Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array
Identifieur interne : 000266 ( Main/Exploration ); précédent : 000265; suivant : 000267Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array
Auteurs : Alison M. Devault [Canada] ; Kevin Mcloughlin [États-Unis] ; Crystal Jaing [États-Unis] ; Shea Gardner [États-Unis] ; Teresita M. Porter [Canada] ; Jacob M. Enk [Canada] ; James Thissen [États-Unis] ; Jonathan Allen [États-Unis] ; Monica Borucki [États-Unis] ; Sharon N. Dewitte [États-Unis] ; Anna N. Dhody [États-Unis] ; Hendrik N. Poinar [Canada]Source :
- Scientific Reports [ 2045-2322 ] ; 2014.
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
Url:
DOI: 10.1038/srep04245
PubMed: 24603850
PubMed Central: 3945050
Affiliations:
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Devault</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>McMaster Ancient DNA Centre, Department of Anthropology, McMaster University</institution>, 1280 Main St W, Hamilton, Ontario L8S4L9,<country>Canada</country></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mcloughlin, Kevin" sort="Mcloughlin, Kevin" uniqKey="Mcloughlin K" first="Kevin" last="Mcloughlin">Kevin Mcloughlin</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Lawrence Livermore National Laboratory</institution>, Livermore, CA 94551,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Jaing, Crystal" sort="Jaing, Crystal" uniqKey="Jaing C" first="Crystal" last="Jaing">Crystal Jaing</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Lawrence Livermore National Laboratory</institution>, Livermore, CA 94551,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Gardner, Shea" sort="Gardner, Shea" uniqKey="Gardner S" first="Shea" last="Gardner">Shea Gardner</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Lawrence Livermore National Laboratory</institution>, Livermore, CA 94551,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Porter, Teresita M" sort="Porter, Teresita M" uniqKey="Porter T" first="Teresita M." last="Porter">Teresita M. Porter</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Department of Biology, McMaster University</institution>, 1280 Main St W, Hamilton, Ontario L8S 4K1,<country>Canada</country></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Enk, Jacob M" sort="Enk, Jacob M" uniqKey="Enk J" first="Jacob M." last="Enk">Jacob M. Enk</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>McMaster Ancient DNA Centre, Department of Anthropology, McMaster University</institution>, 1280 Main St W, Hamilton, Ontario L8S4L9,<country>Canada</country></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Department of Biology, McMaster University</institution>, 1280 Main St W, Hamilton, Ontario L8S 4K1,<country>Canada</country></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Thissen, James" sort="Thissen, James" uniqKey="Thissen J" first="James" last="Thissen">James Thissen</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Lawrence Livermore National Laboratory</institution>, Livermore, CA 94551,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Allen, Jonathan" sort="Allen, Jonathan" uniqKey="Allen J" first="Jonathan" last="Allen">Jonathan Allen</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Lawrence Livermore National Laboratory</institution>, Livermore, CA 94551,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Borucki, Monica" sort="Borucki, Monica" uniqKey="Borucki M" first="Monica" last="Borucki">Monica Borucki</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Lawrence Livermore National Laboratory</institution>, Livermore, CA 94551,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Dewitte, Sharon N" sort="Dewitte, Sharon N" uniqKey="Dewitte S" first="Sharon N." last="Dewitte">Sharon N. Dewitte</name><affiliation wicri:level="1"><nlm:aff id="a4"><institution>Departments of Anthropology and Biological Sciences, University of South Carolina</institution>, Columbia, SC,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Dhody, Anna N" sort="Dhody, Anna N" uniqKey="Dhody A" first="Anna N." last="Dhody">Anna N. Dhody</name><affiliation wicri:level="1"><nlm:aff id="a5"><institution>The College of Physicians of Philadelphia, Mütter Museum</institution>, 19 S 22<sup>nd</sup> St, Philadelphia, PA 19103,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Poinar, Hendrik N" sort="Poinar, Hendrik N" uniqKey="Poinar H" first="Hendrik N." last="Poinar">Hendrik N. Poinar</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>McMaster Ancient DNA Centre, Department of Anthropology, McMaster University</institution>, 1280 Main St W, Hamilton, Ontario L8S4L9,<country>Canada</country></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Department of Biology, McMaster University</institution>, 1280 Main St W, Hamilton, Ontario L8S 4K1,<country>Canada</country></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a6"><institution>Michael G. DeGroote Institute for Infectious Disease Research, McMaster University</institution>, 1280 Main St W, Hamilton, Ontario L8S4L8,<country>Canada</country></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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 <italic>Vibrio cholerae</italic> (cholera) in a 19th century intestinal specimen and <italic>Yersinia pestis</italic> (“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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ortner, D J" uniqKey="Ortner D">D. J. Ortner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rizzi, E" uniqKey="Rizzi E">E. Rizzi</name></author><author><name sortKey="Lari, M" uniqKey="Lari M">M. Lari</name></author><author><name sortKey="Gigli, E" uniqKey="Gigli E">E. Gigli</name></author><author><name sortKey="De Bellis, G" uniqKey="De Bellis G">G. De Bellis</name></author><author><name sortKey="Caramelli, D" uniqKey="Caramelli D">D. Caramelli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Devault, A M" uniqKey="Devault A">A. M. 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Devault</name></noRegion><name sortKey="Enk, Jacob M" sort="Enk, Jacob M" uniqKey="Enk J" first="Jacob M." last="Enk">Jacob M. Enk</name><name sortKey="Enk, Jacob M" sort="Enk, Jacob M" uniqKey="Enk J" first="Jacob M." last="Enk">Jacob M. Enk</name><name sortKey="Poinar, Hendrik N" sort="Poinar, Hendrik N" uniqKey="Poinar H" first="Hendrik N." last="Poinar">Hendrik N. Poinar</name><name sortKey="Poinar, Hendrik N" sort="Poinar, Hendrik N" uniqKey="Poinar H" first="Hendrik N." last="Poinar">Hendrik N. Poinar</name><name sortKey="Poinar, Hendrik N" sort="Poinar, Hendrik N" uniqKey="Poinar H" first="Hendrik N." last="Poinar">Hendrik N. Poinar</name><name sortKey="Porter, Teresita M" sort="Porter, Teresita M" uniqKey="Porter T" first="Teresita M." last="Porter">Teresita M. Porter</name></country><country name="États-Unis"><noRegion><name sortKey="Mcloughlin, Kevin" sort="Mcloughlin, Kevin" uniqKey="Mcloughlin K" first="Kevin" last="Mcloughlin">Kevin Mcloughlin</name></noRegion><name sortKey="Allen, Jonathan" sort="Allen, Jonathan" uniqKey="Allen J" first="Jonathan" last="Allen">Jonathan Allen</name><name sortKey="Borucki, Monica" sort="Borucki, Monica" uniqKey="Borucki M" first="Monica" last="Borucki">Monica Borucki</name><name sortKey="Dewitte, Sharon N" sort="Dewitte, Sharon N" uniqKey="Dewitte S" first="Sharon N." last="Dewitte">Sharon N. Dewitte</name><name sortKey="Dhody, Anna N" sort="Dhody, Anna N" uniqKey="Dhody A" first="Anna N." last="Dhody">Anna N. Dhody</name><name sortKey="Gardner, Shea" sort="Gardner, Shea" uniqKey="Gardner S" first="Shea" last="Gardner">Shea Gardner</name><name sortKey="Jaing, Crystal" sort="Jaing, Crystal" uniqKey="Jaing C" first="Crystal" last="Jaing">Crystal Jaing</name><name sortKey="Thissen, James" sort="Thissen, James" uniqKey="Thissen J" first="James" last="Thissen">James Thissen</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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