The Microbiome Snapshot

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Article by: Erin Carpenter

OMNIgene·GUT facilitating gut microbial collections in remote Himalayan populations


There is so much that can be learned from studying the gut microbiome. The community of bacteria co-habiting with their human host share a curious symbiotic relationship, one that can have a significant affect on health. This is a complex relationship where the abundance and diversity of the microbiome can affect various aspects of human physiology, metabolism, immune response, and psychology. Conversely, many factors within the human host’s control can alter the microbial community, even causing extinction events, such as dietary changes, geographical location, lifestyle, or antibiotic use. When this delicate balance is shifted, this may result in consequences for the host’s health. Therefore, it is essential to characterize the human microbiome and understand what factors alter this complex, reciprocal relationship.

In a recent publication by Aashish Jha and colleagues titled Gut microbiome transition across a lifestyle gradient in Himalaya, the researchers wanted to understand whether differences in traditional lifestyle affect the human gut microbiome and to assess which of the lifestyle associated dietary and environmental factors are associated with the gut bacterial composition.* They had a unique opportunity to study four remote Himalayan populations who shared similar ancestry, cohabited within a small geographical location in the Himalayan foothills, and, until recently, had similar diets and lifestyles. Only within the previous couple of centuries did these tribes transition at varying degrees from seminomadic hunting and gathering to more agrarian means. These tribes represent an interesting human study model to reduce the potential confounding variables of genetics and geographical location, both known to affect microbial populations, in order to better understand how lifestyle and diet influence the gut microbiome.  

The Himalayan populations included in this study were the Chepang, Raute, Raji and Tharu, listed in order of increasing dependence on agriculture. The researchers utilized a customized questionnaire to obtain detailed information regarding the ethno-linguistic, demographic, dietary, behavioural and environmental data of every participant.

In each participant, the gut microbiome needed to be characterized by collecting, transporting and interrogating stool samples. Since the four Himalayan tribes were located in remote areas, cold chain transport was not an available option. Without the ability to freeze samples, it was imperative to capture a snapshot of the bacterial community by preserving the specimens by other methods. The solution was to collect a fresh stool sample using the OMNIgene·GUT fecal collection device (DNA Genotek), allowing the sample to be safely transported at room temperature to Tribhuvan University Institute of Medicine, Kathmandu, where it underwent 16S rRNA sequencing and analysis.

The results of this study were very interesting. As you may have predicted, there was a difference in the beta diversity of the microbial samples from each of the populations studied. There was an observable gradient of beta diversity that mirrored the transition from a traditional foraging diet to a more modern agrarian diet illustrated by the four tribes, indicating that lifestyle strongly influences the gut microbiome even in the absence of industrialism. What was truly surprising, however, was the influence of environmental factors on the microbiome. The results showed that drinking water source and the use of solid cooking fuels were significantly associated with the gut microbiome composition. Furthermore, the alpha diversity did not differ significantly among the four tribes, nor did it differ when the Himalayan tribes were compared relative to the American population. This finding actually conflicts with previous studies showing a higher alpha diversity in traditional populations when compared to westerners. These previous studies, however, typically compared traditional populations in tropical locations to modern populations at different geographical latitudes, which might help to explain the difference. Tropical climates tend to foster higher levels of biodiversity within the environment, which lends itself to greater microbial exposures from diet and daily life.

This study was able to illustrate the adaptation of the human gut microbiome in response to lifestyle and dietary changes from a traditional foraging existence to an agriculturally-dependent and relatively more modern way of life, and was able to largely circumvent the confounders of genetics and geography. This research is incredibly important to ultimately understand how the microbiome and ecosystem interact, and the implications for population health in industrialized modern populations that lack these microbes.

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Jha AR et al. Gut microbiome transition across a lifestyle gradient in Himalaya. BioRxiv. Epub ahead of print (2018). doi:

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