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Subsistence strategies in traditional societies distinguish gut microbiomes.

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 - Nat Commun (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA [2] Universidad Científica del Sur, Lima 18, Perú [3] City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA.

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.

No MeSH data available.


Comparison of the gut microbiomes of Matses, Tunapuco and Norman populations to published data from hunter-gatherer, rural agriculturalist and urban-industrial communities.Analyses were performed on genus-level taxa tables rarefied to 4,000 reads per sample. (a) Principal coordinate analysis of Bray–Curtis distances generated from taxa tables summarized at the genus level. Proportion of variance explained by each principal coordinate axis is denoted in the corresponding axis label. Populations are colour coded by subsistence strategy. Data sets are represented by triangles (this study), circles (Yatsunenko et al.3), and squares (Schnorr et al.1). Ellipses correspond to 95% confidence boundaries for each of the three subsistence categories. (b) Results from Bayesian source-tracking analysis. Source contributions are averaged across samples within the population. (c) Results from Bayesian source tracking for individual samples.
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f3: Comparison of the gut microbiomes of Matses, Tunapuco and Norman populations to published data from hunter-gatherer, rural agriculturalist and urban-industrial communities.Analyses were performed on genus-level taxa tables rarefied to 4,000 reads per sample. (a) Principal coordinate analysis of Bray–Curtis distances generated from taxa tables summarized at the genus level. Proportion of variance explained by each principal coordinate axis is denoted in the corresponding axis label. Populations are colour coded by subsistence strategy. Data sets are represented by triangles (this study), circles (Yatsunenko et al.3), and squares (Schnorr et al.1). Ellipses correspond to 95% confidence boundaries for each of the three subsistence categories. (b) Results from Bayesian source-tracking analysis. Source contributions are averaged across samples within the population. (c) Results from Bayesian source tracking for individual samples.

Mentions: Finally, we compared genus-level taxa abundance profiles between our populations, and those from two previous studies of remote agrarian and hunter-gatherer human gut microbiomes13. PCoA of a Bray–Curtis distance matrix generated from genus-level taxa tables shows a clear separation between traditional and urban-industrial microbiomes (Fig. 3a), consistent across the three different studies. In addition, the hunter-gatherer populations (Matses and Hadza) form a distinct sub-cluster nested within the other traditional populations (Tunapuco, Venezuela and Malawi). To further explore this trend, we performed Bayesian source tracking8 on the Matses, Tunapuco and Norman samples using the previously published data sets as source populations (traditional hunter-gatherer: Hadza; rural agriculturalist: Venezuela, Malawi; and urban-industrial: USA, Italy; Fig. 3b). Consistent with previous analyses, the urban sources formed the primary contribution (~84% average) to the Norman samples, while the combined rural and hunter-gatherer sources accounted for ~95–98% for the Tunapuco and Matses samples. Specifically, the Matses samples had a higher contribution (~58%) from the Hadza hunter-gatherer source, while the Tunapuco samples had a higher contribution (~66%) from the rural Venezuela and Malawi source. Within populations, individuals show variation (Fig. 3c), but overall between ~64 and 85% of individuals have profiles consistent with their subsistence strategy. Thus, while the studies were conducted with differences in sample handling (freezing and desiccation), extraction methods (MoBio PowerSoil and phenol-chloroform) and choice of PCR primers, they nevertheless show a pattern in which two hunter-gatherer populations from two separate continents (Africa and South America) have a greater affinity to each other than to other traditional or urban populations. This is similarly true for the rural agriculturalists in Africa and South America and the urban industrial populations in Europe and North America.


Subsistence strategies in traditional societies distinguish gut microbiomes.

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 - Nat Commun (2015)

Comparison of the gut microbiomes of Matses, Tunapuco and Norman populations to published data from hunter-gatherer, rural agriculturalist and urban-industrial communities.Analyses were performed on genus-level taxa tables rarefied to 4,000 reads per sample. (a) Principal coordinate analysis of Bray–Curtis distances generated from taxa tables summarized at the genus level. Proportion of variance explained by each principal coordinate axis is denoted in the corresponding axis label. Populations are colour coded by subsistence strategy. Data sets are represented by triangles (this study), circles (Yatsunenko et al.3), and squares (Schnorr et al.1). Ellipses correspond to 95% confidence boundaries for each of the three subsistence categories. (b) Results from Bayesian source-tracking analysis. Source contributions are averaged across samples within the population. (c) Results from Bayesian source tracking for individual samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4386023&req=5

f3: Comparison of the gut microbiomes of Matses, Tunapuco and Norman populations to published data from hunter-gatherer, rural agriculturalist and urban-industrial communities.Analyses were performed on genus-level taxa tables rarefied to 4,000 reads per sample. (a) Principal coordinate analysis of Bray–Curtis distances generated from taxa tables summarized at the genus level. Proportion of variance explained by each principal coordinate axis is denoted in the corresponding axis label. Populations are colour coded by subsistence strategy. Data sets are represented by triangles (this study), circles (Yatsunenko et al.3), and squares (Schnorr et al.1). Ellipses correspond to 95% confidence boundaries for each of the three subsistence categories. (b) Results from Bayesian source-tracking analysis. Source contributions are averaged across samples within the population. (c) Results from Bayesian source tracking for individual samples.
Mentions: Finally, we compared genus-level taxa abundance profiles between our populations, and those from two previous studies of remote agrarian and hunter-gatherer human gut microbiomes13. PCoA of a Bray–Curtis distance matrix generated from genus-level taxa tables shows a clear separation between traditional and urban-industrial microbiomes (Fig. 3a), consistent across the three different studies. In addition, the hunter-gatherer populations (Matses and Hadza) form a distinct sub-cluster nested within the other traditional populations (Tunapuco, Venezuela and Malawi). To further explore this trend, we performed Bayesian source tracking8 on the Matses, Tunapuco and Norman samples using the previously published data sets as source populations (traditional hunter-gatherer: Hadza; rural agriculturalist: Venezuela, Malawi; and urban-industrial: USA, Italy; Fig. 3b). Consistent with previous analyses, the urban sources formed the primary contribution (~84% average) to the Norman samples, while the combined rural and hunter-gatherer sources accounted for ~95–98% for the Tunapuco and Matses samples. Specifically, the Matses samples had a higher contribution (~58%) from the Hadza hunter-gatherer source, while the Tunapuco samples had a higher contribution (~66%) from the rural Venezuela and Malawi source. Within populations, individuals show variation (Fig. 3c), but overall between ~64 and 85% of individuals have profiles consistent with their subsistence strategy. Thus, while the studies were conducted with differences in sample handling (freezing and desiccation), extraction methods (MoBio PowerSoil and phenol-chloroform) and choice of PCR primers, they nevertheless show a pattern in which two hunter-gatherer populations from two separate continents (Africa and South America) have a greater affinity to each other than to other traditional or urban populations. This is similarly true for the rural agriculturalists in Africa and South America and the urban industrial populations in Europe and North America.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA [2] Universidad Científica del Sur, Lima 18, Perú [3] City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA.

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.

No MeSH data available.