Gut Microbes最新文献

{"title":"Isolation of derivatives from the food-grade probiotic <i>Lactobacillus johnsonii</i> CNCM I-4884 with enhanced anti-<i>Giardia</i> activity.","authors":"Anne-Sophie Boucard, Saulius Kulakauskas, Jana Alazzaz, Soraya Chaouch, Mohamed Mammeri, Aaron Millan-Oropeza, Carine Machado, Céline Henry, Christine Péchoux, Holger Richly, Michael Gassel, Philippe Langella, Bruno Polack, Isabelle Florent, Luis G Bermúdez-Humarán","doi":"10.1080/19490976.2025.2474149","DOIUrl":"10.1080/19490976.2025.2474149","url":null,"abstract":"<p><p>Giardiasis, a widespread intestinal parasitosis affecting humans and animals, is a growing concern due to the emergence of drug-resistant strains of <i>G. intestinalis</i>. Probiotics offer a promising alternative for preventing and treating giardiasis. Recent studies have shown that the probiotic <i>Lactobacillus johnsonii</i> CNCM I-4884 inhibits <i>G. intestinalis</i> growth both <i>in vitro</i> and <i>in vivo</i>. This protective effect is largely mediated by bile salt hydrolase (BSH) enzymes, which convert conjugated bile acids (BAs) into free forms that are toxic to the parasite. The objective of this study was to use adaptive evolution to develop stress-resistant derivatives of <i>L. johnsonii</i> CNCM I-4884, with the aim of improving its anti-<i>Giardia</i> activity. Twelve derivatives with enhanced resistance to BAs and reduced autolysis were generated. Among them, derivative M11 exhibited the highest <i>in vitro</i> anti-<i>Giardia</i> effect with enhanced BSH activity. Genomic and proteomic analyses of M11 revealed two SNPs and the upregulation of the global stress response by SigB, which likely contributed to its increased BAs resistance and BSH overproduction. Finally, the anti-<i>Giardia</i> efficacy of M11 was validated in a murine model of giardiasis. In conclusion, our results demonstrate that adaptive evolution is an effective strategy to generate robust food-grade bacteria with improved health benefits.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2474149"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction.","authors":"","doi":"10.1080/19490976.2025.2532985","DOIUrl":"10.1080/19490976.2025.2532985","url":null,"abstract":"","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2532985"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12258221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144617173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiota modulate immune cell populations and drive dynamic structural changes in gut-associated lymphoid tissue.","authors":"Pačes Jan, Malinská Nikola, Tušková Liliana, Knížková Karolina, Grobárová Valéria, Zadražil Zdeněk, Hudcovic Tomáš, Michl Anna, Šrůtková Dagmar, Schwarzer Martin, Boes Marianne, Černý Jan","doi":"10.1080/19490976.2025.2543908","DOIUrl":"10.1080/19490976.2025.2543908","url":null,"abstract":"<p><p>Inbred mouse strains provide phenotypic homogeneity between individual mice. However, stochastic morphogenetic events combined with epigenetic changes due to exposure to environmental factors and ontogenic experience result in variability among mice with virtually identical genotypes, reducing the reproducibility of experimental mouse models. Here we used microscopic and cytometric techniques to identify individual patterns in gut-associated lymphoid tissue (GALT) that are induced by exposure to microbiota. By comparing germ-free (GF), conventional (CV) and gnotobiotic mice colonized with a defined minimal mouse microbiota (oMM12) MHC II-EGFP knock-in mice we quantified antigen-presenting cells (APCs) in the lamina propria, cryptopatches (CP), isolated lymphoid follicles (ILFs), Peyer's patches (PPs) and specific sections of the mesenteric lymphoid complex. We found that GF mice had a significantly larger outer intestinal surface area compared to CV and oMM12-colonized mice, which partially compensated for their lower density of the villi in the distal ileum. GF mice also contained fewer APCs than oMM12 mice in the Iamina propria of the villi and had a significantly smaller volume of the solitary intestinal lymphoid tissue (SILT). In both GF and oMM12 mice, PP follicles were significantly smaller compared to CV mice, although number was similar. Concomitantly, the number of pDCs in PPs was significantly lower in GF mice than in CV mice. Moreover, the cecal patch was dispersed into small units in GF mice whereas it was compact in CV mice. Taken together, we here provide further evidence that microbiota regulates SILT differentiation, the size and morphology of PPs, the cellular composition of mesenteric lymph nodes (MLNs) and the morphology of cecal patch. As such, microbiota directly affect not only the functional configuration of the immune system but also the differentiation of lymphoid structures. These findings highlight how standardized microbiota, such as oMM12, can promote reproducibility in animal studies by enabling microbiologically controlled experiments across laboratories.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2543908"},"PeriodicalIF":11.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12351735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144845593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Maternal probiotic exposure enhances CD8 T cell protective neonatal immunity and modulates offspring metabolome to control influenza virus infection.","authors":"Clara Valentin, Patricia Brito Rodrigues, Marko Verce, Sandrine Delbauve, Léa La Palombara, Florine Demaret, Justine Allard, Isabelle Salmon, Patrice D Cani, Arnaud Köhler, Amandine Everard, Véronique Flamand","doi":"10.1080/19490976.2024.2442526","DOIUrl":"https://doi.org/10.1080/19490976.2024.2442526","url":null,"abstract":"<p><p>Maternal gut microbiota composition contributes to the status of the neonatal immune system and could influence the early life higher susceptibility to viral respiratory infections. Using a novel protocol of murine maternal probiotic supplementation, we report that perinatal exposure to <i>Lacticaseibacillus rhamnosus</i> (<i>L.rh</i>) or <i>Bifidobacterium animalis subsp. lactis</i> (<i>B.lac</i>) increases the influenza A/PR8 virus (IAV) clearance in neonates. Following either supplementation, type 1 conventional dendritic cells (cDC1) were amplified in the lymph nodes leading to an enhanced IAV antigen-experienced IFN-γ producing effector CD8 T cells in neonates and IAV-specific resident memory CD8 T cells in adulthood. This was compatible with a higher protection of the offspring upon a secondary infection. Interestingly, only mice born to <i>L.rh</i> supplemented mothers further displayed an increased activation of IFN-γ producing virtual memory CD8 T cells and a production of IL-10 by CD4 and CD8 T cells that could explain a better control of the lung damages upon infection. In the offspring and the mothers, no disturbance of the gut microbiota was observed but, as analyzed through an untargeted metabolomic approach, both exposures modified neonatal plasma metabolites. Among them, we further demonstrated that genistein and 3-(3-hydroxyphenyl)propionic acid recapitulate viral clearance or cDC1 activation in neonates exposed to IAV. We conclude that maternal <i>L.rh</i> or <i>B.lac</i> supplementation confers the neonates specific metabolomic modulations with a better CD8 T cell-mediated immune protection against IAV infection.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2442526"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers.","authors":"Madison Moore, Hunter D Whittington, Rebecca Knickmeyer, M Andrea Azcarate-Peril, Jose M Bruno-Bárcena","doi":"10.1080/19490976.2024.2440120","DOIUrl":"10.1080/19490976.2024.2440120","url":null,"abstract":"<p><p>Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL^-1) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO₂, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2440120"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11660306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Alcaligenes faecalis</i> promotes colitis to colorectal cancer transition through IgA+ B cell suppression and vinculin acetylation.","authors":"Jing Zheng, Chishun Zhou, Zizheng Li, Xin Jin, Yihua Zou, Shasha Bai, Huanjin Zheng, Weichao Ling, Yiru Zhao, Ying Wang, Rong Zhang, Zhongqiu Liu, Linlin Lu","doi":"10.1080/19490976.2025.2473511","DOIUrl":"10.1080/19490976.2025.2473511","url":null,"abstract":"<p><p>Lymphoid tissue-resident commensal bacteria (LRC), a subtype of gut microbiota essential for inflammation-associated carcinogenesis, predominantly attribute to colorectal cancer(CRC), whereas its role was largely unknown. Herein, we found <i>Alcaligenes faecalis</i> (<i>A. faecalis</i>), the main LRC embedded in Peyer's patches, was abundantly enriched in colitis, adenoma, and stage-dependently observed in CRC tissues. Interestingly, <i>A. faecalis</i> alone can not affect intestinal homeostasis, while during colitis, <i>A. faecalis</i> significantly translocated from Peyer's patches to colon, remarkably attenuated immune response abilities of B cells, T cells, and DC cells in PPs, consequently impeded IgA+ B cells homing. Meanwhile, during colitis, the ectopia of <i>A. faecalis</i> in colon tissues, promoted vinculin acetylation by <i>A. faecalis</i>-derived metabolite acetic acid, which impeded intestinal barrier via hindering the binding of vinculin to β-catenin. Our study revealed <i>A. faecalis</i> not only suppress mucosal immune responses via reducing IgA+ B cells in Peyer's patches but also disrupt intestinal barrier via increasing vinculin acetylation, ultimately promoting inflammation-to-cancer transition in CRC.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2473511"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11901412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stevioside mitigates metabolic dysregulation in offspring induced by maternal high-fat diet: the role of gut microbiota-driven thermogenesis.","authors":"Jin Ye, Renjie Shi, Xiaoning Wu, Hua Fan, Yapei Zhao, Xinyun Hu, Lulu Wang, Xiaowei Bo, Dongning Li, Yunshu Ge, Danna Wang, Bing Xia, Zhenting Zhao, Chunxia Xiao, Beita Zhao, Yutang Wang, Xuebo Liu","doi":"10.1080/19490976.2025.2452241","DOIUrl":"10.1080/19490976.2025.2452241","url":null,"abstract":"<p><p>Maternal obesity poses a significant threat to the metabolic profiles of offspring. Microorganisms acquired from the mother early in life critically affect the host's metabolic functions. Natural non-nutritive sweeteners, particularly stevioside (STV), play a crucial role in reducing obesity and affecting gut microbiota composition. Based on this, we hypothesized that maternal STV supplementation could improve the health of mothers and offspring by altering their gut microbiota. Our study found that maternal STV supplementation reduced obesity during pregnancy, decreased abnormal lipid accumulation in offspring mice caused by maternal obesity, and modified the gut microbiota of both dams and offspring, notably increasing the abundance of <i>Lactobacillus apodemi</i> (<i>L. apodemi</i>). Co-housing and fecal microbiota transplant experiments confirmed that gut microbiota mediated the effects of STV on metabolic disorders. Furthermore, treatment with <i>L. apodemi</i> alone replicated the beneficial effects of STV, which were associated with increased thermogenesis. In summary, maternal STV supplementation could alleviate lipid metabolic disorders in offspring by enhancing <i>L. apodemi</i> levels and promoting thermogenic activity, potentially involving changes in bile acid metabolism pathways.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2452241"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine-learning assisted discovery unveils novel interplay between gut microbiota and host metabolic disturbance in diabetic kidney disease.","authors":"I-Wen Wu, Yu-Chieh Liao, Tsung-Hsien Tsai, Chieh-Hua Lin, Zhao-Qing Shen, Yun-Hsuan Chan, Chih-Wei Tu, Yi-Ju Chou, Chi-Jen Lo, Chi-Hsiao Yeh, Chun-Yu Chen, Heng-Chih Pan, Heng-Jung Hsu, Chin-Chan Lee, Mei-Ling Cheng, Wayne Huey-Herng Sheu, Chi-Chun Lai, Huey-Kang Sytwu, Ting-Fen Tsai","doi":"10.1080/19490976.2025.2473506","DOIUrl":"10.1080/19490976.2025.2473506","url":null,"abstract":"<p><p>Diabetic kidney disease (DKD) is a serious healthcare dilemma. Nonetheless, the interplay between the functional capacity of gut microbiota and their host remains elusive for DKD. This study aims to elucidate the functional capability of gut microbiota to affect kidney function of DKD patients. A total of 990 subjects were enrolled consisting of a control group (<i>n</i> = 455), a type 2 diabetes mellitus group (DM, <i>n</i> = 204), a DKD group (<i>n</i> = 182) and a chronic kidney disease group (CKD, <i>n</i> = 149). Full-length sequencing of 16S rRNA genes from stool DNA was conducted. Three findings are pinpointed. Firstly, new types of microbiota biomarkers have been created using a machine-learning (ML) method, namely relative abundance of a microbe, presence or absence of a microbe, and the hierarchy ratio between two different taxonomies. Four different panels of features were selected to be analyzed: (i) DM <i>vs</i>. Control, (ii) DKD <i>vs</i>. DM, (iii) DKD <i>vs</i>. CKD, and (iv) CKD <i>vs</i>. Control. These had accuracy rates between 0.72 and 0.78 and areas under curve between 0.79 and 0.86. Secondly, 13 gut microbiota biomarkers, which are strongly correlated with anthropometric, metabolic and/or renal indexes, concomitantly identified by the ML algorithm and the differential abundance method were highly discriminatory. Finally, the predicted functional capability of a DKD-specific biomarker, <i>Gemmiger</i> spp. is enriched in carbohydrate metabolism and branched-chain amino acid (BCAA) biosynthesis. Coincidentally, the circulating levels of various BCAAs (L-valine, L-leucine and L-isoleucine) and their precursor, L-glutamate, are significantly increased in DM and DKD patients, which suggests that, when hyperglycemia is present, there has been alterations in various interconnected pathways associated with glycolysis, pyruvate fermentation and BCAA biosynthesis. Our findings demonstrate that there is a link involving the gut-kidney axis in DKD patients. Furthermore, our findings highlight specific gut bacteria that can acts as useful biomarkers; these could have mechanistic and diagnostic implications.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2473506"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11901534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncovering <i>de novo</i> polyamine biosynthesis in the gut microbiome and its alteration in inflammatory bowel disease.","authors":"Xinwei Li, Xia Xiao, Shengnan Wang, Biyu Wu, Yixuan Zhou, Pan Deng","doi":"10.1080/19490976.2025.2464225","DOIUrl":"10.1080/19490976.2025.2464225","url":null,"abstract":"<p><p>Polyamines are important gut microbial metabolites known to affect host physiology, yet the mechanisms behind their microbial production remain incompletely understood. In this study, we developed a stable isotope-resolved metabolomic (SIRM) approach to track polyamine biosynthesis in the gut microbiome. Viable microbial cells were extracted from fresh human and mouse feces and incubated anaerobically with [U-¹³C]-labeled inulin (tracer). Liquid chromatography-high resolution mass spectrometry analysis revealed distinct ¹³C enrichment profiles for spermidine (SPD) and putrescine (PUT), indicating that the arginine-agmatine-SPD pathway contributes to SPD biosynthesis in addition to the well-known spermidine synthase pathway (PUT aminopropylation). Species differences were observed in the ¹³C enrichments of polyamines and related metabolites between the human and mouse microbiome. By analyzing the fecal metabolomics and metatranscriptomic data from an inflammatory bowel disease (IBD) cohort, we found significantly higher polyamine levels in IBD patients compared to healthy controls. Further investigations using single-strain SIRM and <i>in silico</i> analyses identified <i>Bacteroides</i> spp. as key contributors to polyamine biosynthesis, harboring essential genes for this process and potentially driving the upregulation of polyamines in IBD. Taken together, this study expands our understanding of polyamine biosynthesis in the gut microbiome and will facilitate the development of precision therapies to target polyamine-associated diseases.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2464225"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11812404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction.","authors":"","doi":"10.1080/19490976.2025.2457204","DOIUrl":"10.1080/19490976.2025.2457204","url":null,"abstract":"","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2457204"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143033087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}