1
|
Philips A, Stolarek I, Kuczkowska B, Juras A, Handschuh L, Piontek J, Kozlowski P, Figlerowicz M. Comprehensive analysis of microorganisms accompanying human archaeological remains. Gigascience 2017; 6:1-13. [PMID: 28609785 PMCID: PMC5965364 DOI: 10.1093/gigascience/gix044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/09/2017] [Accepted: 06/11/2017] [Indexed: 02/01/2023] Open
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.
Collapse
Affiliation(s)
- Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Ireneusz Stolarek
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Bogna Kuczkowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Luiza Handschuh
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Department of Hematology and Bone Marrow Transplantation, University of
Medical Sciences, Poznan, 60-569, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Piotr Kozlowski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan,
60-965, Poland
| |
Collapse
|