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. 2012;7(12):e51146.
doi: 10.1371/journal.pone.0051146. Epub 2012 Dec 12.

Insights from characterizing extinct human gut microbiomes

Raul Y Tito  1 , Dan Knights, Jessica Metcalf, Alexandra J Obregon-Tito, Lauren Cleeland, Fares Najar, Bruce Roe, Karl Reinhard, Kristin Sobolik, Samuel Belknap, Morris Foster, Paul Spicer, Rob Knight, Cecil M Lewis Jr
Affiliations

Insights from characterizing extinct human gut microbiomes

Raul Y Tito et al. PLoS One. 2012.

Abstract

In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (~8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. The geographic distribution and bacterial diversity of the included samples.
These data resulted from comparison of the 16S rRNA V3. Taxon distribution and cluster dendrogram were limited to phyla with a frequency of 5% or more.
Figure 2
Figure 2. Venn-Euler diagram of OTUs at 97% pairwise identity representing 1,045 OTUs.
The sizes of the circles and intersections are proportional to the number of OTUs listed and shared by each sample. Stress value for A is 0.01274982, and it increased in B and C as more samples are added. All the stress values are lower than the predicted value at 0.01 and 0.05, suggesting that the grouping is non-random.
Figure 3
Figure 3. Bayesian source-tracking results for ancient coprolite samples.
Both Rio Zape samples assign partially to the rural African children source, with sample ZA04 also containing a predicted partial match to the modern non-human primate gut source. Caserones sample CA18 assigns almost entirely to the compost source with relatively high confidence; sample CA10 is predicted with low confidence to contain a small proportion of compost (See Figure S5 for variability in proportion estimates). The sources for the Hinds Cave samples were unrecognized given our training data, resulting in nearly complete assignments to the “Unknown” source. When extraction blanks were subjected to 60 cycles of 16S PCR, the amplified microbial community signature assigns to either a skin community or unknown community.
Figure 4
Figure 4. Bayesian source-tracking results for the Tyrolean Iceman and a 1918 soldier glacier mummy (sequence data published in [19]).
The Tyrolean Iceman sample exhibits a substantial degree of similarity to a primate gut, while the soldier mummy assigns mostly to an unknown microbial community, within minor and low-confidence proportions assigning to the primate gut and rural African child gut sources (See Figure S6 for variability in proportion estimates).
See this image and copyright information in PMC

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References

    1. Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, et al. (2006) Metagenomic analysis of the human distal gut microbiome. science 312: 1355. - PMC - PubMed
    1. Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915–1920. - PubMed
    1. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. (2007) The human microbiome project. Nature 449: 804–810. - PMC - PubMed
    1. Blaser M (2011) Antibiotic overuse: Stop the killing of beneficial bacteria. Nature 476: 393–394. - PubMed
    1. Neel JV, Weder AB, Julius S (1998) Type II diabetes, essential hypertension, and obesity as “syndromes of impaired genetic homeostasis”: the “thrifty genotype” hypothesis enters the 21st century. Perspectives in biology and medicine 42: 44–74. - PubMed

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