Gut microbiome changes in response to shifts from rural to urban environments of the Turkana community in Kenya.

Abstract

The human gut microbiome has emerged as an important factor in many traits, including those associated with human health. Change in diversity and community composition of the gut microbiome is linked continuously to various health implications; recently, we are witnessing the rise of a variety of complex diseases related to dramatic changes in daily environments that are maybe related to mismatches between human and microbial evolution as population transit from rural to urban areas. The human gut microbiome composition in industrialized populations is hypothesized to be different from those living in traditional lifestyles. To test this, I studied the Turkana community with an aim of finding out the gut microbiome variations of the traditional and urban group, and the various phenotypic factors that influence the changes. The Turkana gave me an opportunity to understand this, in that it is a unique Nilotic group in Kenya whose population has a common ancestry, but different levels of modernization. Some individuals live a traditional pastoralist lifestyle, while others are sedentary within the Turkana region or urban centers. The transitions from a pastoralist diet centered on meat, blood and milk to an urban diet rich in carbohydrates and fats can give a better understanding of the rising epidemic of chronic metabolic-related diseases around the world. I characterized fecal microbiota of 133 individuals from the Turkana community, 90 - traditional and 43 – urban by paired-end v4 region of 16s rRNA region in the Illumina MiSeq platform. With this data, I asked two main questions: 1) How does the community composition and diversity of the Turkana microbiome compare between traditional and urban groups? 2) How are changes in the microbiome associated with phenotypic variations and the environment? Community structure comparison of the traditional and urban population using UniFrac and Bray Curtis distances showed in the composition of gut microbiome between the two groups. Bacteroidetes, Firmicutes, and Proteobacteria were more abundant in the two populations; the Bacteroidetes were dominant in the urban population while the Firmicutes and Spirochetes dominated the traditional community. For alpha diversity, the traditional and urban people had a different microbial richness and Fisher diversity, but no observed differences with the Shannon and Simpson diversity measures. The ANCOVA correlation results showed that BMI, Age, blood pressure, and residence time in current location correlate microbial richness and Fisher diversity, but Cholesterol and HDL do not. But none of the phenotypes associated with Inverse Simpson, Shannon, and Simpson, could have resulted from not having the sample size necessary to perform the comparisons. In conclusion, the rural to urban areas transition has an impact on the gut microbiome both within and between the populations. I observed a gradual reduction in the microbial diversity in the Turkana population who've moved to urban areas. These, coupled with the loss of beneficial microbiome as has been observed in populations that transited to urban areas several years ago, indicate a possible increased risk to metabolic diseases. Therefore, Future studies should perform a complete sampling of both groups; and determine the metabolic profiles of every sample in order to provide a better understanding of the microbial community structure of the Turkana population.