Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-12

AUTHORS

Kirsten A. Ziesemer, Allison E. Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-García, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. MacDonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis, Corinne Hofman, Christina Warinner

ABSTRACT

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions. More... »

PAGES

16498

References to SciGraph publications

  • 2012-08. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms in THE ISME JOURNAL
  • 2011-09. Bayesian community-wide culture-independent microbial source tracking in NATURE METHODS
  • 2013-12. Metagenomic species profiling using universal phylogenetic marker genes in NATURE METHODS
  • 2012-06. Structure, function and diversity of the healthy human microbiome in NATURE
  • 2015-12. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome in GENOME BIOLOGY
  • 2012-06. Human gut microbiome viewed across age and geography in NATURE
  • 2013-05. Characterizing and measuring bias in sequence data in GENOME BIOLOGY
  • 2015-12. Subsistence strategies in traditional societies distinguish gut microbiomes in NATURE COMMUNICATIONS
  • 2014-12. Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance in THE ISME JOURNAL
  • 2012-09. Diversity, stability and resilience of the human gut microbiota in NATURE
  • 2012-09. Functional interactions between the gut microbiota and host metabolism in NATURE
  • 2012-08. Gut microbiota composition correlates with diet and health in the elderly in NATURE
  • 2014-12. The Earth Microbiome project: successes and aspirations in BMC BIOLOGY
  • 2014-12. Gut microbiome of the Hadza hunter-gatherers in NATURE COMMUNICATIONS
  • 2012-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • 2010-05. QIIME allows analysis of high-throughput community sequencing data in NATURE METHODS
  • 2012-08. Metagenomic microbial community profiling using unique clade-specific marker genes in NATURE METHODS
  • 2010-03. A human gut microbial gene catalogue established by metagenomic sequencing in NATURE
  • 2013-04. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions in NATURE GENETICS
  • 2014-04. Pathogens and host immunity in the ancient human oral cavity in NATURE GENETICS
  • 2015-12. The vocabulary of microbiome research: a proposal in MICROBIOME
  • 2011-02. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries in GENOME BIOLOGY
  • 2006-12. Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces in FRONTIERS IN ZOOLOGY
  • 2013-12. The saliva microbiome of Pan and Homo in BMC MICROBIOLOGY
  • 2014-03. Kraken: ultrafast metagenomic sequence classification using exact alignments in GENOME BIOLOGY
  • 2002-12. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs in BMC BIOINFORMATICS
  • 2010-08. Average genome size: a potential source of bias in comparative metagenomics in THE ISME JOURNAL
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/srep16498

    DOI

    http://dx.doi.org/10.1038/srep16498

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1024141769

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/26563586


    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/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "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": "Bacteria", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Dental Calculus", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Female", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gastrointestinal Microbiome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Amplification", 
            "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": "Male", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Metagenome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Metagenomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Methanobrevibacter", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Microbiota", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Nucleic Acid Conformation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA, Ribosomal, 16S", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Leiden University", 
              "id": "https://www.grid.ac/institutes/grid.5132.5", 
              "name": [
                "Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ziesemer", 
            "givenName": "Kirsten A.", 
            "id": "sg:person.01233741047.71", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01233741047.71"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Oklahoma", 
              "id": "https://www.grid.ac/institutes/grid.266900.b", 
              "name": [
                "Department of Anthropology, University of Oklahoma, Norman, OK, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mann", 
            "givenName": "Allison E.", 
            "id": "sg:person.01302054247.63", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01302054247.63"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Oklahoma", 
              "id": "https://www.grid.ac/institutes/grid.266900.b", 
              "name": [
                "Department of Anthropology, University of Oklahoma, Norman, OK, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Sankaranarayanan", 
            "givenName": "Krithivasan", 
            "id": "sg:person.0676624530.45", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676624530.45"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Copenhagen", 
              "id": "https://www.grid.ac/institutes/grid.5254.6", 
              "name": [
                "Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands", 
                "Center for Geogenetics, University of Copenhagen, Denmark"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Schroeder", 
            "givenName": "Hannes", 
            "id": "sg:person.0601055212.07", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0601055212.07"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Oklahoma", 
              "id": "https://www.grid.ac/institutes/grid.266900.b", 
              "name": [
                "Department of Anthropology, University of Oklahoma, Norman, OK, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ozga", 
            "givenName": "Andrew T.", 
            "id": "sg:person.01156750566.08", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01156750566.08"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Academic Center for Dentistry Amsterdam", 
              "id": "https://www.grid.ac/institutes/grid.424087.d", 
              "name": [
                "Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Brandt", 
            "givenName": "Bernd W.", 
            "id": "sg:person.01356040117.24", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01356040117.24"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Academic Center for Dentistry Amsterdam", 
              "id": "https://www.grid.ac/institutes/grid.424087.d", 
              "name": [
                "Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zaura", 
            "givenName": "Egija", 
            "id": "sg:person.0676564055.21", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676564055.21"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Leiden University", 
              "id": "https://www.grid.ac/institutes/grid.5132.5", 
              "name": [
                "Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Waters-Rist", 
            "givenName": "Andrea", 
            "id": "sg:person.0734202227.11", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0734202227.11"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Leiden University", 
              "id": "https://www.grid.ac/institutes/grid.5132.5", 
              "name": [
                "Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hoogland", 
            "givenName": "Menno", 
            "id": "sg:person.013363667053.59", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013363667053.59"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Max Planck Institute for Evolutionary Anthropology", 
              "id": "https://www.grid.ac/institutes/grid.419518.0", 
              "name": [
                "Department of Anthropology, University of Cape Town, South Africa", 
                "Departament de Prehist\u00f2ria i Arqueologia, Universitat de Val\u00e8ncia, Spain", 
                "Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Salazar-Garc\u00eda", 
            "givenName": "Domingo C.", 
            "id": "sg:person.011611256605.59", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011611256605.59"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of California, Merced", 
              "id": "https://www.grid.ac/institutes/grid.266096.d", 
              "name": [
                "School of Social Sciences, Humanities, and Arts, University of California, Merced, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Aldenderfer", 
            "givenName": "Mark", 
            "id": "sg:person.0763457102.18", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0763457102.18"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of York", 
              "id": "https://www.grid.ac/institutes/grid.5685.e", 
              "name": [
                "Department of Archaeology, University of York, York, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Speller", 
            "givenName": "Camilla", 
            "id": "sg:person.01067513150.73", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01067513150.73"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of York", 
              "id": "https://www.grid.ac/institutes/grid.5685.e", 
              "name": [
                "Department of Archaeology, University of York, York, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hendy", 
            "givenName": "Jessica", 
            "id": "sg:person.01023032002.49", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023032002.49"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of British Columbia", 
              "id": "https://www.grid.ac/institutes/grid.17091.3e", 
              "name": [
                "Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands", 
                "Department of Anthropology, University of British Columbia, Vancouver, Canada"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Weston", 
            "givenName": "Darlene A.", 
            "id": "sg:person.01242622060.76", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242622060.76"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of York", 
              "id": "https://www.grid.ac/institutes/grid.5685.e", 
              "name": [
                "Department of Biology, University of York, York, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "MacDonald", 
            "givenName": "Sandy J.", 
            "id": "sg:person.01046124377.99", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01046124377.99"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of York", 
              "id": "https://www.grid.ac/institutes/grid.5685.e", 
              "name": [
                "Department of Biology, University of York, York, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Thomas", 
            "givenName": "Gavin H.", 
            "id": "sg:person.012515474700.06", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012515474700.06"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of York", 
              "id": "https://www.grid.ac/institutes/grid.5685.e", 
              "name": [
                "Department of Archaeology, University of York, York, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Collins", 
            "givenName": "Matthew J.", 
            "id": "sg:person.012476270300.98", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012476270300.98"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Oklahoma", 
              "id": "https://www.grid.ac/institutes/grid.266900.b", 
              "name": [
                "Department of Anthropology, University of Oklahoma, Norman, OK, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Lewis", 
            "givenName": "Cecil M.", 
            "id": "sg:person.0627332061.87", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0627332061.87"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Leiden University", 
              "id": "https://www.grid.ac/institutes/grid.5132.5", 
              "name": [
                "Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hofman", 
            "givenName": "Corinne", 
            "id": "sg:person.01366365677.04", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366365677.04"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Oklahoma", 
              "id": "https://www.grid.ac/institutes/grid.266900.b", 
              "name": [
                "Department of Anthropology, University of Oklahoma, Norman, OK, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Warinner", 
            "givenName": "Christina", 
            "id": "sg:person.0635474650.16", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635474650.16"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1186/gb-2011-12-2-r18", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000268052", 
              "https://doi.org/10.1186/gb-2011-12-2-r18"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/9780471729259.mc01e05s27", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000284393"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms4654", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000325507", 
              "https://doi.org/10.1038/ncomms4654"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12915-014-0069-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000588445", 
              "https://doi.org/10.1186/s12915-014-0069-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12915-014-0069-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000588445", 
              "https://doi.org/10.1186/s12915-014-0069-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.1314445110", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001934759"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pone.0086251", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002076734"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1475-4754.2012.00707.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003580575"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/bies.201400160", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004096871"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.2906", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004737256", 
              "https://doi.org/10.1038/ng.2906"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11552", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004952443", 
              "https://doi.org/10.1038/nature11552"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1650", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005440831", 
              "https://doi.org/10.1038/nmeth.1650"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.1419136111", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005567414"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1923", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006541515", 
              "https://doi.org/10.1038/nmeth.1923"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-015-0611-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006687810", 
              "https://doi.org/10.1186/s13059-015-0611-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-015-0611-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006687810", 
              "https://doi.org/10.1186/s13059-015-0611-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btr087", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006798251"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11550", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007512293", 
              "https://doi.org/10.1038/nature11550"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11234", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007740093", 
              "https://doi.org/10.1038/nature11234"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/1096-8644(200007)112:3<297::aid-ajpa2>3.0.co;2-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008084193"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/1096-8644(200007)112:3<297::aid-ajpa2>3.0.co;2-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008084193"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1574-6976.1997.tb00351.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008492579"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.f.303", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009032055", 
              "https://doi.org/10.1038/nmeth.f.303"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.f.303", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009032055", 
              "https://doi.org/10.1038/nmeth.f.303"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1223490", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009915545"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btt593", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010435278"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.2066", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010611135", 
              "https://doi.org/10.1038/nmeth.2066"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pone.0051146", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010652605"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btt193", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011287846"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btt193", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011287846"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/database/baq013", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012570686"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev.genet.37.110801.143214", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014567048"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1238286", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015651351"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.3945/ajcn.112.056689", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015858527"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/(sici)1096-8644(199811)107:3<285::aid-ajpa5>3.0.co;2-u", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016119527"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.copbio.2011.11.013", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017075472"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-3-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017682287", 
              "https://doi.org/10.1186/1471-2105-3-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gks1219", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017730157"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.mimet.2003.08.009", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018463188"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1195568", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018660751"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jhevol.2014.10.016", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019933003"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/hmg/ddt398", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020777502"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1742-9994-3-11", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020979005", 
              "https://doi.org/10.1186/1742-9994-3-11"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.copbio.2012.08.005", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021983048"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btp352", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023014918"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1755-0998.2009.02824.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024049630"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1755-0998.2009.02824.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024049630"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkt1244", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024952637"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0047-2484(03)00106-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025397131"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0047-2484(03)00106-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025397131"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btq461", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025904619"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pone.0013963", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026278404"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1098/rstb.2013.0376", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026645780"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/ajpa.20314", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027092251"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/ajpa.20314", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027092251"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.2693", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028082738", 
              "https://doi.org/10.1038/nmeth.2693"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s40168-015-0094-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028795817", 
              "https://doi.org/10.1186/s40168-015-0094-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s40168-015-0094-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028795817", 
              "https://doi.org/10.1186/s40168-015-0094-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2180-13-204", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029792698", 
              "https://doi.org/10.1186/1471-2180-13-204"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/(sici)1096-8644(200002)111:2<211::aid-ajpa7>3.0.co;2-m", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029851078"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pbio.1000546", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030018023"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2014-15-3-r46", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030203790", 
              "https://doi.org/10.1186/gb-2014-15-3-r46"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jas.2006.10.019", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030483492"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.2536", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030790787", 
              "https://doi.org/10.1038/ng.2536"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2014.90", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030819817", 
              "https://doi.org/10.1038/ismej.2014.90"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1098/rspb.2012.1745", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031314963"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11319", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032682406", 
              "https://doi.org/10.1038/nature11319"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.5969107", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034259503"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1128/aem.03006-05", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034568952"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2013-14-5-r51", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034665395", 
              "https://doi.org/10.1186/gb-2013-14-5-r51"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.096651.109", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034877175"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pone.0034131", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036440628"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2012.8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038992953", 
              "https://doi.org/10.1038/ismej.2012.8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2010.29", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041772428", 
              "https://doi.org/10.1038/ismej.2010.29"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1365-313x.2011.04541.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044072615"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1128/aem.00062-07", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045980007"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1128/jb.00542-10", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046395199"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms7505", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046556597", 
              "https://doi.org/10.1038/ncomms7505"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08821", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050498034", 
              "https://doi.org/10.1038/nature08821"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08821", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050498034", 
              "https://doi.org/10.1038/nature08821"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1179/0093469012z.00000000020", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051228698"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ijpp.2013.08.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051882094"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11053", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052378845", 
              "https://doi.org/10.1038/nature11053"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jhevol.2014.06.018", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052760955"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pone.0013042", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053529462"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/pdb.prot5368", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1060411240"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/pdb.prot5448", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1060411299"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.14806/ej.17.1.200", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1067372670"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.3989/tp.2009.09025", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1071808726"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2015-12", 
        "datePublishedReg": "2015-12-01", 
        "description": "To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1038/srep16498", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2520643", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3635862", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3784301", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3793935", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1045337", 
            "issn": [
              "2045-2322"
            ], 
            "name": "Scientific Reports", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "5"
          }
        ], 
        "name": "Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification", 
        "pagination": "16498", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "73039f8c5182df01ab5dd3cdc60d99806076eeaba31d1c0fd2cd822d0edd908e"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "26563586"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "101563288"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/srep16498"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1024141769"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/srep16498", 
          "https://app.dimensions.ai/details/publication/pub.1024141769"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-10T21:24", 
        "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_8687_00000424.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://www.nature.com/articles/srep16498"
      }
    ]
     

    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/srep16498'

    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/srep16498'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/srep16498'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/srep16498'


     

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

    563 TRIPLES      21 PREDICATES      124 URIs      37 LITERALS      25 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/srep16498 schema:about N0c37d25600a0435da5c2ca26923aabab
    2 N13cd42abc18749f29377289c46813105
    3 N1c96261fa5aa4412bd38945f1f3c5632
    4 N1f44a914e51b4a86b54358c0d546c0c4
    5 N21211496310e4157be650f6f783bc4c0
    6 N28b278589d6b480087418fcb1da56d68
    7 N379cf475c9494f42b8dae966538c6e05
    8 N686b7c377616411f86cf481617fd53dc
    9 N8771ee982acf47a6b332b9e042c76f7b
    10 N8ab883e14b3c4cdfae2da0635fc02fff
    11 N9b02de06180843a69021e5d8c37f0572
    12 Na461028c0f6845e59c400d4bc5087172
    13 Na93ed10bb1de482eb91d8590b401e525
    14 Nbb9d2e22acdf4f1185610bc14a3e2978
    15 Ne0c78041e13e4db0a0d4911ec4dd8255
    16 Nf677820de20d4d1684874762019d56b9
    17 anzsrc-for:06
    18 anzsrc-for:0604
    19 schema:author N52312840e0ac4fd49fd1e817e59c9cf0
    20 schema:citation sg:pub.10.1038/ismej.2010.29
    21 sg:pub.10.1038/ismej.2012.8
    22 sg:pub.10.1038/ismej.2014.90
    23 sg:pub.10.1038/nature08821
    24 sg:pub.10.1038/nature11053
    25 sg:pub.10.1038/nature11234
    26 sg:pub.10.1038/nature11319
    27 sg:pub.10.1038/nature11550
    28 sg:pub.10.1038/nature11552
    29 sg:pub.10.1038/ncomms4654
    30 sg:pub.10.1038/ncomms7505
    31 sg:pub.10.1038/ng.2536
    32 sg:pub.10.1038/ng.2906
    33 sg:pub.10.1038/nmeth.1650
    34 sg:pub.10.1038/nmeth.1923
    35 sg:pub.10.1038/nmeth.2066
    36 sg:pub.10.1038/nmeth.2693
    37 sg:pub.10.1038/nmeth.f.303
    38 sg:pub.10.1186/1471-2105-3-2
    39 sg:pub.10.1186/1471-2180-13-204
    40 sg:pub.10.1186/1742-9994-3-11
    41 sg:pub.10.1186/gb-2011-12-2-r18
    42 sg:pub.10.1186/gb-2013-14-5-r51
    43 sg:pub.10.1186/gb-2014-15-3-r46
    44 sg:pub.10.1186/s12915-014-0069-1
    45 sg:pub.10.1186/s13059-015-0611-7
    46 sg:pub.10.1186/s40168-015-0094-5
    47 https://doi.org/10.1002/(sici)1096-8644(199811)107:3<285::aid-ajpa5>3.0.co;2-u
    48 https://doi.org/10.1002/(sici)1096-8644(200002)111:2<211::aid-ajpa7>3.0.co;2-m
    49 https://doi.org/10.1002/1096-8644(200007)112:3<297::aid-ajpa2>3.0.co;2-0
    50 https://doi.org/10.1002/9780471729259.mc01e05s27
    51 https://doi.org/10.1002/ajpa.20314
    52 https://doi.org/10.1002/bies.201400160
    53 https://doi.org/10.1016/j.copbio.2011.11.013
    54 https://doi.org/10.1016/j.copbio.2012.08.005
    55 https://doi.org/10.1016/j.ijpp.2013.08.004
    56 https://doi.org/10.1016/j.jas.2006.10.019
    57 https://doi.org/10.1016/j.jhevol.2014.06.018
    58 https://doi.org/10.1016/j.jhevol.2014.10.016
    59 https://doi.org/10.1016/j.mimet.2003.08.009
    60 https://doi.org/10.1016/s0047-2484(03)00106-4
    61 https://doi.org/10.1073/pnas.1314445110
    62 https://doi.org/10.1073/pnas.1419136111
    63 https://doi.org/10.1093/bioinformatics/btp352
    64 https://doi.org/10.1093/bioinformatics/btq461
    65 https://doi.org/10.1093/bioinformatics/btr087
    66 https://doi.org/10.1093/bioinformatics/btt193
    67 https://doi.org/10.1093/bioinformatics/btt593
    68 https://doi.org/10.1093/database/baq013
    69 https://doi.org/10.1093/hmg/ddt398
    70 https://doi.org/10.1093/nar/gks1219
    71 https://doi.org/10.1093/nar/gkt1244
    72 https://doi.org/10.1098/rspb.2012.1745
    73 https://doi.org/10.1098/rstb.2013.0376
    74 https://doi.org/10.1101/gr.096651.109
    75 https://doi.org/10.1101/gr.5969107
    76 https://doi.org/10.1101/pdb.prot5368
    77 https://doi.org/10.1101/pdb.prot5448
    78 https://doi.org/10.1111/j.1365-313x.2011.04541.x
    79 https://doi.org/10.1111/j.1475-4754.2012.00707.x
    80 https://doi.org/10.1111/j.1574-6976.1997.tb00351.x
    81 https://doi.org/10.1111/j.1755-0998.2009.02824.x
    82 https://doi.org/10.1126/science.1195568
    83 https://doi.org/10.1126/science.1223490
    84 https://doi.org/10.1126/science.1238286
    85 https://doi.org/10.1128/aem.00062-07
    86 https://doi.org/10.1128/aem.03006-05
    87 https://doi.org/10.1128/jb.00542-10
    88 https://doi.org/10.1146/annurev.genet.37.110801.143214
    89 https://doi.org/10.1179/0093469012z.00000000020
    90 https://doi.org/10.1371/journal.pbio.1000546
    91 https://doi.org/10.1371/journal.pone.0013042
    92 https://doi.org/10.1371/journal.pone.0013963
    93 https://doi.org/10.1371/journal.pone.0034131
    94 https://doi.org/10.1371/journal.pone.0051146
    95 https://doi.org/10.1371/journal.pone.0086251
    96 https://doi.org/10.14806/ej.17.1.200
    97 https://doi.org/10.3945/ajcn.112.056689
    98 https://doi.org/10.3989/tp.2009.09025
    99 schema:datePublished 2015-12
    100 schema:datePublishedReg 2015-12-01
    101 schema:description To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.
    102 schema:genre research_article
    103 schema:inLanguage en
    104 schema:isAccessibleForFree true
    105 schema:isPartOf N3ad82e9a1c06475f8bb564d398eb009e
    106 N9334ec24baf648498e0ffadf2d34a906
    107 sg:journal.1045337
    108 schema:name Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
    109 schema:pagination 16498
    110 schema:productId N036deb7fb538432aa27f424d1046b9a8
    111 N83f385a6cdfb447c9fa10dd8159bfd43
    112 Nc353a2c5ccbb49c2ab921c7cdc0d5afb
    113 Ncb7ce773f6ad402c977e23dce5345151
    114 Ncd69e372905c43128867eedda062fc1b
    115 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024141769
    116 https://doi.org/10.1038/srep16498
    117 schema:sdDatePublished 2019-04-10T21:24
    118 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    119 schema:sdPublisher Nf8d6343f41e045de8582907d1cc85b4d
    120 schema:url http://www.nature.com/articles/srep16498
    121 sgo:license sg:explorer/license/
    122 sgo:sdDataset articles
    123 rdf:type schema:ScholarlyArticle
    124 N036deb7fb538432aa27f424d1046b9a8 schema:name doi
    125 schema:value 10.1038/srep16498
    126 rdf:type schema:PropertyValue
    127 N07cceae410d848b7af1c3b4468809f9f rdf:first sg:person.01242622060.76
    128 rdf:rest Nc293bedcd881405aa2f078ceb5a2444f
    129 N0990b64205464b828623b71becacdd92 rdf:first sg:person.01156750566.08
    130 rdf:rest N2263899b16f1407695df918cfe890851
    131 N0c37d25600a0435da5c2ca26923aabab schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    132 schema:name Nucleic Acid Conformation
    133 rdf:type schema:DefinedTerm
    134 N0f7cdc6384fb43138592358cf7484bd4 rdf:first sg:person.012515474700.06
    135 rdf:rest Nad89f883d185435db592ea3c1aac5aaa
    136 N13cd42abc18749f29377289c46813105 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    137 schema:name Metagenome
    138 rdf:type schema:DefinedTerm
    139 N1c96261fa5aa4412bd38945f1f3c5632 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    140 schema:name High-Throughput Nucleotide Sequencing
    141 rdf:type schema:DefinedTerm
    142 N1db58c07dc4f4faab2503331db34b264 rdf:first sg:person.0635474650.16
    143 rdf:rest rdf:nil
    144 N1f44a914e51b4a86b54358c0d546c0c4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    145 schema:name Phylogeny
    146 rdf:type schema:DefinedTerm
    147 N21211496310e4157be650f6f783bc4c0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    148 schema:name Archaeology
    149 rdf:type schema:DefinedTerm
    150 N2263899b16f1407695df918cfe890851 rdf:first sg:person.01356040117.24
    151 rdf:rest Nb39e65d7db4540b38338f2ad01c88dc7
    152 N28b278589d6b480087418fcb1da56d68 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    153 schema:name Microbiota
    154 rdf:type schema:DefinedTerm
    155 N35bf71f5e04f4ec98c4d6f491bb9364e rdf:first sg:person.013363667053.59
    156 rdf:rest N6166d4caf544404cb31c1854548215cc
    157 N379cf475c9494f42b8dae966538c6e05 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    158 schema:name RNA, Ribosomal, 16S
    159 rdf:type schema:DefinedTerm
    160 N3ad82e9a1c06475f8bb564d398eb009e schema:volumeNumber 5
    161 rdf:type schema:PublicationVolume
    162 N4cd0cde1eb7a41aa8b56b64bd74aa728 rdf:first sg:person.01302054247.63
    163 rdf:rest N6313be44aa4746e19a0da5ddb05ada74
    164 N52312840e0ac4fd49fd1e817e59c9cf0 rdf:first sg:person.01233741047.71
    165 rdf:rest N4cd0cde1eb7a41aa8b56b64bd74aa728
    166 N6166d4caf544404cb31c1854548215cc rdf:first sg:person.011611256605.59
    167 rdf:rest N68311be86eba44a3a6b703dd1d0595e2
    168 N6313be44aa4746e19a0da5ddb05ada74 rdf:first sg:person.0676624530.45
    169 rdf:rest Nda3197fc35c9420194977b8cbbbc8849
    170 N68311be86eba44a3a6b703dd1d0595e2 rdf:first sg:person.0763457102.18
    171 rdf:rest Nb830993afebb4154ab8d936a53b3e490
    172 N686b7c377616411f86cf481617fd53dc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    173 schema:name Bacteria
    174 rdf:type schema:DefinedTerm
    175 N7044a6eaf4fe4e45ade7b0cc6966e8a1 rdf:first sg:person.01366365677.04
    176 rdf:rest N1db58c07dc4f4faab2503331db34b264
    177 N83f385a6cdfb447c9fa10dd8159bfd43 schema:name pubmed_id
    178 schema:value 26563586
    179 rdf:type schema:PropertyValue
    180 N8771ee982acf47a6b332b9e042c76f7b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    181 schema:name Methanobrevibacter
    182 rdf:type schema:DefinedTerm
    183 N8ab883e14b3c4cdfae2da0635fc02fff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    184 schema:name Male
    185 rdf:type schema:DefinedTerm
    186 N9334ec24baf648498e0ffadf2d34a906 schema:issueNumber 1
    187 rdf:type schema:PublicationIssue
    188 N991d0cc447d44a0ba814b67ee8091d64 rdf:first sg:person.01023032002.49
    189 rdf:rest N07cceae410d848b7af1c3b4468809f9f
    190 N9b02de06180843a69021e5d8c37f0572 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    191 schema:name Gastrointestinal Microbiome
    192 rdf:type schema:DefinedTerm
    193 Na461028c0f6845e59c400d4bc5087172 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    194 schema:name Female
    195 rdf:type schema:DefinedTerm
    196 Na78d7a5227d549e58ec584089a294b13 rdf:first sg:person.0734202227.11
    197 rdf:rest N35bf71f5e04f4ec98c4d6f491bb9364e
    198 Na93ed10bb1de482eb91d8590b401e525 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    199 schema:name Metagenomics
    200 rdf:type schema:DefinedTerm
    201 Nad89f883d185435db592ea3c1aac5aaa rdf:first sg:person.012476270300.98
    202 rdf:rest Nd442a247b1e249cc86577330bcc0766b
    203 Nb39e65d7db4540b38338f2ad01c88dc7 rdf:first sg:person.0676564055.21
    204 rdf:rest Na78d7a5227d549e58ec584089a294b13
    205 Nb830993afebb4154ab8d936a53b3e490 rdf:first sg:person.01067513150.73
    206 rdf:rest N991d0cc447d44a0ba814b67ee8091d64
    207 Nbb9d2e22acdf4f1185610bc14a3e2978 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    208 schema:name Gene Amplification
    209 rdf:type schema:DefinedTerm
    210 Nc293bedcd881405aa2f078ceb5a2444f rdf:first sg:person.01046124377.99
    211 rdf:rest N0f7cdc6384fb43138592358cf7484bd4
    212 Nc353a2c5ccbb49c2ab921c7cdc0d5afb schema:name readcube_id
    213 schema:value 73039f8c5182df01ab5dd3cdc60d99806076eeaba31d1c0fd2cd822d0edd908e
    214 rdf:type schema:PropertyValue
    215 Ncb7ce773f6ad402c977e23dce5345151 schema:name dimensions_id
    216 schema:value pub.1024141769
    217 rdf:type schema:PropertyValue
    218 Ncd69e372905c43128867eedda062fc1b schema:name nlm_unique_id
    219 schema:value 101563288
    220 rdf:type schema:PropertyValue
    221 Nd442a247b1e249cc86577330bcc0766b rdf:first sg:person.0627332061.87
    222 rdf:rest N7044a6eaf4fe4e45ade7b0cc6966e8a1
    223 Nda3197fc35c9420194977b8cbbbc8849 rdf:first sg:person.0601055212.07
    224 rdf:rest N0990b64205464b828623b71becacdd92
    225 Ne0c78041e13e4db0a0d4911ec4dd8255 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    226 schema:name Dental Calculus
    227 rdf:type schema:DefinedTerm
    228 Nf677820de20d4d1684874762019d56b9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    229 schema:name Humans
    230 rdf:type schema:DefinedTerm
    231 Nf8d6343f41e045de8582907d1cc85b4d schema:name Springer Nature - SN SciGraph project
    232 rdf:type schema:Organization
    233 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    234 schema:name Biological Sciences
    235 rdf:type schema:DefinedTerm
    236 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    237 schema:name Genetics
    238 rdf:type schema:DefinedTerm
    239 sg:grant.2520643 http://pending.schema.org/fundedItem sg:pub.10.1038/srep16498
    240 rdf:type schema:MonetaryGrant
    241 sg:grant.3635862 http://pending.schema.org/fundedItem sg:pub.10.1038/srep16498
    242 rdf:type schema:MonetaryGrant
    243 sg:grant.3784301 http://pending.schema.org/fundedItem sg:pub.10.1038/srep16498
    244 rdf:type schema:MonetaryGrant
    245 sg:grant.3793935 http://pending.schema.org/fundedItem sg:pub.10.1038/srep16498
    246 rdf:type schema:MonetaryGrant
    247 sg:journal.1045337 schema:issn 2045-2322
    248 schema:name Scientific Reports
    249 rdf:type schema:Periodical
    250 sg:person.01023032002.49 schema:affiliation https://www.grid.ac/institutes/grid.5685.e
    251 schema:familyName Hendy
    252 schema:givenName Jessica
    253 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023032002.49
    254 rdf:type schema:Person
    255 sg:person.01046124377.99 schema:affiliation https://www.grid.ac/institutes/grid.5685.e
    256 schema:familyName MacDonald
    257 schema:givenName Sandy J.
    258 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01046124377.99
    259 rdf:type schema:Person
    260 sg:person.01067513150.73 schema:affiliation https://www.grid.ac/institutes/grid.5685.e
    261 schema:familyName Speller
    262 schema:givenName Camilla
    263 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01067513150.73
    264 rdf:type schema:Person
    265 sg:person.01156750566.08 schema:affiliation https://www.grid.ac/institutes/grid.266900.b
    266 schema:familyName Ozga
    267 schema:givenName Andrew T.
    268 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01156750566.08
    269 rdf:type schema:Person
    270 sg:person.011611256605.59 schema:affiliation https://www.grid.ac/institutes/grid.419518.0
    271 schema:familyName Salazar-García
    272 schema:givenName Domingo C.
    273 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011611256605.59
    274 rdf:type schema:Person
    275 sg:person.01233741047.71 schema:affiliation https://www.grid.ac/institutes/grid.5132.5
    276 schema:familyName Ziesemer
    277 schema:givenName Kirsten A.
    278 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01233741047.71
    279 rdf:type schema:Person
    280 sg:person.01242622060.76 schema:affiliation https://www.grid.ac/institutes/grid.17091.3e
    281 schema:familyName Weston
    282 schema:givenName Darlene A.
    283 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242622060.76
    284 rdf:type schema:Person
    285 sg:person.012476270300.98 schema:affiliation https://www.grid.ac/institutes/grid.5685.e
    286 schema:familyName Collins
    287 schema:givenName Matthew J.
    288 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012476270300.98
    289 rdf:type schema:Person
    290 sg:person.012515474700.06 schema:affiliation https://www.grid.ac/institutes/grid.5685.e
    291 schema:familyName Thomas
    292 schema:givenName Gavin H.
    293 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012515474700.06
    294 rdf:type schema:Person
    295 sg:person.01302054247.63 schema:affiliation https://www.grid.ac/institutes/grid.266900.b
    296 schema:familyName Mann
    297 schema:givenName Allison E.
    298 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01302054247.63
    299 rdf:type schema:Person
    300 sg:person.013363667053.59 schema:affiliation https://www.grid.ac/institutes/grid.5132.5
    301 schema:familyName Hoogland
    302 schema:givenName Menno
    303 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013363667053.59
    304 rdf:type schema:Person
    305 sg:person.01356040117.24 schema:affiliation https://www.grid.ac/institutes/grid.424087.d
    306 schema:familyName Brandt
    307 schema:givenName Bernd W.
    308 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01356040117.24
    309 rdf:type schema:Person
    310 sg:person.01366365677.04 schema:affiliation https://www.grid.ac/institutes/grid.5132.5
    311 schema:familyName Hofman
    312 schema:givenName Corinne
    313 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366365677.04
    314 rdf:type schema:Person
    315 sg:person.0601055212.07 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
    316 schema:familyName Schroeder
    317 schema:givenName Hannes
    318 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0601055212.07
    319 rdf:type schema:Person
    320 sg:person.0627332061.87 schema:affiliation https://www.grid.ac/institutes/grid.266900.b
    321 schema:familyName Lewis
    322 schema:givenName Cecil M.
    323 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0627332061.87
    324 rdf:type schema:Person
    325 sg:person.0635474650.16 schema:affiliation https://www.grid.ac/institutes/grid.266900.b
    326 schema:familyName Warinner
    327 schema:givenName Christina
    328 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635474650.16
    329 rdf:type schema:Person
    330 sg:person.0676564055.21 schema:affiliation https://www.grid.ac/institutes/grid.424087.d
    331 schema:familyName Zaura
    332 schema:givenName Egija
    333 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676564055.21
    334 rdf:type schema:Person
    335 sg:person.0676624530.45 schema:affiliation https://www.grid.ac/institutes/grid.266900.b
    336 schema:familyName Sankaranarayanan
    337 schema:givenName Krithivasan
    338 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676624530.45
    339 rdf:type schema:Person
    340 sg:person.0734202227.11 schema:affiliation https://www.grid.ac/institutes/grid.5132.5
    341 schema:familyName Waters-Rist
    342 schema:givenName Andrea
    343 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0734202227.11
    344 rdf:type schema:Person
    345 sg:person.0763457102.18 schema:affiliation https://www.grid.ac/institutes/grid.266096.d
    346 schema:familyName Aldenderfer
    347 schema:givenName Mark
    348 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0763457102.18
    349 rdf:type schema:Person
    350 sg:pub.10.1038/ismej.2010.29 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041772428
    351 https://doi.org/10.1038/ismej.2010.29
    352 rdf:type schema:CreativeWork
    353 sg:pub.10.1038/ismej.2012.8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038992953
    354 https://doi.org/10.1038/ismej.2012.8
    355 rdf:type schema:CreativeWork
    356 sg:pub.10.1038/ismej.2014.90 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030819817
    357 https://doi.org/10.1038/ismej.2014.90
    358 rdf:type schema:CreativeWork
    359 sg:pub.10.1038/nature08821 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050498034
    360 https://doi.org/10.1038/nature08821
    361 rdf:type schema:CreativeWork
    362 sg:pub.10.1038/nature11053 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052378845
    363 https://doi.org/10.1038/nature11053
    364 rdf:type schema:CreativeWork
    365 sg:pub.10.1038/nature11234 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007740093
    366 https://doi.org/10.1038/nature11234
    367 rdf:type schema:CreativeWork
    368 sg:pub.10.1038/nature11319 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032682406
    369 https://doi.org/10.1038/nature11319
    370 rdf:type schema:CreativeWork
    371 sg:pub.10.1038/nature11550 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007512293
    372 https://doi.org/10.1038/nature11550
    373 rdf:type schema:CreativeWork
    374 sg:pub.10.1038/nature11552 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004952443
    375 https://doi.org/10.1038/nature11552
    376 rdf:type schema:CreativeWork
    377 sg:pub.10.1038/ncomms4654 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000325507
    378 https://doi.org/10.1038/ncomms4654
    379 rdf:type schema:CreativeWork
    380 sg:pub.10.1038/ncomms7505 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046556597
    381 https://doi.org/10.1038/ncomms7505
    382 rdf:type schema:CreativeWork
    383 sg:pub.10.1038/ng.2536 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030790787
    384 https://doi.org/10.1038/ng.2536
    385 rdf:type schema:CreativeWork
    386 sg:pub.10.1038/ng.2906 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004737256
    387 https://doi.org/10.1038/ng.2906
    388 rdf:type schema:CreativeWork
    389 sg:pub.10.1038/nmeth.1650 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005440831
    390 https://doi.org/10.1038/nmeth.1650
    391 rdf:type schema:CreativeWork
    392 sg:pub.10.1038/nmeth.1923 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006541515
    393 https://doi.org/10.1038/nmeth.1923
    394 rdf:type schema:CreativeWork
    395 sg:pub.10.1038/nmeth.2066 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010611135
    396 https://doi.org/10.1038/nmeth.2066
    397 rdf:type schema:CreativeWork
    398 sg:pub.10.1038/nmeth.2693 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028082738
    399 https://doi.org/10.1038/nmeth.2693
    400 rdf:type schema:CreativeWork
    401 sg:pub.10.1038/nmeth.f.303 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009032055
    402 https://doi.org/10.1038/nmeth.f.303
    403 rdf:type schema:CreativeWork
    404 sg:pub.10.1186/1471-2105-3-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017682287
    405 https://doi.org/10.1186/1471-2105-3-2
    406 rdf:type schema:CreativeWork
    407 sg:pub.10.1186/1471-2180-13-204 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029792698
    408 https://doi.org/10.1186/1471-2180-13-204
    409 rdf:type schema:CreativeWork
    410 sg:pub.10.1186/1742-9994-3-11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020979005
    411 https://doi.org/10.1186/1742-9994-3-11
    412 rdf:type schema:CreativeWork
    413 sg:pub.10.1186/gb-2011-12-2-r18 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000268052
    414 https://doi.org/10.1186/gb-2011-12-2-r18
    415 rdf:type schema:CreativeWork
    416 sg:pub.10.1186/gb-2013-14-5-r51 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034665395
    417 https://doi.org/10.1186/gb-2013-14-5-r51
    418 rdf:type schema:CreativeWork
    419 sg:pub.10.1186/gb-2014-15-3-r46 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030203790
    420 https://doi.org/10.1186/gb-2014-15-3-r46
    421 rdf:type schema:CreativeWork
    422 sg:pub.10.1186/s12915-014-0069-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000588445
    423 https://doi.org/10.1186/s12915-014-0069-1
    424 rdf:type schema:CreativeWork
    425 sg:pub.10.1186/s13059-015-0611-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006687810
    426 https://doi.org/10.1186/s13059-015-0611-7
    427 rdf:type schema:CreativeWork
    428 sg:pub.10.1186/s40168-015-0094-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028795817
    429 https://doi.org/10.1186/s40168-015-0094-5
    430 rdf:type schema:CreativeWork
    431 https://doi.org/10.1002/(sici)1096-8644(199811)107:3<285::aid-ajpa5>3.0.co;2-u schema:sameAs https://app.dimensions.ai/details/publication/pub.1016119527
    432 rdf:type schema:CreativeWork
    433 https://doi.org/10.1002/(sici)1096-8644(200002)111:2<211::aid-ajpa7>3.0.co;2-m schema:sameAs https://app.dimensions.ai/details/publication/pub.1029851078
    434 rdf:type schema:CreativeWork
    435 https://doi.org/10.1002/1096-8644(200007)112:3<297::aid-ajpa2>3.0.co;2-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008084193
    436 rdf:type schema:CreativeWork
    437 https://doi.org/10.1002/9780471729259.mc01e05s27 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000284393
    438 rdf:type schema:CreativeWork
    439 https://doi.org/10.1002/ajpa.20314 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027092251
    440 rdf:type schema:CreativeWork
    441 https://doi.org/10.1002/bies.201400160 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004096871
    442 rdf:type schema:CreativeWork
    443 https://doi.org/10.1016/j.copbio.2011.11.013 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017075472
    444 rdf:type schema:CreativeWork
    445 https://doi.org/10.1016/j.copbio.2012.08.005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021983048
    446 rdf:type schema:CreativeWork
    447 https://doi.org/10.1016/j.ijpp.2013.08.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051882094
    448 rdf:type schema:CreativeWork
    449 https://doi.org/10.1016/j.jas.2006.10.019 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030483492
    450 rdf:type schema:CreativeWork
    451 https://doi.org/10.1016/j.jhevol.2014.06.018 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052760955
    452 rdf:type schema:CreativeWork
    453 https://doi.org/10.1016/j.jhevol.2014.10.016 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019933003
    454 rdf:type schema:CreativeWork
    455 https://doi.org/10.1016/j.mimet.2003.08.009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018463188
    456 rdf:type schema:CreativeWork
    457 https://doi.org/10.1016/s0047-2484(03)00106-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025397131
    458 rdf:type schema:CreativeWork
    459 https://doi.org/10.1073/pnas.1314445110 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001934759
    460 rdf:type schema:CreativeWork
    461 https://doi.org/10.1073/pnas.1419136111 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005567414
    462 rdf:type schema:CreativeWork
    463 https://doi.org/10.1093/bioinformatics/btp352 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023014918
    464 rdf:type schema:CreativeWork
    465 https://doi.org/10.1093/bioinformatics/btq461 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025904619
    466 rdf:type schema:CreativeWork
    467 https://doi.org/10.1093/bioinformatics/btr087 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006798251
    468 rdf:type schema:CreativeWork
    469 https://doi.org/10.1093/bioinformatics/btt193 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011287846
    470 rdf:type schema:CreativeWork
    471 https://doi.org/10.1093/bioinformatics/btt593 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010435278
    472 rdf:type schema:CreativeWork
    473 https://doi.org/10.1093/database/baq013 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012570686
    474 rdf:type schema:CreativeWork
    475 https://doi.org/10.1093/hmg/ddt398 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020777502
    476 rdf:type schema:CreativeWork
    477 https://doi.org/10.1093/nar/gks1219 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017730157
    478 rdf:type schema:CreativeWork
    479 https://doi.org/10.1093/nar/gkt1244 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024952637
    480 rdf:type schema:CreativeWork
    481 https://doi.org/10.1098/rspb.2012.1745 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031314963
    482 rdf:type schema:CreativeWork
    483 https://doi.org/10.1098/rstb.2013.0376 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026645780
    484 rdf:type schema:CreativeWork
    485 https://doi.org/10.1101/gr.096651.109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034877175
    486 rdf:type schema:CreativeWork
    487 https://doi.org/10.1101/gr.5969107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034259503
    488 rdf:type schema:CreativeWork
    489 https://doi.org/10.1101/pdb.prot5368 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060411240
    490 rdf:type schema:CreativeWork
    491 https://doi.org/10.1101/pdb.prot5448 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060411299
    492 rdf:type schema:CreativeWork
    493 https://doi.org/10.1111/j.1365-313x.2011.04541.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1044072615
    494 rdf:type schema:CreativeWork
    495 https://doi.org/10.1111/j.1475-4754.2012.00707.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1003580575
    496 rdf:type schema:CreativeWork
    497 https://doi.org/10.1111/j.1574-6976.1997.tb00351.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1008492579
    498 rdf:type schema:CreativeWork
    499 https://doi.org/10.1111/j.1755-0998.2009.02824.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1024049630
    500 rdf:type schema:CreativeWork
    501 https://doi.org/10.1126/science.1195568 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018660751
    502 rdf:type schema:CreativeWork
    503 https://doi.org/10.1126/science.1223490 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009915545
    504 rdf:type schema:CreativeWork
    505 https://doi.org/10.1126/science.1238286 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015651351
    506 rdf:type schema:CreativeWork
    507 https://doi.org/10.1128/aem.00062-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045980007
    508 rdf:type schema:CreativeWork
    509 https://doi.org/10.1128/aem.03006-05 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034568952
    510 rdf:type schema:CreativeWork
    511 https://doi.org/10.1128/jb.00542-10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046395199
    512 rdf:type schema:CreativeWork
    513 https://doi.org/10.1146/annurev.genet.37.110801.143214 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014567048
    514 rdf:type schema:CreativeWork
    515 https://doi.org/10.1179/0093469012z.00000000020 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051228698
    516 rdf:type schema:CreativeWork
    517 https://doi.org/10.1371/journal.pbio.1000546 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030018023
    518 rdf:type schema:CreativeWork
    519 https://doi.org/10.1371/journal.pone.0013042 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053529462
    520 rdf:type schema:CreativeWork
    521 https://doi.org/10.1371/journal.pone.0013963 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026278404
    522 rdf:type schema:CreativeWork
    523 https://doi.org/10.1371/journal.pone.0034131 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036440628
    524 rdf:type schema:CreativeWork
    525 https://doi.org/10.1371/journal.pone.0051146 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010652605
    526 rdf:type schema:CreativeWork
    527 https://doi.org/10.1371/journal.pone.0086251 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002076734
    528 rdf:type schema:CreativeWork
    529 https://doi.org/10.14806/ej.17.1.200 schema:sameAs https://app.dimensions.ai/details/publication/pub.1067372670
    530 rdf:type schema:CreativeWork
    531 https://doi.org/10.3945/ajcn.112.056689 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015858527
    532 rdf:type schema:CreativeWork
    533 https://doi.org/10.3989/tp.2009.09025 schema:sameAs https://app.dimensions.ai/details/publication/pub.1071808726
    534 rdf:type schema:CreativeWork
    535 https://www.grid.ac/institutes/grid.17091.3e schema:alternateName University of British Columbia
    536 schema:name Department of Anthropology, University of British Columbia, Vancouver, Canada
    537 Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
    538 rdf:type schema:Organization
    539 https://www.grid.ac/institutes/grid.266096.d schema:alternateName University of California, Merced
    540 schema:name School of Social Sciences, Humanities, and Arts, University of California, Merced, USA
    541 rdf:type schema:Organization
    542 https://www.grid.ac/institutes/grid.266900.b schema:alternateName University of Oklahoma
    543 schema:name Department of Anthropology, University of Oklahoma, Norman, OK, USA
    544 rdf:type schema:Organization
    545 https://www.grid.ac/institutes/grid.419518.0 schema:alternateName Max Planck Institute for Evolutionary Anthropology
    546 schema:name Departament de Prehistòria i Arqueologia, Universitat de València, Spain
    547 Department of Anthropology, University of Cape Town, South Africa
    548 Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    549 rdf:type schema:Organization
    550 https://www.grid.ac/institutes/grid.424087.d schema:alternateName Academic Center for Dentistry Amsterdam
    551 schema:name Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands
    552 rdf:type schema:Organization
    553 https://www.grid.ac/institutes/grid.5132.5 schema:alternateName Leiden University
    554 schema:name Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
    555 rdf:type schema:Organization
    556 https://www.grid.ac/institutes/grid.5254.6 schema:alternateName University of Copenhagen
    557 schema:name Center for Geogenetics, University of Copenhagen, Denmark
    558 Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
    559 rdf:type schema:Organization
    560 https://www.grid.ac/institutes/grid.5685.e schema:alternateName University of York
    561 schema:name Department of Archaeology, University of York, York, UK
    562 Department of Biology, University of York, York, UK
    563 rdf:type schema:Organization
     




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


    ...