Gut microbiome (Cambridge, England)最新文献_第3页

MetaFunc: Taxonomic and Functional Analyses of High Throughput Sequencing for Microbiomes MetaFunc:微生物组高通量测序的分类和功能分析

Gut microbiome (Cambridge, England) Pub Date : 2023-01-01 DOI: 10.1017/gmb.2022.12

Arielle Kae Sulit, Tyler Kolisnik, Frank A Frizelle, Rachel Purcell, Sebastian Schmeier

{"title":"MetaFunc: Taxonomic and Functional Analyses of High Throughput Sequencing for Microbiomes","authors":"Arielle Kae Sulit, Tyler Kolisnik, Frank A Frizelle, Rachel Purcell, Sebastian Schmeier","doi":"10.1017/gmb.2022.12","DOIUrl":"https://doi.org/10.1017/gmb.2022.12","url":null,"abstract":"Abstract The identification of functional processes taking place in microbiome communities augment traditional microbiome taxonomic studies, giving a more complete picture of interactions taking place within the community. While there are applications that perform functional annotation on metagenomes or metatranscriptomes, very few of these are able to link taxonomic identity to function or are limited by their input types or databases used. Here we present MetaFunc, a workflow which takes RNA sequences as input reads, and from these (1) identifies species present in the microbiome sample and (2) provides gene ontology annotations associated with the species identified. In addition, MetaFunc allows for host gene analysis, mapping the reads to a host genome, and separating these reads, prior to microbiome analyses. Differential abundance analysis for microbe taxonomies, and differential gene expression analysis and gene set enrichment analysis may then be carried out through the pipeline. A final correlation analysis between microbial species and host genes can also be performed. Finally, MetaFunc builds an R shiny application that allows users to view and interact with the microbiome results. In this paper, we showed how MetaFunc can be applied to metatranscriptomic datasets of colorectal cancer.","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135077882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Towards the characterization of sustainable diet’s gut microbiota composition and functions 可持续饮食肠道菌群组成及功能的研究

Gut microbiome (Cambridge, England) Pub Date : 2023-01-01 DOI: 10.1017/gmb.2023.13

Mariana Lares-Michel, Zyanya Reyes-Castillo, Fatima Ezzahra Housni

{"title":"Towards the characterization of sustainable diet’s gut microbiota composition and functions","authors":"Mariana Lares-Michel, Zyanya Reyes-Castillo, Fatima Ezzahra Housni","doi":"10.1017/gmb.2023.13","DOIUrl":"https://doi.org/10.1017/gmb.2023.13","url":null,"abstract":"Abstract The gut microbiome is a key element for health preservation and disease prevention. Nevertheless, defining a healthy gut microbiome is complex since it is modulated by several factors, such as host genetics, sex, age, geographical zone, drug use, and, especially, diet. Although a healthy diet has proven to increase microbial alpha and beta diversity and to promote the proliferation of health-related bacteria, considering the current environmental and nutritional crisis, such as climate change, water shortage, loss of diversity, and the obesity pandemic, it should be highlighted that a healthy diet is not always sustainable. Sustainable diets are dietary patterns that promote all dimensions of people’s health and well-being while exerting low pressure on the environment, and being accessible, affordable, safe, equitable, and culturally acceptable. Examples of diets that tend to be sustainable are the Planetary Health Diet of the EAT-Lancet Commission or territorial diets such as the Mediterranean and the Traditional Mexican diet (milpa diet), adapted to specific contexts. These diets are principally plant-based but include small or moderate amounts of animal-based foods. Characterising the effects of sustainable diets on gut microbiota is urgent to ensure that the benefits for human health are aligned with environmental preservation and respect the sociocultural aspects of individuals.","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135360957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gut physiology meets microbiome science. 肠道生理学与微生物组科学的结合。

Gut microbiome (Cambridge, England) Pub Date : 2022-12-12 eCollection Date: 2023-01-01 DOI: 10.1017/gmb.2022.10

Hannelore Daniel

{"title":"Gut physiology meets microbiome science.","authors":"Hannelore Daniel","doi":"10.1017/gmb.2022.10","DOIUrl":"https://doi.org/10.1017/gmb.2022.10","url":null,"abstract":"Research on the gut microbiome has gained high popularity and almost every disease has meanwhile been linked to alterations in microbiome composition. Typically assessed via stool samples, the microbiome displays a huge diversity with a multitude of environmental parameters already identified as contributing to its character. Despite impressive scientific progress, normal microbiome diversity remains largely unexplained and it is tempting to speculate some of the yet unexplained variance is hidden in normal gut physiology. Although a few genome/phenome-wide associations studies have recently highlighted physiological parameters such as stool frequency, known as contributing to microbiome diversity, there is a large knowledge base from decades of basic research on gut functions that can be explored for possible links to stool features and microbiome characteristics. And, when extrapolating findings from faecal samples to the biology in the intestinal lumen or the mucosal microenvironment, gut anatomy and physiology features need to be considered. Similarly, differences in anatomy and physiology between rodents and humans need attention when discussing findings in animals in relation to human physiology and nutrition.","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"4 ","pages":"e1"},"PeriodicalIF":0.0,"publicationDate":"2022-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302554","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

Determining the metabolic fate of human milk oligosaccharides: it may just be more complex than you think? 确定母乳低聚糖的代谢命运：它可能比你想象的更复杂？

Gut microbiome (Cambridge, England) Pub Date : 2022-09-07 eCollection Date: 2022-01-01 DOI: 10.1017/gmb.2022.8

Peter Philip James Jackson, Anisha Wijeyesekera, Robert Adrian Rastall

引用次数: 0

Modulating the gut microenvironment as a treatment strategy for irritable bowel syndrome: a narrative review. 调节肠道微环境作为肠易激综合征的治疗策略:叙述性回顾

Gut microbiome (Cambridge, England) Pub Date : 2022-08-25 eCollection Date: 2022-01-01 DOI: 10.1017/gmb.2022.6

Cristina Iribarren, Lujain Maasfeh, Lena Öhman, Magnus Simrén

引用次数: 0

The microbiome in adult acute appendicitis. 成人急性阑尾炎的微生物组

Gut microbiome (Cambridge, England) Pub Date : 2022-08-04 eCollection Date: 2022-01-01 DOI: 10.1017/gmb.2022.7

Mei Sze Lee, Arielle Sulit, Frank Frizelle, Rachel Purcell

{"title":"The microbiome in adult acute appendicitis.","authors":"Mei Sze Lee, Arielle Sulit, Frank Frizelle, Rachel Purcell","doi":"10.1017/gmb.2022.7","DOIUrl":"10.1017/gmb.2022.7","url":null,"abstract":"Acute appendicitis is a common acute surgical emergency; however, the pathogenesis of adult appendicitis remains poorly understood. The microbiome is increasingly thought to play a key role in inflammatory disease of the bowel and similarly, may play a role in appendicitis. This study aimed to characterise the microbiome of adult acute appendicitis in a prospective cohort. We recruited 60 adults with acute appendicitis and 20 healthy controls. Rectal swabs were taken from each patient. After DNA extraction, 16S rRNA amplicon sequencing was carried out for analysis of diversity and taxonomic abundance. Phylogenetic sequencing of the samples indicated that there is a difference between the microbial composition of those with acute appendicitis and healthy controls, with a statistically significant decrease in alpha diversity in rectal swabs of appendicitis patients compared to healthy controls. At the genus level, we saw an increased abundance of potential pathogens, for example, Parvimonas and Acinetobacter, and a decrease in commensal taxa such as Faecalibacterium, Blautia and Lachnospiraceae in appendicitis patients compared to healthy controls. There was a reduction in diversity and loss of commensals in the microbiome of those with acute appendicitis, which may play a role in the cascade leading to acute appendicitis or the result of this.","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":" ","pages":"e8"},"PeriodicalIF":0.0,"publicationDate":"2022-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47023191","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

Alterations in infant gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME technology. 接触草甘膦和 Roundup 和/或使用 SHIME 技术的孢子制剂后，婴儿肠道微生物组的组成和代谢发生变化。

Gut microbiome (Cambridge, England) Pub Date : 2022-07-26 eCollection Date: 2022-01-01 DOI: 10.1017/gmb.2022.5

Robin Mesnage, Marta Calatayud, Cindy Duysburgh, Massimo Marzorati, Michael N Antoniou

{"title":"Alterations in infant gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME technology.","authors":"Robin Mesnage, Marta Calatayud, Cindy Duysburgh, Massimo Marzorati, Michael N Antoniou","doi":"10.1017/gmb.2022.5","DOIUrl":"https://doi.org/10.1017/gmb.2022.5","url":null,"abstract":"Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. We describe the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology. SHIME microbiota culture was undertaken in the presence of a concentration of 100-mg/L glyphosate and the same glyphosate equivalent concentration of Roundup. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large-scale disturbances, including an increased abundance of long-chain polyunsaturated fatty acids. Changes in bacterial composition measured by qPCR and 16S rRNA suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota.","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"3 ","pages":"e6"},"PeriodicalIF":0.0,"publicationDate":"2022-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302555","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

Microbial lactate utilisation and the stability of the gut microbiome. 微生物乳酸利用率和肠道微生物组的稳定性

Gut microbiome (Cambridge, England) Pub Date : 2022-05-04 eCollection Date: 2022-01-01 DOI: 10.1017/gmb.2022.3

Petra Louis, Sylvia Helen Duncan, Paul Owen Sheridan, Alan William Walker, Harry James Flint

{"title":"Microbial lactate utilisation and the stability of the gut microbiome.","authors":"Petra Louis, Sylvia Helen Duncan, Paul Owen Sheridan, Alan William Walker, Harry James Flint","doi":"10.1017/gmb.2022.3","DOIUrl":"10.1017/gmb.2022.3","url":null,"abstract":"The human large intestinal microbiota thrives on dietary carbohydrates that are converted to a range of fermentation products. Short-chain fatty acids (acetate, propionate and butyrate) are the dominant fermentation acids that accumulate to high concentrations in the colon and they have health-promoting effects on the host. Although many gut microbes can also produce lactate, it usually does not accumulate in the healthy gut lumen. This appears largely to be due to the presence of a relatively small number of gut microbes that can utilise lactate and convert it to propionate, butyrate or acetate. There is increasing evidence that these microbes play important roles in maintaining a healthy gut environment. In this review, we will provide an overview of the different microbes involved in lactate metabolism within the gut microbiota, including biochemical pathways utilised and their underlying energetics, as well as regulation of the corresponding genes. We will further discuss the potential consequences of perturbation of the microbiota leading to lactate accumulation in the gut and associated disease states and how lactate-utilising bacteria may be employed to treat such diseases.","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":" ","pages":"e3"},"PeriodicalIF":0.0,"publicationDate":"2022-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47263021","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

Dried chicory root improves bowel function, benefits intestinal microbial trophic chains and increases faecal and circulating short chain fatty acids in subjects at risk for type 2 diabetes. 干菊苣根改善肠道功能，有益于肠道微生物营养链，并增加2型糖尿病患者的粪便和循环短链脂肪酸

Gut microbiome (Cambridge, England) Pub Date : 2022-04-28 eCollection Date: 2022-01-01 DOI: 10.1017/gmb.2022.4

Marie-Luise Puhlmann, Roosa Jokela, Katja Catharina Wilhelmina van Dongen, Thi Phuong Nam Bui, Roland Willem Jan van Hangelbroek, Hauke Smidt, Willem Meindert de Vos, Edith Johanna Maria Feskens

{"title":"Dried chicory root improves bowel function, benefits intestinal microbial trophic chains and increases faecal and circulating short chain fatty acids in subjects at risk for type 2 diabetes.","authors":"Marie-Luise Puhlmann, Roosa Jokela, Katja Catharina Wilhelmina van Dongen, Thi Phuong Nam Bui, Roland Willem Jan van Hangelbroek, Hauke Smidt, Willem Meindert de Vos, Edith Johanna Maria Feskens","doi":"10.1017/gmb.2022.4","DOIUrl":"10.1017/gmb.2022.4","url":null,"abstract":"We investigated the impact of dried chicory root in a randomised, placebo-controlled trial with 55 subjects at risk for type 2 diabetes on bowel function, gut microbiota and its products, and glucose homeostasis. The treatment increased stool softness (+1.1 ± 0.3 units; p = 0.034) and frequency (+0.6 ± 0.2 defecations/day; p < 0.001), strongly modulated gut microbiota composition (7 % variation; p = 0.001), and dramatically increased relative levels (3-4-fold) of Anaerostipes and Bifidobacterium spp., in a dose-dependent, reversible manner. A synthetic community, including selected members of these genera and a Bacteroides strain, generated a butyrogenic trophic chain from the product. Faecal acetate, propionate and butyrate increased by 25.8 % (+13.0 ± 6.3 mmol/kg; p = 0.023) as did their fasting circulating levels by 15.7 % (+7.7 ± 3.9 μM; p = 0.057). In the treatment group the glycaemic coefficient of variation decreased from 21.3 ± 0.94 to 18.3 ± 0.84 % (p = 0.004), whereas fasting glucose and HOMA-ir decreased in subjects with low baseline Blautia levels (-0.3 ± 0.1 mmol/L fasting glucose; p = 0.0187; -0.14 ± 0.1 HOMA-ir; p = 0.045). Dried chicory root intake rapidly and reversibly affects bowel function, benefits butyrogenic trophic chains, and promotes glycaemic control.","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":"3 1","pages":"e4"},"PeriodicalIF":0.0,"publicationDate":"2022-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11407914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45022875","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

Involvement of microbiota and short-chain fatty acids on non-alcoholic steatohepatitis when induced by feeding a hypercaloric diet rich in saturated fat and fructose. 喂食富含饱和脂肪和果糖的高热量饮食诱导的非酒精性脂肪性肝炎与微生物群和短链脂肪酸的关系

Gut microbiome (Cambridge, England) Pub Date : 2022-04-08 eCollection Date: 2022-01-01 DOI: 10.1017/gmb.2022.2

Iñaki Milton-Laskibar, Laura Judith Marcos-Zambrano, Saioa Gómez-Zorita, Enrique Carrillo de Santa Pau, Alfredo Fernández-Quintela, Jose Alfredo Martínez, María Puy Portillo

{"title":"Involvement of microbiota and short-chain fatty acids on non-alcoholic steatohepatitis when induced by feeding a hypercaloric diet rich in saturated fat and fructose.","authors":"Iñaki Milton-Laskibar, Laura Judith Marcos-Zambrano, Saioa Gómez-Zorita, Enrique Carrillo de Santa Pau, Alfredo Fernández-Quintela, Jose Alfredo Martínez, María Puy Portillo","doi":"10.1017/gmb.2022.2","DOIUrl":"10.1017/gmb.2022.2","url":null,"abstract":"Consumption of high-energy-yielding diets, rich in fructose and lipids, is a factor contributing to the current increase in non-alcoholic fatty liver disease prevalence. Gut microbiota composition and short-chain fatty acids (SCFAs) production alterations derived from unhealthy diets are considered putative underlying mechanisms. This study aimed to determine relationships between changes in gut microbiota composition and SCFA levels by comparing rats featuring diet-induced steatohepatitis with control counterparts fed a standard diet. A high-fat high-fructose (HFHF) feeding induced higher body, liver and mesenteric adipose tissue weights, increased liver triglyceride content and serum transaminase, glucose, non-HDL-c and MCP-1 levels. Greater liver malondialdehyde levels and glutathione peroxidase activity were also observed after feeding the hypercaloric diet. Regarding gut microbiota composition, a lowered diversity and increased abundances of bacteria from the Clostridium sensu stricto 1, Blautia, Eubacterium coprostanoligenes group, Flavonifractor, and UBA1819 genera were found in rats featuring diet-induced steatohepatitis, as well as higher isobutyric, valeric and isovaleric acids concentrations. These results suggest that hepatic alterations produced by a hypercaloric HFHF diet may be related to changes in overall gut microbiota composition and abundance of specific bacteria. The shift in SCFA levels produced by this unbalanced diet cannot be discarded as potential mediators of the reported hepatic and metabolic alterations.","PeriodicalId":73187,"journal":{"name":"Gut microbiome (Cambridge, England)","volume":" ","pages":"e5"},"PeriodicalIF":0.0,"publicationDate":"2022-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48271976","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