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Gut microbiome transition across a lifestyle gradient in Himalaya

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...

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Autores principales: Jha, Aashish R., Davenport, Emily R., Gautam, Yoshina, Bhandari, Dinesh, Tandukar, Sarmila, Ng, Katharine M., Fragiadakis, Gabriela K., Holmes, Susan, Gautam, Guru Prasad, Leach, Jeff, Sherchand, Jeevan Bahadur, Bustamante, Carlos D., Sonnenburg, Justin L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237292/
https://www.ncbi.nlm.nih.gov/pubmed/30439937
http://dx.doi.org/10.1371/journal.pbio.2005396
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author Jha, Aashish R.
Davenport, Emily R.
Gautam, Yoshina
Bhandari, Dinesh
Tandukar, Sarmila
Ng, Katharine M.
Fragiadakis, Gabriela K.
Holmes, Susan
Gautam, Guru Prasad
Leach, Jeff
Sherchand, Jeevan Bahadur
Bustamante, Carlos D.
Sonnenburg, Justin L.
author_facet Jha, Aashish R.
Davenport, Emily R.
Gautam, Yoshina
Bhandari, Dinesh
Tandukar, Sarmila
Ng, Katharine M.
Fragiadakis, Gabriela K.
Holmes, Susan
Gautam, Guru Prasad
Leach, Jeff
Sherchand, Jeevan Bahadur
Bustamante, Carlos D.
Sonnenburg, Justin L.
author_sort Jha, Aashish R.
collection PubMed
description 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.
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spelling pubmed-62372922018-12-01 Gut microbiome transition across a lifestyle gradient in Himalaya Jha, Aashish R. Davenport, Emily R. Gautam, Yoshina Bhandari, Dinesh Tandukar, Sarmila Ng, Katharine M. Fragiadakis, Gabriela K. Holmes, Susan Gautam, Guru Prasad Leach, Jeff Sherchand, Jeevan Bahadur Bustamante, Carlos D. Sonnenburg, Justin L. PLoS Biol Research Article 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. Public Library of Science 2018-11-15 /pmc/articles/PMC6237292/ /pubmed/30439937 http://dx.doi.org/10.1371/journal.pbio.2005396 Text en © 2018 Jha et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Jha, Aashish R.
Davenport, Emily R.
Gautam, Yoshina
Bhandari, Dinesh
Tandukar, Sarmila
Ng, Katharine M.
Fragiadakis, Gabriela K.
Holmes, Susan
Gautam, Guru Prasad
Leach, Jeff
Sherchand, Jeevan Bahadur
Bustamante, Carlos D.
Sonnenburg, Justin L.
Gut microbiome transition across a lifestyle gradient in Himalaya
title Gut microbiome transition across a lifestyle gradient in Himalaya
title_full Gut microbiome transition across a lifestyle gradient in Himalaya
title_fullStr Gut microbiome transition across a lifestyle gradient in Himalaya
title_full_unstemmed Gut microbiome transition across a lifestyle gradient in Himalaya
title_short Gut microbiome transition across a lifestyle gradient in Himalaya
title_sort gut microbiome transition across a lifestyle gradient in himalaya
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237292/
https://www.ncbi.nlm.nih.gov/pubmed/30439937
http://dx.doi.org/10.1371/journal.pbio.2005396
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