Insights from Characterizing Extinct Human Gut Microbiomes

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.

Captivity humanizes the primate microbiome

“…Taxonomy assignment, diversity analysis, and principal coordinate analysis were obtained through QIIME with default settings and using custom R scripts. Published data used in our meta-analysis (17,23,40,41) were analyzed similarly. Microbiome-based phylogenies for SI Appendix, Fig.…”

Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease

“…The results of analyses on gut microbiome show that ancient microbiota are different than the modern cosmopolitan human microbiomes and appear more related to rural microbiota. 3 Similar changes can be expected in oral microbiome too. Comparison of the present microbiome with that of ancient may enable us to understand the shift of microorganisms due to various factors such as change in lifestyle, diet and use of antimicrobials.…”

Origins of an Unmarked Georgia Cemetery Using Ancient DNA Analysis

“…Teeth or bone were pulverized using sterile tools by researchers equipped with sterile gowns, hair nets and marks. DNA was extracted in an ISO 7 (class 10,000) HEPA-filtration, positive pressure clean room using previously established salting out extraction methods (Tito et al 2012;Tito et al 2008). In brief, the salting out protocol involved lysing the pulverized skeletal material overnight, followed by a Proteinase K (Invitrogen) incubation, and a subsequent washing and eluting of the DNA (Tito et al 2012;Tito et al 2008).…”

“…DNA was extracted in an ISO 7 (class 10,000) HEPA-filtration, positive pressure clean room using previously established salting out extraction methods (Tito et al 2012;Tito et al 2008). In brief, the salting out protocol involved lysing the pulverized skeletal material overnight, followed by a Proteinase K (Invitrogen) incubation, and a subsequent washing and eluting of the DNA (Tito et al 2012;Tito et al 2008). Seven of these samples (F001, F017, F024, F035, F051, F096, F100) were replicated at Washington State University (WSU) using a modified protocol of Kemp et al(2007) described by Moss et al (2014).…”