Asian Microbiome Project Phase 1_Gut Microbiota of healthy Beijing Children

Asia differs substantially among and within its regions populated by diverse ethnic groups, which maintain their own respective cultures and dietary habits. To address the diversity in the Asian gut microbiota that functions as an interface between the food that people eat and their health, we characterized the fecal bacterial community of 303 children living in urban and rural regions in five countries spanning temperate and tropical areas of Asia. We used 454-pyrotag sequencing and quantitative real-time PCR to classify and quantify bacterial 16S rRNA genes in feces. The variation of the microbiota profiled for the 303 children was diverged into two clusters exhibiting a tradeoff gradient between Prevotella and Bifidobacterium/Bacteroides. Most children from Japan and majority from China and Taiwan harbored a Bifidobacterium/Bacteroides-enriched type (BB-enterotype) microbiota, whereas children from Indonesia tended to harbor a Prevotella-enriched type (P-enterotype). Comparative analysis of the bacterial community structure indicated that the BB-enterotype contained comparatively fewer bacterial phylotypes in each child but varied among children. The P-enterotype was shaped by a relatively more conserved bacterial community that shared a higher number of phylotypes, in particular, a highly diversified phylogenetic group that is closely related to Prevotella copri. Random-forest analysis based on species-level fecal-bacterial composition segregated the samples from China, Japan, and Indonesia at a high probability, but filled the gaps between China and Japan and China and Indonesia with samples from Taiwan and Thailand, respectively, which mirrored the geographical location of these countries. The microbiota of children in Japan exhibited remarkably low diversity both within and among individuals, and contained notably reduced amounts of Enterobacteriaceae and certain other bacteria that are indicators of poor hygiene. These differences in the microbiota of Asian children might reflect their living environment and also their unique dietary habits.