Subsistence strategies in traditional societies distinguish gut microbiomes

Alexandra J. Obregon-Tito; Raul Y. Tito; Jessica Metcalf; Krithivasan Sankaranarayanan; Jose C. Clemente; Luke K. Ursell; Zhenjiang Zech Xu; Will Van Treuren; Rob Knight; Patrick M. Gaffney; Paul Spicer; Paul Lawson; Luis Marin-Reyes; Omar Trujillo-Villarroel; Morris Foster; Emilio Guija-Poma; Luzmila Troncoso-Corzo; Christina Warinner; Andrew T. Ozga; Cecil M. Lewis

doi:10.1038/ncomms7505

Subsistence strategies in traditional societies distinguish gut microbiomes

Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, Paul Spicer, Paul Lawson, Luis Marin-Reyes, Omar Trujillo-Villarroel, Morris Foster, Emilio Guija-Poma, Luzmila Troncoso-Corzo, Christina Warinner, Andrew T. Ozga, Cecil M. Lewis

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Abstract

Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth × 26-513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.

Original language	English
Article number	6505
Journal	Nature Communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms7505
State	Published - Mar 2015

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Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P. M., Spicer, P., Lawson, P., Marin-Reyes, L., Trujillo-Villarroel, O., Foster, M., Guija-Poma, E., Troncoso-Corzo, L., Warinner, C., Ozga, A. T., & Lewis, C. M. (2015). Subsistence strategies in traditional societies distinguish gut microbiomes. Nature Communications, 6, Article 6505. https://doi.org/10.1038/ncomms7505

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title = "Subsistence strategies in traditional societies distinguish gut microbiomes",

abstract = "Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth × 26-513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.",

author = "Obregon-Tito, {Alexandra J.} and Tito, {Raul Y.} and Jessica Metcalf and Krithivasan Sankaranarayanan and Clemente, {Jose C.} and Ursell, {Luke K.} and {Zech Xu}, Zhenjiang and {Van Treuren}, Will and Rob Knight and Gaffney, {Patrick M.} and Paul Spicer and Paul Lawson and Luis Marin-Reyes and Omar Trujillo-Villarroel and Morris Foster and Emilio Guija-Poma and Luzmila Troncoso-Corzo and Christina Warinner and Ozga, {Andrew T.} and Lewis, {Cecil M.}",

year = "2015",

month = mar,

doi = "10.1038/ncomms7505",

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journal = "Nature Communications",

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Obregon-Tito, AJ, Tito, RY, Metcalf, J, Sankaranarayanan, K, Clemente, JC, Ursell, LK, Zech Xu, Z, Van Treuren, W, Knight, R, Gaffney, PM, Spicer, P, Lawson, P, Marin-Reyes, L, Trujillo-Villarroel, O, Foster, M, Guija-Poma, E, Troncoso-Corzo, L, Warinner, C, Ozga, AT & Lewis, CM 2015, 'Subsistence strategies in traditional societies distinguish gut microbiomes', Nature Communications, vol. 6, 6505. https://doi.org/10.1038/ncomms7505

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AU - Obregon-Tito, Alexandra J.

AU - Tito, Raul Y.

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AU - Sankaranarayanan, Krithivasan

AU - Clemente, Jose C.

AU - Ursell, Luke K.

AU - Zech Xu, Zhenjiang

AU - Van Treuren, Will

AU - Knight, Rob

AU - Gaffney, Patrick M.

AU - Spicer, Paul

AU - Lawson, Paul

AU - Marin-Reyes, Luis

AU - Trujillo-Villarroel, Omar

AU - Foster, Morris

AU - Guija-Poma, Emilio

AU - Troncoso-Corzo, Luzmila

AU - Warinner, Christina

AU - Ozga, Andrew T.

AU - Lewis, Cecil M.

PY - 2015/3

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N2 - Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth × 26-513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.

AB - Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth × 26-513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.

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SN - 2041-1723

VL - 6

JO - Nature Communications

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Subsistence strategies in traditional societies distinguish gut microbiomes

Abstract

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