Diversity and enterotype in gut bacterial community of adults in Taiwan

Abstract

BackgroundGastrointestinal microbiota, particularly gut microbiota, is associated with human health. The biodiversity of gut microbiota is affected by ethnicities and environmental factors such as dietary habits or medicine intake, and three enterotypes of the human gut microbiome were announced in 2011. These enterotypes are not significantly correlated with gender, age, or body weight but are influenced by long-term dietary habits. However, to date, only two enterotypes (predominantly consisting of Bacteroides and Prevotella) have shown these characteristics in previous research; the third enterotype remains ambiguous. Understanding the enterotypes can improve the knowledge of the relationship between microbiota and human health.ResultsWe obtained 181 human fecal samples from adults in Taiwan. Microbiota compositions were analyzed using next-generation sequencing (NGS) technology, which is a culture-independent method of constructing microbial community profiles by sequencing 16S ribosomal DNA (rDNA). In these samples, 17,675,898 sequencing reads were sequenced, and on average, 215 operational taxonomic units (OTUs) were identified for each sample. In this study, the major bacteria in the enterotypes identified from the fecal samples were Bacteroides, Prevotella, and Enterobacteriaceae, and their correlation with dietary habits was confirmed. A microbial interaction network in the gut was observed on the basis of the amount of short-chain fatty acids, pH value of the intestine, and composition of the bacterial community (enterotypes). Finally, a decision tree was derived to provide a predictive model for the three enterotypes. The accuracies of this model in training and independent testing sets were 97.2 and 84.0%, respectively.ConclusionsWe used NGS technology to characterize the microbiota and constructed a predictive model. The most significant finding was that Enterobacteriaceae, the predominant subtype, could be a new subtype of enterotypes in the Asian population.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3261-6) contains supplementary material, which is available to authorized users.

Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities

“…In another context, some studies reported that Ruminococcus was a major ecotype [ 30 – 32 ], including one which analyzed data from native populations from different countries [ 33 ]. In particular, Enterobacteriaceae belonged to the third major ecotype among Taiwanese [ 34 ]. However, these discrepancies need to be clarified with more attention to sample size, and sampling methods and variations.…”

Comparative genomics of Bifidobacterium species isolated from marmosets and humans

“…However, closer examination shows that the predominant species are different among the three marmoset colonies considered in this study (Figure ). Studies that view microbiomes with similar distributions of phyla or genera as an “enterotype” may tend to overlook important variation within members of the enterotype (Arumugam et al, ; Koren et al, ; Liang et al, ; Wu et al, ). For instance, putative aliphatic sulfonate ABC transporter genes were found in B. callitrichos and not in B. reuteri (Figure ) , and there are >500 other proteins that are not shared between strains of these two species (Figure ).…”

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“…Recently, some metagenome‐wide association studies (MGWAS) showed that the variations in human genome are associated with certain microbiome signature . The human enterotypes are determined by gut microbiota composition and have been suggested to be associated with response to diet . The taxonomic composition, richness, diversity and temporal stability may contribute to distinct functional properties in different enterotypes .…”

“…For example, while the PBS or normal saline were generally used for dilution of probiotics, some studies used the skim milk for resuspension 52 or generation of fermented milk 41,46 (Table 1) 60 Recently, some metagenome-wide association studies (MGWAS) showed that the variations in human genome are associated with certain microbiome signature. 61,62 The human enterotypes are determined by gut microbiota composition 63,64 and have been suggested to be associated with response to diet. 65 The taxonomic composition, richness, diversity and temporal stability may contribute to distinct functional properties in different enterotypes.…”