Gut microbes reports最新文献

Halogenated flame retardant exposure was associated with pediatric gut microbiome profiles in a Canadian cohort. 在一项加拿大队列研究中，卤代阻燃剂暴露与儿童肠道微生物群谱有关。

Gut microbes reports Pub Date : 2026-10-18 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2747517

Yidan Zhang, Feng Gao, Peng Gao, Yihan Fan, Xinlei Wang, Yuqiu Yang, Anthony Gagnon, Guillaume Martinez, Virginie Gillet, Jiping Zhu, Jean-Philippe Bellenger, Andrea A Baccarelli, Larissa Takser, Yike Shen

{"title":"Halogenated flame retardant exposure was associated with pediatric gut microbiome profiles in a Canadian cohort.","authors":"Yidan Zhang, Feng Gao, Peng Gao, Yihan Fan, Xinlei Wang, Yuqiu Yang, Anthony Gagnon, Guillaume Martinez, Virginie Gillet, Jiping Zhu, Jean-Philippe Bellenger, Andrea A Baccarelli, Larissa Takser, Yike Shen","doi":"10.1080/29933935.2026.2747517","DOIUrl":"10.1080/29933935.2026.2747517","url":null,"abstract":"Environmental chemical exposures have been linked to gut microbiome dysregulation and adverse health outcomes in children. Halogenated flame retardants (HFRs) are persistent chemicals with substantial early-life exposure, yet evidence on their effects on the pediatric gut microbiome remains limited. We examined associations between HFR exposures and the gut microbiome among 8-12-y-old children from the GESTation and Environment (GESTE) cohort in Sherbrooke, Canada. In a multi-matrix, multi-omics design, 10 HFRs were quantified in plasma (n = 140) and stool (n = 182), with shotgun metagenomic and metatranscriptomic sequencing characterized microbial species and functional pathways. After false discovery rate correction, plasma BDE-47 and BDE-99 were inversely associated with Clostridium sp. CAG:221 and Bacteroides dorei, respectively (q < 0.2). Stool BDE-153 was negatively associated with short-chain fatty acid-producing taxa, including Eubacterium spp. and Roseburia intestinalis, and positively associated with Alistipes putredinis and Faecalibacterium spp. Stool BDE-153 and anti-DP were associated with higher activity of pathways involved in phospholipid homeostasis and 4-aminobutanoate degradation. Mediation analysis suggested that Faecalibacterium spp. partly mediated the association between stool BDE-153 and cytidine diphosphate-diacylglycerol biosynthesis. Our findings suggest that childhood HFR exposure is associated with alterations in gut microbiome composition and function, with potential implications for pediatric health.","PeriodicalId":519879,"journal":{"name":"Gut microbes reports","volume":"3 1","pages":"2747517"},"PeriodicalIF":0.0,"publicationDate":"2026-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13682408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149240889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbiome-targeted dietary therapy in health and disease: Challenges, opportunities, and pathways forward. 以微生物群为目标的饮食治疗在健康和疾病：挑战、机遇和前进的途径。

Gut microbes reports Pub Date : 2026-10-09 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2744027

Alice S Day, Anissa M Armet, Srinivas Kamath, Paul M Joyce, Robert V Bryant, Heather K Armstrong

{"title":"Microbiome-targeted dietary therapy in health and disease: Challenges, opportunities, and pathways forward.","authors":"Alice S Day, Anissa M Armet, Srinivas Kamath, Paul M Joyce, Robert V Bryant, Heather K Armstrong","doi":"10.1080/29933935.2026.2744027","DOIUrl":"https://doi.org/10.1080/29933935.2026.2744027","url":null,"abstract":"The gut microbiome has an established role in health and disease, and can be manipulated by diet, positioning microbiome-targeted dietary therapies as potential therapeutics. Mounting evidence supports dietary patterns rich in fermentable fibers and lower in nutrient-poor processed foods; however, there are individual, local, and system-wide complexities to adopting and sustaining dietary change as part of therapeutic dietary strategies. Wider adoption of diet therapy is also limited by critical factors that interfere and influence treatment outcomes, the most significant being inter-individual variability in response to dietary therapy, which remains poorly characterized and understood, hindering advancements in precision nutrition. This review examines the role of the gut microbiome in health and disease and describes barriers and solutions for developing and implementing microbiome-targeted dietary interventions as therapeutic strategies. We organize these barriers into three domains: biological, behavioral, and policy and systems, moving from molecular and individual-level mechanisms to population-level systems, and identify evidence gaps and candidate measurable outcomes to guide future research and dietary guideline development.","PeriodicalId":519879,"journal":{"name":"Gut microbes reports","volume":"3 1","pages":"2744027"},"PeriodicalIF":0.0,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13656811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149187477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the interplay between dietary plant glycolipids and gut microbiota: A systematic review. 探索膳食植物糖脂与肠道微生物群之间的相互作用：系统综述。

Gut microbes reports Pub Date : 2026-09-26 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2676398

Anastasia Cartegnie, Eva Larrieu, Marie-Caroline Michalski, Cécile Vors

{"title":"Exploring the interplay between dietary plant glycolipids and gut microbiota: A systematic review.","authors":"Anastasia Cartegnie, Eva Larrieu, Marie-Caroline Michalski, Cécile Vors","doi":"10.1080/29933935.2026.2676398","DOIUrl":"10.1080/29933935.2026.2676398","url":null,"abstract":"Considering the shift towards plant-based diets, it becomes necessary to better understand the roles of plant-derived nutrients in health. Despite their abundance in green plants, the role of plant glycolipids (GLs) in metabolic health remains scarcely known. Gut microbiota is a key actor in the regulation of host health, whose interplay with diet is complex. This systematic review examines the available evidence on potential interactions between dietary plant GLs and the gut microbiota. A structured search strategy was used to identify preclinical and human studies assessing the impact of plant GLs on the gut microbiota composition or the potential degradation of plant GLs by gut bacteria. Among 345 screened records, 13 studies were finally included. Both animal- and human-based evidence suggest that plant GLs may impact the gut microbiota composition, with beneficial effects for host by promoting a healthy gut bacterial ecosystem (increase in gut health-related bacteria and a reduction in some pathobionts). Some GLs exhibit in vitro antibacterial properties, and several pathways of GL bacterial degradation have been described, suggesting that the gut microbiota uses plant GLs as a source of nutrients. Such promising evidence highlights the potential prebiotic role of plant GLs and encourages further study of the gut-associated metabolic effects of plant GLs in humans.","PeriodicalId":519879,"journal":{"name":"Gut microbes reports","volume":"3 1","pages":"2676398"},"PeriodicalIF":0.0,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13618843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149076883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gut microbiome dysbiosis and functional alterations in Campylobacter-associated gastroenteritis using metagenomic approaches. 利用宏基因组方法研究弯曲杆菌相关肠胃炎的肠道微生物群失调和功能改变。

Gut microbes reports Pub Date : 2026-08-18 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2688065

Bilal Djeghout, Alise J Ponsero, Nuno Pedroso, George M Savva, Ngozi Elumogo, Nicol Janecko

{"title":"Gut microbiome dysbiosis and functional alterations in Campylobacter-associated gastroenteritis using metagenomic approaches.","authors":"Bilal Djeghout, Alise J Ponsero, Nuno Pedroso, George M Savva, Ngozi Elumogo, Nicol Janecko","doi":"10.1080/29933935.2026.2688065","DOIUrl":"https://doi.org/10.1080/29933935.2026.2688065","url":null,"abstract":"Campylobacter species are a major cause of bacterial gastroenteritis worldwide. Using shotgun metagenomic sequencing of stool samples from PCR-confirmed Campylobacter-positive patients and symptomatic PCR-negative controls, we reveal dysbiosis marked by reduced species richness (median Shannon diversity was significantly lower in the Campylobacter-positive group [3.24] vs. Campylobacter-negative group [3.63], P = 0.038), taxonomic shifts toward inflammation-associated taxa (Campylobacteriaceae, Enterobacteriaceae, Pasteurellaceae), and depletion of key commensals involved in short-chain fatty acid (SCFA) production (Ruminococcaceae, Bacteroidaceae, Eubacteriaceae). These changes define a distinct microbial signature of infection, suggestive of a perturbed gut environment with reduced colonization resistance and impaired barrier function. Despite these taxonomic and ecological disruptions, resistome profiling showed no increase in the burden or diversity of antimicrobial resistance genes (ARGs), suggesting that the observed microbiome disruption may not lead to broader expansion of ARGs in the gut microbiome. Whole-genome sequencing of cultured Campylobacter jejuni and C. coli isolates revealed common ARGs, including bla OXA-193, tet(O), and gyrA_T86I, some of which overlapped with metagenomic findings. Moreover, metagenomics identified low-abundance Campylobacter species in PCR-negative controls, underscoring the need for greater taxonomic resolution. These results delineate a Campylobacter-associated microbial and functional footprint in the human gut, with implications for diagnostics and antimicrobial stewardship.","PeriodicalId":519879,"journal":{"name":"Gut microbes reports","volume":"3 1","pages":"2688065"},"PeriodicalIF":0.0,"publicationDate":"2026-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13488468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148804504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Longitudinal multi-omic dynamics in hospitalized COVID-19 patients based on disease severity. 基于疾病严重程度的住院COVID-19患者的纵向多基因组动力学

Gut microbes reports Pub Date : 2026-08-13 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2712728

Christopher M Basting, Ty A Schroeder, Robin Shields-Cutler, Erik Swanson, Candace Guerrero, Charlotte R Hemmila, Courtney A Broedlow, Ashma Chakrawarti, Adrian Velez, Ross Cromarty, Agostino Riva, Alessandro Torre, Alessia Lai, Luca Schifanella, Nichole R Klatt

{"title":"Longitudinal multi-omic dynamics in hospitalized COVID-19 patients based on disease severity.","authors":"Christopher M Basting, Ty A Schroeder, Robin Shields-Cutler, Erik Swanson, Candace Guerrero, Charlotte R Hemmila, Courtney A Broedlow, Ashma Chakrawarti, Adrian Velez, Ross Cromarty, Agostino Riva, Alessandro Torre, Alessia Lai, Luca Schifanella, Nichole R Klatt","doi":"10.1080/29933935.2026.2712728","DOIUrl":"https://doi.org/10.1080/29933935.2026.2712728","url":null,"abstract":"Despite a decline in global COVID-19 cases, severe disease requiring hospitalization remains a significant health burden. Microbial dysbiosis and microbial translocation have been implicated in COVID-19 severity through their contributions to systemic inflammation, yet the temporal dynamics of the microbiome and related metabolites across disease severity are not well defined. To address this, we conducted a longitudinal study of 22 hospitalized COVID-19 patients in Milan, Italy, classified as moderate, severe, or critical by the WHO criteria. Rectal and nasal microbiomes, plasma cytokines, bile acids, fatty acids, and gut barrier damage markers were measured at up to three timepoints over an average of 9 d. Critically ill patients exhibited sustained elevations in pro-inflammatory cytokines (IL-6, IL-8, and TNFα), increased gut barrier damage markers (LBP, zonulin, and sCD14), early depletion of beneficial commensals (including Faecalibacterium prausnitzii), and expansion of opportunistic pathogens such as Hungatella hathewayi and Erysipelatoclostridium ramosum. These microbial shifts were accompanied by the progressive loss of secondary and conjugated bile acids and increased levels of branched- and medium-chain fatty acids. Correlation analyses linked commensal taxa to reduced gut barrier damage and opportunistic pathogens to IL-6. Together, these findings define distinct trajectories associated with COVID-19 severity and highlight the importance of early interventions targeting microbial dysbiosis.","PeriodicalId":519879,"journal":{"name":"Gut microbes reports","volume":"3 1","pages":"2712728"},"PeriodicalIF":0.0,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13475324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148765880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gut microbiota as a driver of variable antihypertensive drug response: A narrative review. 肠道微生物群作为可变抗高血压药物反应的驱动因素：一项叙述性综述。

Gut microbes reports Pub Date : 2026-08-13 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2717017

Victor Zheng, Disha Patel, Tao Yang

{"title":"Gut microbiota as a driver of variable antihypertensive drug response: A narrative review.","authors":"Victor Zheng, Disha Patel, Tao Yang","doi":"10.1080/29933935.2026.2717017","DOIUrl":"https://doi.org/10.1080/29933935.2026.2717017","url":null,"abstract":"Hypertension is a major global burden to human health. Despite the availability of multiple classes of antihypertensive medications, a considerable number of patients still have uncontrolled or treatment-resistant hypertension. The gut microbiota is increasingly recognized as a regulator of blood pressure, and fecal microbiota transfer from hypertensive patients has been shown to increase blood pressure in experimental rodent recipients. Although antihypertensive medications remain the mainstay of treatment and are more readily applicable than microbiota-based therapies, gut microbiota may influence how these medications work. Gut microbes contain diverse enzymes involved in drug metabolism and can also affect host physiology in response. Emerging research has identified the gut microbiota as an important modifier of therapeutic drug efficacy. In this review, we summarize the current evidence supporting the role of the gut microbiota as a modifier of antihypertensive drug response. We also propose that future studies focus on identifying gut microbial features and bacterial species that may be used to improve the blood pressure-lowering efficacy of antihypertensive medications.","PeriodicalId":519879,"journal":{"name":"Gut microbes reports","volume":"3 1","pages":"2717017"},"PeriodicalIF":0.0,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13475318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148765624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Isolation and characterization of seven phages infecting gut Bacteroides. 7种感染肠道拟杆菌的噬菌体的分离与鉴定。

Gut microbes reports Pub Date : 2026-07-31 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2709722

Krushe Mundru, Khalida Khatun, Yolanda Y Huang

引用次数: 0

Assessment of nutrient intake by gut microbiota enterotype in Japanese subjects. 日本受试者肠道菌群肠型对营养摄入的评估。

Gut microbes reports Pub Date : 2026-07-30 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2705623

Tomohisa Takagi, Ryo Inoue, Akira Ohshima, Machi Oda, Hiroshi Sakazume, Kenta Ogawa, Tomohide Tanaka, Tomo Tominaga, Yoichi Mihara, Norihiro Ouchi, Atsuo Adachi, Tadaaki Kamitani, Satoaki Matoba, Jin Narumoto, Katsura Mizushima, Takeshi Yasuda, Hiroaki Kitae, Kazuhiko Uchiyama, Yuji Naito

{"title":"Assessment of nutrient intake by gut microbiota enterotype in Japanese subjects.","authors":"Tomohisa Takagi, Ryo Inoue, Akira Ohshima, Machi Oda, Hiroshi Sakazume, Kenta Ogawa, Tomohide Tanaka, Tomo Tominaga, Yoichi Mihara, Norihiro Ouchi, Atsuo Adachi, Tadaaki Kamitani, Satoaki Matoba, Jin Narumoto, Katsura Mizushima, Takeshi Yasuda, Hiroaki Kitae, Kazuhiko Uchiyama, Yuji Naito","doi":"10.1080/29933935.2026.2705623","DOIUrl":"10.1080/29933935.2026.2705623","url":null,"abstract":"Japanese gut microbiota forms community clusters and shares some compositional features with Western enterotypes, although the relationship between enterotypes and habitual nutrient intake in Japanese adults remains unclear. We analyzed data from 770 community-dwelling adults. Enterotypes were assigned based on 16S rRNA gene profiles using a support vector machine model, and taxonomic annotations were updated using the SILVA 138 database. Dietary intake and nutrient intake were assessed, and differences among enterotypes were examined. Candidate nutrients and food groups potentially associated with enterotypes were prioritized using a SHapley Additive explanation (SHAP)-based interpretation of the XGBoost models and were further evaluated using linear discriminant analysis. Five enterotypes (Types A-E) were identified and exhibited insufficient dietary fiber and excessive salt intake. Types A and C showed the highest and lowest overall nutrient intake scores, respectively. Although predictive performance for nutrient intake and food-group intake was modest, linear discriminant analysis based on SHAP-prioritized features revealed distinct but partially overlapping dietary signatures among enterotypes. Correlation analyses identified associations between key bacterial taxa and enterotype-specific dietary features, which reflect complex combinations of nutrients and food groups. These findings may contribute to the development of enterotype-aware dietary strategies to promote a healthy gut microbiota.","PeriodicalId":519879,"journal":{"name":"Gut microbes reports","volume":"3 1","pages":"2705623"},"PeriodicalIF":0.0,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13432868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148671998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Isolation and characterization of a novel lytic bacteriophage for Faecalibacterium prausnitzii, a key member of the human gut microbiota. prausnitzii粪杆菌（Faecalibacterium prausnitzii）一种新型裂解噬菌体的分离和鉴定。

Gut microbes reports Pub Date : 2026-07-29 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2708416

Mikaela Whitty, Maria Jelinic, Grant R Drummond, Antony Vinh, Steve Petrovski

{"title":"Isolation and characterization of a novel lytic bacteriophage for Faecalibacterium prausnitzii, a key member of the human gut microbiota.","authors":"Mikaela Whitty, Maria Jelinic, Grant R Drummond, Antony Vinh, Steve Petrovski","doi":"10.1080/29933935.2026.2708416","DOIUrl":"10.1080/29933935.2026.2708416","url":null,"abstract":"Faecalibacterium prausnitzii is a dominant and health-associated member of the human gastrointestinal tract that is consistently depleted in individuals with metabolic, cardiovascular, and psychiatric disorders. Despite its importance in gut health, little is known about the bacteriophages (or phages) that infect this species. Phages are increasingly recognized as key regulators of bacterial population dynamics in the gut microbiota; however, while prophages of F. prausnitzii have been described, no lytic phages targeting this bacterium have been reported. Here, we describe the isolation and characterization of the first lytic F. prausnitzii bacteriophage, vB_Fpr_FP01. Whole-genome sequencing and comparative genomics analysis demonstrate that FP01 represents a novel species, clustering within a genus that includes an uncharacterized phage within the class Caudovirales. Comparative analysis also identified closely related viral sequences in the human gut virome dataset, suggesting that related phages occur in gut-associated environments. These findings expand the current knowledge of F. prausnitzii-associated phages and provide a framework for future studies investigating phage‒host interactions and their role in shaping gut microbial communities.","PeriodicalId":519879,"journal":{"name":"Gut microbes reports","volume":"3 1","pages":"2708416"},"PeriodicalIF":0.0,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13432834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148671982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gut bacterial O-demethylation in microbiome-dependent drug response. 肠道细菌o -去甲基化在微生物组依赖性药物反应中的作用。

Gut microbes reports Pub Date : 2026-07-27 eCollection Date: 2026-01-01 DOI: 10.1080/29933935.2026.2709263

Cheng-Kai Chiang, Braden S Dibello, Joshua Park, Jess Rondinella, Qihao Wu

引用次数: 0