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Sci Rep. 2014 Mar 6;4:4245. doi: 10.1038/srep04245.

Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.

Author information

1
McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada.
2
Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
3
Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada.
4
1] McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada [2] Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada.
5
Departments of Anthropology and Biological Sciences, University of South Carolina, Columbia, SC, USA.
6
The College of Physicians of Philadelphia, Mütter Museum, 19 S 22nd St, Philadelphia, PA 19103, USA.
7
1] McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada [2] Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada [3] Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L8, Canada.

Abstract

Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis ("Black Death" plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.

PMID:
24603850
PMCID:
PMC3945050
DOI:
10.1038/srep04245
[Indexed for MEDLINE]
Free PMC Article

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