Gut Microbes最新文献

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Gut microbes metabolize strawberry phytochemicals and mediate their beneficial effects on vascular inflammation. 肠道微生物代谢草莓植物化学物质并介导其对血管炎症的有益作用。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2025-01-06 DOI: 10.1080/19490976.2024.2446375
Chrissa Petersen, Adhini Kuppuswamy Satheesh Babu, Ceres Mattos Della Lucia, Henry A Paz, Lisard Iglesias-Carres, Ying Zhong, Thunder Jalili, J David Symons, Kartik Shankar, Andrew P Neilson, Umesh D Wankhade, Pon Velayutham Anandh Babu
{"title":"Gut microbes metabolize strawberry phytochemicals and mediate their beneficial effects on vascular inflammation.","authors":"Chrissa Petersen, Adhini Kuppuswamy Satheesh Babu, Ceres Mattos Della Lucia, Henry A Paz, Lisard Iglesias-Carres, Ying Zhong, Thunder Jalili, J David Symons, Kartik Shankar, Andrew P Neilson, Umesh D Wankhade, Pon Velayutham Anandh Babu","doi":"10.1080/19490976.2024.2446375","DOIUrl":"https://doi.org/10.1080/19490976.2024.2446375","url":null,"abstract":"<p><p>Evidence suggests that a healthy gut microbiome is essential for metabolizing dietary phytochemicals. However, the microbiome's role in metabolite production and the influence of gut dysbiosis on this process remain unclear. Further, studies on the relationship among gut microbes, metabolites, and biological activities of phytochemicals are limited. We addressed this knowledge gap using strawberry phytochemicals as a model. C57BL/6J mice were fed a standard diet [C]; strawberry-supplemented diet (~2 human servings) [CS]; strawberry-supplemented diet and treated with antibiotics (to deplete gut microbes) [CSA]; high-fat diet (HFD) [HF]; strawberry-supplemented HFD [HS]; and strawberry-supplemented HFD and treated with antibiotics [HSA] for 12 weeks. First, antibiotic treatment suppressed the production of selected metabolites (CSA <i>vs</i>. CS), and <i>p</i>-coumaric acid was identified as a strawberry-derived microbial metabolite. Second, HFD-induced dysbiosis negatively affected metabolite production (HS <i>vs</i>. HF), and hippuric acid was identified as a microbial metabolite in HFD conditions. Third, dietary strawberries improved HFD-induced vascular inflammation (HS <i>vs</i>. HF). However, antibiotic treatment reduced metabolite production and abolished the vascular effects of strawberries (HSA <i>vs</i>. HS), indicating the importance of gut microbes in mediating the vascular benefits of strawberries <i>via</i> metabolites. Fourth, strawberry supplementation decreased <i>Coprobacillus</i> that was positively associated with vascular inflammation, whereas it increased <i>Lachnospiraceae</i> that was negatively associated with vascular inflammation and positively associated with hippuric acid. Fifth, hippuric acid was negatively associated with vascular inflammation. Our study fills in some pieces of the giant puzzle regarding the influence of gut microbes on the biological activities of phytochemicals. HFD-induced gut dysbiosis negatively impacts metabolite production and a strong association exists among gut microbes, strawberry-derived microbial metabolites, and the vascular benefits of dietary strawberries. Further, our study provides significant proof of concept to warrant future research on the use of strawberries as a nutritional strategy to prevent vascular complications.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2446375"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142931580","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}
引用次数: 0
Clostridioides difficile binary toxin CDT induces biofilm-like persisting microcolonies. 艰难梭菌二元毒素CDT诱导生物膜样持续微菌落。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2024-12-24 DOI: 10.1080/19490976.2024.2444411
Jazmin Meza-Torres, Jean-Yves Tinevez, Aline Crouzols, Héloïse Mary, Minhee Kim, Lise Hunault, Susan Chamorro-Rodriguez, Emilie Lejal, Pamela Altamirano-Silva, Déborah Groussard, Samy Gobaa, Johann Peltier, Benoit Chassaing, Bruno Dupuy
{"title":"<i>Clostridioides difficile</i> binary toxin CDT induces biofilm-like persisting microcolonies.","authors":"Jazmin Meza-Torres, Jean-Yves Tinevez, Aline Crouzols, Héloïse Mary, Minhee Kim, Lise Hunault, Susan Chamorro-Rodriguez, Emilie Lejal, Pamela Altamirano-Silva, Déborah Groussard, Samy Gobaa, Johann Peltier, Benoit Chassaing, Bruno Dupuy","doi":"10.1080/19490976.2024.2444411","DOIUrl":"https://doi.org/10.1080/19490976.2024.2444411","url":null,"abstract":"<p><p>Clinical symptoms of <i>Clostridioides difficile</i> infection (CDI) range from diarrhea to pseudomembranous colitis. A major challenge in managing CDI is the high rate of relapse. Several studies correlate the production of CDT binary toxin by clinical strains of <i>C. difficile</i> with higher relapse rates. Although the mechanism of action of CDT on host cells is known, its exact contribution to CDI is still unclear. To understand the physiological role of CDT during CDI, we established two hypoxic relevant intestinal models, Transwell and Microfluidic Intestine-on-Chip systems. Both were challenged with the epidemic strain UK1 CDT<sup>+</sup> and its isogenic CDT<sup>-</sup> mutant. We report that CDT induces mucin-associated microcolonies that increase <i>C. difficile</i> colonization and display biofilm-like properties by enhancing <i>C. difficile</i> resistance to vancomycin. Importantly, biofilm-like microcolonies were also observed in the cecum and colon of infected mice. Hence, our study shows that CDT induces biofilm-like microcolonies, increasing <i>C. difficile</i> persistence and risk of relapse.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2444411"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885583","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}
引用次数: 0
Hypoglycemic effect of C. butyricum-pMTL007-GLP-1 engineered probiotics on type 2 diabetes mellitus. 丁酸梭菌- pmtl007 - glp -1工程益生菌对2型糖尿病的降糖作用。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2025-01-02 DOI: 10.1080/19490976.2024.2447814
Dexi Zhou, Shengjie Li, Gang Hu, Yufan Wang, Zhanghua Qi, Xuan Xu, Jing Wei, Qiong Liu, Tingtao Chen
{"title":"Hypoglycemic effect of <i>C. butyricum</i>-pMTL007-GLP-1 engineered probiotics on type 2 diabetes mellitus.","authors":"Dexi Zhou, Shengjie Li, Gang Hu, Yufan Wang, Zhanghua Qi, Xuan Xu, Jing Wei, Qiong Liu, Tingtao Chen","doi":"10.1080/19490976.2024.2447814","DOIUrl":"https://doi.org/10.1080/19490976.2024.2447814","url":null,"abstract":"<p><p>Diabetes mellitus (DM) is a complex metabolic disease characterized by hyperglycemia. Recently, the incidence of diabetes has increased exponentially, and it is estimated to become the seventh leading cause of global mortality by 2030. Glucagon-like peptide-1 (GLP-1), a hormone derived from the intestine, has been demonstrated to exert remarkable hypoglycemic effects. However, its limitation lies in its short plasma half-life, necessitating the continuous intravenous injection of GLP-1 drugs to achieve efficacy. Here, we engineered <i>Clostridium butyricum</i> to continuously express and deliver GLP-1 (denoted as Cb-GLP-1), and assessed its therapeutic efficacy in type 2 diabetes mellitus (T2DM) mice. We demonstrated that administration of Cb-GLP-1 effectively lowered blood glucose levels, regulated dyslipidemia, and ameliorated hepatic impairment in T2DM mice. Furthermore, Cb-GLP-1 treatment facilitated insulin secretion by retarding islet cell apoptosis and activating the glucagon-like peptide 1 receptor/adenylate cyclase/protein kinase A (GLP-1 R/AC/PKA) signaling pathway. Gut microbiota analysis revealed that Cb-GLP-1 restored gut homeostasis disrupted in T2DM mice, as indicated by the decreased abundance of <i>Lactobacillus</i> and <i>Providencia</i> genera in response to Cb-GLP-1 treatment. Collectively, the intestinal microbiota regulation and hypoglycemic effect of the engineered strain Cb-GLP-1 presents a promising approach for diabetes management.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2447814"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914573","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}
引用次数: 0
Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential. 青少年袖式胃切除术后肠道微生物群的变化与增加的口腔相关分类群和促炎潜力。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2025-02-19 DOI: 10.1080/19490976.2025.2467833
Cynthia O Akagbosu, Kathryn E McCauley, Sivaranjani Namasivayam, Hector N Romero-Soto, Wade O'Brien, Mickayla Bacorn, Eric Bohrnsen, Benjamin Schwarz, Shreni Mistry, Andrew S Burns, P Juliana Perez-Chaparro, Qing Chen, Phoebe LaPoint, Anal Patel, Lauren E Krausfeldt, Poorani Subramanian, Brian A Sellers, Foo Cheung, Richard Apps, Iyadh Douagi, Shira Levy, Evan P Nadler, Suchitra K Hourigan
{"title":"Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential.","authors":"Cynthia O Akagbosu, Kathryn E McCauley, Sivaranjani Namasivayam, Hector N Romero-Soto, Wade O'Brien, Mickayla Bacorn, Eric Bohrnsen, Benjamin Schwarz, Shreni Mistry, Andrew S Burns, P Juliana Perez-Chaparro, Qing Chen, Phoebe LaPoint, Anal Patel, Lauren E Krausfeldt, Poorani Subramanian, Brian A Sellers, Foo Cheung, Richard Apps, Iyadh Douagi, Shira Levy, Evan P Nadler, Suchitra K Hourigan","doi":"10.1080/19490976.2025.2467833","DOIUrl":"10.1080/19490976.2025.2467833","url":null,"abstract":"<p><p>Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown. Here, we show that adolescents exhibit significant gut microbiome and metabolome shifts several months after laparoscopic vertical sleeve gastrectomy (VSG), with increased alpha diversity and notably with enrichment of oral-associated taxa. To assess causality of the microbiome/metabolome changes in phenotype, pre-VSG and post-VSG stool was transplanted into germ-free mice. Post-VSG stool was not associated with any beneficial outcomes such as adiposity reduction compared pre-VSG stool. However, post-VSG stool exhibited a potentially inflammatory phenotype with increased intestinal Th17 and decreased regulatory T cells. Concomitantly, we found elevated fecal calprotectin and an enrichment of proinflammatory pathways in a subset of adolescents post-VSG. We show that in some adolescents, microbiome changes post-VSG may have inflammatory potential, which may be of importance considering the increased incidence of inflammatory bowel disease post-VSG.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2467833"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11845021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457594","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}
引用次数: 0
Staphylococcus warneri dampens SUMOylation and promotes intestinal inflammation. 沃氏葡萄球菌抑制sumo酰化并促进肠道炎症。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2025-01-16 DOI: 10.1080/19490976.2024.2446392
Léa Loison, Marion Huré, Benjamin Lefranc, Jérôme Leprince, Christine Bôle-Feysot, Moïse Coëffier, David Ribet
{"title":"<i>Staphylococcus warneri</i> dampens SUMOylation and promotes intestinal inflammation.","authors":"Léa Loison, Marion Huré, Benjamin Lefranc, Jérôme Leprince, Christine Bôle-Feysot, Moïse Coëffier, David Ribet","doi":"10.1080/19490976.2024.2446392","DOIUrl":"10.1080/19490976.2024.2446392","url":null,"abstract":"<p><p>Gut bacteria play key roles in intestinal physiology, via the secretion of diversified bacterial effectors. Many of these effectors remodel the host proteome, either by altering transcription or by regulating protein post-translational modifications. SUMOylation, a ubiquitin-like post-translational modification playing key roles in intestinal physiology, is a target of gut bacteria. Mutualistic gut bacteria can promote SUMOylation, via the production of short- or branched-chain fatty acids (SCFA/BCFA). In contrast, several pathogenic bacteria were shown to dampen SUMOylation in order to promote infection. Here, we demonstrate that <i>Staphylococcus warneri</i>, a natural member of the human gut microbiota, decreases SUMOylation in intestinal cells. We identify that Warnericin RK, a hemolytic toxin secreted by <i>S. warneri</i>, targets key components of the host SUMOylation machinery, leading to the loss of SUMO-conjugated proteins. We further demonstrate that Warnericin RK promotes inflammation in intestinal and immune cells using both SUMO-dependent and SUMO-independent mechanisms. We finally show that Warnericin RK regulates the expression of genes involved in intestinal tight junctions. Together, these results highlight the diversity of mechanisms used by bacteria from the gut microbiota to manipulate host SUMOylation. They further highlight that changes in gut microbiota composition may impact intestinal inflammation, by altering the equilibrium between bacterial effectors promoting or dampening SUMOylation.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2446392"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004536","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}
引用次数: 0
The gut-skin axis: a bi-directional, microbiota-driven relationship with therapeutic potential. 肠道-皮肤轴:一个双向的,微生物群驱动的关系与治疗潜力。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2025-03-06 DOI: 10.1080/19490976.2025.2473524
Maira Jimenez-Sanchez, Larissa S Celiberto, Hyungjun Yang, Ho Pan Sham, Bruce A Vallance
{"title":"The gut-skin axis: a bi-directional, microbiota-driven relationship with therapeutic potential.","authors":"Maira Jimenez-Sanchez, Larissa S Celiberto, Hyungjun Yang, Ho Pan Sham, Bruce A Vallance","doi":"10.1080/19490976.2025.2473524","DOIUrl":"10.1080/19490976.2025.2473524","url":null,"abstract":"<p><p>This review explores the emerging term \"gut-skin axis\" (GSA), describing the bidirectional signaling that occurs between the skin and the gastrointestinal tract under both homeostatic and disease conditions. Central to GSA communication are the gut and skin microbiota, the microbial communities that colonize these barrier surfaces. By influencing diverse host pathways, including innate immune, vitamin D receptor, and Aryl hydrocarbon receptor signaling, a balanced microbiota contributes to both tissue homeostasis and host defense. In contrast, microbiota imbalance, or dysbiosis at one site, can lead to local barrier dysfunction, resulting in the activation of signaling pathways that can disrupt tissue homeostasis at the other site, potentially leading to inflammatory skin conditions such as atopic dermatitis and psoriasis, or gut diseases like Inflammatory Bowel Disease. To date, most research on the GSA has examined the impact of the gut microbiota and diet on skin health, but recent studies show that exposing the skin to ultraviolet B-light can beneficially modulate both the gut microbiome and intestinal health. Thus, despite the traditional focus of clinicians and researchers on these organ systems as distinct, the GSA offers new opportunities to better understand the pathogenesis of cutaneous and gastrointestinal diseases and promote health at both sites.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2473524"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11901370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572727","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}
引用次数: 0
Anti-interleukin-23 treatment linked to improved Clostridioides difficile infection survival. 抗白细胞介素-23治疗与艰难梭菌感染存活率提高有关。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2025-03-21 DOI: 10.1080/19490976.2025.2480195
Gregory R Madden, Robert Preissner, Saskia Preissner, William A Petri
{"title":"Anti-interleukin-23 treatment linked to improved <i>Clostridioides difficile</i> infection survival.","authors":"Gregory R Madden, Robert Preissner, Saskia Preissner, William A Petri","doi":"10.1080/19490976.2025.2480195","DOIUrl":"10.1080/19490976.2025.2480195","url":null,"abstract":"<p><p><i>Clostridioides difficile</i> is a leading cause of healthcare-associated infection, and an unacceptably high proportion of patients with <i>C. difficile</i> infection die despite conventional antibiotic treatment. Host-directed immunotherapy has been proposed as an ideal treatment modality for <i>C. difficile</i> infection to mitigate the underlying toxin-mediated pathogenic immune response while sparing protective gut microbes. Interleukin-23 monoclonal antibody inhibitors are used extensively to control pro-inflammatory Th17 immune pathways in psoriasis and inflammatory bowel disease that are similarly important during <i>C. difficile</i> infection. We used a large retrospective electronic health record database to test the hypothesis that hospitalized patients with <i>C. difficile</i> infection who are on anti-IL-23 treatment will have improved survival compared to patients without anti-IL-23. A total of 9,301 anti-IL-23 patients had significantly lower probability of all-cause death within 30 d (0.54%) compared with 1:1 propensity-matched control patients (3.1%). IL-23 inhibition is a promising adjunct to <i>C. difficile</i> treatment, and further clinical trials repositioning anti-IL-23 monoclonal antibodies from psoriasis and inflammatory bowel disease to <i>C. difficile</i> infection are warranted.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2480195"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669815","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}
引用次数: 0
Maternal consumption of urbanized diet compromises early-life health in association with gut microbiota. 母亲的城市化饮食消费损害了与肠道微生物群相关的早期生命健康。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2025-04-02 DOI: 10.1080/19490976.2025.2483783
Rong Huang, Guicheng Zhou, Jie Cai, Cha Cao, Zhenjun Zhu, Qingping Wu, Fen Zhang, Yu Ding
{"title":"Maternal consumption of urbanized diet compromises early-life health in association with gut microbiota.","authors":"Rong Huang, Guicheng Zhou, Jie Cai, Cha Cao, Zhenjun Zhu, Qingping Wu, Fen Zhang, Yu Ding","doi":"10.1080/19490976.2025.2483783","DOIUrl":"10.1080/19490976.2025.2483783","url":null,"abstract":"<p><p>Urbanization has significantly transformed dietary habits worldwide, contributing to a globally increased burden of non-communicable diseases and altered gut microbiota landscape. However, it is often overlooked that the adverse effects of these dietary changes can be transmitted from the mother to offspring during early developmental stages, subsequently influencing the predisposition to various diseases later in life. This review aims to delineate the detrimental effects of maternal urban-lifestyle diet (urbanized diet) on early-life health and gut microbiota assembly, provide mechanistic insights on how urbanized diet mediates mother-to-offspring transfer of bioactive substances in both intrauterine and extrauterine and thus affects fetal and neonatal development. Moreover, we also further propose a framework for developing microbiome-targeted precision nutrition and diet strategies specifically for pregnant and lactating women. The establishment of such knowledge can help develop proactive preventive measures from the beginning of life, ultimately reducing the long-term risk of disease and improving public health outcomes.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2483783"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11988223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772221","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}
引用次数: 0
Best practices for developing microbiome-based disease diagnostic classifiers through machine learning. 通过机器学习开发基于微生物组的疾病诊断分类器的最佳实践。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2025-04-04 DOI: 10.1080/19490976.2025.2489074
Peikun Li, Min Li, Wei-Hua Chen
{"title":"Best practices for developing microbiome-based disease diagnostic classifiers through machine learning.","authors":"Peikun Li, Min Li, Wei-Hua Chen","doi":"10.1080/19490976.2025.2489074","DOIUrl":"10.1080/19490976.2025.2489074","url":null,"abstract":"<p><p>The human gut microbiome, crucial in various diseases, can be utilized to develop diagnostic models through machine learning (ML). The specific tools and parameters used in model construction such as data preprocessing, batch effect removal and modeling algorithms can impact model performance and generalizability. To establish an generally applicable workflow, we divided the ML process into three above-mentioned steps and optimized each sequentially using 83 gut microbiome cohorts across 20 diseases. We tested a total of 156 tool-parameter-algorithm combinations and benchmarked them according to internal- and external- AUCs. At the data preprocessing step, we identified four data preprocessing methods that performed well for regression-type algorithms and one method that excelled for non-regression-type algorithms. At the batch effect removal step, we identified the \"ComBat\" function from the <i>sva</i> R package as an effective batch effect removal method and compared the performance of various algorithms. Finally, at the ML algorithm selection step, we found that Ridge and Random Forest ranked the best. Our optimized work flow performed similarly comparing with previous exhaustive methods for disease-specific optimizations, thus is generally applicable and can provide a comprehensive guideline for constructing diagnostic models for a range of diseases, potentially serving as a powerful tool for future medical diagnostics.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2489074"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788275","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}
引用次数: 0
Post sleeve gastrectomy-enriched gut commensal Clostridia promotes secondary bile acid increase and weight loss. 套管胃切除术后富含肠道共生梭菌促进继发性胆汁酸增加和体重减轻。
IF 12.2 1区 医学
Gut Microbes Pub Date : 2025-12-01 Epub Date: 2025-02-06 DOI: 10.1080/19490976.2025.2462261
Shaoqian Zhao, Huibin Lin, Wen Li, Xiaoqiang Xu, Qihan Wu, Zhifeng Wang, Juan Shi, Yufei Chen, Lingxia Ye, Liuqing Xi, Lijia Chen, Mingyang Yuan, Junlei Su, Aibo Gao, Jiabin Jin, Xiayang Ying, Xiaolin Wang, Yaorui Ye, Yingkai Sun, Yifei Zhang, Xiaxing Deng, Baiyong Shen, Weiqiong Gu, Guang Ning, Weiqing Wang, Jie Hong, Jiqiu Wang, Ruixin Liu
{"title":"Post sleeve gastrectomy-enriched gut commensal Clostridia promotes secondary bile acid increase and weight loss.","authors":"Shaoqian Zhao, Huibin Lin, Wen Li, Xiaoqiang Xu, Qihan Wu, Zhifeng Wang, Juan Shi, Yufei Chen, Lingxia Ye, Liuqing Xi, Lijia Chen, Mingyang Yuan, Junlei Su, Aibo Gao, Jiabin Jin, Xiayang Ying, Xiaolin Wang, Yaorui Ye, Yingkai Sun, Yifei Zhang, Xiaxing Deng, Baiyong Shen, Weiqiong Gu, Guang Ning, Weiqing Wang, Jie Hong, Jiqiu Wang, Ruixin Liu","doi":"10.1080/19490976.2025.2462261","DOIUrl":"10.1080/19490976.2025.2462261","url":null,"abstract":"<p><p>The gut microbiome is altered after bariatric surgery and is associated with weight loss. However, the commensal bacteria involved and the underlying mechanism remain to be determined. We performed shotgun metagenomic sequencing in obese subjects before and longitudinally after sleeve gastrectomy (SG), and found a significant enrichment in microbial species in Clostridia and bile acid metabolizing genes after SG treatment. Bile acid profiling further revealed decreased primary bile acids (PBAs) and increased conjugated secondary bile acids (C-SBAs) after SG. Specifically, glycodeoxycholic acid (GDCA) and taurodeoxycholic acid (TDCA) were increased at different follow-ups after SG, and were associated with the increased abundance of Clostridia and body weight reduction. Fecal microbiome transplantation with post-SG feces increased SBA levels, and alleviated body weight gain in the recipient mice. Furthermore, both Clostridia-enriched spore-forming bacteria and GDCA supplementation increased the expression of genes responsible for lipolysis and fatty acid oxidation in adipose tissue and reduced adiposity via Takeda G-protein-coupled receptor 5 (TGR5) signaling. Our findings reveal post-SG gut microbiome and C-SBAs as contributory to SG-induced weight loss, in part via TGR5 signaling, and suggest SBA-producing gut microbes as a potential therapeutic target for obesity intervention.</p>","PeriodicalId":12909,"journal":{"name":"Gut Microbes","volume":"17 1","pages":"2462261"},"PeriodicalIF":12.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143364581","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}
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