Gut microbiome transition across a lifestyle gradient in Himalaya

Abstract

The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle. Whether shifts away from the foraging lifestyle that characterize much of humanity’s past influence the gut microbiome, and to what degree, remains unclear. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in traditional human lifestyles. These groups led seminomadic hunting–gathering lifestyles until transitioning to varying levels of agricultural dependence upon farming. The Tharu began farming 250–300 years ago, the Raute and Raji transitioned 30–40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut-associated microbes and find that differences in the lifestyles of Himalayan foragers and farmers are strongly correlated with microbial community variation. Furthermore, the gut microbiomes of all four traditional Himalayan populations are distinct from that of the Americans, indicating that industrialization may further exacerbate differences in the gut community. The Chepang foragers harbor an elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of the populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. The gut microbiomes of Raute and Raji reveal an intermediate state between the Chepang and Tharu, indicating that divergence from a stereotypical foraging microbiome can occur within a single generation. Our results also show that environmental factors such as drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across lifestyles. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of determining how large-scale gut microbiome reconfiguration impacts human biology.

Vulnerability of the industrialized microbiota

“…1A) (30). A study comparing the industrialized microbiota with that of three Nepalese populations living on a gradient from foraging to farming showed the shift in microbiota composition that takes place as populations depart from a foraging lifestyle (31). Intermediate states of lifestyle change toward urbanization are accompanied by less extreme but evident changes in the microbiota (Fig.…”

“…The recent shift to consuming largely sterile food and water has likely also influenced the microbiota. For example, the source of drinking water was significantly associated with microbiota composition in the cross-sectional study of Nepalese individuals living on a lifestyle gradient, as well as the Hadza (31). As industrial populations removed microbes from drinking water, the burden of diseases such as cholera and other waterborne illnesses decreased.…”

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach

“…A catalogue of microbes and their entire genomic contents in a particular environment is known as the microbiome. Recent studies in humans have demonstrated that the gut microbiome is influenced by lifestyle, likely due to differences in diet and environment associated with human subsistence [1][2][3][4] and that it plays an important role in health and disease [5][6][7]. There are many similarities between human and pet microbiomes [8] and emerging evidence suggests that gut microbiota may also act as an important regulator of health and diseases in household pets [9][10][11][12].…”

Problems with the concept of gut microbiota dysbiosis

“…Indeed, six per cent of the Hadzas showed Treponemas also in the serum samples, raising further doubts about their overall health status. While we have data that show how microbiota composition changes occur in a genetically homogenous population transitioning to different food production systems, we still lack data on how these changes affect human physiology and health along this gradient (Jha et al, 2018).…”