Comprehensive analysis of microorganisms accompanying human archaeological remains

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.

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt

“…In light of their DNA damage pattern, it is reasonable to assume that these are truly ancient environmental bacteria that populated archeological sediments. The contamination of archeological remains by environmental bacteria is indeed well expected, as already documented in previous paleomicrobiological aDNA studies 15 , 18 , 37 . For the relative abundances of bacterial families detected across the samples, please see Supplementary Data 2 .…”

“…Alternatively, ancient DNA (aDNA) analysis based on shotgun metagenomic sequencing is emerging as an attractive and reliable opportunity to directly investigate the microbial ecology of our ancestors 12 – 15 . Paleomicrobiological aDNA studies have traditionally been conducted on dental calculus and bones 15 – 18 , providing landmark information on ancient pathogens and oral microbial communities.…”

“…Alternatively, ancient DNA (aDNA) analysis based on shotgun metagenomic sequencing is emerging as an attractive and reliable opportunity to directly investigate the microbial ecology of our ancestors 12 – 15 . Paleomicrobiological aDNA studies have traditionally been conducted on dental calculus and bones 15 – 18 , providing landmark information on ancient pathogens and oral microbial communities. However, given that stools are widely acknowledged as a proxy of the gut microbiome structure 19 , the metagenomics of aDNA from paleofeces, also known as coprolites, represents the only way to gain insight into the ancient human gut microbiome 2 .…”

Microbial community types and signature-like soil bacterial patterns from fortified prehistoric hills of Thuringia (Germany)

“…8 Normalized numbers of reads (ppm values, 0 set to "20") for samples no. 4c (Röderburg, diamonds) and 9a (Theuern, squares) versus the reads of the inner part of Lange Bahn in comparison with the samples from outside Lange Bahn (open circles), selected OTUs corresponding to Table 7 of the supplementary material sample specific and less dependent on geographical origin (Philips et al 2017).…”

“…The investigation of microbial ancient DNA from human remains (Philips et al 2017) was motivated by the recognition of pathogens (Rollo and Marota 1999;Moodley et al 2009), on the one hand. On the other hand, profiling of soil microbial DNA was used for characterization of archaeological objects (Lenehan et al 2017) and evaluation of degradation and preservation conditions (McNamara et al 2005;Douterelo et al 2010;Xu et al 2017).…”