Abstract
Human gut microbiota plays important roles in harvesting energy from the diet, stimulating the proliferation of the intestinal epithelium, developing the immune system, and regulating fat storage in the host. Characterization of gut microbiota, however, has been limited to western people and is not sufficiently extensive to fully describe microbial communities. In this study, we investigated the overall composition of the gut microbiota and its host specificity and temporal stability in 20 Koreans using 454-pyrosequencing with barcoded primers targeting the V1 to V3 region of the bacterial 16S rRNA gene. A total of 303,402 high quality reads covered each sample and 8,427 reads were analyzed on average. The results were compared with those of individuals from the USA, China and Japan. In general, microbial communities were dominated by five previously identified phyla: Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Proteobacteria. UPGMA cluster analysis showed that the species composition of gut microbiota was host-specific and stable over the duration of the test period, but the relative abundance of each member fluctuated. 43 core Korean gut microbiota were identified by comparison of sequences from each individual, of which 15 species level phylotypes were related to previously-reported butyrate-producing bacteria. UniFrac analysis revealed that human gut microbiota differed between countries: Korea, USA, Japan and China, but tended to vary less between individual Koreans, suggesting that gut microbial composition is related to internal and external characteristics of each country member such as host genetics and diet styles.
Highlights
After the completion of the Human Genome Project (HGP), many scientists were disappointed by the announcement that the human genome contained only around 20,000 protein coding genes rather than the 100,000 originally estimated because the number of gene was thought to be insufficient to solve the mysteries of human health and disease
For the estimation of gut microbial diversity, all the pyrosequencing reads were subjected to operational taxonomic unit (OTU) determination
When all sequences were clustered with representatives under conditions demanding 90% to 100% sequence identity, the number of operational taxonomic units (OTUs) varied between 2,284 and 62,095 (Figure S1)
Summary
After the completion of the Human Genome Project (HGP), many scientists were disappointed by the announcement that the human genome contained only around 20,000 protein coding genes rather than the 100,000 originally estimated because the number of gene was thought to be insufficient to solve the mysteries of human health and disease. The colon contains between 1011 and 1012 microbial cells per ml and this extremely high population density is associated with a number of total genes that is two orders of magnitude higher than that contained in the human genome [3]. Recent study estimated 9,000,000 unique human gut microbial genes with culture-independent sequence data and complete human gut bacterial genomes [4]. Co-evolution with these great microbial ecosystems serves important functions for the human host by presenting nutrients from diets [5], resisting the colonization of pathogens [6], stimulating the proliferation of the intestinal epithelium [7], and regulating fat storage [8]. Numerous diseases, including type 1 diabetes (T1D) [9], inflammatory bowel disease (IBD) [10], and gastric and colonic cancers [11,12], have been shown to be linked to dysbiosis of microbial communities
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