Comprehensive analysis of microorganisms accompanying human archaeological remains.

Anna Philips,Piotr Kozlowski,Bogna Kuczkowska,Marek Figlerowicz,Anna Juras,Luiza Handschuh,Janusz Piontek,Ireneusz Stolarek

doi:10.1093/gigascience/gix044

Abstract

Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.

Highlights

During the last 2 decades, a number of methods that permit isolation and sequencing of ancient DNA extracted from archaeological specimens have been elaborated
It is noteworthy that we identified within our samples Propionibacterium phage—a double-stranded DNA virus that is associated with oral microbiome [47, 48]
A traditional approach based on the analysis of a singular 16S rRNA marker gene [64] is limited to the identification of bacteria/archaea at the genus level at most, being less accurate [65]

Summary

Background

During the last 2 decades, a number of methods that permit isolation and sequencing of ancient DNA (aDNA) extracted from archaeological specimens have been elaborated. For each sample, we calculated the DNA damage values separately for the following groups of bacterial species: (i) environmental; (ii) all human-related; (iii) oral; (iv) gut; and (v) potential pathogens We compared these values with corresponding values determined for the endogenous human aDNA in the same sample. The highest differences between the levels of human and microbial DNA damage were observed for environmental bacteria that showed very little DNA damage (on average: δs = 0.1767; δd = 0.0264; (1/λ1) = 1.3089) Different DNA damage levels in environmental and human-related bacteria did not result from differences in the stability of bacterial genomes but from their age

Discussion

Experimental procedures

Bioinformatics procedures

Findings

Availability of supporting data and materials