title: Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.
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.
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada.
authors.forename: Alison M
authors.initials: AM
authors.lastname: Devault
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: McLoughlin
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
authors.forename: Crystal
authors.initials: C
authors.lastname: Jaing
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
authors.forename: Shea
authors.initials: S
authors.lastname: Gardner
authors.affiliation: Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada.
authors.forename: Teresita M
authors.initials: TM
authors.lastname: Porter
authors.affiliation: 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.
authors.forename: Jacob M
authors.initials: JM
authors.lastname: Enk
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
authors.forename: James
authors.initials: J
authors.lastname: Thissen
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Allen
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
authors.forename: Monica
authors.initials: M
authors.lastname: Borucki
authors.affiliation: Departments of Anthropology and Biological Sciences, University of South Carolina, Columbia, SC, USA.
authors.forename: Sharon N
authors.initials: SN
authors.lastname: DeWitte
authors.affiliation: The College of Physicians of Philadelphia, Mütter Museum, 19 S 22nd St, Philadelphia, PA 19103, USA.
authors.forename: Anna N
authors.initials: AN
authors.lastname: Dhody
authors.affiliation: 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.
authors.forename: Hendrik N
authors.initials: HN
authors.lastname: Poinar
mesh_terms: D001106:Archaeology; D019295:Computational Biology; D004269:DNA, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D014734:Vibrio cholerae / Q000145:classification / Q000235:genetics; D015010:Yersinia pestis / Q000145:classification / Q000235:genetics
chemical_list: D004269:DNA, Bacterial