Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-05

AUTHORS

Alison M. Devault, Kevin McLoughlin, Crystal Jaing, Shea Gardner, Teresita M. Porter, Jacob M. Enk, James Thissen, Jonathan Allen, Monica Borucki, Sharon N. DeWitte, Anna N. Dhody, Hendrik N. Poinar

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. More... »

PAGES

4245

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/srep04245

DOI

http://dx.doi.org/10.1038/srep04245

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1020758762

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24603850


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Microbiology", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Archaeology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Computational Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "High-Throughput Nucleotide Sequencing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oligonucleotide Array Sequence Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phylogeny", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Vibrio cholerae", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Yersinia pestis", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "McMaster University", 
          "id": "https://www.grid.ac/institutes/grid.25073.33", 
          "name": [
            "McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Devault", 
        "givenName": "Alison M.", 
        "id": "sg:person.01057437460.01", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01057437460.01"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Lawrence Livermore National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.250008.f", 
          "name": [
            "Lawrence Livermore National Laboratory, Livermore, CA 94551, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "McLoughlin", 
        "givenName": "Kevin", 
        "id": "sg:person.01110130055.95", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01110130055.95"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Lawrence Livermore National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.250008.f", 
          "name": [
            "Lawrence Livermore National Laboratory, Livermore, CA 94551, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Jaing", 
        "givenName": "Crystal", 
        "id": "sg:person.01145317730.80", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01145317730.80"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Lawrence Livermore National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.250008.f", 
          "name": [
            "Lawrence Livermore National Laboratory, Livermore, CA 94551, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gardner", 
        "givenName": "Shea", 
        "id": "sg:person.01116430457.09", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01116430457.09"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "McMaster University", 
          "id": "https://www.grid.ac/institutes/grid.25073.33", 
          "name": [
            "Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Porter", 
        "givenName": "Teresita M.", 
        "id": "sg:person.0607762407.10", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0607762407.10"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "McMaster University", 
          "id": "https://www.grid.ac/institutes/grid.25073.33", 
          "name": [
            "McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada", 
            "Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Enk", 
        "givenName": "Jacob M.", 
        "id": "sg:person.01207123576.96", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01207123576.96"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Lawrence Livermore National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.250008.f", 
          "name": [
            "Lawrence Livermore National Laboratory, Livermore, CA 94551, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Thissen", 
        "givenName": "James", 
        "id": "sg:person.01125555740.52", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01125555740.52"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Lawrence Livermore National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.250008.f", 
          "name": [
            "Lawrence Livermore National Laboratory, Livermore, CA 94551, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Allen", 
        "givenName": "Jonathan", 
        "id": "sg:person.0651572762.41", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0651572762.41"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Lawrence Livermore National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.250008.f", 
          "name": [
            "Lawrence Livermore National Laboratory, Livermore, CA 94551, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Borucki", 
        "givenName": "Monica", 
        "id": "sg:person.01124467130.52", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01124467130.52"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of South Carolina", 
          "id": "https://www.grid.ac/institutes/grid.254567.7", 
          "name": [
            "Departments of Anthropology and Biological Sciences, University of South Carolina, Columbia, SC, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "DeWitte", 
        "givenName": "Sharon N.", 
        "id": "sg:person.0647333303.58", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0647333303.58"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "College of Physicians of Philadelphia", 
          "id": "https://www.grid.ac/institutes/grid.418804.1", 
          "name": [
            "The College of Physicians of Philadelphia, M\u00fctter Museum, 19 S 22nd St, Philadelphia, PA 19103, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dhody", 
        "givenName": "Anna N.", 
        "id": "sg:person.01016412266.41", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01016412266.41"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "McMaster University", 
          "id": "https://www.grid.ac/institutes/grid.25073.33", 
          "name": [
            "McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada", 
            "Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada", 
            "Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L8, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Poinar", 
        "givenName": "Hendrik N.", 
        "id": "sg:person.0676355246.40", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676355246.40"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1007/s13353-013-0145-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001211173", 
          "https://doi.org/10.1007/s13353-013-0145-1"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35097083", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007834691", 
          "https://doi.org/10.1038/35097083"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35097083", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007834691", 
          "https://doi.org/10.1038/35097083"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35097083", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007834691", 
          "https://doi.org/10.1038/35097083"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1297-9686-44-21", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009930584", 
          "https://doi.org/10.1186/1297-9686-44-21"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jvi.02690-09", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010722302"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.3201/eid1301.060837", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012317562"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(05)80360-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013618994"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1238286", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015651351"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-11-668", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016736182", 
          "https://doi.org/10.1186/1471-2164-11-668"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ncomms1701", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018056965", 
          "https://doi.org/10.1038/ncomms1701"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ijpp.2011.01.002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022130639"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0022631", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022891993"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.242579699", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031701959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkr1079", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032911085"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1056/nejmoa1308663", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033308693"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0140-6736(05)17745-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034724012"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro1476", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038598481", 
          "https://doi.org/10.1038/nrmicro1476"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro1476", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038598481", 
          "https://doi.org/10.1038/nrmicro1476"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature10549", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042284160", 
          "https://doi.org/10.1038/nature10549"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1809", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042710160", 
          "https://doi.org/10.1038/nrg1809"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1809", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042710160", 
          "https://doi.org/10.1038/nrg1809"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0029973", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048372864"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2009-10-3-r25", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049583368", 
          "https://doi.org/10.1186/gb-2009-10-3-r25"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bfgp/elr027", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050134641"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.120618.111", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052850693"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2144/000113809", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1069096399"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2015-05", 
    "datePublishedReg": "2015-05-01", 
    "description": "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. ", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/srep04245", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1045337", 
        "issn": [
          "2045-2322"
        ], 
        "name": "Scientific Reports", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "4"
      }
    ], 
    "name": "Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array", 
    "pagination": "4245", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "62e9400f530f18377da05bdea193f532c6768454d77119bf13b80eec464affbc"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "24603850"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101563288"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/srep04245"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1020758762"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/srep04245", 
      "https://app.dimensions.ai/details/publication/pub.1020758762"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T22:19", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8690_00000424.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/articles/srep04245"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/srep04245'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/srep04245'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/srep04245'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/srep04245'


 

This table displays all metadata directly associated to this object as RDF triples.

270 TRIPLES      21 PREDICATES      61 URIs      30 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/srep04245 schema:about N44a9bd7eb2564f899dabfa0dabfe3ab2
2 N4e8afd28a7f447e8b7449f9f50ff523d
3 N51a249c1e2c64284bb0f4372a0ba84e2
4 N540da9adf2a54277a04c961530bef836
5 N650a0a205b81408ca4b4e64fbbb0e27f
6 N7a7a043f03a24301ac67e2b0de863bdc
7 N99f1d281e14d4f81a73c3a96d14284c7
8 Ne432163011eb4e438db4bc74eb32f140
9 Nfd9f31b027c14f508ced56ede4d499cc
10 anzsrc-for:06
11 anzsrc-for:0605
12 schema:author N502da22c310147999de529bcb98b2355
13 schema:citation sg:pub.10.1007/s13353-013-0145-1
14 sg:pub.10.1038/35097083
15 sg:pub.10.1038/nature10549
16 sg:pub.10.1038/ncomms1701
17 sg:pub.10.1038/nrg1809
18 sg:pub.10.1038/nrmicro1476
19 sg:pub.10.1186/1297-9686-44-21
20 sg:pub.10.1186/1471-2164-11-668
21 sg:pub.10.1186/gb-2009-10-3-r25
22 https://doi.org/10.1016/j.ijpp.2011.01.002
23 https://doi.org/10.1016/s0022-2836(05)80360-2
24 https://doi.org/10.1016/s0140-6736(05)17745-9
25 https://doi.org/10.1056/nejmoa1308663
26 https://doi.org/10.1073/pnas.242579699
27 https://doi.org/10.1093/bfgp/elr027
28 https://doi.org/10.1093/nar/gkr1079
29 https://doi.org/10.1101/gr.120618.111
30 https://doi.org/10.1126/science.1238286
31 https://doi.org/10.1128/jvi.02690-09
32 https://doi.org/10.1371/journal.pone.0022631
33 https://doi.org/10.1371/journal.pone.0029973
34 https://doi.org/10.2144/000113809
35 https://doi.org/10.3201/eid1301.060837
36 schema:datePublished 2015-05
37 schema:datePublishedReg 2015-05-01
38 schema:description 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.
39 schema:genre research_article
40 schema:inLanguage en
41 schema:isAccessibleForFree true
42 schema:isPartOf N1c0493cc774f4824a7f563173bb82cc6
43 Nc77524b60e784ff0b1122ce955c98008
44 sg:journal.1045337
45 schema:name Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array
46 schema:pagination 4245
47 schema:productId N709dedb83fad4503affcbd46be318df0
48 N87f3ac41d5fd4e87a86edb977e46a62e
49 N8bae6a629b764d428fbb2bbc4af77c59
50 Nca8daee8d3e94e89a500f35d22b58eed
51 Ne96cb42ac1a247c0816062f3480ea62d
52 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020758762
53 https://doi.org/10.1038/srep04245
54 schema:sdDatePublished 2019-04-10T22:19
55 schema:sdLicense https://scigraph.springernature.com/explorer/license/
56 schema:sdPublisher N077baf6eab9e4bebad0d7992e2baa363
57 schema:url http://www.nature.com/articles/srep04245
58 sgo:license sg:explorer/license/
59 sgo:sdDataset articles
60 rdf:type schema:ScholarlyArticle
61 N00d9d024cd4d49a2a8b5381de3139264 rdf:first sg:person.0676355246.40
62 rdf:rest rdf:nil
63 N05485db03be54ab3bbbf253e894bd70c rdf:first sg:person.01125555740.52
64 rdf:rest N0cbb3eb19ab4480c9dded1edb123f5a8
65 N077baf6eab9e4bebad0d7992e2baa363 schema:name Springer Nature - SN SciGraph project
66 rdf:type schema:Organization
67 N0cbb3eb19ab4480c9dded1edb123f5a8 rdf:first sg:person.0651572762.41
68 rdf:rest N420141504a6942e2a9655d6b1b090fcd
69 N143d0e37d5dc4f3a807950498cbb818e rdf:first sg:person.01016412266.41
70 rdf:rest N00d9d024cd4d49a2a8b5381de3139264
71 N1c0493cc774f4824a7f563173bb82cc6 schema:issueNumber 1
72 rdf:type schema:PublicationIssue
73 N3b3229f8353f4c7c8fc4c14285a6d8d6 rdf:first sg:person.0607762407.10
74 rdf:rest Ncdfe3c3080cb4c6abded33e9654abab4
75 N420141504a6942e2a9655d6b1b090fcd rdf:first sg:person.01124467130.52
76 rdf:rest Ne29c27c2d53e48e796701d731dde3e35
77 N44a9bd7eb2564f899dabfa0dabfe3ab2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name DNA, Bacterial
79 rdf:type schema:DefinedTerm
80 N4e8afd28a7f447e8b7449f9f50ff523d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Vibrio cholerae
82 rdf:type schema:DefinedTerm
83 N502da22c310147999de529bcb98b2355 rdf:first sg:person.01057437460.01
84 rdf:rest N868d4fac7f9d45c5afc87a3482e44eba
85 N51a249c1e2c64284bb0f4372a0ba84e2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
86 schema:name Archaeology
87 rdf:type schema:DefinedTerm
88 N540da9adf2a54277a04c961530bef836 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
89 schema:name Oligonucleotide Array Sequence Analysis
90 rdf:type schema:DefinedTerm
91 N650a0a205b81408ca4b4e64fbbb0e27f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
92 schema:name Phylogeny
93 rdf:type schema:DefinedTerm
94 N6edce20afd5f43988fbe03d393908b69 rdf:first sg:person.01145317730.80
95 rdf:rest Na505a02df9754d01a4ddfff023f7dbbb
96 N709dedb83fad4503affcbd46be318df0 schema:name doi
97 schema:value 10.1038/srep04245
98 rdf:type schema:PropertyValue
99 N7a7a043f03a24301ac67e2b0de863bdc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
100 schema:name Humans
101 rdf:type schema:DefinedTerm
102 N868d4fac7f9d45c5afc87a3482e44eba rdf:first sg:person.01110130055.95
103 rdf:rest N6edce20afd5f43988fbe03d393908b69
104 N87f3ac41d5fd4e87a86edb977e46a62e schema:name pubmed_id
105 schema:value 24603850
106 rdf:type schema:PropertyValue
107 N8bae6a629b764d428fbb2bbc4af77c59 schema:name nlm_unique_id
108 schema:value 101563288
109 rdf:type schema:PropertyValue
110 N99f1d281e14d4f81a73c3a96d14284c7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name High-Throughput Nucleotide Sequencing
112 rdf:type schema:DefinedTerm
113 Na505a02df9754d01a4ddfff023f7dbbb rdf:first sg:person.01116430457.09
114 rdf:rest N3b3229f8353f4c7c8fc4c14285a6d8d6
115 Nc77524b60e784ff0b1122ce955c98008 schema:volumeNumber 4
116 rdf:type schema:PublicationVolume
117 Nca8daee8d3e94e89a500f35d22b58eed schema:name readcube_id
118 schema:value 62e9400f530f18377da05bdea193f532c6768454d77119bf13b80eec464affbc
119 rdf:type schema:PropertyValue
120 Ncdfe3c3080cb4c6abded33e9654abab4 rdf:first sg:person.01207123576.96
121 rdf:rest N05485db03be54ab3bbbf253e894bd70c
122 Ne29c27c2d53e48e796701d731dde3e35 rdf:first sg:person.0647333303.58
123 rdf:rest N143d0e37d5dc4f3a807950498cbb818e
124 Ne432163011eb4e438db4bc74eb32f140 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Yersinia pestis
126 rdf:type schema:DefinedTerm
127 Ne96cb42ac1a247c0816062f3480ea62d schema:name dimensions_id
128 schema:value pub.1020758762
129 rdf:type schema:PropertyValue
130 Nfd9f31b027c14f508ced56ede4d499cc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
131 schema:name Computational Biology
132 rdf:type schema:DefinedTerm
133 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
134 schema:name Biological Sciences
135 rdf:type schema:DefinedTerm
136 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
137 schema:name Microbiology
138 rdf:type schema:DefinedTerm
139 sg:journal.1045337 schema:issn 2045-2322
140 schema:name Scientific Reports
141 rdf:type schema:Periodical
142 sg:person.01016412266.41 schema:affiliation https://www.grid.ac/institutes/grid.418804.1
143 schema:familyName Dhody
144 schema:givenName Anna N.
145 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01016412266.41
146 rdf:type schema:Person
147 sg:person.01057437460.01 schema:affiliation https://www.grid.ac/institutes/grid.25073.33
148 schema:familyName Devault
149 schema:givenName Alison M.
150 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01057437460.01
151 rdf:type schema:Person
152 sg:person.01110130055.95 schema:affiliation https://www.grid.ac/institutes/grid.250008.f
153 schema:familyName McLoughlin
154 schema:givenName Kevin
155 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01110130055.95
156 rdf:type schema:Person
157 sg:person.01116430457.09 schema:affiliation https://www.grid.ac/institutes/grid.250008.f
158 schema:familyName Gardner
159 schema:givenName Shea
160 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01116430457.09
161 rdf:type schema:Person
162 sg:person.01124467130.52 schema:affiliation https://www.grid.ac/institutes/grid.250008.f
163 schema:familyName Borucki
164 schema:givenName Monica
165 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01124467130.52
166 rdf:type schema:Person
167 sg:person.01125555740.52 schema:affiliation https://www.grid.ac/institutes/grid.250008.f
168 schema:familyName Thissen
169 schema:givenName James
170 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01125555740.52
171 rdf:type schema:Person
172 sg:person.01145317730.80 schema:affiliation https://www.grid.ac/institutes/grid.250008.f
173 schema:familyName Jaing
174 schema:givenName Crystal
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01145317730.80
176 rdf:type schema:Person
177 sg:person.01207123576.96 schema:affiliation https://www.grid.ac/institutes/grid.25073.33
178 schema:familyName Enk
179 schema:givenName Jacob M.
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01207123576.96
181 rdf:type schema:Person
182 sg:person.0607762407.10 schema:affiliation https://www.grid.ac/institutes/grid.25073.33
183 schema:familyName Porter
184 schema:givenName Teresita M.
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0607762407.10
186 rdf:type schema:Person
187 sg:person.0647333303.58 schema:affiliation https://www.grid.ac/institutes/grid.254567.7
188 schema:familyName DeWitte
189 schema:givenName Sharon N.
190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0647333303.58
191 rdf:type schema:Person
192 sg:person.0651572762.41 schema:affiliation https://www.grid.ac/institutes/grid.250008.f
193 schema:familyName Allen
194 schema:givenName Jonathan
195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0651572762.41
196 rdf:type schema:Person
197 sg:person.0676355246.40 schema:affiliation https://www.grid.ac/institutes/grid.25073.33
198 schema:familyName Poinar
199 schema:givenName Hendrik N.
200 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676355246.40
201 rdf:type schema:Person
202 sg:pub.10.1007/s13353-013-0145-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001211173
203 https://doi.org/10.1007/s13353-013-0145-1
204 rdf:type schema:CreativeWork
205 sg:pub.10.1038/35097083 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007834691
206 https://doi.org/10.1038/35097083
207 rdf:type schema:CreativeWork
208 sg:pub.10.1038/nature10549 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042284160
209 https://doi.org/10.1038/nature10549
210 rdf:type schema:CreativeWork
211 sg:pub.10.1038/ncomms1701 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018056965
212 https://doi.org/10.1038/ncomms1701
213 rdf:type schema:CreativeWork
214 sg:pub.10.1038/nrg1809 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042710160
215 https://doi.org/10.1038/nrg1809
216 rdf:type schema:CreativeWork
217 sg:pub.10.1038/nrmicro1476 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038598481
218 https://doi.org/10.1038/nrmicro1476
219 rdf:type schema:CreativeWork
220 sg:pub.10.1186/1297-9686-44-21 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009930584
221 https://doi.org/10.1186/1297-9686-44-21
222 rdf:type schema:CreativeWork
223 sg:pub.10.1186/1471-2164-11-668 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016736182
224 https://doi.org/10.1186/1471-2164-11-668
225 rdf:type schema:CreativeWork
226 sg:pub.10.1186/gb-2009-10-3-r25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049583368
227 https://doi.org/10.1186/gb-2009-10-3-r25
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1016/j.ijpp.2011.01.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022130639
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1016/s0022-2836(05)80360-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013618994
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1016/s0140-6736(05)17745-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034724012
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1056/nejmoa1308663 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033308693
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1073/pnas.242579699 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031701959
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1093/bfgp/elr027 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050134641
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1093/nar/gkr1079 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032911085
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1101/gr.120618.111 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052850693
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1126/science.1238286 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015651351
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1128/jvi.02690-09 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010722302
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1371/journal.pone.0022631 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022891993
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1371/journal.pone.0029973 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048372864
252 rdf:type schema:CreativeWork
253 https://doi.org/10.2144/000113809 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069096399
254 rdf:type schema:CreativeWork
255 https://doi.org/10.3201/eid1301.060837 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012317562
256 rdf:type schema:CreativeWork
257 https://www.grid.ac/institutes/grid.250008.f schema:alternateName Lawrence Livermore National Laboratory
258 schema:name Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
259 rdf:type schema:Organization
260 https://www.grid.ac/institutes/grid.25073.33 schema:alternateName McMaster University
261 schema:name Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada
262 McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada
263 Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L8, Canada
264 rdf:type schema:Organization
265 https://www.grid.ac/institutes/grid.254567.7 schema:alternateName University of South Carolina
266 schema:name Departments of Anthropology and Biological Sciences, University of South Carolina, Columbia, SC, USA
267 rdf:type schema:Organization
268 https://www.grid.ac/institutes/grid.418804.1 schema:alternateName College of Physicians of Philadelphia
269 schema:name The College of Physicians of Philadelphia, Mütter Museum, 19 S 22nd St, Philadelphia, PA 19103, USA
270 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...