Dataset Information

Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions.

ABSTRACT: Enterotypes are used for classifying individuals based on the gut microbiome. A number of studies are available to find the Enterotypes in healthy individuals; however, most of them lack comparisons at the world level. We analyzed the healthy human gut microbiomes of 495 datasets available in the European Nucleotide Archive (ENA) database derived from fifteen countries from four continents. Firmicutes and Bacteroidetes were the two most abundant phyla in the healthy human gut, worldwide. A high ratio of Proteobacteriato Actinobacteria and a low abundance of Prevotella were identified as the indicators of IBD. Prevotella, Bacteroides, and Bifidobacterium were identified as the Enterotypes in the inter-continental comparisons. At the intra-continental level, two (Bacteroides and Ruminococcaceae), four (Faecalibacterium, Bacteroides, Prevotella, and Clostridiales), and two (Prevotella, Bacteroides/Bifidobacterium) Enterotypes were identified in the American, European, and Asian continents, respectively. In addition, a high abundance of the unknown genus of Ruminococcaeae was observed in the Colombian human gut microbiome. A substantial impact of the geographical distance was observed on human gut microbiome variations, demonstrating a cumulative effect of factors, including dietary habits, genetics, lifestyle, environment, and climate, etc.

SUBMITTER: Mobeen F

PROVIDER: S-EPMC6563668 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions.

Mobeen Fauzul F Sharma Vikas V Tulika Prakash P

Bioinformation 20181229 9

Enterotypes are used for classifying individuals based on the gut microbiome. A number of studies are available to find the Enterotypes in healthy individuals; however, most of them lack comparisons at the world level. We analyzed the healthy human gut microbiomes of 495 datasets available in the European Nucleotide Archive (ENA) database derived from fifteen countries from four continents. Firmicutes and Bacteroidetes were the two most abundant phyla in the healthy human gut, worldwide. A high ...[more]

PMID: 31223215

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Project description:Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene.Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents.Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.

Dataset Information

Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions.

Publications

Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions.

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