Population Stratification in the Gut Microbiota of Bali is Associated with Transitional Lifestyle

Abstract

Background: Human living conditions, such as food availability and the built environment, contribute to environmental forces that influence gut microbiota composition. Understanding the impact of the environment on microbiota assembly and its association with human health has multiple potential applications. Indonesia is a densely populated country that has been undergoing a dramatic societal change for the past two decades. It is distinctive in that it occupies an archipelago that imposes diverse geographic and cultural boundaries. The relationship between diet, microbiota, and health is poorly known in Indonesians and represents a natural study for the interaction between ethnogeographic factors and nutrition in microbiota assembly. Results: Here we show the first comprehensive report of the gut microbiota in adults from Bali, Indonesia (n=41). Their microbiotas clustered into two distinct community types: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community. The Type-P individuals had lower alpha diversity (p <0.001, Shannon) and more incidence of obesity. The two community types are significantly different in their inter-genus co-abundance pattern (p <0.001, ANOSIM, Wilcoxon test). Further analyses with diet and obesity data showed that the presence of two distinct community types in Bali is a significant confounder for identifying health markers. In a multi-country dataset (n=257), the Bali microbiota indicates a transitional state from a subsistent (Prevotella-dominant) to industrial (Bacteroides-dominant) society. The two largest axes in a Principal Coordinate Analysis of weighted UniFrac distance explained the majority of variance between samples across countries (49.1%). Microbial dissimilarity across populations is significantly associated with Prevotella and Bacteriodes abundance (p <0.001, Generalized Additive Model). Conclusion: Our data showed that lifestyle transitions have a strong influence on the frequency of microbiota community types in a population. The Bali microbiota is undergoing a shift towards a Bacteroides-dominant community which reflects the ongoing transition of nutrition, socio-economy, and lifestyle the society. Although enterotypes obscured the detection of health markers, our findings collectively suggest that enterotypes may be useful in future studies for informing population-level stratification in large heterogenetic datasets.

US Immigration Westernizes the Human Gut Microbiome

“…Previous work has established that diet and geographical environment are two principal determinants of microbiome structure and function (De Filippo et al, 2010; Febinia, 2017; Gomez et al, 2016; Kwok et al, 2014; Obregon-Tito et al, 2015; Rothschild et al, 2018; Schnorr et al, 2014; Yatsunenko et al, 2012). Rural indigenous populations have been found to harbor substantial biodiversity in their gut microbiomes, including novel microbial taxa not found in industrialized populations (Clemente et al, 2015; Gomez et al, 2016; Obregon-Tito et al, 2015; Schnorr et al, 2014; Smits et al, 2017; Yatsunenko et al, 2012).…”