Gut microbiome (Cambridge, England)最新文献

{"title":"Erratum: The effects of inorganic nitrate and inulin co-ingestion on circulating metabolites and blood pressure in young adults: a pilot double-blind randomised crossover trial - CORRIGENDUM.","authors":"Jessica Virgili, Gwenaelle Le Gall, Anni Vanhatalo, Bert Bond, David Vauzour, Luciana Torquati","doi":"10.1017/gmb.2025.10010","DOIUrl":"10.1017/gmb.2025.10010","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1017/gmb.2025.10008.].</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e15"},"PeriodicalIF":0.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139760","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":"Human DNA hijacking microbiota surveys: causes and consequences in colon related 16s rRNA amplicon sequencing.","authors":"Leandro Di Gloria, Lorenzo Casbarra, Marta Bastiani, Gabriele Memoli, Matteo Ramazzotti","doi":"10.1017/gmb.2025.10012","DOIUrl":"10.1017/gmb.2025.10012","url":null,"abstract":"<p><p>The efficiency of polymerase chain reaction (PCR) decreases under suboptimal conditions, such as low template concentration combined with high concentrations of similar sequences. Under these circumstances, mis-priming can occur, leading to the generation of erroneous copies. Specifically, in 16S amplicon sequencing of human intestinal biopsy samples, host off-target sequences are frequently generated and subsequently sequenced, particularly when the commonly used V3-V4 primers are employed. This issue not only introduces errors in data interpretation but also results in the unnecessary consumption of sequencing depth. In response to this challenge, we analysed over 1,300 publicly available V3-V4 amplicon sequences related to the human colon, profiling the colon microbiota while elucidating the biases introduced by host off-targets. Briefly, our findings reveal that unaddressed host DNA contamination can lead to false bacterial identifications and obscure significant differences in microbiota composition. Furthermore, we identified human sequences on chromosomes 5, 11, and 17 as the main contributors to the majority of off-target sequences. Finally, we suggest practical approaches to mitigate this issue without altering the original protocol design, retaining the widely used V3-V4 primers. In particular, using a C3 spacer-modified nucleotide targeting the off-target sequence is here proposed as a promising strategy acting upstream of the off-target generation.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e14"},"PeriodicalIF":0.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139771","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":"The effects of inorganic nitrate and inulin co-ingestion on circulating metabolites and blood pressure in young adults: a pilot double-blind randomised crossover trial.","authors":"Jessica Virgili, Gwenaelle Le Gall, Anni Vanhatalo, Bert Bond, David Vauzour, Luciana Torquati","doi":"10.1017/gmb.2025.10008","DOIUrl":"10.1017/gmb.2025.10008","url":null,"abstract":"<p><p>Dietary patterns enriched in fermentable fibre (such as inulin) and inorganic nitrate are linked to cardiovascular benefits, possibly mediated by gut microbiota-derived bioactive compounds including short-chain fatty acids (SCFAs) and nitric oxide (NO). However, the potential synergistic effects remain unclear. We conducted a randomised, double-blind, crossover study to investigate the acute effects of inulin (15 g; INU), nitrate (400 mg; NO₃ ^-), and their combination (INU + NO₃ ^-) on plasma nitrate and nitrite levels, SCFAs, and blood pressure (BP) in 20 adults. Plasma nitrate and nitrite were significantly elevated following INU + NO₃ ^- and NO₃ ^- compared to INU (<i>p</i> < 0.001). Plasma SCFAs were increased after INU + NO₃ ^- and INU, but the incremental AUC was not statistically significant, likely due to large inter-individual variability. No significant main effects were observed on BP; however, inverse correlations were identified between peak plasma nitrite and diastolic BP (r_s = -0.61, <i>p</i> = 0.004) and mean arterial pressure (MAP) (r_s = -0.59, <i>p</i> = 0.005) following INU + NO₃ ^-. Peak nitrate concentrations were inversely correlated with diastolic BP following NO₃ ^- (r_s = -0.47, <i>p</i> = 0.004). Co-supplementation with inulin and nitrate did not enhance plasma nitrate/nitrite or BP beyond nitrate alone but modulated SCFA profiles, suggesting potential interactions between fibre fermentation and nitrate metabolism for cardiovascular health.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e11"},"PeriodicalIF":0.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12277101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144683706","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":"Sex hormones and diets rich in polyunsaturated ω-6/ω-3 fatty acids modify microbiota distinctly in a mouse model of Alzheimer's disease.","authors":"Lara Ordoñez-Gutierrez, Francisco Wandosell","doi":"10.1017/gmb.2025.10005","DOIUrl":"10.1017/gmb.2025.10005","url":null,"abstract":"<p><p>There is considerable data suggesting that the gut microbiota (GM) contributes to health and regulates host immunity and influences brain function, findings with implications for neurodegenerative diseases, such as Alzheimer's Disease (AD). In the present study, using three non-fat diets with different ratios of unsaturated ω-6/ω-3 fatty acids (FAs)(high or low), we analyzed how minor differences in diet can affect the microbiota of amyloid precursor protein/Presenilin 1 transgenic (APP/PS1 [TG]) mice, a mice model of AD, next, we studied how the levels of sex hormones may affect the GM. The data obtained show that sex hormones in males fed our standard diet (S) modified alpha and beta diversity, whereas no differences were observed in TG mice compared with wild-type mice. Moreover, there were significant differences in both alpha or beta diversity in mice fed with an H or L diet compared with an S diet. In conclusion, our data indicate that the levels of sex hormones or differences in the ω-6/ω-3 FA ratio alter the GM more than expected. Thus, it is tantalizing to propose that low levels of ω-3 FAs in APP/PS1 mice fed an \"H\" diet may be responsible for modifying some bacterial genera, exacerbating the basal neuropathology in this AD model.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e10"},"PeriodicalIF":0.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700543","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":"The effect of dietary transition on infant microbiota composition and metabolic activity captured with the simulator of the human intestinal microbial ecosystem (SHIME).","authors":"Shadi Pakroo, Samira Soltani, Armin Tarrah, Gisèle LaPointe","doi":"10.1017/gmb.2025.10007","DOIUrl":"10.1017/gmb.2025.10007","url":null,"abstract":"<p><p>The Simulator of the Human Intestinal Microbial Ecosystem (SHIME) system was provided with baby feed for one week to stabilise the microbial community, followed by a 10-day period with baby feed and another 10-day period with adult feed. The study was conducted using sterilised and standardised feed formulations, which model dietary conditions in vitro. Following the transition from baby to adult feed, a significant reduction in the proportion of butyrate in comparison to total SCFA was found after transitioning to adult feed in both the transverse colon and distal colon bioreactors. Our findings suggest that abrupt early-life dietary changes from simple to complex carbohydrates as well as the exclusion of bovine milk proteins can transiently lower the ability of the microbiota to produce butyrate. The lack of additional microbial input leads to a delay or impairment of the adaptation to the modified feed composition. However, given the short treatment duration and sterilised feed composition, these findings should be interpreted within the limitations of this in vitro model. A reduction in butyrate concentration following the transition to adult feed may reflect a temporary shift in microbial metabolic activity rather than a long-term impact on energy extraction efficiency in vivo.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e9"},"PeriodicalIF":0.0,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12231521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144585689","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":"Exploration of novel bioactive compounds from the microbiome of fish and shellfish as an alternative to replace antibiotic drugs in aquaculture farming.","authors":"Arvind Diwan, Sanjay Harke, Archana N Panche","doi":"10.1017/gmb.2025.6","DOIUrl":"10.1017/gmb.2025.6","url":null,"abstract":"<p><p>The use of antibiotics in fish and shrimp aquaculture all over the world was found to be only partially successful in preventing infectious diseases. However, their overuse has resulted in the contamination of closed aquatic ecosystems, reduced antibiotic resistance in organisms that fight infectious diseases, and compromised the effectiveness of various antibiotic medications in controlling diseases. Excessive use of antibiotics damages aquaculture species and impacts human health, also rendering the most potent antibiotics increasingly ineffective, with limited alternatives. Therefore, intensive research efforts have been made to replace antibiotics with other protocols and methods like vaccines, phage therapy, quorum quenching technology, probiotics, prebiotics, chicken egg yolk antibody (IgY), and plant therapy,\" etc. Though all these methods have great potential, many of them are still in the experimental stage, except for fish vaccines. All these alternative technologies need to be carefully standardized and evaluated before implementation. In recent times, after realizing the importance of the gut microbiome community in maintaining the health of animals, efforts have been made to use the microbiome strains for the prevention of pathogenic bacterial and viral infections. Now it has been experimentally proven that animals should possess a healthy microbiome community in their gut tract to strengthen the immune system and prevent the entry of harmful pathogens. Investigations are now being carried out on the derivation of various bioactive compounds from the gut microbiome strains and their structural profile and functionality using the molecular tools of metagenomics and bioinformatics. Such newly discovered compounds from microbiomes can be used as potential alternatives to replace antibiotic drugs in the aquaculture industry. These alternatives are likely to emerge as breakthroughs in animal health management and farming, with effects on cost efficiency, species health, productivity, and yield enhancement. Therefore, introducing new micro-innovative technologies into an overall health management plan will be highly beneficial.</p>","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"6 ","pages":"e8"},"PeriodicalIF":0.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12179545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478129","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":"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}

{"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 10¹⁵ 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}

{"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}

{"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}