Anna Pii Hjørne, Martin Steen Mortensen, Tine Rask Licht, Martin Frederik Laursen
{"title":"Loperamide increases mouse gut transit time in a dose-dependent manner with treatment duration-dependent effects on distinct gut microbial taxa.","authors":"Anna Pii Hjørne, Martin Steen Mortensen, Tine Rask Licht, Martin Frederik Laursen","doi":"10.1017/gmb.2025.5","DOIUrl":"https://doi.org/10.1017/gmb.2025.5","url":null,"abstract":"<p><p>Intestinal transit time has been recognized as an important factor in shaping the gut microbiota, although causality remains to be firmly demonstrated. The aim of this study was to evaluate the effect of different loperamide doses on the mouse intestinal transit time and to investigate the effects of increasing transit time on the gut microbial community. Loperamide significantly increased the transit time in a dose-dependent manner. Additionally, we observed a significant difference between the control group and the loperamide-treated groups in the abundance of the bacterial families <i>Bacteroidaceae, Erysipelotrichaceae, Porphyromonadaceae</i>, and <i>Akkermansiaceae</i> after 7 days of loperamide treatment, with the bacterial families responding to the increased transit time at different rates. Fermentation of faeces obtained from the same mice, with or without loperamide, demonstrated that the observed effects on gut microbiota <i>in vivo</i> were not a result of direct interactions between loperamide and the gut microbiota but rather a consequence of loperamide-induced increased intestinal transit time. In the cecum of the mice, we found higher levels of propionate in the high-dose group compared to the control and low-dose groups. Collectively, our findings establish that an altered transit time is causal to changes in the composition and activity of the microbiome.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e7"},"PeriodicalIF":0.0,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12056420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058659","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}
Pavan K Mantravadi, Basavaraj S Kovi, Sabbasani Rajasekhara Reddy, Ganesh Pandian Namasivayam, Karunakaran Kalesh, Anutthaman Parthasarathy
{"title":"Probing and manipulating the gut microbiome with chemistry and chemical tools.","authors":"Pavan K Mantravadi, Basavaraj S Kovi, Sabbasani Rajasekhara Reddy, Ganesh Pandian Namasivayam, Karunakaran Kalesh, Anutthaman Parthasarathy","doi":"10.1017/gmb.2025.4","DOIUrl":"https://doi.org/10.1017/gmb.2025.4","url":null,"abstract":"<p><p>The human gut microbiome represents an extended \"second genome\" harbouring about 10<sup>15</sup> microbes containing >100 times the number of genes as the host. States of health and disease are largely mediated by host-microbial metabolic interplay, and the microbiome composition also underlies the differential responses to chemotherapeutic agents between people. Chemical information will be the key to tackle this complexity and discover specific gut microbiome metabolism for creating more personalised interventions. Additionally, rising antibiotic resistance and growing awareness of gut microbiome effects are creating a need for non-microbicidal therapeutic interventions. We classify chemical interventions for the gut microbiome into categories like molecular decoys, bacterial conjugation inhibitors, colonisation resistance-stimulating molecules, \"prebiotics\" to promote the growth of beneficial microbes, and inhibitors of specific gut microbial enzymes. Moreover, small molecule probes, including click chemistry probes, artificial substrates for assaying gut bacterial enzymes and receptor agonists/antagonists, which engage host receptors interacting with the microbiome, are some other promising developments in the expanding chemical toolkit for probing and modulating the gut microbiome. This review explicitly excludes \"biologics\" such as probiotics, bacteriophages, and CRISPR to concentrate on chemistry and chemical tools like chemoproteomics in the gut-microbiome context.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e6"},"PeriodicalIF":0.0,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12056425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144001491","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}
Luana Greco, Federica Rubbino, Clarissa Ferrari, Michela Cameletti, Fabio Grizzi, Fabrizio Bonelli, Alberto Malesci, Massimiliano Mazzone, Luigi Ricciardiello, Luigi Laghi
{"title":"Association of <i>Fusobacterium nucleatum</i> with colorectal cancer molecular subtypes and its outcome: a systematic review.","authors":"Luana Greco, Federica Rubbino, Clarissa Ferrari, Michela Cameletti, Fabio Grizzi, Fabrizio Bonelli, Alberto Malesci, Massimiliano Mazzone, Luigi Ricciardiello, Luigi Laghi","doi":"10.1017/gmb.2025.3","DOIUrl":"https://doi.org/10.1017/gmb.2025.3","url":null,"abstract":"<p><p>Colorectal cancer (CRC) represents a relevant public health problem, with high incidence and mortality in Western countries. CRC can occur as sporadic (65%-75%), common familial (25%), or as a consequence of an inherited predisposition (up to 10%). While unravelling its genetic basis has been a long trip leading to relevant clinical implementation over more than 30 years, other contributing factors remain to be clarified. Among these, micro-organisms have emerged as critical players in the development and progression of the disease, as well as for CRC treatment response. <i>Fusobacterium nucleatum</i> (<i>Fn</i>) has been associated with CRC development in both pre-clinical models and clinical settings. <i>Fusobacteria</i> are core members of the human oral microbiome, while being less prevalent in the healthy gut, prompting questions about their localization in CRC and its precursor lesions. This review aims to critically discuss the evidence connecting <i>Fn</i> with CRC pathogenesis, its molecular subtypes and clinical outcomes.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e5"},"PeriodicalIF":0.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029271","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}
Patricia Sanz Morales, Anisha Wijeyesekera, M Denise Robertson, Giles Major, Claire L Boulangé, Peter Philip James Jackson, Carlos Guillermo Poveda Turrado, Glenn R Gibson
{"title":"An <i>in vitro</i> batch culture study to assess the fermentation of human milk oligosaccharides by faecal microbiota from healthy and irritable bowel syndrome stool donors.","authors":"Patricia Sanz Morales, Anisha Wijeyesekera, M Denise Robertson, Giles Major, Claire L Boulangé, Peter Philip James Jackson, Carlos Guillermo Poveda Turrado, Glenn R Gibson","doi":"10.1017/gmb.2025.2","DOIUrl":"https://doi.org/10.1017/gmb.2025.2","url":null,"abstract":"<p><p>This study explored the effects of different human milk oligosaccharides (HMOs), solely and in combination, on gut microbiota composition and metabolic activity (organic acid production), using anaerobic <i>in vitro</i> batch culture fermenters. The aim was to compare prebiotic effects of HMOs (2'FL, 3'FL, 3'SL, 6'SL, LNT, LNnT, and 1:1 ratio mixes of 2'FL/3'SL and 3'SL/LNT) in faecal samples from irritable bowel syndrome (IBS) donors and healthy controls, and to determine the best-performing HMO in IBS. Fluorescent <i>in situ</i> hybridisation coupled with flow cytometry was utilised to study microbiota changes in major colonic genera, and organic acid production was assessed by gas chromatography. IBS donors had different starting microbial profiles compared to healthy controls and lower levels of organic acids. In response to HMOs, there were alterations in both the control and IBS faecal microbiomes. In IBS donor fermenters, <i>Bifidobacterium</i>, <i>Faecalibacterium</i>, total bacterial numbers, and organic acid production significantly increased post-HMO intervention. When comparing the effect of HMO interventions on the microbiota and organic acid production, a mix of 3'SL/LNT HMOs may be the most promising intervention for IBS patients.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e4"},"PeriodicalIF":0.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12034501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144059043","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}
Manahil M Bineid, Litai Liu, Eduard F Ventura, Sakshi Bansal, Katherine Curi-Quinto, Juana Del Valle-Mendoza, Gemma E Walton, Karani Santhanakrishnan Vimaleswaran
{"title":"The effect of probiotics, prebiotics and synbiotics on gut microbial community profile in overweight and obese Latin American and Caribbean populations: a systematic review of human trials.","authors":"Manahil M Bineid, Litai Liu, Eduard F Ventura, Sakshi Bansal, Katherine Curi-Quinto, Juana Del Valle-Mendoza, Gemma E Walton, Karani Santhanakrishnan Vimaleswaran","doi":"10.1017/gmb.2024.12","DOIUrl":"10.1017/gmb.2024.12","url":null,"abstract":"<p><p>Oral supplementation with probiotics, prebiotics, and synbiotics is a novel potential complementary therapy for addressing overweight and obesity through gut microbiota modulation. This systematic review provides a comprehensive summary of the existing evidence to guide future research. Literature searches were conducted in four databases to identify human trials published until May 2024 that examined the impact of probiotic, prebiotic, or synbiotic interventions on faecal microbiota composition changes in overweight and obese participants from Latin American and Caribbean populations (LACPs). Of the 13,090 identified records, five randomised controlled trials (RCTs) from Brazil, Mexico, and Chile met the inclusion criteria for this review. The included RCTs evaluated different forms of therapies over short-term interventions (6 or 8 weeks), with sample sizes ranging from 21 to 39 participants across the studies. Variations in the reported outcomes were observed due to differences in supplement formulation, dosage, population characteristics, and methodological heterogeneity. The findings indicate that the available data are inadequate to establish definitive conclusions regarding the impact of biotic treatments on gut microbiota profiles in LACP. Further research with larger sample sizes and precise microbiota analysis is required to elucidate the implications of dietary interventions on gut microbiota in obesity and related disorders.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e2"},"PeriodicalIF":0.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411844","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}
{"title":"Partially hydrolyzed guar gum attenuates symptoms and modulates the gut microbiota in a model of SARS-CoV-2 infection.","authors":"Jiayue Yang, Isaiah Song, Misa Saito, Tenagy Hartanto, Takeshi Ichinohe, Shinji Fukuda","doi":"10.1017/gmb.2024.7","DOIUrl":"10.1017/gmb.2024.7","url":null,"abstract":"<p><p>The coronavirus disease 2019 (COVID-19) pandemic has caused health issues worldwide. Studies have suggested that modulation of the gut microbiota could attenuate the severity of COVID-19 symptoms. In light of this, we explored the effects of the prebiotic dietary fibre partially hydrolyzed guar gum (PHGG) on SARS-CoV-2 infection in a Syrian hamster model, hypothesizing that modulation of the gut microbiome and intestinal metabolites through PHGG administration would improve COVID-19 disease outcomes. Eight hamsters each were assigned to the PHGG administration and control groups. The PHGG group was given a diet supplemented with 5% PHGG for two weeks. Consequently, PHGG improved the host survival rate to 100% compared to 25% of the control group (P = 0.003) and attenuated morbid weight loss. Another non-infected set of hamsters was used for the analysis of the gut microbiome composition with 16S rRNA amplicon sequencing, serum, and faecal metabolites with GC-MS and LC-MS. PHGG altered the gut microbiome composition and increased the relative abundances of <i>Ileibacterium</i>, <i>Bifidobacterium</i>, and <i>Prevotella.</i> Furthermore, it elevated the concentrations of faecal valeric acid, propionic acid, ursodeoxycholic acid, and serum deoxycholic acid. Taken together, our data suggest that the prebiotic PHGG modulates gut metabolites and has the potential to reduce COVID-19 morbidity.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e1"},"PeriodicalIF":0.0,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411828","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}
Usha Longwani, Ashok K Sharma, Aditya S Malwe, Shubham K Jaiswal, Vineet K Sharma
{"title":"GutBugDB: a web resource to predict the human gut microbiome-mediated biotransformation of biotic and xenobiotic molecules.","authors":"Usha Longwani, Ashok K Sharma, Aditya S Malwe, Shubham K Jaiswal, Vineet K Sharma","doi":"10.1017/gmb.2024.15","DOIUrl":"10.1017/gmb.2024.15","url":null,"abstract":"<p><p>There has been a growing recognition of the significant role played by the human gut microbiota in altering the bioavailability as well as the pharmacokinetic and pharmacodynamic aspects of orally ingested xenobiotic and biotic molecules. The determination of species-specific contributions to the metabolism of biotic and xenobiotic molecules has the potential to aid in the development of new therapeutic and nutraceutical molecules that can modulate human gut microbiota. Here we present \"GutBugDB,\" an open-access digital repository that provides information on potential gut microbiome-mediated biotransformation of biotic and xenobiotic molecules using the predictions from the GutBug tool. This database is constructed using metabolic proteins from 690 gut bacterial genomes and 363,872 protein enzymes assigned with their EC numbers (with representative Expasy ID and domains present). It provides information on gut microbiome enzyme-mediated metabolic biotransformation for 1439 FDA-approved drugs and nutraceuticals. GutBugDB is publicly available at https://metabiosys.iiserb.ac.in/gutbugdb/.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e3"},"PeriodicalIF":0.0,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411827","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}
Ni Shi, Sushma Nepal, Rachel Hoobler, Cristina Menni, Mary C Playdon, Daniel Spakowicz, Philippa M Wells, Claire J Steves, Steven K Clinton, Fred K Tabung
{"title":"Pro-inflammatory and hyperinsulinaemic dietary patterns are associated with specific gut microbiome profiles: a TwinsUK cohort study.","authors":"Ni Shi, Sushma Nepal, Rachel Hoobler, Cristina Menni, Mary C Playdon, Daniel Spakowicz, Philippa M Wells, Claire J Steves, Steven K Clinton, Fred K Tabung","doi":"10.1017/gmb.2024.14","DOIUrl":"10.1017/gmb.2024.14","url":null,"abstract":"<p><p>Metabolic dietary patterns, including the Empirical Dietary Index for Hyperinsulinaemia (EDIH) and Empirical Dietary Inflammatory Pattern (EDIP), are known to impact multiple chronic diseases, but the role of the colonic microbiome in mediating such relationships is poorly understood. Among 1,610 adults with faecal 16S rRNA data in the TwinsUK cohort, we identified the microbiome profiles for EDIH and EDIP (from food frequency questionnaires) cross-sectionally using elastic net regression. We assessed the association of the dietary pattern-related microbiome profile scores with circulating biomarkers in multivariable-adjusted linear regression. In addition, we used PICRUSt2 to predict biological pathways associated with the enriched microbiome profiles, and further screened pathways for associations with the dietary scores in linear regression analyses. Microbiome profile scores developed with 32 (EDIH) and 15 (EDIP) genera were associated with higher insulin and homeostatic model assessment of insulin resistance. Six genera were associated with both dietary scores: <i>Ruminococcaceae_UCG-008, Lachnospiraceae_UCG-008, Defluviitaleaceae_UCG-011 Anaeroplasma</i>, inversely and <i>Negativibacillus, Streptococcus</i>, positively. Further, pathways in fatty acid biosynthesis, sugar acid degradation, and mevalonate metabolism were associated with insulinaemic and inflammatory diets. Dietary patterns that exert metabolic effects on insulin and inflammation may influence chronic disease risk by modulating gut microbial composition and function.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"5 ","pages":"e12"},"PeriodicalIF":0.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11658949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866371","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}
{"title":"Has the two decades of research on the gut microbiome resulted in making healthier choices?","authors":"M Andrea Azcarate-Peril","doi":"10.1017/gmb.2024.13","DOIUrl":"10.1017/gmb.2024.13","url":null,"abstract":"<p><p>The gut microbiome is widely recognized for its significant contribution to maintaining human health across all life stages, from infancy to adulthood and beyond. This perspective article focuses on the impacts of well-supported microbiome research on global caesarean delivery rates, breastfeeding practices, and antimicrobial use. The article also explores the impact of dietary choices, particularly those involving ultra-processed foods, on the gut microbiota and their potential contribution to conditions like obesity, metabolic syndrome, and inflammatory diseases. This perspective aims to emphasize the need for updated guidelines and policy interventions to address the increasing global trends of caesarean deliveries, reduced breastfeeding, overuse of antibiotics, and consumption of highly processed foods to counter their adverse effects on gut health.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"5 ","pages":"e10"},"PeriodicalIF":0.0,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11658936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866369","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}
Yvonne E Finnegan, Holly R Neill, Emily J Prpa, Bruno Pot
{"title":"\"Gut\" to grips with the science of the microbiome - a symposium report.","authors":"Yvonne E Finnegan, Holly R Neill, Emily J Prpa, Bruno Pot","doi":"10.1017/gmb.2024.8","DOIUrl":"10.1017/gmb.2024.8","url":null,"abstract":"<p><p>The latest Yakult Science Study Day was held virtually on 2 November 2023. Aimed at healthcare professionals, researchers, and students, a variety of experts explored the latest gut microbiome research and what it means in practice. The morning sessions discussed the role of the microbiome in health and disease, the rapid advancements in DNA sequencing and implications for personalised nutrition, the current state of evidence on health benefits associated with fermented foods, prebiotics and probiotics and the challenges involved in interpreting research in this area. The afternoon session considered the emerging research on the microbiota-gut-brain axis in mediating effects of food on mood, the bidirectional impact of menopause on the gut microbiota, and the interplay between the gut and skin with implications for the treatment of rare and common skin disorders. The session ended with an update on the use of faecal microbiota transplant in both research and clinical practice. Undoubtedly, the gut microbiome is emerging as a key conductor of human health, both in relation to gastrointestinal and non-gastrointestinal outcomes. As research continues to elucidate mechanisms of action and confirm their effects in human trials, the gut microbiome should be a key consideration within a holistic approach to health moving forward.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"5 ","pages":"e11"},"PeriodicalIF":0.0,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11658944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866249","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}