility and RIF. All experts agree that microbial dysbiosis characterized by an imbalance among the dominant Lactobacillus species is associated with RIF leading to increased inflammation hence poor reproductive outcomes. Probiotics have emerged as possible therapies that restore microbial equilibrium while reducing inflammation and enhancing the intactness of the genital epithelium barrier. All experts have strongly supported the use of Lactobacillus-based oral probiotic supplementation particularly for preventing miscarriages and maintaining pregnancy. All the experts unanimously agreed that oral probiotic supplementation, particularly Lactobacillus-based, should be considered as a potential method to prevent miscarriages and aid in maintaining pregnancy. They recommend oral probiotic use prior to embryo transfer to enhance implantation and pregnancy rates. This expert opinion emphasizes the value of probiotics as a safe and non-invasive approach to treating infertility and RIF. By fostering a balanced microbiome, probiotics may increase the likelihood of successful pregnancies.},
}

@article {pmid40271290,
year = {2025},
author = {Patki, A and Kunjimoideen, K and Sawankar, S and Tyagi, R and Hegde, V and Budi, J},
title = {Expert Opinion on the Use of Probiotics in Recurrent Pregnancy Loss.},
journal = {Cureus},
volume = {17},
number = {3},
pages = {e81056},
doi = {10.7759/cureus.81056},
pmid = {40271290},
issn = {2168-8184},
abstract = {Recurrent pregnancy loss (RPL) involves multiple consecutive miscarriages in early pregnancy, affecting a significant number of Indian women and placing substantial physical and emotional stress on expecting couples. This expert consensus aims to highlight probiotics as a promising option for enhancing fertility and supporting successful pregnancy outcomes, offering hope to individuals and couples affected by RPL. A group of fourteen experts with diverse expertise in gynecology, obstetrics, and fertility from across India gathered between June 29 and June 30, 2024. According to the experts, advanced maternal age emerges as an independent risk factor for miscarriage, with increased risks among older Indian women. The major contributors to RPL include thyroid disease and polycystic ovarian disease. Experts emphasize that the vaginal microbiome dysbiosis, characterized by the reduced dominance of Lactobacilli, is associated with adverse pregnancy outcome, such as preterm birth, early pregnancy loss, and increased events of RPL. Oral probiotic supplementation, particularly strains like L. acidophilus and L. rhamnosus, may improve embryo implantation, reduce miscarriage risk, and support pregnancy maintenance. A healthy lifestyle choice and minimal use of antibiotics are important in creating a positive reproductive outcome. The present expert opinion supports the potential benefits of probiotics, particularly Lactobacillus species, in managing RPL and improving reproductive outcomes. By promoting a balanced microbiota, reducing inflammation, and modulating immune responses, probiotics may play a critical role in enhancing reproductive success.},
}

@article {pmid40271058,
year = {2025},
author = {Cheng, X and He, J and Yang, Y and He, Y and Chen, G and Ling, B and Wang, A},
title = {Targeted metabolomics unravels the mechanism by phenylpropanoid-rich of the peel of Zea mays L. ameliorates metabolic disorders in diabetic mice through gut microbiota modulation.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1551713},
doi = {10.3389/fphar.2025.1551713},
pmid = {40271058},
issn = {1663-9812},
abstract = {BACKGROUND: Diabetes is one common clinical symptoms of metabolic disorders. The peel of Zea mays L. is a folk remedy for diabetes that has not been thoroughly studied. The effects and mechanisms on diabetes complicated glucose and lipid metabolism disorders are still unknown now.

PURPOSE: The research is intended to elucidate the constituent of phenylpropanoid enriched of Zea mays L. (YMP), and investigate the treatment and mechanism on amending glucose and lipid metabolism disorders.

METHODS: The constituents of YMP were systematacially identified by HPLC-Q-TOF-MS/MS and NMR. To assess the effects of varying YMP doses, diabetic mice induced by streptozotocin and a high-fat diet were divided into groups. Targeted serum metabolomics investigations were conducted using UHPLC-LTQ-Orbitrap MS. Moreover, 16S rRNA analysis was employed to elucidate the intricate mechanisms through the gut microbiota modulates lipid and glucose metabolism.

RESULTS: It demonstrated that the primary component of YMP was luteolin. At a high dosage of 160 mg/kg/day, YMP considerably reduced the values of the oral glucose tolerance test, insulin, and blood glucose (p < 0.001). After administration, insulin resistance indexes decreased. YMP reversed the accumulation of glycogen in the liver and reduced hepatic lipid deposition. Compared to MOD group, the concentration of luteolin is higher and its metabolite, indicating that luteolin may be adequately absorbed and have an influence on the circulatory system. The results of 16S rRNA sequencing demonstrated that YMP and gut microbiota interacted to positively regulate beneficial bacteria such as Bifidobacterium, Ligilactobacillus, and Lactobacillus.

CONCLUSION: This work investigated the regulating effect of YMP on the liver glycolipid metabolism for the first time, and it also showed the underlying mechanism through gut microbiota. According to these studies, YMP has a lot of potential to be used as a supplemental treatment for complex metabolic illnesses like diabetes. It offered empirical support for the use of alternative medicine in the area to treat complex problems of glucose and lipid metabolism in diabetes.},
}

@article {pmid40270934,
year = {2025},
author = {Erdrich, S and Gelissen, IC and Vuyisich, M and Toma, R and Harnett, JE},
title = {An association between poor oral health, oral microbiota, and pain identified in New Zealand women with central sensitisation disorders: a prospective clinical study.},
journal = {Frontiers in pain research (Lausanne, Switzerland)},
volume = {6},
number = {},
pages = {1577193},
doi = {10.3389/fpain.2025.1577193},
pmid = {40270934},
issn = {2673-561X},
abstract = {INTRODUCTION: The portal to the gastrointestinal tract is the oral cavity, with transient and permanent microbial residents. Oral pathogens are implicated in the aetiology of several chronic conditions. To date, the role of oral health and the oral microbiota in the aetiology of pain in sensitisation disorders have not been explored. Here, we examined associations between self-reported oral health, the oral microbiome, and various pain presentations in women.

METHODS: Oral health in women was assessed using the WHO oral health questionnaire. Body pain, migraine, and abdominal pain were determined using validated instruments. Saliva samples were evaluated using metatranscriptomics for relative gene abundance. Demographic and clinical characteristics data were evaluated for relationships between oral health scores, pain measures, and the oral microbiota at three taxa levels.

RESULTS: Participants in the lowest quintiles for oral health were more likely to suffer migraine headaches (χ [2] = 23.24, df 4, p < 0.001) and higher body pain scores. Four oral pathogenic species were significantly associated with SF36 bodily pain (q < 0.05) after controlling for confounders. Relative abundance of Gardnerella (genus) correlated moderately with oral health scores (ρ = -0.346, q = 0.001), while Lancefieldella (genus) and Mycoplasma salivarius were associated with migraine.

DISCUSSION: Low oral health scores correlated with higher pain scores. Both were associated with higher relative abundance of oral pathobionts. This suggests a potential role for the oral microbiota in the aetiology of pain experienced by women with migraine headache and abdominal and body pain. These findings prompt consideration of an oral microbiome-nervous system axis.

TRIAL REGISTRATION: The study was registered with the Australia and New Zealand Clinical Trials Registry (ANZCTR), registration number ACTRN12620001337965, on 11/12/2020 https://www.anzctr.org.au/, and with the World Health Organisation, UTN: U1111-1258-5108.},
}

@article {pmid40270828,
year = {2025},
author = {Akther, SM and Hu, J and Miller, G and Shi, W},
title = {Foot traffic on turf primarily shaped the endophytic bacteriome of the soil-rhizosphere-root continuum.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1488371},
doi = {10.3389/fmicb.2025.1488371},
pmid = {40270828},
issn = {1664-302X},
abstract = {Foot traffic on turf can cause grass wear-stress and soil compaction, adversely impacting turf health. The root microbiome, consisting of diverse microbes, plays a crucial role in enhancing plant resilience to abiotic stressors. However, the effects of foot traffic on these microbes and the mechanisms they employ to help plant survival remain largely unknown. Here, we investigated how foot traffic affected microbial communities of the root endosphere, rhizosphere, and bulk soil in Bermudagrass (Cynodon spp.) and Zoysiagrass (Zoysia spp.) turfs. Foot traffic was simulated to mimic six professional football games per week using a modified Baldree traffic simulator. High-throughput amplicon sequencing targeting 16S rRNA for bacteria and ITS for fungi was employed to analyze microbial communities. Foot traffic slightly and significantly reduced soil moisture and inorganic nitrogen, likely due to soil compaction and associated impairment on microbial activity. Microbial alpha diversity varied across microhabitats, with no discernible effect of foot traffic. However, microbial community composition was impacted by foot traffic, being more pronounced on bacteria of the root endosphere and on fungi of the bulk soil. In light of the genetic potential predicted by PICRUSt2, foot traffic enriched a few pathways of the endophytic bacteriome, including nitrifier denitrification (PWY7084) and mannosylglycerate biosynthesis (PWY5656). This indicated that root endophytes could help turfgrass to tolerate foot traffic via controls on the concentration of nitric oxide, the signaling molecule for root growth, and mannosylglycerate, the compatible solute for protecting enzymes against osmotic stress. Foot traffic also enhanced degradation pathways of carbohydrates and 4-coumarate, the constituent of turfgrass cell walls (PWY-3801, PWY-2221, PWY-7046), indicating the faster turnover of root tissues. Along the root-rhizosphere-bulk soil continuum, the bacteriome varied substantially in composition and also exhibited contrasting genetic potentials from stress alleviation to nutrient supply in coping with grass growth. But foot traffic had little effect on the genetic potential of bacteriome in rhizosphere and bulk soil. Our findings indicated that the endophytic bacteriome was more sensitive to foot traffic than the bacteriome in the rhizosphere and bulk soil and could potentially help turf survival via influences on plant signal molecules and compatible solutes.},
}

@article {pmid40270827,
year = {2025},
author = {Duan, T and Ren, Z and Jiang, H and Ding, Y and Wang, H and Wang, F},
title = {Gut microbiome signature in response to neoadjuvant chemoradiotherapy in patients with rectal cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1543507},
doi = {10.3389/fmicb.2025.1543507},
pmid = {40270827},
issn = {1664-302X},
abstract = {BACKGROUND: Rectal cancer remains a leading cause of cancer-associated mortality, especially in advanced cases with limited treatment options. Emerging evidence suggests that the gut microbiome may influence the therapeutic efficacy of neoadjuvant chemoradiotherapy (CRT).

OBJECTIVE: This study aimed to explore the dynamic changes in gut microbiome composition and metabolic pathways in rectal cancer patients undergoing CRT.

METHODS: Paired fecal samples were collected from rectal cancer patients pre- and post-CRT. 16S rRNA amplicon sequencing and proteomics analysis were conducted to investigate microbial and metabolic alterations.

RESULTS: Significant shifts in the microbiome were observed, with Fusobacterium, Subdoligranulum, Prevotella, Alloprevotella, and Bacteroides being enriched pre-CRT, while Streptococcus, Megamonas, Megasphaera, Escherichia-Shigella, and Olsenella became dominant post-CRT. Metabolic analysis revealed upregulated carbohydrate metabolism and downregulated lipid and energy metabolism.

CONCLUSION: These findings identify potential microbial biomarkers and metabolic pathways associated with CRT response, offering insights into personalized treatment strategies.},
}

@article {pmid40270813,
year = {2025},
author = {Hernández-García, JA and Bernal, JS and Antony-Babu, S and Villa-Tanaca, L and Hernández-Rodríguez, C and De-la-Vega-Camarillo, E},
title = {Teosinte-derived SynCom and precision biofertilization modulate the maize microbiome, enhancing growth, yield, and soil functionality in a Mexican field.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1534327},
doi = {10.3389/fmicb.2025.1534327},
pmid = {40270813},
issn = {1664-302X},
abstract = {Modern agriculture faces the challenge of optimizing fertilization practices while maintaining soil resilience and microbial diversity, both critical for sustainable crop production. We evaluated the effects of multiple fertilization strategies on soil microbial communities and plant performance, comparing conventional methods (urea-based and phosphorus fertilizers applied manually or via drone-assisted precision delivery) with biofertilization using a synthetic microbial consortium (SynCom) derived from teosinte-associated microbes. This SynCom consisted of seven bacterial strains: Serratia nematodiphila EDR2, Klebsiella variicola EChLG19, Bacillus thuringiensis EML22, Pantoea agglomerans EMH25, Bacillus thuringiensis EBG39, Serratia marcescens EPLG52, and Bacillus tropicus EPP72. High-throughput sequencing revealed significant shifts in bacterial and fungal communities across treatments. Untreated soils showed limited diversity, dominated by Enterobacteriaceae (>70%). Conventional fertilization gradually reduced Enterobacteriaceae while increasing Pseudomonas and Lysinibacillus populations. Drone-assisted conventional fertilization notably enhanced Acinetobacter and Rhizobiales growth. Biofertilization treatments produced the most pronounced shifts, reducing Enterobacteriaceae below 50% while significantly increasing beneficial taxa like Bacillus, Pantoea, and Serratia. Network analysis demonstrated that microbial interaction complexity increased across treatments, with Bacillus emerging as a keystone species. Drone-assisted biofertilization fostered particularly intricate microbial networks, enhancing synergistic relationships involved in nutrient cycling and biocontrol, though maintaining the stability of these complex interactions requires careful monitoring. Our findings provide key insights into how precision biofertilization with teosinte-derived microbial consortia can sustainably reshape the maize microbiome, improving crop performance and soil resilience.},
}

@article {pmid40270812,
year = {2025},
author = {Fagerlund, A and Møretrø, T and Jensen, MR and Langsrud, S and Moen, B},
title = {Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1541481},
doi = {10.3389/fmicb.2025.1541481},
pmid = {40270812},
issn = {1664-302X},
abstract = {Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.},
}

@article {pmid40270772,
year = {2025},
author = {Ganesan, R and Thirumugan, D},
title = {Editorial: Microbiome-based metabolomics revolution in health and microbial metabolites redefinition.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1582602},
doi = {10.3389/fcimb.2025.1582602},
pmid = {40270772},
issn = {2235-2988},
}

@article {pmid40270679,
year = {2025},
author = {Kelliher, JM and Johnson, LYD and Rodriguez, FE and Saunders, JK and Kroeger, ME and Hanson, B and Robinson, AJ and Anthony, WE and Van Goethem, MW and Kiledal, A and Shibl, AA and de Andrade, AAS and Ettinger, CL and Gupta, CL and Robinson, CRP and Zuniga, C and Sprockett, D and Machado, DT and Skoog, EJ and Oduwole, I and Rothman, JA and Prime, K and Lane, KR and Lemos, LN and Karstens, L and McCauley, M and Seyoum, MM and Elmassry, MM and Guzel, M and Longley, R and Roux, S and Pitot, TM and Eloe-Fadrosh, EA},
title = {A cost and community perspective on the barriers to microbiome data reuse.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1585717},
doi = {10.3389/fbinf.2025.1585717},
pmid = {40270679},
issn = {2673-7647},
abstract = {Microbiome research is becoming a mature field with a wealth of data amassed from diverse ecosystems, yet the ability to fully leverage multi-omics data for reuse remains challenging. To provide a view into researchers' behavior and attitudes towards data reuse, we surveyed over 700 microbiome researchers to evaluate data sharing and reuse challenges. We found that many researchers are impeded by difficulties with metadata records, challenges with processing and bioinformatics, and problems with data repository submissions. We also explored the cost constraints of data reuse at each step of the data reuse process to better understand "pain points" and to provide a more quantitative perspective from sixteen active researchers. The bioinformatics and data processing step was estimated to be the most time consuming, which aligns with some of the most frequently reported challenges from the community survey. From these two approaches, we present evidence-based recommendations for how to address data sharing and reuse challenges with concrete actions for future work.},
}

@article {pmid40270620,
year = {2025},
author = {Chen, X and Lin, WY and Zhang, FW and Guo, LQ and Ge, H and Ge, DZ and Tan, JJ and Liu, BC and Wang, RR and Zhang, L},
title = {Investigation of oral microbiome composition in elderly Chinese patients with hypertension: a cross-sectional study.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2489603},
doi = {10.1080/20002297.2025.2489603},
pmid = {40270620},
issn = {2000-2297},
abstract = {BACKGROUND: Hypertension is a prevalent metabolic disorder in the elderly, with its pathogenesis linked to gut microbiota dysbiosis. Recent studies suggested that oral microbiota may also play a role in hypertension development, yet its relationship with hypertension in the elderly remains underexplored.

OBJECTIVE: This cross-sectional study aimed to examine the structure of the oral microbiota and its association with hypertension in elderly patients, providing insights into hypertension prevention and treatment.

METHODS: A total of 206 subjects (60-89 years) were categorized into normal (CON) and hypertensive (HTN) groups, based on the Chinese Hypertension Guidelines. Saliva samples were analyzed using 16S rRNA gene sequencing.

RESULTS: Oral microbiota composition was significantly influenced by blood pressure. At the phylum level, Synergistetes and Spirochaetes were more significantly abundant in the HTN group, while at the genus level Treponema and Leptothrix was higher, Actinomyces and Capnocytophaga were lower in HTN. Random Forest analysis identified 15 key microbiota as strong discriminators of HTN (AUC 0.74). Blood pressure was negatively correlated with Actinomycetes and positively correlated with Leptothrix. PICRUST2 analysis revealed elevated chlorinated compound degradation in HTN patients.

CONCLUSIONS: This study identified distinct oral microbiota in elderly hypertensive patients, highlighting the role of the oral microbiome in hypertension pathogenesis.},
}

@article {pmid40270532,
year = {2025},
author = {Ma, J and Wang, M and Sun, Y and Zheng, Y and Lai, S and Zhang, Y and Wu, Y and Jiang, C and Shen, F},
title = {Cockroach Microbiome Disrupts Indoor Environmental Microbial Ecology with Potential Public Health Implications.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {4},
pages = {380-391},
doi = {10.1021/envhealth.4c00216},
pmid = {40270532},
issn = {2833-8278},
abstract = {Cockroaches pose a significant global public health concern. However, besides the well-recognized cockroach-induced allergy, the potential impact of the cockroach microbiome on human health through various means is not yet fully elucidated. This study aimed to clarify the health impacts of cockroaches by investigating the microbial interactions among cockroaches, the indoor environment, and humans. We simultaneously collected cockroach, indoor environment (indoor air and floor dust), and human (exhaled breath condensate and skin) samples from residential areas in five cities representing distinct climate zones in China. The 16S rDNA sequencing results revealed that cockroaches harbor diverse bacterial populations that vary across different cities. The prevalence of potential pathogenic bacteria (PPB) in cockroaches ranged from 1.1% to 58.9%, with dominant resistance genes conferring resistance to tetracycline, macrolide, and beta-lactam. The relationships between the cockroach microbiome and the associated environmental and human microbiomes were explored by using fast expectation-maximization microbial source tracking (FEAST). The potential contribution of cockroach bacteria to the floor dust-borne microbiome and indoor airborne microbiome was estimated to be 5.6% and 1.3%, respectively. Similarly, the potential contribution of cockroach PPB to the floor dust-borne microbiome and indoor airborne microbiome was calculated to be 4.0% and 1.2%, respectively. In residences with cockroach infestations, the contribution of other sources to the indoor environment was slightly increased. Collectively, the role of cockroaches in the transmission of microorganisms, particularly pathogenic bacteria and antibiotic resistance genes, cannot be overlooked.},
}

@article {pmid40270495,
year = {2025},
author = {Hakimiha, N and Jahani Sherafat, S and Laakso, EL and Fekrazad, R},
title = {Photobiomodulation and the oral-gut microbiome axis: therapeutic potential and challenges.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1555704},
doi = {10.3389/fmed.2025.1555704},
pmid = {40270495},
issn = {2296-858X},
abstract = {This Perspective article explores the challenges associated with the direct application of photobiomodulation (PBM) to the gut and presents a novel hypothesis for indirect gut health modulation through oral microbiome alteration. Given the difficulties in delivering PBM effectively to deep gastrointestinal tissues, an alternative approach involves targeting the oral microbiome, which has a demonstrated relationship with the gut microbiome. Research indicates that PBM applied to the oral cavity could selectively alter microbial composition. This alteration may, via the oral-gut microbiome axis, indirectly impact gut health. This hypothesis, supported by preliminary studies, suggests that oral PBM could offer a promising non-invasive strategy for managing gut-related disorders. Furthermore, there may be a link between the oral microbiome and brain diseases. Given the proximity to the brain, PBM-induced changes in the oral microbiota could indirectly help prevent neurological disorders. However, further investigation is necessary to comprehensively elucidate the underlying mechanisms and therapeutic implications of this approach.},
}

@article {pmid40270276,
year = {2025},
author = {Li, H and Xue, R and Di, Y and Cheng, X and Li, S and Li, J and Fan, Q and Zhang, Y and Zhang, Y},
title = {Potential mechanisms underlying pathological fatigue-induced cardiac dysfunction.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {8},
pages = {e70511},
doi = {10.1096/fj.202500202R},
pmid = {40270276},
issn = {1530-6860},
support = {//FREE Fund/ ; },
mesh = {Animals ; Male ; *Fatigue/complications/physiopathology/metabolism ; Rats ; Gastrointestinal Microbiome/physiology ; *Heart Diseases/etiology/metabolism/physiopathology ; Myocardium/metabolism/pathology ; Rats, Sprague-Dawley ; Disease Models, Animal ; },
abstract = {Pathological fatigue has emerged as a significant contributor to cardiac dysfunction. Unfortunately, suitable animal models to study cardiac dysfunction caused by fatigue are lacking, and the underlying mechanisms remain unclear. This study aimed to establish a pathological fatigue model induced by 5-week combined stress and explore the mechanisms of cardiac dysfunction triggered by fatigue. Five-week combined stress induced fatigue-like phenotypes, which included reluctance to move, reduced exercise endurance, and muscle strength. Moreover, the 5-week combined stress resulted in a significant reduction in both EF and FS, along with a marked upregulation of several myocardial injury biomarkers, thereby confirming the presence of abnormal cardiac function. Targeted metabolomics analysis indicated that 80% of the differential metabolites were downregulated, suggesting a hypometabolic profile in the heart. Interestingly, among the downregulated fatty acid metabolites, we identified two bacterial metabolites, namely acetate and butyrate. More importantly, we observed an inverse correlation between the levels of acetate and butyrate and the concentrations of certain cardiac injury markers. We then observed disturbances in gut bacteria, and group differences at the genus level revealed that all six differential bacteria, which ranked in the top 10 in terms of relative abundance, may directly or indirectly influence the production of acetic acid and butyric acid. Among them, the abundance of Akkermansia bacteria was positively correlated with reduced acetic acid levels. In summary, the present study provides a novel animal model of pathological fatigue-induced cardiac dysfunction and suggests that hypometabolic features and gut microbiota dysbiosis may be an important mechanism.},
}

Animals
Male
*Fatigue/complications/physiopathology/metabolism
Rats
Gastrointestinal Microbiome/physiology
*Heart Diseases/etiology/metabolism/physiopathology
Myocardium/metabolism/pathology
Rats, Sprague-Dawley
Disease Models, Animal

@article {pmid40270118,
year = {2025},
author = {Murtaza, N and Collins, L and Yao, CK and Thwaites, PA and Veitch, P and Varney, JE and Gill, PA and Gibson, PR and Morrison, M and Muir, JG},
title = {Effects of dietary FODMAP content on the faecal microbiome and gastrointestinal physiology in healthy adults: a randomised, controlled cross-over feeding study.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-39},
doi = {10.1017/S0007114525000868},
pmid = {40270118},
issn = {1475-2662},
abstract = {The effect dietary FODMAPs (fermentable oligo-, di- and mono-saccharides and polyols) in healthy adults is poorly documented. This study compared specific effects of low and moderate FODMAP intake (relative to typical intake) on the faecal microbiome, participant-reported outcomes and gastrointestinal physiology. In a single-blind cross-over study, 25 healthy participants were randomised to one of two provided diets, 'low' (LFD) <4 g/d or 'moderate' (MFD) 14-18 g/d, for 3 weeks each, with ≥2-week washout between. Endpoints were assessed in the last week of each diet. The faecal bacterial/archaeal and fungal communities were characterised in 18 participants in whom high quality DNA was extracted by 16S rRNA and ITS2 profiling, and by metagenomic sequencing. There were no differences in gastrointestinal or behavioural symptoms (fatigue, depression, anxiety), or in faecal characteristics and biochemistry (including short-chain fatty acids). Mean colonic transit time (telemetry) was 23 (95% confidence interval: 15, 30) h with the MFD compared with 34 (24, 44) h with LFD (n=12; p=0.009). Fungal diversity (richness) increased in response to MFD, but bacterial richness was reduced, coincident with expansion of the relative abundances of Bifidobacterium, Anaerostipes, and Eubacterium. Metagenomic analysis showed expansion of polyol-utilising Bifidobacteria, and Anaerostipes with MFD. In conclusion, short-term alterations of FODMAP intake are not associated with symptomatic, stool or behavioural manifestations in healthy adults, but remarkable shifts within the bacterial and mycobiome populations were observed. These findings emphasise the need to quantitatively assess all microbial Domains and their interrelationships to improve understanding of consequences of diet on gut function.},
}

@article {pmid40270072,
year = {2025},
author = {Kim, CW and Ku, KB and Hwang, I and Jung, HE and Kim, KD and Lee, HK},
title = {Differential responses of lung and intestinal microbiota to SARS-CoV-2 infection: a comparative study of the Wuhan and Omicron strains in K18-hACE2 Tg mice.},
journal = {Laboratory animal research},
volume = {41},
number = {1},
pages = {11},
pmid = {40270072},
issn = {1738-6055},
support = {RS-2023-NR077244, RS-2024-00439735//National Research Foundation of Korea/ ; RS-2024-00342560//National Research Foundation of Korea/ ; K-GRC GO! KRICT project BSF24-113//Korea Research Institute of Chemical Technology/ ; },
abstract = {BACKGROUND: The COVID-19 pandemic, caused by SARS-CoV-2, has led to the emergence of viral variants with distinct characteristics. Understanding the differential impacts of SARS-CoV-2 variants is crucial for effective public health response and treatment development. We investigated the differential effects of the original Wuhan strain and the emergent Omicron variant of SARS-CoV-2 using a K18-hACE2 transgenic mouse model. We compared the mortality rates, viral loads, and histopathological changes in lung and tracheal tissues, as well as alterations in the lung and intestinal microbiota following infection.

RESULTS: Our findings revealed significant differences between the variants, with the Wuhan strain causing higher mortality rates, severe lung pathology, and elevated viral loads compared to the Omicron variant. Microbiome analyses uncovered novel and distinct shifts in the lung and intestinal microbiota associated with each variant, providing evidence for variant-specific microbiome alterations. These changes suggest microbiome-related mechanisms that might modulate disease severity and host responses to SARS-CoV-2 infection.

CONCLUSIONS: This study highlights critical differences between the Wuhan strain and Omicron variant in terms of mortality, lung pathology, and microbiota changes, emphasizing the role of the microbiome in influencing disease outcomes. Novel findings include the identification of variant-specific microbiota shifts, which underscore potential microbiome-related mechanisms underlying differences in disease severity. These insights pave the way for future research exploring microbiome-targeted interventions to mitigate the impacts of SARS-CoV-2 and other viral infections.},
}

@article {pmid40270064,
year = {2025},
author = {Basu, A and Chalasani, D and Sarma, PVSRN and Uikey, S and Chenna, VR and Choudhari, PL and Podile, AR},
title = {Influence of genotype, nodule position, and edaphic factors on microbial diversity and assembly of pigeonpea (Cajanus cajan) root nodules in Indian soils.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {41},
pmid = {40270064},
issn = {2524-6372},
abstract = {BACKGROUND: Pigeonpea (Cajanus cajan) is an important legume crop in semi-arid regions with multiple uses. The microbial diversity within its root nodules in Indian soils remains poorly explored. We investigated the bacterial diversity of pigeonpea root nodules across different genotypes and soil types to identify the factors driving their assembly. Using a metagenomic approach and high-throughput sequencing of the 16S rRNA gene, we analyzed the nodule microbiomes of three pigeonpea genotypes (Asha, Durga, and Mannem Konda Kandi) grown in three different soil types (Alfisol, Vertisol, and Inceptisol) and wild pigeonpea (C. scarabaeoides) in its native soil.

RESULTS: Our results indicated that pigeonpea nodules harbor diverse rhizobial and non-rhizobial endophytes and that host genotype, nodule position, soil type, and other edaphic factors influence significant variation in the microbial community structure. The core nodule microbiome was dominated by Proteobacteria and Bacteroidetes. Bradyrhizobium and Ensifer were predominant among the rhizobial taxa, and non-rhizobial genera such as Pseudomonas, Chitinophaga, and Limnobacter were also abundant. Edaphic factors, particularly soil type, pH, and nutrient availability, had a stronger influence on the nodule bacterial community composition than the host genotype. Although bulk soil exhibited higher bacterial diversity, nodule microbiomes were less diverse but more specialized, indicating host-mediated selection. A comparison of the nodule microbiomes of wild and cultivated pigeonpea revealed distinct differences, with the core nodule microbiome of wild pigeonpea dominated by Bradyrhizobium, while that of cultivated pigeonpea exhibited a diverse bacterial community.

CONCLUSIONS: These findings demonstrate that soil properties play a more critical role than host genetics in shaping the pigeonpea nodule microbiome, emphasizing the importance of environmental conditions in symbiotic interactions. The differences between wild and cultivated genotypes suggest that domestication has altered microbial recruitment strategies. This study provides foundational insights into the factors driving microbial assembly in pigeonpea nodules, with implications for improving crop productivity through targeted microbial management. Future research should explore the functional roles of these microbial communities to optimize their use in sustainable agriculture.},
}

@article {pmid40269989,
year = {2025},
author = {Wang, Z and Wu, Q and Shen, W and Wan, F and He, J and Liu, L and Tang, S and Tan, Z},
title = {Cooling redistributed endotoxin across different biofluids via modulating the ruminal microbiota and metabolome without altering quorum sensing signal levels in heat-stressed beef bulls.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {38},
pmid = {40269989},
issn = {2524-4671},
support = {32302764//National Natural Science Foundation of China/ ; 2024JJ5179//Hunan Provincial Natural Science Foundation/ ; 22A0168//Hunan Provincial Education Department/ ; 2022A02001-1//Science and Technology Department of Xinjiang Uygur Autonomous Region/ ; 2021RC4060//Hunan Provincial Science and Technology Department/ ; },
abstract = {BACKGROUND: Cooling is one of the most common and economical methods to ameliorate heat stress (HS), and it has been discovered to alter the lipopolysaccharide (LPS) endotoxin level in ruminants. However, whether the endotoxin variation induced by cooling relates to the quorum sensing (QS) within the ruminal microflora remains unknown. The current study was consequently performed to examine whether cooling could influence the endotoxin distribution across different biofluids, ruminal microbiota, and ruminal metabolisms through affecting the QS of rumen microorganisms in beef cattle exposed to HS. Thirty-two Simmental bulls were used as experimental animals and randomly assigned to either the control (CON) group, or the mechanical ventilation and water spray (MVWS) treatment. The temperature-humidity index (THI) was recorded throughout this trial, and samples of the rumen liquid, blood, and urine were collected.

RESULTS: Cooling significantly lowered (P < 0.05) the temperature-humidity index (THI), ruminal endotoxin, and endotoxin concentration and excretion in urine, and significantly raised endotoxin level in blood (P < 0.05), but did not change the ruminal concentrations of QS signals including 3-OXO-C6-HSL and the AI-2 (P > 0.05). The linear discriminant analysis effect size (LEfSe) analysis revealed that Prevotellaceae, Rikenellaceae, Monoglobales and their affiliated members, as well as other bacterial taxa were significantly differently (P < 0.05) enriched between the two treatments. The Tax4Fun2 prediction suggested that QS function was upregulated in MVWS compared to CON. The metabolomic analysis indicated that cooling altered the ruminal metabolism profile and downregulated the pathways of lysine degradation, phenylalanine, tyrosine and tryptophan biosynthesis, and ubiquinone and other terpenoid-quinone biosynthesis. The significant (P < 0.05) correlations of the differential bacteria and metabolites with endotoxin and QS molecules were also demonstrated through Spearman analysis.

CONCLUSIONS: Based on the results of this trial, it could be speculated that the cooling reshaped the endotoxin distribution across different biofluids through manipulating ruminal microbiota and metabolome, which might involve the participation of QS. Further investigations are warranted to disclose and verify the mechanisms for those correlations found in this study.},
}

@article {pmid40269973,
year = {2025},
author = {An, J and Ge, Y and He, H and Ge, H and Li, J and Li, Z and Liu, L and Wang, Z and Lan, X and Shen, W and Cheng, A and Wan, F},
title = {Dietary L-leucine supplementation improves ruminal fermentation parameters and epithelium development in fattening Angus beef cattle.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {60},
pmid = {40269973},
issn = {1674-9782},
support = {2022YFD1301101-1//National Key R&D Program/ ; 32172758//National Natural Science Foundation of China/ ; 2024BBF01008//Key Research and Development Program of Ningxia/ ; },
abstract = {BACKGROUND: In this study, the effects of L-leucine (Leu) on rumen fermentation parameters, rumen epithelium development, amino acid composition, rumen bacterial communities and rumen metabolites in beef cattle were investigated. Twenty-four fattening Angus females of similar initial weight (575.5 ± 22.1 kg) were randomly assigned to 2 treatments with 4 replicate pens (3 cattle per pen). They were fed either a basal diet or a basal diet supplemented with 6.0 g L-Leu/100 kg BW/d for 120 d.

RESULTS: (1) Leu increased the ruminal concentrations of total volatile fatty acid (VFA) (P = 0.017), propionate (P = 0.023), isovalerate (P = 0.001), and branched-chain volatile fatty acid (BCVFA) (P = 0.01) at 4 h post-feeding. It also tended to increase acetate (P = 0.083) and decrease the ammonia-N (NH3-N) concentration (P = 0.055), but it did not affect ruminal pH (P > 0.1). Leu also increased microbial crude protein (MCP) (P = 0.026) at 4 h post-feeding, but decreased MCP at 8 h post-feeding (P = 0.010). (2) Supplementation with L-Leu increased the ruminal concentrations of phenylalanine (P = 0.011), lysine (P = 0.034), and tyrosine (P = 0.033), while decreasing the cystine concentration (P = 0.010). (3) Leu increased the thickness of the stratum spinosum and basal (P < 0.05), while decreasing the thickness of the stratum granulosum (P < 0.05). (4) Leu upregulated the relative mRNA abundance of genes involved in tight junction proteins (P < 0.05) and VFA absorption and metabolism (P < 0.01) in the rumen epithelium. This upregulation was positively correlated with the concentrations ruminal isovalerate and BCVFA (P < 0.01). (5) L-Leu did not affect the diversity and richness of ruminal microbes (P > 0.05), but differential bacterial biomarkers (LEfSe, LDA > 2) were either positively or negatively correlated with ruminal MCP, NH3-N, and BCVFA concentrations (P < 0.001). Additionally, differential bacterial metabolites (OPLS-DA, VIP > 1.5) were primarily enriched in the amino acid metabolism pathway and the cofactors and vitamins metabolism pathway (P < 0.05).

CONCLUSIONS: Dietary supplementation with L-Leu altered rumen fermentation parameters and patterns, improved rumen epithelial morphology, and enhanced the expression of genes related to VFA absorption and metabolism in the rumen epithelium of beef cattle.},
}

@article {pmid40269688,
year = {2025},
author = {Zhang, WD and Liu, YY and Li, MM and Du, H and Huang, KY and Feng, YY and Ma, CW and Wei, XX and Wang, XQ and Ran, JH},
title = {Decoding endosperm endophytes in Pinus armandi: a crucial indicator for host response to climate change.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {239},
pmid = {40269688},
issn = {1471-2180},
support = {2022YFF130170//National Key Research and Development Program of China/ ; XDA23080000//the Strategic Priority Research Program, CAS/ ; 31770238//the National Natural Science Foundation of China/ ; 2012070//Youth Innovation Promotion Association, CAS/ ; },
mesh = {*Endophytes/genetics/classification/isolation & purification/physiology ; *Climate Change ; *Pinus/microbiology ; *Endosperm/microbiology ; Phylogeny ; China ; Microbiota ; Transcriptome ; Biodiversity ; Ascomycota/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: Plant-associated microorganisms significantly contribute to plant survival in diverse environments. However, limited information is available regarding the involvement of endophytes in responding to climate change and their potential to enhance host plants' adaptation to future environmental shifts. Pinus armandi, endemic to China and widely distributed in climate-sensitive regions, serves as an ideal subject for investigating microbiome interactions that assist host plants in climate change response. Despite this, a comprehensive understanding of the diversity, community composition, and factors influencing endosperm endophytes in P. armandi, as well as the response of these endophytes to climate change, remains elusive.

RESULTS: In this study, transcriptome data from 55 P. armandi samples from 13 populations were analyzed to evaluate the composition and diversity of active endosperm endophytes and predict their response to future climate change. The results revealed variations in community composition, phylogenetic diversity, and interaction network between the northern and southern groups. Temperature and precipitation correlated with endosperm endophytic species richness and diversity. Under projected future climate conditions, the northern group exhibits greater genomic vulnerability and anticipates increased threats, reflecting a corresponding trend in endosperm endophytes, particularly within the Ascomycota community.

CONCLUSION: The consistent threat trend from climate change impacting both hosts and endophytes emphasizes the potential importance of host-related fungi as crucial indicators for predicting future climate impacts. Meanwhile, this study establishes an initial framework for exploring host-microbial interactions within the context of climate warming and provides valuable insights for studies related to plant protection.},
}

*Endophytes/genetics/classification/isolation & purification/physiology
*Climate Change
*Pinus/microbiology
*Endosperm/microbiology
Phylogeny
China
Microbiota
Transcriptome
Biodiversity
Ascomycota/genetics/classification/isolation & purification

@article {pmid40269516,
year = {2025},
author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D},
title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf177},
pmid = {40269516},
issn = {1477-4054},
support = {U24HG006620/NH/NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Metagenomics/methods ; *Metagenome ; *Microbiota ; *Gastrointestinal Microbiome ; Computational Biology/methods ; Algorithms ; },
abstract = {UNLABELLED: The continuously decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal of identifying microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here, we propose a novel backward variable selection method based on the hyperdimensional computing (HDC) paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.

AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the HDC paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics
*Metagenomics/methods
*Metagenome
*Microbiota
*Gastrointestinal Microbiome
Computational Biology/methods
Algorithms

@article {pmid40269515,
year = {2025},
author = {Sirasani, JP and Gardner, C and Jung, G and Lee, H and Ahn, TH},
title = {Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf176},
pmid = {40269515},
issn = {1477-4054},
support = {2430236//National Science Foundation/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Biomarkers/blood ; },
abstract = {Advances in next-generation sequencing have resulted in a growing understanding of the microbiome and its role in human health. Unlike traditional microbiome analysis, blood and tissue microbiome analyses focus on the detection and characterization of microbial DNA in blood and tissue, previously considered a sterile environment. In this review, we discuss the challenges and methodologies associated with analyzing these samples, particularly emphasizing blood and tissue microbiome research. Key preprocessing steps-including the removal of ribosomal RNA, host DNA, and other contaminants-are critical to reducing noise and accurately capturing microbial evidence. We also explore how taxonomic profiling tools, machine learning, and advanced normalization techniques address contamination and low microbial biomass, thereby improving reliability. While it offers the potential for identifying microbial involvement in systemic diseases previously undetectable by traditional methods, this methodology also carries risks and lacks universal acceptance due to concerns over reliability and interpretation errors. This paper critically reviews these factors, highlighting both the promise and pitfalls of using blood and tissue microbiome analyses as a tool for biomarker discovery.},
}

Humans
*Microbiota/genetics
*Computational Biology/methods
High-Throughput Nucleotide Sequencing
Machine Learning
Biomarkers/blood

@article {pmid40269473,
year = {2025},
author = {Khan, MAW and Bohannan, BJM and Meyer, KM and Womack, AM and Nüsslein, K and Grover, JP and Mazza Rodrigues, JL},
title = {Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70088},
doi = {10.1111/1758-2229.70088},
pmid = {40269473},
issn = {1758-2229},
support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; DEB 14422214//National Science Foundation/ ; },
mesh = {*Rainforest ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Microbiota ; Metagenomics/methods ; Metagenome ; *Archaea/genetics/metabolism/classification/isolation & purification ; Soil/chemistry ; Viruses/genetics/classification/metabolism/isolation & purification ; Machine Learning ; Brazil ; },
abstract = {The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long-term established pastures in the Amazon. Machine learning-derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein-coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein-coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long-term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long-term established pastures with implications for the C and N cycles.},
}

*Rainforest
*Soil Microbiology
*Bacteria/genetics/metabolism/classification/isolation & purification
*Microbiota
Metagenomics/methods
Metagenome
*Archaea/genetics/metabolism/classification/isolation & purification
Soil/chemistry
Viruses/genetics/classification/metabolism/isolation & purification
Machine Learning
Brazil

@article {pmid40269247,
year = {2025},
author = {Brasier, N and Niederberger, C and Zanella, M and Othman, A and Schlapbach, R and Kunz, L and Dittmann, A and Reeve, K and Prummer, M and Goldhahn, J},
title = {The molecular signature of heat stress in sweat reveals non-invasive biomarker candidates for health monitoring.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {650},
pmid = {40269247},
issn = {2399-3642},
mesh = {Humans ; *Sweat/chemistry/metabolism ; *Biomarkers/analysis/metabolism ; *Heat-Shock Response ; Male ; Female ; Adult ; Proteomics/methods ; Cross-Over Studies ; Young Adult ; },
abstract = {Heat stress is a significant public health challenge that leads to an increased risk of serious health deterioration, injuries, and loss of economic productivity. While the gold standard for monitoring heat stress continues to remain with population-based measurements, a straight-forward person-centered approach is lacking. Sweat can supply a wealth of molecular information, ranging from protein levels to levels of metabolites; it is thus a promising monitoring biofluid. A thorough investigation of sweat's molecular signature during heat stress is called for. We conducted a cross-over study on healthy participants with personalized heat-stress visits to investigate heat stress's proteomic and molecular signatures in sweat. Through mass-spectrometry analysis, we identified multiple candidate biomarkers ranging from amino acids to microbiome metabolites and proteins. To the best of our knowledge, these biomarker candidates represent the first successful approach to metabolically differentiate between various heat stressors thereby enabling their acute monitoring. While these biomarker candidates need further investigation to confirm their clinical value, many have already been identified as directly associated with heat stress in animals and plants. Once further investigated, next-generation wearable devices for person-centered, on-skin sweat-analysing platforms could be developed that would transform health management during exposure to heat stress.},
}

Humans
*Sweat/chemistry/metabolism
*Biomarkers/analysis/metabolism
*Heat-Shock Response
Male
Female
Adult
Proteomics/methods
Cross-Over Studies
Young Adult

@article {pmid40269196,
year = {2025},
author = {Verspohl, V and van Egmond, M and Kneisel, L and Reese, F and Thelen, AC and Korten, N and Neumann, M and Schaack, L and Voelz, C and Käver, L and Herpertz-Dahlmann, B and Beyer, C and Seitz, J and Trinh, S},
title = {Chronic starvation induces microglial cell depletion in an activity-based anorexia model.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14132},
pmid = {40269196},
issn = {2045-2322},
mesh = {Animals ; *Microglia/pathology/metabolism/drug effects ; Disease Models, Animal ; Rats ; Fatty Acids, Omega-3/administration & dosage/pharmacology ; *Anorexia/pathology ; Astrocytes/metabolism/pathology/drug effects ; *Starvation/pathology/complications ; Probiotics/administration & dosage/pharmacology ; Brain/pathology/metabolism ; Male ; *Anorexia Nervosa/pathology/metabolism ; Cell Proliferation ; },
abstract = {Anorexia nervosa (AN) is a severe psychiatric disease with a largely unknown pathophysiology. AN leads to reduced brain volume and a disbalance of the gut microbiome suggesting the involvement of the gut-brain-axis. Also, in the activity-based anorexia (ABA) animal model mimicking AN brain volume loss is observed. This study investigated the impact of chronic starvation on brain cell populations and evaluated the potential protective effects of omega-3 fatty acids (FA) and probiotics in rats. We used a chronic ABA model and provided daily oral supplementation of omega-3 FA and probiotics. Immunohistochemistry and qPCR were used to analyze GFAP-positive astrocytes, IBA1-positive microglia, OLIG1/2-positive oligodendrocytes, MAP2-positive neurons and Ki-67-positive proliferating cells in the cerebral cortex and corpus callosum. We found a significant reduction of astrocytes and microglia in all ABA groups, likely due to reduced proliferating cells. Reduced running wheel activity and reduced amount of food needed to sustain body weight were observed in animals with supplementation with omega-3 FA and probiotics but we did not observe alterations in brain cells that could be attributed to these supplementations. Our results indicate that glial cell depletion potentially underlies the diminished brain volume found in ABA rats. Omega-3 FA and probiotics show potential for reducing AN-related symptoms and merit further study as a therapeutic approach.},
}

Animals
*Microglia/pathology/metabolism/drug effects
Disease Models, Animal
Rats
Fatty Acids, Omega-3/administration & dosage/pharmacology
*Anorexia/pathology
Astrocytes/metabolism/pathology/drug effects
*Starvation/pathology/complications
Probiotics/administration & dosage/pharmacology
Brain/pathology/metabolism
Male
*Anorexia Nervosa/pathology/metabolism
Cell Proliferation

@article {pmid40269132,
year = {2025},
author = {Kumar, T and Rekhi, A and Lee, Y and Tran, J and Nagtalon, AGD and Rohatgi, S and Cyphert, EL},
title = {Leveraging the microbiome to combat antibiotic resistant gynecological infections.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {32},
pmid = {40269132},
issn = {2731-8745},
abstract = {The vaginal resistome can be considered a collection of the resistant determinants in the vaginal microbiome. Here we review the vaginal resistome including the microbes and resistant genes harbored in common gynecological infections, vaginal microbes that participate in horizontal gene transfer, host factors that contribute to the resistome, and common therapies. Finally, we provide perspective on technologies that can be leveraged to study the vaginal resistome and remaining challenges.},
}

@article {pmid40269059,
year = {2025},
author = {Aljutaily, T and Aladhadh, M and Alsaleem, KA and Alharbi, HF and Barakat, H and Aljumayi, H and Moustafa, MMA and Rehan, M},
title = {Gut microbiota diversity in obese rats treated with intermittent fasting, probiotic-fermented camel milk with or without dates and their combinations.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14204},
pmid = {40269059},
issn = {2045-2322},
support = {QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Camelus ; Rats ; *Obesity/microbiology/diet therapy ; *Probiotics/administration & dosage ; *Fasting ; *Milk ; Male ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Biodiversity ; Cultured Milk Products ; Intermittent Fasting ; },
abstract = {Dietary alternatives help effectively in obesity management. The present study examines the gut microbiota diversity in obesity-induced rats treated with intermittent fasting, fermented camel milk (FCM), and FCM-incorporated Sukkari date or their combinations. The metagenomic analysis of the gut microbiome through 16 S rRNA revealed 226 families, 499 genera, and 879 bacterial species. In the taxonomy distributions and heatmap analysis, Bacteroidota (i.e., Prevotella) had the uppermost relative abundance in groups before treatments (Before_Groups, most samples clustered in one sub-cluster) reached 80.50% in sample S11 (Before_G2), whereas Firmicutes (i.e., Lactobacillus) presented the dominant in groups after treatments (After_Groups, generality samples grouped in another sub-cluster) and counted 70.86% in sample S88 (After_G6), reflecting potential short-chain fatty acids production. The alpha and beta diversity explored by Shannon and PCoA indices presented high diversity in most groups after treatment. Deferribacterota and Fusobacteriota, in addition to Stenotrophomonas and Listeria, were the key phylotypes in the treated groups at the Phylum and genus levels, respectively. The proposed functional pathways involving mannan, rhamnose I, glucose, and xylose degradation were the most supported pathways in After_Groups with potential carbohydrate degradation. Eventually, intermittent fasting and probiotic fermented camel milk increased microbiome diversity and accelerated weight loss, preventing health issues.},
}

Animals
*Gastrointestinal Microbiome/genetics
Camelus
Rats
*Obesity/microbiology/diet therapy
*Probiotics/administration & dosage
*Fasting
*Milk
Male
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Biodiversity
Cultured Milk Products
Intermittent Fasting

@article {pmid40268958,
year = {2025},
author = {Luo, Q and Gao, H and Xiang, Y and Li, J and Dong, L and Wang, X and Liu, F and Guo, Y and Shen, C and Ding, Q and Qin, C and Liang, G and Wen, L},
title = {The dynamics of microbiome and virome in migratory birds of southwest China.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {64},
pmid = {40268958},
issn = {2055-5008},
mesh = {Animals ; China ; *Virome ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; *Charadriiformes/microbiology/virology ; Animal Migration ; *Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Birds/microbiology/virology ; Metagenomics ; Phylogeny ; },
abstract = {Migratory birds carry pathogens, posing a significant threat to environmental and human health. We documented the metatranscriptome and RNA virome of 896 stool samples from migratory birds and environmental samples over four consecutive years in southwest China. Our analysis identified Catellicoccus marimammalium as the predominant bacterium in the gut of black-headed gulls, with an average relative abundance of 79.3%. Strain-level analysis of C. marimammalium revealed a dominant population with some longitudinal diversity over the four years. Additionally, the gut of black-headed gulls was found to harbor numerous viruses, including a novel hepatovirus. Lysates of cells of C. marimammalium but not other bacteria derived from black-headed gulls could inhibit the replication of human hepatovirus, suggesting a potential regulatory role for gut commensal bacteria in modulating viral carriage. These findings enhance our understanding of the microbiome and RNA virome diversity in migratory birds and provide insights into the modulation of asymptomatic infections.},
}

Animals
China
*Virome
Feces/microbiology/virology
*Gastrointestinal Microbiome
*Charadriiformes/microbiology/virology
Animal Migration
*Bacteria/classification/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
*Birds/microbiology/virology
Metagenomics
Phylogeny

@article {pmid40268913,
year = {2025},
author = {Yuan, J and Sun, B and Li, M and Yang, C and Zhang, L and Chen, N and Chen, F and Li, L},
title = {OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {63},
pmid = {40268913},
issn = {2055-5008},
support = {82070566//National Natural Science Foundation of China/ ; J230029//Beijing Natural Science Foundation/ ; 2022YFA1206100 and 2022YFE0118300//National Key R&D Program of China/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; *Inflammatory Bowel Diseases/microbiology ; *Saliva/microbiology/chemistry ; *Proteomics/methods ; Workflow ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Bacterial Proteins/analysis/genetics ; Microbiota ; Female ; Male ; Mouth/microbiology ; Proteome/analysis ; Adult ; },
abstract = {The human oral microbiome has been associated with multiple inflammatory conditions including inflammatory bowel disease (IBD). Identifying functional changes in oral microbiome by metaproteomics helps understanding the factors driving dysbiosis related to intestinal diseases. However, enriching bacterial cells from oral samples (such as saliva and mouth rinse) rich in host proteins is challenging. Here, we present an Optimized Salivary MetaProteomic sample analysis workflow (OSaMPle) to enrich salivary bacteria and reduce host-derived interferences for in-depth analysis of the oral metaproteome. Compared to a conventional approach, OSaMPle improved the identification of bacterial peptides and proteins by 3.2 folds and 1.7 folds, respectively. Furthermore, applying OSaMPle to analyze mouth rinse samples from IBD patients revealed significant alterations in bacterial protein expressions under disease conditions. Specifically, proteins involved in the fatty acid elongation pathway in Peptostreptococcus were significantly less abundant in IBD patients, whereas proteins associated with the TCA cycle in Neisseria were significantly more abundant. The OSaMPle workflow is capable of processing small-volume oral samples and adaptable to high-throughput automation. It holds promise as a strategy for investigating the functional responses of oral microbiomes under disease conditions and identifying disease-associated microbes with their proteins, providing critical insights for detecting disease-related biomarkers within the oral microbiome.},
}

Humans
*Dysbiosis/microbiology
*Inflammatory Bowel Diseases/microbiology
*Saliva/microbiology/chemistry
*Proteomics/methods
Workflow
*Bacteria/classification/genetics/isolation & purification/metabolism
Bacterial Proteins/analysis/genetics
Microbiota
Female
Male
Mouth/microbiology
Proteome/analysis
Adult

@article {pmid40268833,
year = {2025},
author = {Ravindra, K and Kaur, M and Mor, S},
title = {Impacts of microplastics on gut health: Current status and future directions.},
journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40268833},
issn = {0975-0711},
abstract = {BACKGROUND AND OBJECTIVES: Microplastics are pervasive environmental pollutants, attracting significant concern due to their potential adverse effects on ecosystems and human health. This study hypothesizes that microplastics may significantly impact gastrointestinal (GI) health through various mechanisms. The objective of this systematic review is to explore the effects of microplastics on GI health, focusing on animal models such as mice, fish and earthworms.

METHODS: A systematic review approach was employed, analyzing studies that investigate the impact of microplastics on the gut microbiota, gut barrier integrity and GI inflammation. The review includes a synthesis of findings from multiple animal models.

RESULTS: The review reveals consistent evidence that microplastics can disrupt the gut microbiota, impair the gut barrier, and induce inflammatory responses in the GI tract. Statistical analysis shows a significant correlation between microplastic exposure and GI health deterioration across various animal models.

CONCLUSIONS: The findings underscore the harmful effects of microplastics on GI health, emphasizing the urgent need for policy interventions to reduce plastic pollution. Implementing measures to limit the production and usage of disposable plastics is crucial for mitigating the risks posed by microplastic contamination to promote environmental sustainability and safeguard human well-being.},
}

@article {pmid40268586,
year = {2025},
author = {Harris, CS and Conley, YP and Bai, J and Hammer, MJ},
title = {The Use of Biomarkers in Precision Health Symptom Science-Opportunities and Challenges.},
journal = {Seminars in oncology nursing},
volume = {},
number = {},
pages = {151886},
doi = {10.1016/j.soncn.2025.151886},
pmid = {40268586},
issn = {1878-3449},
abstract = {OBJECTIVES: Precision health symptom science applies person-centered approaches to elucidate interindividual differences in patients' symptom experiences and incorporates omics methods with social, societal, and environmental determinants of health to develop symptom management strategies. By filling scientific gaps related to patients' symptom experiences and their underlying mechanisms, interventions can be developed to improve quality of life and outcomes. The purposes of this article are to describe symptom phenotype development; review analytical approaches to identify a symptom phenotype; and discuss common and emerging methods for biomarker discovery and their implications in precision health symptom science.

METHODS: Peer-reviewed research studies, review articles, and scientific expertise were synthesized to provide a broad overview of several methods of biomarker discovery and their implications for precision health symptom science.

RESULTS: Approaches to symptom phenotype development and analytical methods for phenotype identification were reviewed. Common (ie, genomic, epigenomic, transcriptomic, proteomic, metabolomic, microbiome) and emerging (ie, polygenic risk scores, microRNA, epigenetic clocks, allostatic load, wearables) methods for biomarker discovery were described. Each method provides unique information to improve our understanding of the complex biological processes that underlie symptoms and may be used for risk prediction, screening, surveillance, and treatment response.

CONCLUSIONS: While the exemplar approaches to conducting precision health symptom science were shared through an oncology lens, they are generalizable across acute and chronic conditions.

Symptom biomarker identification is inherently complex and the methods for biomarker collection, processing, measurement, and analysis are continually evolving. Therefore, symptom scientists need to form transdisciplinary teams with experts in omics methodologies and bioinformatics. Despite the challenges, symptom scientists are well suited to lead the way in precision health symptom science to reduce symptom burden and improve quality of life among patients with various chronic conditions.},
}

@article {pmid40268434,
year = {2025},
author = {Nakao, T and Shimada, M and Tokunaga, T and Nishi, M and Kashihara, H and Takasu, C and Wada, Y and Yoshimoto, T},
title = {The number of teeth is a prognostic indicator for chemotherapy in colorectal cancer.},
journal = {The journal of medical investigation : JMI},
volume = {72},
number = {1.2},
pages = {134-138},
doi = {10.2152/jmi.72.134},
pmid = {40268434},
issn = {1349-6867},
mesh = {Humans ; Male ; Female ; *Colorectal Neoplasms/drug therapy/mortality ; Retrospective Studies ; Middle Aged ; Aged ; Prognosis ; *Tooth ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: The oral and gut microbiomes are linked to prognosis in colorectal cancer patients undergoing surgery, chemotherapy, or radiotherapy. Dysbiosis in the oral microbiome can lead to tooth decay, periodontitis, and gingivitis, resulting in tooth loss. This study examined the relationship between tooth count and chemotherapy outcomes in colorectal cancer patients.

METHOD: This retrospective cohort study involved 42 patients receiving chemotherapy for unresectable advanced or metastatic colorectal cancer at Tokushima University Hospital between October 2016 and December 2021. Prior to chemotherapy, dental panoramic radiographs were taken to determine tooth count. Patients were grouped based on the number of teeth (≥17 vs. ≤16), and overall survival (OS), progression-free survival (PFS), and adverse events were compared.

RESULTS: Patients with ≤16 teeth had significantly worse OS than those with ≥17 teeth (p = 0.024). PFS tended to be worse in patients with ≤16 teeth, albeit without significance (p = 0.097). The incidence of various adverse events did not differ between the groups. Anemia was the most common adverse event in patients with ≤16 teeth. Conversely, neutropenia was the most common adverse event in patients with ≥17 teeth.

CONCLUSION: The number of teeth could be easily examined prognostic factor for chemotherapy in colorectal cancer. J. Med. Invest. 72 : 134-138, February, 2025.},
}

Humans
Male
Female
*Colorectal Neoplasms/drug therapy/mortality
Retrospective Studies
Middle Aged
Aged
Prognosis
*Tooth
Adult
Aged, 80 and over

@article {pmid40195978,
year = {2025},
author = {Roy, A and Meregini, S and Cho, HJ and Chen, Z and Zaki, A and Argula, T and Beutler, B and SoRelle, JA},
title = {N-glycosylation enzyme Mpi is essential for mucin O-glycosylation, host-microbe homeostasis, Paneth cell defense, and metabolism.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {40195978},
issn = {2693-5015},
support = {K08 AI155832/AI/NIAID NIH HHS/United States ; R01 AI125581/AI/NIAID NIH HHS/United States ; R01 DK135511/DK/NIDDK NIH HHS/United States ; U19 AI100627/AI/NIAID NIH HHS/United States ; },
abstract = {Intestinal homeostasis relies on a protective mucus layer that separates bacteria from the host, with Muc2 as its primary component. This secreted, gel-forming mucin is heavily O-glycosylated, allowing it to retain water and support beneficial bacteria. For the first time, we demonstrate that Muc2 N-glycosylation plays a critical in mucin maturation, O-glycosylation, barrier integrity, and the prevention of dysbiosis. Using mouse models with global and intestine-specific N-glycan deficiency- caused by the loss of the mannose producing enzyme, Mpi- we uncover an unexpected link between N-glycosylation and intestinal homeostasis. Our findings reveal that Mpi hypomorphic mice are highly sensitive to DSS-induced colitis, while Mpi [flox]; Villin [Cre] mice spontaneously develop disease, exhibiting increased ER stress and dysbiosis. Additionally, electron microscopy, proteomics, and gene expression analyses of goblet and Paneth cells indicate immaturity, mitochondrial loss, and disruptions in lipid metabolism. These results highlight the fundamental role of N-glycosylation in maintaining intestinal homeostasis.},
}

@article {pmid40271438,
year = {2017},
author = {Lu, J and Breitwieser, FP and Thielen, P and Salzberg, SL},
title = {Bracken: estimating species abundance in metagenomics data.},
journal = {PeerJ. Computer science},
volume = {3},
number = {},
pages = {},
doi = {10.7717/peerj-cs.104},
pmid = {40271438},
issn = {2376-5992},
abstract = {Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.},
}

@article {pmid40267905,
year = {2025},
author = {Zhang, J and Wang, B and Xu, H and Liu, W and Yu, J and Wang, Q and Yu, H and Wei, JW and Dai, R and Zhou, J and He, Y and Zou, D and Yang, J and Ban, X and Hu, Q and Meng, X and Liu, YX and Wang, B and Hu, B and Wang, M and Xin, P and Chu, J and Li, C and Garrido-Oter, R and Yu, P and van Dijk, ADJ and Dong, L and Bouwmeester, H and Gao, S and Huang, A and Chu, C and Li, J and Bai, Y},
title = {Root microbiota regulates tiller number in rice.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.03.033},
pmid = {40267905},
issn = {1097-4172},
abstract = {Rice tillering is an important agronomic trait regulated by plant genetic and environmental factors. However, the role and mechanism of the root microbiota in modulating rice tillering have not been explored. Here, we examined the root microbiota composition and tiller numbers of 182 genome-sequenced rice varieties grown under field conditions and uncovered a significant correlation between root microbiota composition and rice tiller number. Using cultivated bacterial isolates, we demonstrated that various members of the root microbiota can regulate rice tillering in both laboratory and field conditions. Genetic, biochemical, and structural analyses revealed that cyclo(Leu-Pro), produced by the tiller-inhibiting bacterium Exiguobacterium R2567, activates the rice strigolactone (SL) signaling pathway by binding to the SL receptor OsD14, thus regulating tillering. The present work provides insight into how the root microbiota regulates key agronomic traits and offers a promising strategy for optimizing crop growth by harnessing the root microbiota in sustainable agriculture.},
}

@article {pmid40267755,
year = {2025},
author = {Situ, Y and Zhang, P and Zhang, C and Jiang, A and Zhang, N and Zhu, L and Mou, W and Liu, Z and Wong, HZH and Zhang, J and Cheng, Q and Lin, A and Luo, P},
title = {The metabolic dialogue between intratumoural microbes and cancer: implications for immunotherapy.},
journal = {EBioMedicine},
volume = {115},
number = {},
pages = {105708},
doi = {10.1016/j.ebiom.2025.105708},
pmid = {40267755},
issn = {2352-3964},
abstract = {The tumour microenvironment (TME) exerts a profound influence on cancer progression and treatment outcomes. Recent investigations have elucidated the crucial role of intratumoural microbiota and their metabolites in shaping the TME and modulating anti-tumour immunity. This review critically assesses the influence of intratumoural microbial metabolites on the TME and cancer immunotherapy. We systematically analyse how microbial-derived glucose, amino acid, and lipid metabolites modulate immune cell function, cytokine secretion, and tumour growth. The roles of specific metabolites, including lactate, short-chain fatty acids, bile acids, and tryptophan derivatives, are comprehensively examined in regulating immune responses and tumour progression. Furthermore, we investigate the potential of these metabolites to augment the efficacy of cancer immunotherapies, with particular emphasis on immune checkpoint inhibitors. By delineating the mechanisms through which microbial metabolites influence the TME, this review provides insights into novel microbiome-based therapeutic strategies, thereby highlighting a promising frontier in personalised cancer medicine.},
}

@article {pmid40267682,
year = {2025},
author = {Deokar, GS and Pathak, VA and Kshirsagar, SJ and Al-Asmari, F and Nirmal, N},
title = {Enhancement of vitamin B12 in plant-based food through microbial fermentation-a sustainable food system.},
journal = {Food chemistry},
volume = {484},
number = {},
pages = {144437},
doi = {10.1016/j.foodchem.2025.144437},
pmid = {40267682},
issn = {1873-7072},
abstract = {Vitamin B12 deficiency represents a notable health concern, especially among individuals adhering to plant-based dietary patterns. Understanding the biochemical mechanisms of in-situ B12 synthesis by gut microbiome and prebiotic supplementation is important for microbial fermentation strategies. This article discusses the mechanisms and applications of microbial fermentation in augmenting B12 levels, focusing on its significance in fortifying plant-derived food products. Microbial fermentation stands as a promising avenue for enhancing vitamin B12 content in plant-based foods, addressing a critical dietary concern among vegetarians and vegans. Moreover, bioavailability, regulatory considerations, and large-scale production remain a challenge and provide a scope for improvements. Future research should be focused on optimizing fermentation conditions, improving B12 stability in fortified foods, and assessing its long-term impact on human health.},
}

@article {pmid40267563,
year = {2025},
author = {Jian, Z and Wu, H and Yan, S and Li, T and Zhao, R and Zhao, J and Zi, X and Wang, K and Huang, Y and Gu, D and Zhao, S and Ge, C and Jia, J and Liu, L and Xu, Z and Dou, T},
title = {Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis.},
journal = {Poultry science},
volume = {104},
number = {7},
pages = {105138},
doi = {10.1016/j.psj.2025.105138},
pmid = {40267563},
issn = {1525-3171},
abstract = {The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.},
}

@article {pmid40267504,
year = {2025},
author = {Hu, X and Gu, X and Li, H and Wang, H and Tang, D},
title = {Global Trends in Artificial Intelligence and Sepsis-Related Research: A Bibliometric Analysis.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002598},
pmid = {40267504},
issn = {1540-0514},
abstract = {BACKGROUND: In the field of bibliometrics, although some studies have conducted literature reviews and analyses on sepsis, these studies mainly focus on specific areas or technologies, such as the relationship between the gut microbiome and sepsis, or immunomodulatory treatments for sepsis. However, there are still few studies that provide comprehensive bibliometric analyses of global scientific publications related to AI in sepsis research.

OBJECTIVE: The aim of this study is to assess the global trend analysis of AI applications in sepsis based on publication output, citations, co-authorship between countries, and co-occurrence of author keywords.

METHODS: A total of 4,382 papers published from 2015 to December 2024 were retrieved and downloaded from the SCIE database in WOS. After selecting the document types as articles and reviews, and conducting eligibility checks on titles and abstracts, the final bibliometric analysis using VOSviewer and CiteSpace included 4,209 papers.

RESULTS: The number of published papers increased sharply starting in 2021, accounting for 58.14% (2,447/4,209) of all included papers. The United States and China together account for approximately 60.16% (2,532/4,209) of the total publications. Among the top 10 institutions in AI research on sepsis, seven are located in the United States. Rishikesan Kamaleswaran is the most contributing author, with PLOS ONE having more citations in this field than other journals. SCIENTIFIC REPORTS is also the most influential journal (NP = 106, H-index = 23, IF: 3.8).

CONCLUSION: This study highlights the popular areas of AI research, provides a comprehensive overview of the research trends of AI in sepsis, and offers potential collaboration and future research prospects. To make AI-based clinical research sufficiently persuasive in sepsis practice, collaborative research is needed to improve the maturity and robustness of AI-driven models.},
}

@article {pmid40267287,
year = {2025},
author = {Chen, D and Zhang, T and Cui, H and Gu, J and Xuan, P},
title = {KNDM: A Knowledge Graph Transformer and Node Category Sensitive Contrastive Learning Model for Drug and Microbe Association Prediction.},
journal = {Journal of chemical information and modeling},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jcim.5c00186},
pmid = {40267287},
issn = {1549-960X},
abstract = {It has been proven that the microbiome in human bodies can promote or inhibit the treatment effects of the drugs by affecting their toxicities and activities. Therefore, identifying drug-related microbes helps in understanding how drugs exert their functions under the influence of these microbes. Most recent methods for drug-related microbe prediction are developed based on graph learning. However, those methods fail to fully utilize the diverse characteristics of drug and microbe entities from the perspective of a knowledge graph, as well as the contextual relationships among multiple meta-paths from the meta-path perspective. Moreover, previous methods overlook the consistency between the entity features derived from the knowledge graph and the node semantic features extracted from the meta-paths. To address these limitations, we propose a knowledge-graph transformer and node category-sensitive contrastive learning-based drug and microbe association prediction model (KNDM). This model learns the diverse features of drug and microbe entities, encodes the contextual relationships across multiple meta-paths, and integrates the feature consistency. First, we construct a knowledge graph consisting of drug and microbe entities, which aids in revealing similarities and associations between any two entities. Second, considering the heterogeneity of entities in the knowledge graph, we propose an entity category-sensitive transformer to integrate the diversity of multiple entity types and the various relationships among them. Third, multiple meta-paths are constructed to capture and embed the semantic relationships based on similarities and associations among drug and microbe nodes. A meta-path semantic feature learning strategy with recursive gating is proposed to capture specific semantic features of individual meta-paths while fusing contextual relationships among multiple meta-paths. Finally, we develop a node-category-sensitive contrastive learning strategy to enhance the consistency between entity features and node semantic features. Extensive experiments demonstrate that KNDM outperforms eight state-of-the-art drug-microbe association prediction models, while ablation studies validate the effectiveness of its key innovations. Additionally, case studies on candidate microbes associated with three drugs-curcumin, epigallocatechin gallate, and ciprofloxacin-further showcase KNDM's capability to identify potential drug-microbe associations.},
}

@article {pmid40267282,
year = {2025},
author = {Yang, Z and Chen, H and Zhong, GH and Liu, J},
title = {cAMP-Mediated Biofilm eDNA Transfer Facilitates the Resilience of Soil Microbiome to Agrochemical Stress.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00961},
pmid = {40267282},
issn = {1520-5118},
abstract = {Soil microorganisms utilize extracellular DNA (eDNA)-based biofilms as a defense against xenobiotics. However, the specific effects and transfer pathways of eDNA under persistent agrochemical exposure remain unclear. This study examined the transfer dynamics of carbofuran-hydrolase gene pchA from Pseudomonas stutzeri PS21. During biofilm formation, pchA was released from eDNA, leading to an enrichment of beneficial microorganisms such as Acidobacteria and Elusimicrobia, which enhanced organic compound metabolism and improved soil microbiome resilience. An increase in the pchA-associated mobile genetic elements and the colocalization of pchA with other bacterial species indicated the potential horizontal gene transfer (HGT) under carbofuran exposure. Additionally, carbofuran triggered a cAMP-dependent apoptotic pathway, leading to a 59.6% increase in pchA copy number, which suggested that cAMP played a role in initiating HGT. In conclusion, the cAMP-mediated interspecific transfer of pchA could enhance microbial coadaptation to carbofuran contamination, thereby strengthening the collective defense of soil microbiome against agrochemical stress.},
}

@article {pmid40267215,
year = {2025},
author = {Gabby, ME and Bandara, A and Outrata, LM and Ebohon, O and Ahmad, SS and Dressler, JM and McClune, ME and Trimble, RN and Mullen, L and Jutras, BL},
title = {A high-resolution screen identifies a preexisting beta-lactam that specifically treats Lyme disease in mice.},
journal = {Science translational medicine},
volume = {17},
number = {795},
pages = {eadr9091},
doi = {10.1126/scitranslmed.adr9091},
pmid = {40267215},
issn = {1946-6242},
mesh = {Animals ; *Lyme Disease/drug therapy/microbiology ; Borrelia burgdorferi/drug effects ; Mice ; *beta-Lactams/therapeutic use/pharmacology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Humans ; Microbial Sensitivity Tests ; Drug Evaluation, Preclinical ; },
abstract = {Lyme disease, caused by Borrelia burgdorferi in the United States, is an escalating human health problem that can cause severe disease if not properly treated. Doxycycline is the primary treatment option for Lyme disease; however, several concerns are associated with high-dose doxycycline treatment. For example, doxycycline is a broad-spectrum antibiotic and kills beneficial bacteria. Doxycycline is also known to produce unwanted off-target effects in eukaryotic cells. Some at-risk populations such as young children cannot be prescribed doxycycline, and in addition to these shortcomings, the treatment appears to fail in 10 to 20% of cases. We reasoned that safe, alternative therapies may currently exist but have not yet been found because of the challenges associated with drug screening approaches. We screened nearly 500 US Food and Drug Administration-approved compounds using an array of physiological, cellular, and molecular techniques. Top-performing candidates were counter screened to identify compounds that did not affect other bacterial phyla. Piperacillin emerged as a compound that eradicated B. burgdorferi at low-nanomolar concentrations by specifically interfering with the unusual, multizonal peptidoglycan synthesis pattern common to the Borrelia clade. Mechanistic in vitro studies identified the cellular target of piperacillin in B. burgdorferi and produced key insights that may explain both the specificity and efficacy of the compound. Further, in vivo studies using an experimental mouse infection model demonstrated that piperacillin treated animals at a 100-fold lower dose than the effective dose of doxycycline without affecting the murine microbiome. Our findings suggest that piperacillin may offer clinicians another therapeutic option for Lyme disease.},
}

Animals
*Lyme Disease/drug therapy/microbiology
Borrelia burgdorferi/drug effects
Mice
*beta-Lactams/therapeutic use/pharmacology
*Anti-Bacterial Agents/therapeutic use/pharmacology
Humans
Microbial Sensitivity Tests
Drug Evaluation, Preclinical

@article {pmid40267015,
year = {2025},
author = {Incharoen, T and Charoensook, R and Tartrakoon, W and Numthuam, S and Sunanta, Y and Jimenez, G and Loor, JJ},
title = {Dietary Bacillus toyonensis BCT-7112[T] Supplementation Influences Performance, Egg Quality, Ammonia Emission, and Cecal Microbiome in Laying Ducks.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030259},
pmid = {40267015},
issn = {2306-7381},
support = {R2561A064//Rubinum S.A., Spain, and Center of Excellence for Agricultural and Livestock Innovation, Faculty of Agriculture Natural Resources and Environment, Naresuan University, Phitsanulok, Thailand/ ; },
abstract = {This study evaluated the effects of Bacillus toyonensis BCT-7112[T] on laying duck performance, egg quality, ammonia emission, and cecal microbiota. Two hundred twenty 32-week-old Khaki Campbell ducks were assigned to four dietary treatments (0, 200, 500, or 1000 ppm Toyocerin[®] 10[9] premixture, containing 1 × 10[9] B. toyonensis BCT-7112[T] CFU/g) with five replicate pens of eleven birds each. Data on productivity, egg quality, and ammonia emissions were collected weekly, and cecal microbiota were analyzed at 44 weeks of age. Supplementation with 1000 ppm B. toyonensis BCT-7112[T] significantly increased average egg weight (p < 0.001) and eggshell thickness (p = 0.007). Egg mass also improved at higher supplementation levels (p < 0.05), though feed intake, feed conversion, daily egg production, and most egg quality parameters were unaffected (p > 0.05). Ammonia emissions in litter decreased significantly (p < 0.05) with probiotic inclusion. Cecal microbiota analysis revealed higher diversity in ducks fed 1000 ppm, with a notable shift in predominant phyla from Bacteroidetes (35.12%) and Firmicutes (34.93%) in the controls to Bacteroidetes (40.52%), Firmicutes (34.08%), and Deferribacteres (9.54%) in the treated ducks. The findings suggest that 1000 ppm B. toyonensis BCT-7112[T] enhances egg production, eggshell quality, and microbial diversity while reducing ammonia emissions in laying duck systems.},
}

@article {pmid40266957,
year = {2025},
author = {Sun, J and Liang, S and Gu, X and Xu, J and Wang, X and Wang, Z and Tao, H and Wang, J and Han, B},
title = {Effects of Dietary Supplementation with Yeast Hydrolysate on Immune Function, Fecal Short Chain Fatty Acids, and Intestinal Health in Cats.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030239},
pmid = {40266957},
issn = {2306-7381},
support = {CAAS-ASTIP-2023-IFR-14//Central Public-interest Scientific Institution Basal Research Fund/ ; },
abstract = {Yeast hydrolysate (YH) is rich in amino acids and other nutrients, and as a nutritional supplement it has been widely used in daily nutritional supplements for livestock. However, the role of YH in domestic pets, especially cats, has not yet been determined. The objective of this research was to study the effects of different concentrations of YH on the healthy cats. All cats were randomly divided into four treatments: the control group (T0, n = 6, without YH), treatment 1 (T1, the low concentration group, 0.8% of YH, n = 6), treatment 2 (T2, the middle concentration group, 1.5% of YH, n = 6), and treatment 3 (T3, the high concentration group, 4% of YH, n = 6), and the blood biochemistry, immune indexes and odorous substances in the feces, and microbiome of cats were determined on day 28. Our results showed that YH could increase the immunoglobulin G (IgG) level in the serum (p < 0.01) and reduce 3-methylindole content in the feces (p < 0.01). The acetic acid in the feces of T2 treatment (1.5%YH) was apparently increased compared to the control treatment (p < 0.05). The blood biochemistry indexes were not affected by the YH. Compared to the control group, there was no significant difference in the abundance at the phylum level. On the genus level, the abundance of g_Ruminocococcaceae and g_Lachnospiraceae, the beneficial bacteria in the gut, were decreased in the treatment T3 compared to treatment T1 (p < 0.05), but there was no significance between T1 and T2, which suggested that a high concentration of YH may be negative for gut health. So, the research showed that 1.5% of YH could be the best concentration for the improvement of immunity and gut health for cats.},
}

@article {pmid40266944,
year = {2025},
author = {Herzog, F and Crissman, KR and Beckers, KF and Zhou, G and Liu, CC and Sones, JL},
title = {Lactobacillus Genus Complex Probiotic-Induced Changes on the Equine Clitoral Microbiome.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030232},
pmid = {40266944},
issn = {2306-7381},
support = {2022//Louisiana State University Charles V. Cusimano/ ; },
abstract = {Dysbiosis of the lower reproductive tract (LRT) in mares may play a role in clinical diseases, including endometritis and placentitis. Metagenomic/metagenetic analysis of bacterial DNA can identify organisms that are not readily cultured and, thus, may go undetected. In this study, we tested the following hypotheses: (1) the clitoris of estrual mares harbors a unique resident microbiome, (2) topical Lactobacillus genus complex (LGC)-containing probiotic will alter the equine clitoral microbiome, and (3) early pregnancy rates following clitoral LGC application will not differ significantly from industry standards. Mares (n = 12) in estrus had sterile clitoral swabs collected (0) prior to daily topical LGC for 4 days. Second (12 h) and third clitoral swabs (48 h) were collected following final LGC application. During the next estrus, the mares were bred by artificial insemination. Genomic DNA was extracted and used for 16S rRNA sequencing via the Illumina Miseq platform. Abundance was evaluated via Friedman test with pairwise Dunn's post hoc comparisons. Statistical significance was set at p < 0.05. Compared to time 0, Desulfobacterota decreased and Corynebacterium spp. increased at 12 h and 48 h compared to 0, while Actinobacillus and Fusobacterium spp. increased in a time-dependent manner. Furthermore, Mobiluncus spp. and Christensenellacea_R-7_group decreased at 12 h and 48 h compared to 0. LGC changed the beta but not alpha diversity at both 12 h and 48 h. Mares with LGC application achieved an 85% pregnancy rate in the subsequent estrus. Future investigations are needed to understand the role of the LRT microbiome and probiotics in equine breeding.},
}

@article {pmid40266930,
year = {2025},
author = {Bakker, J and Nederlof, RA and Stumpel, J and de la Garza, MA},
title = {Recent Advances in the Etiology, Diagnosis, and Treatment of Marmoset Wasting Syndrome.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030203},
pmid = {40266930},
issn = {2306-7381},
abstract = {One of the primary challenges encountered in managing captive callitrichids is a group of gastrointestinal disorders that are collectively known as Marmoset Wasting Syndrome (MWS). Unfortunately, MWS is still not well understood. It is suggested that MWS has a multifactorial etiology; stress, infection, malnutrition, malabsorption, and enteritis or colitis may be associated with MWS. Usually, animals demonstrate more than one of the following clinical signs: progressive weight loss, alopecia, chronic diarrhea, muscle atrophy, hypoproteinemia, and anemia. Recent advances in diagnostics, mostly noninvasive fecal and urine tests, yielded promising results. Good treatment results have been achieved with the administration of glucocorticoids and tranexamic acid, although no cure has been found yet. Probiotics and gel diets also demonstrated to be potentially useful. However, once animals are affected by MWS, treatments eventually become ineffective, and animals will inevitably require euthanasia to prevent further suffering. Preventative measures should be aimed at reducing stress and optimizing housing, husbandry, and diets. More research is warranted to elucidate the pathogenesis of MWS in captive callitrichids and to refine diagnostic and treatment methods.},
}

@article {pmid40266902,
year = {2025},
author = {Kerek, Á and Román, I and Szabó, Á and Pézsa, NP and Jerzsele, Á},
title = {Antibiotic Resistance Gene Expression in Veterinary Probiotics: Two Sides of the Coin.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030217},
pmid = {40266902},
issn = {2306-7381},
support = {RRF-2.3.1-21-2022-00001//National Recovery Fund/ ; },
abstract = {The rapid proliferation of antimicrobial resistance has emerged as one of the most pressing animal and public health challenges of our time. Probiotics, extensively employed in human and veterinary medicine, are instrumental in maintaining a balanced microbiome and mitigating its disruption during antibiotic therapy. While their numerous benefits are well documented, probiotics also present potential risks, notably the capacity to harbor antimicrobial resistance genes. This genetic reservoir could contribute to the emergence and spread of antimicrobial resistance by facilitating the horizontal transfer of resistance genes to pathogenic bacteria within the gut. This review critically examines the presence of antimicrobial resistance genes in commonly used probiotic strains, explores the underlying mechanisms of resistance, and provides a balanced analysis of the benefits and risks associated with their use. By addressing these dual aspects, this paper highlights the need for vigilant evaluation of probiotics to preserve their therapeutic potential while minimizing public health risks.},
}

@article {pmid40266732,
year = {2025},
author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX},
title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030269},
pmid = {40266732},
issn = {2075-4450},
support = {Hermes 57545//Universidad Nacional de Colombia/ ; },
abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.},
}

@article {pmid40266727,
year = {2025},
author = {Ngando, FJ and Tang, H and Zhang, X and Zhang, X and Yang, F and Shang, Y and Cai, J and Guo, Y and Zhao, L and Zhang, C},
title = {Effects of Feeding Sources and Different Temperature Changes on the Gut Microbiome Structure of Chrysomya megacephala (Diptera: Calliphoridae).},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030283},
pmid = {40266727},
issn = {2075-4450},
support = {No.82371895//National Natural Science Foundation of China/ ; No. 2022JJ40671//the Human Natural Science Foundation/ ; },
abstract = {Chrysomya megacephala (Diptera: Calliphoridae), commonly referred to as the oriental latrine fly, is a synanthropic blowfly species frequently associated with decomposing organic matter. This study sought to investigate the influence of various feeding substrates and temperature conditions, specifically constant temperatures of 15, 25, 35 °C, and variable temperatures averaging 23.31 °C, on the gut microbiome of C. megacephala. The microbiome analysis was conducted using the Illumina HiSeq platform for 16S rRNA gene sequencing in Changsha, China. Across all experimental conditions, the gut microbiome of C. megacephala yielded 1257 operational taxonomic units (OTUs), which were categorized into 26 phyla, 72 classes, 165 orders, 270 families, 516 genera, and 794 species. The study showed significant differences in the gut microbiome of C. megacephala between different feeding sources and temperature conditions across the lifespan. Low temperature had the potential to reduce the proportion abundance of bacterial communities in the gut microbiome, while high and variable temperature increased them. Metabolism was the main predicted function with diverse phenotypic characters in the gut microbiota of C. megacephala. The presence of diverse bacterial phenotypes in the gut microbiome of C. megacephala highlights its significant interest for medicine and offers promising applications in industry and agriculture.},
}

@article {pmid40266445,
year = {2025},
author = {Chellappoo, A and Baedke, J and Meloni, M},
title = {From genetic to postgenomic determinisms: The role of the environment reconsidered : Introduction to the collection 'Postgenomic determinisms: Environmental narratives after the century of the gene'.},
journal = {History and philosophy of the life sciences},
volume = {47},
number = {2},
pages = {23},
pmid = {40266445},
issn = {1742-6316},
support = {BA 5808/2-1//Deutsche Forschungsgemeinschaft/ ; BA 5808/2-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Environment ; *Genetic Determinism ; *Genomics ; *Gene-Environment Interaction ; *Genetics/history ; },
abstract = {In the past twenty years, conceptual and technological shifts in the life sciences have unseated the causal primacy of the gene. The picture emerging from 'postgenomic' science is one that emphasises multifactorial dependencies between the environment, development, and the genome, and blurs boundaries between biological individuals, and between the body and the environment. Despite the rejection of genetic determinism within postgenomics, forms of determinism nevertheless persist. The environment is often conceptualised in postgenomic research in a narrow and constrained way, affording an outsized causal role to certain environmental factors while neglecting the influence of others. This carries ethical and social implications, including for understandings of race and motherhood. This topical collection interrogates the environmental determinisms developing within postgenomic science, through investigation of their conceptual foundations, histories, and social contexts across a range of postgenomic fields.},
}

Humans
*Environment
*Genetic Determinism
*Genomics
*Gene-Environment Interaction
*Genetics/history

@article {pmid40266410,
year = {2025},
author = {van Boom, KM and Kohn, TA and Tordiffe, ASW},
title = {Methionine, threonine and glutamic acid adapted pathways in captive cheetahs on a glycine-supplemented diet.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {21},
number = {3},
pages = {56},
pmid = {40266410},
issn = {1573-3890},
mesh = {Animals ; *Glycine/metabolism/administration & dosage ; *Acinonyx/metabolism/blood ; *Threonine/metabolism/blood ; Dietary Supplements ; *Methionine/metabolism/blood ; *Glutamic Acid/metabolism/blood/urine ; Diet ; Animal Feed/analysis ; Male ; Female ; },
abstract = {BACKGROUND: Captive cheetahs are prone to a range of unusual diseases potentially linked to unnatural diets high in muscle meat and low in collagen-rich animal fibre. In the wild, cheetahs typically eat whole prey diets not easily replicated in a captive setting. Glycine is the most abundant amino acid in collagen with a key role in several metabolic pathways such as collagen biosynthesis. Several recent studies suggest that endogenous glycine production may be limited in several species.

OBJECTIVES: Using untargeted [1]H- nuclear magnetic resonance, the metabolic changes in the urine and serum of 10 adult captive cheetahs on a glycine-supplemented diet were investigated.

METHODS: Cheetahs were fed either a meat only (control) or glycine-supplemented meat diet (30 g glycine per 1 kg meat) for four weeks, followed by a four-week cross-over. Urine and blood samples were collected at baseline and after each intervention.

RESULTS: A total of 151 and 60 metabolites were identified in the urine and serum, respectively. Specifically, dimethylsulphone, proline, fructose, dimethylamine, trimethylamine, pyroglutamic acid, 1,3-diaminopropane, dihydrothymine, methylmalonic acid and pimelic acid contributed to metabolome differences in the urine. In serum, glutamic acid, threonine, α-aminobutyric acid, glucose-6-phosphate, ethanolamine, methionine and propionic acid were highlighted. These metabolites play various metabolic roles in energy production, immune function, protein and collagen biosynthesis or as products of gut microbiome fermentation.

CONCLUSION: Glycine supplementation influenced threonine sparing, pyrimidine biosynthesis pathways and bacterial fermentation products, although the implications of these findings on the health of captive cheetahs is unknown. Future studies should use a targeted approach to further elaborate on these pathways.},
}

Animals
*Glycine/metabolism/administration & dosage
*Acinonyx/metabolism/blood
*Threonine/metabolism/blood
Dietary Supplements
*Methionine/metabolism/blood
*Glutamic Acid/metabolism/blood/urine
Diet
Animal Feed/analysis
Male
Female

@article {pmid40266381,
year = {2025},
author = {Cuny, MAC and Gloder, G and Bourne, ME and Kalisvaart, SN and Verreth, C and Crauwels, S and Cusumano, A and Lievens, B and Poelman, EH},
title = {Parasitoid Calyx Fluid and Venom Affect Bacterial Communities in Their Lepidopteran Host Labial Salivary Glands.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {33},
pmid = {40266381},
issn = {1432-184X},
support = {ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; },
mesh = {Animals ; *Salivary Glands/microbiology ; *Wasps/physiology ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Microbiota ; Larva/parasitology/microbiology ; Host-Parasite Interactions ; *Butterflies/microbiology/parasitology ; Hemolymph/microbiology ; Polydnaviridae/physiology ; *Wasp Venoms/pharmacology ; *Moths/microbiology/parasitology ; },
abstract = {The influence of gut and gonad bacterial communities on insect physiology, behaviour, and ecology is increasingly recognised. Parasitism by parasitoid wasps alters many physiological processes in their hosts, including gut bacterial communities. However, it remains unclear whether these changes are restricted to the gut or also occur in other tissues and fluids, and the mechanisms underlying such changes are unknown. We hypothesise that host microbiome changes result from the injection of calyx fluid (that contain symbiotic viruses known as polydnaviruses) and venom during parasitoid oviposition and that these effects vary by host tissue. To test this, we microinjected Pieris brassicae caterpillars with calyx fluid and venom from Cotesia glomerata, using saline solution and natural parasitism by C. glomerata as controls. We analysed changes in the bacterial community composition in the gut, regurgitate, haemolymph, and labial salivary glands of the host insects. Multivariate analysis revealed distinct bacterial communities across tissues and fluids, with high diversity in the salivary glands and haemolymph. Parasitism and injection of calyx fluid and venom significantly altered bacterial communities in the salivary glands. Differential abundance analysis showed that parasitism affected bacterial relative abundance in the haemolymph, and that Wolbachia was only found in the haemolymph of parasitized caterpillars. Altogether, our findings reveal that parasitism influences the host haemolymph microbiome, and both parasitism and injection of calyx fluid and venom drive changes in the bacterial community composition within the host salivary glands. Given that the composition of salivary glands can influence plant response to herbivory, we discuss these results in the broader context of plant-parasitoid interactions.},
}

Animals
*Salivary Glands/microbiology
*Wasps/physiology
*Bacteria/classification/genetics/isolation & purification/drug effects
*Microbiota
Larva/parasitology/microbiology
Host-Parasite Interactions
*Butterflies/microbiology/parasitology
Hemolymph/microbiology
Polydnaviridae/physiology
*Wasp Venoms/pharmacology
*Moths/microbiology/parasitology

@article {pmid40266380,
year = {2025},
author = {Çakır, B and Sönmezoğlu, BG and Şahin, EÖ and Köroğlu, M and Aksoy, NÖ},
title = {Evaluation of ocular surface microbiota in children with blepharoconjunctivitis.},
journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie},
volume = {},
number = {},
pages = {},
pmid = {40266380},
issn = {1435-702X},
support = {2022-09-32-106//Sakarya Üniversitesi/ ; },
abstract = {PURPOSE: To investigate the conjunctival and eyelid margin bacterial microbiota in children with blepharoconjunctivitis by using 16S rDNA amplicon sequencing.

METHODS: In this prospective cross-sectional study, 20 children aged between 3-15 years with blepharoconjunctivitis or blepharokeratokonjunctivitis formed Blepharitis Group and 21 children aged between 3-15 years without any ocular and sysemic diseases except mild refractive errors formed Control Group. Swap samples from all children were taken. The alpha diversity of the ocular surface microbiota within each group were evaluated by using Shannon's, Simpson, and Chao index. Beta diversity was evaluated by Bray Curtis index.

RESULTS: Microbiological diversity was higher in the patient group than in the control group. According to Shannon's, Simpson, and Chao index, there were statistically difference between groups (p: 0.000013, p:000003 p: 0.00235, respectively). According to the Bray Curtis index, the healthy eye microbiome in the control group is observed to be highly similar, consistent with other analyses, and the overlapping cluster with the blepharitis eye microbiome is quite low (pco1: 40.93%). Sphingoblump, Micrococus, Lacnospiracebacterium, Stenothermophilus, Aurelmonass, Micrococus, Blatiabeum, Delfiacdiovorans and Vellonella densities were found to be higher in the patient group.

CONCLUSION: Both alpha and beta diversity analyses were significantly higher in pediatric age group patients with blepharitis. In addition, Lacnospiracebacterium, Stenothermophilus, Aurelmonass, Micrococus, Blatiabeum, Delfiacdiovorans and Vellonella densities were found to be higher, which may lead to future studies focused on diagnosis and treatment.},
}

@article {pmid40266093,
year = {2025},
author = {Zou, Y and Pu, L and Guo, A and Li, Y and Liu, Y and Wang, Y and Ding, Y and Du, X and Guo, X and Zhang, S and Cai, X and Wang, S},
title = {Helminth reshapes host gut microbiota and immunoregulation by deploying an antimicrobial program of innate immunity.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2496447},
doi = {10.1080/19490976.2025.2496447},
pmid = {40266093},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/immunology ; Animals ; *Immunity, Innate ; Mice ; Macrophages/immunology ; T-Lymphocytes, Regulatory/immunology ; Antimicrobial Cationic Peptides/immunology ; Mice, Inbred C57BL ; Lactobacillus ; },
abstract = {Helminths can manipulate their host's gut microbiota, with the expansion of the lactobacilli population being a common feature. This process profoundly influences host immunoregulation, yet the underlying mechanisms remain almost unknown. Using a tissue-dwelling helminth model (larval Echinococcus multilocularis) while validating key findings from other helminth infections, we show that helminths harness the antibacterial program of host innate immunity to transform the host gut microbiome and control gut microbiota-mediated immunity. Using multifaceted techniques, we elucidate that cathelicidin-related antimicrobial peptide (CRAMP), derived from the expanded CD11b[+]CD206[+] macrophages rather than the intestinal epithelial cells, is the key component that enters into the gut ecological system and enhances the fitness of Lactobacillus by selectively killing gram-negative microbes like enterobacteria. Furthermore, through in vitro cell culturing and in vivo dietary intervention experiments, we demonstrate that this regulation from innate immunity is boosted via toll-like receptor signaling by helminth's secretory products, which could be sufficiently tuned down by dietary vitamin D through its receptor and cyp27b1. Importantly, using microbiota-targeted treatment methods, we prove that this signaling bolsters gut microbiota-mediated host intestinal Foxp3[+] Treg cell expansion and parasite survival and that therapies targeting this signaling are effective in treating infection. We outline a dietary micronutrient-dependent mechanism by which helminths leverage host innate immunity to edit the host gut microbiome and thereby control immunosuppression precisely.},
}

*Gastrointestinal Microbiome/immunology
Animals
*Immunity, Innate
Mice
Macrophages/immunology
T-Lymphocytes, Regulatory/immunology
Antimicrobial Cationic Peptides/immunology
Mice, Inbred C57BL
Lactobacillus

@article {pmid40265782,
year = {2025},
author = {Soultatos, SK and Chatzaki, A and Karas, PA and Papadaki, AA and Kalantzakis, GS and Psarras, G and Goumas, DE and Karpouzas, DG and Markakis, EA},
title = {Biocontrol Potential of Raw Olive Mill Waste Against Verticillium dahliae in Vegetable Crops.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/plants14060867},
pmid = {40265782},
issn = {2223-7747},
abstract = {Verticillium wilt caused by the soil-borne fungus Verticillium dahliae causes severe losses to a broad range of economically important crops worldwide. Chemical disease management is ineffective; thus, alternative control strategies are needed. Olive-producing countries face the challenge of managing olive mill wastewater (OMW) in an environmentally friendly and agronomically beneficial manner. The proper use of OMW supported by scientific research has been proposed as a valuable means for successful disease management. In this respect, we tested whether soil application of raw OMW can protect vegetable crops against V. dahliae and investigated the potential disease-suppressive mechanisms. OMW inhibited significantly fungal growth, sporulation, hyphae width, and conidial and microsclerotial germination in vitro, and these effects were dose-dependent. Moreover, the addition of OMW in the soil provided sufficient protection of eggplant and tomato against V. dahliae in planta. The high OMW-conferred protection of eggplant was gradually decreased, possibly due to the decreased phenolic content in OMW over time. Bioassays with sterilized soil substrate and OMW, along with isolated microbial strains, revealed that soil- and OMW-originated microbes had no role in disease suppression. Moreover, split-root set-ups suggested a non-systemic OMW-induced resistance mechanism. Root-drench application of OMW in eggplant and tomato plants did not cause significant alterations in the structure of the plant microbiome that could be associated with disease suppressiveness.},
}

@article {pmid40265726,
year = {2025},
author = {Rawat, A and Han, B and Patel, N and Allehaibi, H and Rosado, AS and Hirt, H},
title = {Symbiotic plant-bacterial-fungal interaction orchestrates ethylene and auxin signaling for optimized plant growth.},
journal = {The Plant journal : for cell and molecular biology},
volume = {122},
number = {2},
pages = {e70174},
doi = {10.1111/tpj.70174},
pmid = {40265726},
issn = {1365-313X},
support = {BAS/1/1062-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Symbiosis/physiology ; *Arabidopsis/microbiology/growth & development/physiology ; *Indoleacetic Acids/metabolism ; *Ethylenes/metabolism ; Signal Transduction ; *Enterobacter/physiology ; *Basidiomycota/physiology ; Endophytes/physiology ; Plant Growth Regulators/metabolism ; Rhizosphere ; Plant Development ; Plant Roots/microbiology ; },
abstract = {The complex and mutual interactions between plants and their associated microbiota are key for plant survival and fitness. From the myriad of microbes that exist in the soil, plants dynamically engineer their surrounding microbiome in response to varying environmental and nutrient conditions. The notion that the rhizosphere bacterial and fungal community acts in harmony with plants is widely acknowledged, yet little is known about how these microorganisms interact with each other and their host plants. Here, we explored the interaction of two well-studied plant beneficial endophytes, Enterobacter sp. SA187 and the fungus Serendipita indica. We show that these microbes show inhibitory growth in vitro but act in a mutually positive manner in the presence of Arabidopsis as a plant host. Although both microbes can promote plant salinity tolerance, plant resilience is enhanced in the ternary interaction, revealing that the host plant has the ability to positively orchestrate the interactions between microbes to everyone's benefit. In conclusion, this study advances our understanding of plant-microbiome interaction beyond individual plant-microbe relationships, unveiling a new layer of complexity in how plants manage microbial communities for optimal growth and stress resistance.},
}

*Symbiosis/physiology
*Arabidopsis/microbiology/growth & development/physiology
*Indoleacetic Acids/metabolism
*Ethylenes/metabolism
Signal Transduction
*Enterobacter/physiology
*Basidiomycota/physiology
Endophytes/physiology
Plant Growth Regulators/metabolism
Rhizosphere
Plant Development
Plant Roots/microbiology

@article {pmid40265594,
year = {2025},
author = {Zhang, D and Zhang, Z and Liao, L and Dong, B and Xiong, X and Qin, X and Fan, X},
title = {Impact of fecal microbiota transplantation on lung function and gut microbiome in an ARDS rat model: A multi-omics analysis including 16S rRNA sequencing, metabolomics, and transcriptomics.},
journal = {International journal of immunopathology and pharmacology},
volume = {39},
number = {},
pages = {3946320251333982},
doi = {10.1177/03946320251333982},
pmid = {40265594},
issn = {2058-7384},
mesh = {Animals ; *Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; *Fecal Microbiota Transplantation/methods ; *Respiratory Distress Syndrome/therapy/microbiology/metabolism/physiopathology/genetics ; *Lung/metabolism/physiopathology/microbiology ; *RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Disease Models, Animal ; Rats ; Male ; *Transcriptome ; Multiomics ; },
abstract = {OBJECTIVE: Acute respiratory distress syndrome (ARDS) is a severe pulmonary condition characterized by inflammation and lung damage, frequently resulting in poor clinical outcomes. Recent studies suggest that the gut-lung axis, mediated by gut microbiota, is critical in ARDS progression. This study investigates the therapeutic potential of fecal microbiota transplantation (FMT) in an ARDS rat model (n = 6).

INTRODUCTION: The pathogenesis of ARDS involves complex interactions between the lungs and gut, with microbiota playing a key role. Understanding the effects of FMT on lung function and gut microbiota may provide new therapeutic strategies for ARDS management.

METHODS: Sprague-Dawley rats were pre-treated with a broad-spectrum antibiotic cocktail to create a germ-free state and subsequently exposed to intranasal lipopolysaccharide to induce ARDS. The rats then received FMT treatment. Lung samples were analyzed using histopathology and transcriptomics. Fecal samples were analyzed using 16S rRNA sequencing and metabolomics.

RESULTS: FMT treatment significantly reduced lung injury and improved pulmonary function, as evidenced by increased partial pressure of arterial oxygen (PaO2) and decreased partial pressure of arterial carbon dioxide (PaCO2). FMT also significantly altered in gut microbiota composition by regulating the gut microbiota composition of Akkermansia and Lactobacillus, restoring the abundance of genera such as Muribaculaceae, Clostridia_UCG-014, Prevotella, and Adlercreutzia, while reducing Romboutsia. FMT restored key metabolic pathways involved in lipid metabolism, amino acid biosynthesis, and immune regulation, including the modulation of immune pathways like mTOR signaling. These alterations contribute to reduced lung injury and improved pulmonary function.

CONCLUSION: These findings indicate that FMT may exert its beneficial effects in ARDS by modulating the gut microbiota and enhancing metabolic and immune responses. However, given that this study remains in the preclinical stage, further validation in clinical studies is necessary before considering clinical application.},
}

Animals
*Gastrointestinal Microbiome
Rats, Sprague-Dawley
*Fecal Microbiota Transplantation/methods
*Respiratory Distress Syndrome/therapy/microbiology/metabolism/physiopathology/genetics
*Lung/metabolism/physiopathology/microbiology
*RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Disease Models, Animal
Rats
Male
*Transcriptome
Multiomics

@article {pmid40265492,
year = {2025},
author = {Wang, B and Zheng, X and Zhang, X},
title = {Extracorporeal Shock Wave Therapy (ESWT) in burn scar microbiome modulation: critical analysis of methodological rigor and translational potential.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000002411},
pmid = {40265492},
issn = {1743-9159},
}

@article {pmid40265464,
year = {2025},
author = {Yan, X and Xie, F and Yang, S and Sun, Y and Lei, Y and Ren, Q and Si, H and Li, Z and Qiu, Q},
title = {Metagenomic Insights into the Rumen Microbiome in Solid and Liquid Fractions of Yaks and their Differences Compared to Other Ruminants.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12984},
pmid = {40265464},
issn = {1749-4877},
support = {32225009//National Natural Science Foundation of China/ ; 32122083//National Natural Science Foundation of China/ ; 32402780//National Natural Science Foundation of China/ ; XDA26040301//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.},
}

@article {pmid40265160,
year = {2025},
author = {Fässler, D and Heinken, A and Hertel, J},
title = {Characterising functional redundancy in microbiome communities via relative entropy.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1482-1497},
pmid = {40265160},
issn = {2001-0370},
abstract = {Functional redundancy has been hypothesised to be at the core of the well-evidenced relation between high ecological microbiome diversity and human health. Here, we conceptualise and operationalise functional redundancy on a single-trait level for functionally annotated microbial communities, utilising an information-theoretic approach based on relative entropy that also allows for the quantification of functional interdependency across species. Via constraint-based microbiome community modelling of a public faecal metagenomic dataset, we demonstrate that the strength of the relation between species diversity and functional redundancy is dependent on specific attributes of the function under consideration such as the rarity and the occurring functional interdependencies. Moreover, by integrating faecal metabolome data, we highlight that measures of functional redundancy have correlates in the host's metabolome. We further demonstrate that microbiomes sampled from colorectal cancer patients display higher levels of species-species functional interdependencies than those of healthy controls. By analysing microbiome community models from an inflammatory bowel disease (IBD) study, we show that although species diversity decreased in IBD subjects, functional redundancy increased for certain metabolites, notably hydrogen sulphide. This finding highlights their potential to provide valuable insights beyond species diversity. Here, we formalise the concept of functional redundancy in microbial communities and demonstrate its usefulness in real microbiome data, providing a foundation for a deeper understanding of how microbiome diversity shapes the functional capacities of a microbiome.},
}

@article {pmid40264979,
year = {2025},
author = {Zhong, Y and Chi, H and Wu, T and Fan, W and Su, H and Li, R and Jiang, W and Du, X and Ma, Z},
title = {Diversity of rhizosphere microbial communities in different rice varieties and their diverse adaptive responses to saline and alkaline stress.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537846},
pmid = {40264979},
issn = {1664-302X},
abstract = {Rice rhizosphere microbiota plays a crucial role in crop yield and abiotic stress tolerance. However, little is known about how the composition and function of rhizosphere soil microbial communities respond to soil salinity, alkalinity, and rice variety in rice paddy ecosystems. In this study, we analyzed the composition and function of rhizosphere soil microbial communities associated with two rice varieties (Jida177 and Tongxi933) cultivated in soils with different levels of salinity-alkalinity in Northeast China using a metagenomics approach. Our results indicate that the rhizospheres of Jida177 and Tongxi933 rice varieties harbor distinct microbial communities, and these microbial communities are differentiated based on both soil salinity-alkalinity and rice varieties. Furthermore, the observed differences in rice yield and grain quality between the Jida177 and Tongxi933 rice varieties suggest that these changes may be attributed to alterations in the rhizosphere microbiome under varying salinity conditions. These findings may pave the way for more efficient soil management and deeper understanding of the potential effects of soil salinization on the rice rhizosphere system.},
}

@article {pmid40264974,
year = {2025},
author = {Wong, SH and Wu, WKK},
title = {Editorial: Roles of gut microbiota in cancers of the gastrointestinal tract.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1585090},
pmid = {40264974},
issn = {1664-302X},
}

@article {pmid40264836,
year = {2025},
author = {Fiala, O and Hanzlova, M and Borska, L and Fiala, Z and Holmannova, D},
title = {Beyond physical exhaustion: Understanding overtraining syndrome through the lens of molecular mechanisms and clinical manifestation.},
journal = {Sports medicine and health science},
volume = {7},
number = {4},
pages = {237-248},
pmid = {40264836},
issn = {2666-3376},
abstract = {BACKGROUND: Overtraining Syndrome (OTS) is a condition resulting from excessive physical activity without adequate recovery, predominantly affecting elite athletes and military personnel. While overreaching can be a temporary state, non-functional overreaching may progress to chronic OTS. This review explores various hypotheses regarding the pathogenesis of OTS, including glycogen depletion, dysregulated cytokine response, oxidative stress, and alterations in the autonomic nervous system function. It also highlights the systemic impact of OTS on multiple organ systems, immune function, and overall health, linking the condition to chronic inflammation and an increased disease susceptibility. Additionally, it addresses the role of the gut microbiome in health modulation through physical activity.

METHODS: This narrative review was conducted through a structured search of peer-reviewed journal articles in databases such as PubMed, Web of Science, and Google Scholar, focusing on studies involving human participants and published in English.

RESULTS: OTS has systemic effects on multiple organ systems, immune function, and overall health, leading to chronic inflammation and increased disease susceptibility. Athletes with OTS exhibit higher morbidity rates, influenced by factors such as sleep deprivation and stress. The review also emphasizes the role of the gut microbiome as a significant modulator of health through physical activity.

CONCLUSION: Balanced training and recovery are crucial for preventing OTS and maintaining optimal health and quality of life in physically active individuals. Understanding the complex pathophysiology of OTS is essential for developing effective prevention and treatment strategies.},
}

@article {pmid40264799,
year = {2025},
author = {Dadi, P and Pauling, CW and Shrivastava, A and Shah, DD},
title = {Synthesis of versatile neuromodulatory molecules by a gut microbial glutamate decarboxylase.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112289},
pmid = {40264799},
issn = {2589-0042},
abstract = {Dysbiosis of the microbiome correlates with many neurological disorders, yet very little is known about the chemistry that controls the production of neuromodulatory molecules by gut microbes. Here, we found that an enzyme glutamate decarboxylase (BfGAD) of a gut microbe Bacteroides fragilis forms multiple neuromodulatory molecules such as γ-aminobutyric acid (GABA), hypotaurine, taurine, homotaurine, and β-alanine. We evolved BfGAD and doubled its taurine productivity. Additionally, we increased its specificity toward the substrate L-glutamate. Here, we provide a chemical strategy via which the BfGAD activity could be fine-tuned. In future, this strategy could be used to modulate the production of neuromodulatory molecules by gut microbes.},
}

@article {pmid40264541,
year = {2025},
author = {Wu, Y and Azevedo, P and Jin, S and Xu, H and Lei, H and Verschuren, L and Rodas-Gonzalez, A and Nyachoti, M and Yang, C},
title = {Feed efficiency and fecal microbiome of nursery pigs from parents with divergent breeding value for feed conversion ratio.},
journal = {Translational animal science},
volume = {9},
number = {},
pages = {txaf026},
pmid = {40264541},
issn = {2573-2102},
abstract = {Improving feed efficiency (FE) is essential for the swine industry's economic and environmental sustainability. Genetic selection, particularly through estimating breeding values for feed conversion ratio (EBV_FCR), is a common strategy to enhance FE. However, the biological mechanisms underlying phenotypic variations in FE between pigs with different EBV_FCR values are not fully understood. This study investigates these mechanisms by examining growth performance, nutrient and energy digestibility, and fecal microbiota composition and functionality of pigs at the nursery stage. The study involved 128 pigs, weaned at 21 d (±2 d) and with an initial body weight of 6.87 kg (±0.34 kg). These pigs, selected from dam and sire lines with divergent EBV_FCR values, were randomly assigned to 32 pens with four pigs each. Pigs were fed a corn and soybean meal-based diet, divided into two feeding phases of 2 wk each, under similar rearing conditions. Results indicated no significant differences in average daily feed intake (ADFI), average daily body weight gain (ADG), or feed efficiency (FE, gain:feed) between pigs from different EBV_FCR lines (P > 0.05). Similarly, nutrient digestibility showed no significant variation (P > 0.05). While the overall fecal microbiota taxonomic composition was similar between the groups, there was a trend toward higher beta diversity in the microbiota of pigs from parents with lower EBV_FCR (high efficiency pigs, H pigs) (P < 0.083). Carbohydrate and amino acid metabolism were predominant in all pigs, regardless of genetic background, with similar predicted microbiota functionality across groups. The study concluded that genetic differences based on parents divergent EBV_FCR did not affect growth performance, nutrient utilization, or microbiota characteristics at the nursery stage. This suggests that while EBV_FCR based genetic selection does not impact early-stage performance or microbiome responses, its effects may differ in older pigs, warranting further research.},
}

@article {pmid40264335,
year = {2025},
author = {Barasarathi, J and Perveen, K and Khan, F and Muthukumaran, M and Debnath, A and Behera, M and Pongen, M and Sayyed, R and Mastinu, A},
title = {Targeting Agrobacterium tumefaciens: A Computational Study on Quorum Sensing Inhibition.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70041},
doi = {10.1002/jobm.70041},
pmid = {40264335},
issn = {1521-4028},
support = {//King Saud University, Riyadh, Saudi Arabia, Researchers Supporting Project Number RSP2025R358 and University of Brescia, "ex 60% - Mastinu"./ ; },
abstract = {Crown gall disease, caused by Agrobacterium tumefaciens, results in significant loss in agricultural productivity losses due to induced tumor-like growths on various crops. The virulence of A. tumefaciens is controlled by its quorum sensing (QS) system, specifically through the TraR protein, which regulates the expression of genes essential for pathogenicity and plasmid transfer. Beyond pathogenic interactions, QS plays a crucial role in the plant microbiome, influencing symbiosis, competition, and plant health. This study aimed to identify QS inhibitors (QSIs) that disrupt TraR-mediated signaling as a novel approach to mitigate crown gall disease while exploring broader implications for plant-microbe interactions. Using a combination of molecular docking, molecular dynamics (MD) simulations, and protein-protein interaction analysis, we screened a library of potential QSIs and identified N-phenylselenourea as a potent candidate with a binding affinity of -8 kcal/mol to TraR. MD simulations confirmed the stability of this compound within the TraR binding pocket, with strong interactions observed with key residues such as Tyr53 and Asp70. Gene Ontology (GO) enrichment analysis supported these findings, highlighting the disruption of critical pathogenic pathways. Our findings underscore the dual benefits of QSIs, offering a targeted strategy to control A. tumefaciens infections while potentially enhancing plant-microbiome interactions for improved plant health. This study lays the groundwork for developing sustainable agricultural practices by leveraging QS disruption to manage plant diseases and promote beneficial microbial communities.},
}

@article {pmid40264322,
year = {2025},
author = {Jain, MS and Prasanthi, S and Bommala, ND and Goudanavar, P and Naveen, NR},
title = {Harnessing the Human Microbiome for Innovative Drug Delivery Systems: Exploring Pharmacomicrobiomics and Targeted Therapies.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128354250250326045943},
pmid = {40264322},
issn = {1873-4286},
abstract = {The human gut microbiome has emerged as a crucial component of health and disease, presenting novel opportunities for the development of drug delivery systems based on microbiome interactions. This paper explores advanced strategies utilizing microorganisms, engineered bacteria, viruses, and bacteria-encapsulated nanoparticles as next-generation therapeutic vehicles. Focusing on analytical approaches to phage therapy and bio-hybrid bacteria for targeted drug delivery, the article highlights recent breakthroughs in colon-specific targeting for gastrointestinal disorders. The study also delves into the emerging field of pharmacomicrobiomics, with an emphasis on applications in cancer, cardiovascular, digestive, and nervous system treatments, specifically targeting key drug classes such as ACE inhibitors, proton-pump inhibitors, and NSAIDs. Challenges related to cytotoxicity and toxicity are addressed, offering proposals for safer therapeutic applications. This review underscores the transformative potential of the microbiome in personalized medicine and targeted drug delivery, with a focus on its integration with advanced technologies to optimize therapeutic outcomes.},
}

@article {pmid40264268,
year = {2025},
author = {Yang, Q and Zhang, X and Luo, Y and Jiang, Y and You, J and Li, C and Ye, F and Chen, T and Chen, Q},
title = {Ameliorative effect of "intestinal-vaginal" probiotics on 5-fluorouracil-induced microbial dysbiosis in colorectal cancer.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00940e},
pmid = {40264268},
issn = {2042-650X},
abstract = {The interaction between the gut microbiome and cancer chemotherapy has been extensively studied. However, the exact role of the vaginal microbiome in chemotherapy remains unknown. To address this issue, we established a colorectal cancer chemotherapy mouse model. Here, we confirmed that 5-fluorouracil induced dysbiosis in both the vaginal and gut microbiomes, presenting a new challenge for conventional chemotherapy. Therefore, we innovatively propose an "intestinal-vaginal" probiotics administration strategy, which involves the simultaneous delivery of probiotics to both the gut and vagina, aiming to enhance chemotherapy efficacy while alleviating dysbiosis and associated side effects. Our results indicate that, compared to gut-only probiotic intervention, "intestinal-vaginal" probiotics administration significantly enhanced the anticancer efficacy of 5-fluorouracil by upregulating the p53 pathway. Furthermore, regarding gastrointestinal side effects, "intestinal-vaginal" probiotics more effectively reduced the release of vomit-associated neurotransmitters (e.g., 5-HT and SP), while also alleviating mucositis by downregulating the NF-κB pathway. Additionally, "intestinal-vaginal" probiotics outperformed the oral probiotic by increasing beneficial microbiota and reducing pathogenic bacteria. Notably, regarding vaginal side effects, "intestinal-vaginal" probiotics significantly inhibited the NF-κB inflammatory pathway and pro-apoptotic proteins, and improved vaginal dysbiosis compared to vaginal-only probiotics. These findings provide the first evidence of the significant potential of the "intestinal-vaginal" probiotics delivery approach as an adjunctive cancer therapy, which offers a novel perspective on the synergistic interactions between host microbiota communities.},
}

@article {pmid40264255,
year = {2025},
author = {Allkja, J and Bakri, A and Short, B and Gilmour, A and Brown, JL and Bal, AM and Newby, KJM and Jenkins, T and Short, RD and Williams, C and Ramage, G},
title = {Investigating the Prevalence of Fungi in Diabetic Ulcers: An Under-Recognised Contributor to Polymicrobial Biofilms.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {4},
pages = {e70025},
doi = {10.1111/apm.70025},
pmid = {40264255},
issn = {1600-0463},
support = {EP/V005839/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {Humans ; *Biofilms/growth & development ; *Diabetic Foot/microbiology ; Female ; Male ; *Fungi/isolation & purification/classification/genetics ; Middle Aged ; Aged ; *Coinfection/microbiology/epidemiology ; Prevalence ; Real-Time Polymerase Chain Reaction ; Aged, 80 and over ; Adult ; },
abstract = {Diabetic foot ulcers (DFUs) are common complications for diabetic patients, often exacerbated by complex polymicrobial biofilm infections. While the majority of DFU studies are bacterial focused, fungi have also been identified. This study aims to investigate the prevalence of fungi in DFUs, as well as their potential role and influence on persistence and wound healing. Consecutive DFU swabs were collected from 128 patients (n = 349). Fungal positivity was assessed using enhanced culture and real-time qPCR. Routine microbiology cultures were carried out as part of standard care in the clinics, and their results were then compared to our laboratory investigation. Routine and enhanced culture resulted in similar rates of fungal detection (~9%), whereas qPCR resulted in a higher rate of detection (31%). Notably, the predominant yeast Candida parapsilosis was present in ischaemic and penetrating bone wounds. These findings support existing evidence of fungal presence in DFUs. We demonstrated that routine diagnostic methods are sufficient for fungal detection, but enhanced culture methods allow for more precise fungal identification. Finally, while fungal presence does not appear to impact patient outcomes in our study, their role within these infections remains poorly understood, and further studies are needed to fully understand their relationship to the microbiome.},
}

Humans
*Biofilms/growth & development
*Diabetic Foot/microbiology
Female
Male
*Fungi/isolation & purification/classification/genetics
Middle Aged
Aged
*Coinfection/microbiology/epidemiology
Prevalence
Real-Time Polymerase Chain Reaction
Aged, 80 and over
Adult

@article {pmid40264170,
year = {2025},
author = {Mayer, T and Teutloff, E and Unger, K and Lehenberger, P and Agler, MT},
title = {Deterministic colonization arises early during the transition of soil bacteria to the phyllosphere and is shaped by plant-microbe interactions.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {102},
pmid = {40264170},
issn = {2049-2618},
support = {390713860//Deutsche Forschungsgemeinschaft/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Soil Microbiology ; *Plant Leaves/microbiology ; *Bacteria/classification/genetics/isolation & purification/growth & development ; Germination ; Phylogeny ; Pseudomonas/genetics ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Host Microbial Interactions ; },
abstract = {BACKGROUND: Upon seed germination, soil bacteria are activated to transition to the plant and eventually colonize mature tissues like leaves. These bacteria are poised to significantly influence plant health, but we know little about their colonization routes. We studied the mechanisms of the transition of soil bacteria to germinating plants and leaves using an in-planta isolation approach and by experimentally manipulating inoculation times. We then tested how plant-microbe-microbe interactions shape assembly mechanisms in natural soil communities by amending soil with a trackable, labeled strain of the opportunistic pathogen Pseudomonas viridiflava (Pv3D9).

RESULTS: We identified 27 diverse genera of leaf-associated bacteria that could transition alone from a few cells near a germinating plant to mature leaves, suggesting that the soil-to-leaf transition is probably important for them in nature. Indeed, when plants were only inoculated by soil after the emergence of true leaves, less diverse bacteria transitioned to mature leaves via different colonization mechanisms than when plants germinated in the presence of soil microorganisms. In particular, deterministic processes drove the colonization of phylogenetic bins dominated by Pedobacter, Enterobacter, Stenotrophomonas, Janthinobacterium, Pseudomonas, and Chryseobacterium only in the natural soil-to-leaf transition. Host genotype and soil amendments with Pv3D9, both of which affect host physiology, had strong effects on mainly deterministic colonization.

CONCLUSIONS: Diverse bacteria transition from soil to leaves during natural colonization, resulting in characteristic diversity in healthy leaf microbiomes. The mechanisms of colonization are a mix of stochastic processes, which will be largely shaped by competition, and deterministic processes which are more responsive to factors that shape host physiology. In the chase toward targeted manipulation of microbiomes, identifying these mechanisms for a given host and environment provides important information. Developing targeted treatments, however, will require further dissection of the pathways by which host factors drive stochastic and deterministic transitions from soil to leaves. Video Abstract.},
}

*Soil Microbiology
*Plant Leaves/microbiology
*Bacteria/classification/genetics/isolation & purification/growth & development
Germination
Phylogeny
Pseudomonas/genetics
Microbiota
RNA, Ribosomal, 16S/genetics
Soil/chemistry
Host Microbial Interactions

@article {pmid40264132,
year = {2025},
author = {Zhou, M and Wu, L and Sun, X and Liu, M and Wang, Y and Yang, B and Ai, H and Chen, C and Huang, L},
title = {Assessing the relationship between the gut microbiota and growth traits in Chinese indigenous pig breeds.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {284},
pmid = {40264132},
issn = {1746-6148},
support = {3226200298//National Natural Science Foundation of China/ ; 2022YFA1304204//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Swine/growth & development/microbiology ; Feces/microbiology ; China ; RNA, Ribosomal, 16S/genetics ; Cecum/microbiology ; Bacteria/classification/genetics ; East Asian People ; },
abstract = {BACKGROUND: Gut microbiota plays crucial roles in host metabolism, diseases and development. It has also been reported to be associated with growth performance in pigs. However, the bacterial species influencing pig growth performance have not been isolated, and the mechanisms remain unclear.

RESULTS: In this study, we collected 500 gut microbial samples from two Chinese indigenous pig breeds, including 244 fecal samples from Bamaxiang (BMX) pigs and 256 cecum content samples from Erhualian (EHL) pigs, to investigate the relationship between gut microbiota and pig growth traits. Bacterial compositions were determined by 16 S rRNA gene sequencing, and association analysis was performed using a two-part model. We found that the Firmicutes-to-Bacteroidota ratio in fecal samples from BMX pigs was negatively associated with average daily gain (P = 0.0085). Amplicon sequence variants (ASVs) belonging to Prevotella and three ASVs annotated to Oscillospiraceae were negatively associated with pig growth traits, while ASVs annotated to Muribaculaceae and Rikenellaceae showed positive correlations with growth traits in BMX fecal samples. In cecum content samples from EHL pigs, ASVs belonging to Prevotella, Lactobacillus delbrueckii, and Lachnospiraceae were negatively associated with growth performance, whereas one ASV belonging to Rikenellaceae demonstrated a positive association. Predicted functional capacity analysis revealed that metabolic pathways related to the digestive system, glycan biosynthesis and metabolism, signaling molecules and interactions, and xenobiotics biodegradation and metabolism were positively associated with pig growth traits. Conversely, the excretory system pathway showed a negative correlation. These pathways were found to correlate with growth trait-associated bacterial ASVs, suggesting that alterations in gut bacterial composition led to functional capacity shifts in the gut microbiome, subsequently affecting porcine growth.

CONCLUSIONS: Our results gave significant insights about the effect of gut microbiota on pig growth and provided important evidence to support further isolation of bacterial taxa that influence pig growth for elucidating their mechanisms.},
}

Animals
*Gastrointestinal Microbiome
Swine/growth & development/microbiology
Feces/microbiology
China
RNA, Ribosomal, 16S/genetics
Cecum/microbiology
Bacteria/classification/genetics
East Asian People

@article {pmid40264013,
year = {2025},
author = {Peng, Y and Zhang, X and Wang, G and Li, Z and Lai, X and Yang, B and Chen, B and Du, G},
title = {The gut microbial community structure of the oriental armyworm Mythimna separata (Walker) (Lepidoptera: Noctuidae) affects the the virulence of the entomopathogenic fungus Metarhizium rileyi.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {232},
pmid = {40264013},
issn = {1471-2180},
support = {202202AE090036//Major Science and Technology Project of Yunnan and Kunming/ ; 202301AT070487//Science and Technology Department of Yunnan Province Basic Research Project/ ; },
mesh = {Animals ; *Metarhizium/pathogenicity ; *Gastrointestinal Microbiome ; Virulence ; Larva/microbiology ; *Moths/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Mythimna separata, the oriental armyworm, is a lepidopteran pest that threatens cereal crops. In the current study, two strains (XSBN200920 and JHML200710) of entomopathogenic fungus Metarhizium rileyi were tested for virulence against oriental armyworms. When treated with spore suspensions of both strains at a concentration of 1.0 × 10[8] spores/mL, the 3rd instar larvae's survival rate was considerably different (P < 0.01). The median lethal time of the insects exposed to XSBN200920 was about 3 d longer than that of JHML200710. The results of 16S ribosomal RNA sequencing showed that Chao1 richness in the JHML200710 treatment group was significantly decreased compared with the CK (0.02% Tween 80). The dominant gut bacteria species at the phylum level were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota in the three groups. The CK group had a much higher associated abundance of cyanobacteria than the other two fungal treatment groups. Sixteen genera revealed significant variations in the gut bacteria of the insects at the genus level. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional gene and enzyme analysis showed that when compared with the CK group, the XSBN200920 treatment group showed a significant reduction in six aspects, including betalain biosynthesis, spliceosome, and neuroactive ligand-receptor interaction. These findings suggested that healthy and fungus-infected insects' intestinal microbial community structure differed significantly. And the virulence of M. rileyi is closely linked to its ability to alter the structure of the intestinal microbiome of insects. The results offer a starting point for examining the relationship between the gut microbial diversity of oriental armyworms and variations in the virulence of pathogenic fungi.},
}

Animals
*Metarhizium/pathogenicity
*Gastrointestinal Microbiome
Virulence
Larva/microbiology
*Moths/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification

@article {pmid40263877,
year = {2025},
author = {Qu, C and Liang, S and Wang, K and He, Y and Ju, W and Sun, Y and Miao, J},
title = {EPA-enriched lipid from Apostichopus japonicus byproducts mitigates UVB-induced oxidative stress and inflammation by gut-skin axis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {208},
number = {},
pages = {116085},
doi = {10.1016/j.foodres.2025.116085},
pmid = {40263877},
issn = {1873-7145},
mesh = {Animals ; *Ultraviolet Rays/adverse effects ; *Oxidative Stress/drug effects/radiation effects ; *Skin/drug effects/radiation effects/metabolism ; *Stichopus/chemistry ; Gastrointestinal Microbiome/drug effects ; *Inflammation/prevention & control ; *Eicosapentaenoic Acid/pharmacology ; *Lipids/pharmacology/chemistry ; Antioxidants/pharmacology ; },
abstract = {The tremendous byproducts from sea cucumber processing discarded as waste bring serious environmental and economic challenges. The abundant EPA in sea cucumber intestines indicates the potential for lipid development. However, there is little study on how these lipids affect skin health. Using REM techniques, this study prepared lipids from Apostichopus japonicus intestines (AJIL) with a 26.63 % EPA content, which displayed DPPH scavenging capacity in vitro. Administration of AJIL showed significant skin repair effects by reducing the symptoms of UVB-induced skin tissue damage, preventing epidermal thickening and increasing hydroxyproline content to protect collagen. AJIL suppressed oxidative stress and inflammation by significantly reducing ROS and MDA levels and enhancing GPx and CAT activity, as well as inhibiting the expression of inflammatory cytokines such as TNF-α, NF-κB, IL-1β and IL-6. By upregulating Nrf2, HO-1 and NQO-1 and downregulating Keap1, AJIL activated the Keap1-Nrf2 signaling pathways. Furthermore, AJIL regulated the composition and structure of gut microbiome, especially significantly increasing the SCFA-producing and anti-inflammatory bacteria like Muribacuclaceae, Alloprevotella, Bacteroides and Prevotellaceae, then improved key metabolic pathways. Overall, AJIL mediated the gut-skin axis to prevent UVB-induced skin damage and revealed potential as a natural skin protection candidate, which transformed discarded sea cucumber intestines into valuable resources for skin health.},
}

Animals
*Ultraviolet Rays/adverse effects
*Oxidative Stress/drug effects/radiation effects
*Skin/drug effects/radiation effects/metabolism
*Stichopus/chemistry
Gastrointestinal Microbiome/drug effects
*Inflammation/prevention & control
*Eicosapentaenoic Acid/pharmacology
*Lipids/pharmacology/chemistry
Antioxidants/pharmacology

@article {pmid40263874,
year = {2025},
author = {Huang, X and Li, R and Xu, J and Kang, J and Chen, X and Han, B and Xue, Y},
title = {Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome.},
journal = {Food research international (Ottawa, Ont.)},
volume = {208},
number = {},
pages = {116061},
doi = {10.1016/j.foodres.2025.116061},
pmid = {40263874},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; *Viruses/genetics/classification ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology/virology ; Bacteriophages/genetics ; *Metabolome ; Multiomics ; },
abstract = {The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.},
}

*Fermentation
*Microbiota
Fungi/metabolism/genetics
*Bacteria/metabolism/genetics
*Viruses/genetics/classification
Metagenomics
Food Microbiology
*Fermented Foods/microbiology/virology
Bacteriophages/genetics
*Metabolome
Multiomics

@article {pmid40263778,
year = {2025},
author = {Peng, L and Zeng, H and Wan, L and Yang, X and Bai, Q and Huang, J and Liu, Z},
title = {Effects of microbial fermentation on tea in alleviating obesity symptoms: Insights from microbiome and metabolomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {208},
number = {},
pages = {116111},
doi = {10.1016/j.foodres.2025.116111},
pmid = {40263778},
issn = {1873-7145},
mesh = {*Fermentation ; *Tea/chemistry/microbiology ; *Obesity/metabolism ; *Metabolomics ; Animals ; Polyphenols/analysis ; Male ; *Microbiota ; Camellia sinensis/microbiology/chemistry ; Mice ; Anti-Obesity Agents/pharmacology ; Mice, Inbred C57BL ; },
abstract = {Previous studies imply that dark tea has more advantages in facilitating the growth of Akkermansia which may be beneficial to anti-obesity. However, whether those benefits are affected by the unique processing (microbial fermentation) of dark tea remains unclear. Moreover, although there are many reports regarding the comparison of anti-obesity effects among different types of tea, the insights into the relationship between tea pharmacological component and the therapeutic effects are still limited due to the ununified tea raw material. In our study, the anti-obesity effects of non-microbial fermentation tea (NFT) and microbial fermentation tea (FT) are investigated and compared. By controlling for the raw material source, the effects of microbial fermentation on tea in alleviating obesity symptoms are effectively isolated. Our results suggested that even though NFT and FT showed distinctive differences in terms of ingredients, they exerted similar properties in attenuating overweight, regulating glucolipid metabolism, and alleviating hepatic dysfunction. The underlying mechanisms could be that NFT and FT displayed similar effects in promoting the proliferation of Akkermansia as well as enhancing the production of short-chain fatty acids. Furthermore, tea chemical constituent analyses exhibited that although microbial fermentation caused differences in polyphenol profiling between NFT and FT, it didn't remarkably influence the polyphenol content in tea which is strongly associated with the growth of Akkermansia. This might be root cause of the comparable effects on alleviating obesity symptoms between NFT and FT groups. Together, the current data supplied valuable information on the relationship among the microbial fermentation of tea, tea bioactivities, and obesity symptoms for mankind to understand.},
}

*Fermentation
*Tea/chemistry/microbiology
*Obesity/metabolism
*Metabolomics
Animals
Polyphenols/analysis
Male
*Microbiota
Camellia sinensis/microbiology/chemistry
Mice
Anti-Obesity Agents/pharmacology
Mice, Inbred C57BL

@article {pmid40263590,
year = {2025},
author = {Kadibalban, AS and Künstner, A and Schröder, T and Zauleck, J and Witt, O and Marinos, G and Kaleta, C},
title = {Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40263590},
issn = {1744-4292},
support = {EXC2167//Deutsche Forschungsgemeinschaft (DFG)/ ; KA 3541/20-1//ExoMod/ ; },
abstract = {Type 2 diabetes (T2D) presents a global health concern, with evidence highlighting the role of the human gut microbiome in metabolic diseases. This study employs metabolic modelling to elucidate changes in host-microbiome interactions in T2D. Glucose levels, diet, 16S sequences and metadata were collected for 1866 individuals. In addition, microbial community models, and ecological interactions were simulated for the gut microbiomes. Our findings revealed a significant decrease in metabolic fluxes provided by the host's diet to the microbiome in T2D patients, accompanied by increased within-community exchanges. Moreover, the diabetic microbiomes shift towards increased exploitative ecological interactions at the expense of collaborative interactions. The reduced microbiome-to-host butyrate flux, along with decreased fluxes of amino acids (including tryptophan), nucleotides, and B vitamins from the host's diet, further highlight the dysregulation in microbial-host interactions in diabetes. In addition, microbiomes of T2D patients exhibit enrichment in energy metabolism, indicative of increased metabolic activity and antagonism. This study sheds light on the increased microbiome autonomy and antagonism accompanying diabetes, and provides candidate metabolic targets for intervention studies and experimental validation.},
}

@article {pmid40263502,
year = {2025},
author = {Canderan, J and Ye, Y},
title = {Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13926},
pmid = {40263502},
issn = {2045-2322},
support = {R01AI143254//U.S. Department of Health & Human Services | NIH | Center for Information Technology (Center for Information Technology, National Institutes of Health)/ ; EF-202545//National Science Foundation (NSF)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/metabolism ; Humans ; *Proteomics/methods ; *Bacterial Proteins/metabolism ; Aspergillus/metabolism ; },
abstract = {Microbiome research has revealed associations between microbial species and colorectal cancer (CRC). Most of the existing research relied on metagenomic data. We leveraged a tool that we recently developed for detecting human and microbial peptides from (meta)proteomics data to reanalyze Clinical Proteomic Tumor Analysis Consortium CRC proteomics datasets. Our analyses revealed potential microbial species and proteins that are associated with CRC, especially when analyzing multiplexed proteomics data consisting of cancerous and healthy tissue taken from the same individuals. Many of the identified proteins are associated with species with known links to CRC, such as the fungi Aspergillus kawachii, but many are unstudied or their specific roles unknown. Proteins from other microbial species, such as Paenibacillus cellulosilyticus, were also identified in the samples. We showed that Aspergillus kawachii and others are depleted overall in cancer samples, which is consistent with a previous genomic-based multi-cohort study. Our analysis also revealed that some proteins belonging to this species are more abundantly detected, while others in this and other species are not. Further, we showed that microbial identifications could be used to build predictive models for tumor detection, but caution needs to be taken when applying such models trained on one dataset to another due to the substantial impacts of different experimental techniques on peptide detection profiles.},
}

*Colorectal Neoplasms/microbiology/metabolism
Humans
*Proteomics/methods
*Bacterial Proteins/metabolism
Aspergillus/metabolism

@article {pmid40263165,
year = {2025},
author = {Tan, J and Chen, R and Gan, D and Ou, M and Wu, Y and Jie, H and Xu, Y and Huang, J},
title = {Correlation between Lactobacillus of Vaginal Microbiota and the Pregnancy Outcomes for Patients Experiencing Recurrent Miscarriage.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {40263165},
issn = {1933-7205},
support = {2022A1515012599//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
abstract = {The etiology of recurrent miscarriage (RM) is complex, with the vaginal microbiota (VM) being an important factor associated with RM. We aimed to establish the VM composition in both patients with RM and healthy women and further investigate relationship between the subsequent pregnancy outcomes of patients with RM and VM, to explain the potential mechanism of VM in RM to some extent. A cohort study compared the VM between 34 patients with RM and 15 healthy women using a sequencing technique based on Type IIB restriction enzymes for the microbiome (2bRAD-M). Further comparison was made between 11 patients with clinical miscarriages (CM) and 13 patients with ongoing pregnancies (OP) in the RM group who conceived naturally. To determine the VM composition, the 2bRAD-M library was prepared, and sequence and bioinformatics analyses were conducted. The composition of the VM exhibited notable differences between the non-RM and RM groups, with significant findings for alpha diversity (p < 0.05) and beta diversity (p = 0.01). Further analysis between the RM-OP and RM-CM groups revealed a significant difference in Lactobacillus (97.81% ± 2.71% vs. 53.37% ± 46.42%, p = 0.03). Other uncommon species, such as Cutibacterium acnes (C. acnes) (p = 0.04) were found significantly increase in the RM-CM group. Functional annotation analysis revealed 47 related signaling pathways between the two groups. The results of this study indicate that Lactobacillus is associated with subsequent miscarriages and that C. acnes is closely related to pregnancy outcomes of patients with RM.},
}