Dynamics of metatranscription in the inflammatory bowel disease gut microbiome View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-01-08

AUTHORS

Melanie Schirmer, Eric A. Franzosa, Jason Lloyd-Price, Lauren J. McIver, Randall Schwager, Tiffany W. Poon, Ashwin N. Ananthakrishnan, Elizabeth Andrews, Gildardo Barron, Kathleen Lake, Mahadev Prasad, Jenny Sauk, Betsy Stevens, Robin G. Wilson, Jonathan Braun, Lee A. Denson, Subra Kugathasan, Dermot P. B. McGovern, Hera Vlamakis, Ramnik J. Xavier, Curtis Huttenhower

ABSTRACT

Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes and metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn’s disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study’s results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD. More... »

PAGES

337-346

Journal

TITLE

Nature Microbiology

ISSUE

3

VOLUME

3

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41564-017-0089-z

DOI

http://dx.doi.org/10.1038/s41564-017-0089-z

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1099939086

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/29311644


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/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "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/2008/0605", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Microbiology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Adolescent", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Adult", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Child", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Colitis, Ulcerative", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Crohn Disease", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Dysbiosis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Feces", 
        "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 Expression Profiling", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Inflammatory Bowel Diseases", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Longitudinal Studies", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Male", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Metagenomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phenotype", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Young Adult", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "The Broad Institute of MIT and Harvard, Cambridge, MA, USA", 
            "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Schirmer", 
        "givenName": "Melanie", 
        "id": "sg:person.0735243706.58", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0735243706.58"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "The Broad Institute of MIT and Harvard, Cambridge, MA, USA", 
            "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Franzosa", 
        "givenName": "Eric A.", 
        "id": "sg:person.0772302366.11", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772302366.11"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "The Broad Institute of MIT and Harvard, Cambridge, MA, USA", 
            "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lloyd-Price", 
        "givenName": "Jason", 
        "id": "sg:person.01305635227.39", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305635227.39"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "The Broad Institute of MIT and Harvard, Cambridge, MA, USA", 
            "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "McIver", 
        "givenName": "Lauren J.", 
        "id": "sg:person.0735340465.29", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0735340465.29"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Schwager", 
        "givenName": "Randall", 
        "id": "sg:person.015641574201.36", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015641574201.36"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The Broad Institute of MIT and Harvard, Cambridge, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "The Broad Institute of MIT and Harvard, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Poon", 
        "givenName": "Tiffany W.", 
        "id": "sg:person.01070777175.16", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01070777175.16"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.32224.35", 
          "name": [
            "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ananthakrishnan", 
        "givenName": "Ashwin N.", 
        "id": "sg:person.01162263474.10", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01162263474.10"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.32224.35", 
          "name": [
            "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Andrews", 
        "givenName": "Elizabeth", 
        "id": "sg:person.010766323545.03", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010766323545.03"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA", 
          "id": "http://www.grid.ac/institutes/grid.50956.3f", 
          "name": [
            "The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Barron", 
        "givenName": "Gildardo", 
        "id": "sg:person.0616153736.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0616153736.46"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.239573.9", 
          "name": [
            "Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lake", 
        "givenName": "Kathleen", 
        "id": "sg:person.01120622312.65", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01120622312.65"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA", 
          "id": "http://www.grid.ac/institutes/grid.189967.8", 
          "name": [
            "Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Prasad", 
        "givenName": "Mahadev", 
        "id": "sg:person.01050244072.18", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050244072.18"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Vatche and Tamar Manoukian Division of Digestive Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA", 
          "id": "http://www.grid.ac/institutes/grid.19006.3e", 
          "name": [
            "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA", 
            "Vatche and Tamar Manoukian Division of Digestive Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sauk", 
        "givenName": "Jenny", 
        "id": "sg:person.0734646245.51", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0734646245.51"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.32224.35", 
          "name": [
            "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stevens", 
        "givenName": "Betsy", 
        "id": "sg:person.0617342215.97", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0617342215.97"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.32224.35", 
          "name": [
            "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wilson", 
        "givenName": "Robin G.", 
        "id": "sg:person.01107263510.81", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01107263510.81"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA", 
          "id": "http://www.grid.ac/institutes/grid.19006.3e", 
          "name": [
            "Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Braun", 
        "givenName": "Jonathan", 
        "id": "sg:person.01157070417.56", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157070417.56"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH, USA", 
          "id": "http://www.grid.ac/institutes/grid.239573.9", 
          "name": [
            "Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Denson", 
        "givenName": "Lee A.", 
        "id": "sg:person.01066161527.57", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01066161527.57"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Children\u2019s Healthcare of Atlanta, Atlanta, GA, USA", 
          "id": "http://www.grid.ac/institutes/grid.428158.2", 
          "name": [
            "Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA", 
            "Children\u2019s Healthcare of Atlanta, Atlanta, GA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kugathasan", 
        "givenName": "Subra", 
        "id": "sg:person.01147172155.49", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01147172155.49"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA", 
          "id": "http://www.grid.ac/institutes/grid.50956.3f", 
          "name": [
            "The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "McGovern", 
        "givenName": "Dermot P. B.", 
        "id": "sg:person.012743332661.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012743332661.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The Broad Institute of MIT and Harvard, Cambridge, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "The Broad Institute of MIT and Harvard, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Vlamakis", 
        "givenName": "Hera", 
        "id": "sg:person.0773476547.34", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773476547.34"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.116068.8", 
          "name": [
            "The Broad Institute of MIT and Harvard, Cambridge, MA, USA", 
            "Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA", 
            "Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA", 
            "Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Xavier", 
        "givenName": "Ramnik J.", 
        "id": "sg:person.0717130066.82", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717130066.82"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "The Broad Institute of MIT and Harvard, Cambridge, MA, USA", 
            "Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Huttenhower", 
        "givenName": "Curtis", 
        "id": "sg:person.01214462502.85", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01214462502.85"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/ismej.2015.127", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006611214", 
          "https://doi.org/10.1038/ismej.2015.127"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.3589", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028162909", 
          "https://doi.org/10.1038/nmeth.3589"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrc3613", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012572377", 
          "https://doi.org/10.1038/nrc3613"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrgastro.2015.150", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003936311", 
          "https://doi.org/10.1038/nrgastro.2015.150"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.3176", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023901695", 
          "https://doi.org/10.1038/nmeth.3176"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ncomms7528", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047959844", 
          "https://doi.org/10.1038/ncomms7528"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s11302-015-9475-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044492550", 
          "https://doi.org/10.1007/s11302-015-9475-2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmicrobiol.2017.4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1083801915", 
          "https://doi.org/10.1038/nmicrobiol.2017.4"
        ], 
        "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.10.1038/nature11209", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027248000", 
          "https://doi.org/10.1038/nature11209"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2012-13-9-r79", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029450096", 
          "https://doi.org/10.1186/gb-2012-13-9-r79"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-90-481-9078-2_6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005457539", 
          "https://doi.org/10.1007/978-90-481-9078-2_6"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2018-01-08", 
    "datePublishedReg": "2018-01-08", 
    "description": "Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes\u00a0and\u00a0metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn\u2019s disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study\u2019s results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.", 
    "genre": "article", 
    "id": "sg:pub.10.1038/s41564-017-0089-z", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2436126", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2500444", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.3806830", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.5475480", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2439042", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2690017", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2439002", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1052984", 
        "issn": [
          "2058-5276"
        ], 
        "name": "Nature Microbiology", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "3", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "3"
      }
    ], 
    "keywords": [
      "inflammatory bowel disease", 
      "microbial gene expression", 
      "Human Microbiome Project", 
      "species-specific biases", 
      "genomic abundance", 
      "predominant transcription", 
      "Integrative Human Microbiome Project", 
      "gut microbiome", 
      "different organisms", 
      "metagenomic abundance", 
      "microbiome functionality", 
      "non-IBD control patients", 
      "transcriptional activity", 
      "transcript levels", 
      "microbial organisms", 
      "gene expression", 
      "individual microorganisms", 
      "Microbiome Project", 
      "gut microorganisms", 
      "metagenomic profiles", 
      "fecal metagenomes", 
      "functional potential", 
      "exacerbation of IBD", 
      "organisms", 
      "microbial characteristics", 
      "phenotypical changes", 
      "aberrant immune response", 
      "metagenomes", 
      "transcription", 
      "microbiome", 
      "informative relative", 
      "microbial factors", 
      "abundance", 
      "bowel disease", 
      "ulcerative colitis", 
      "control patients", 
      "digestive tract", 
      "Crohn's disease", 
      "microorganisms", 
      "inflamed gut", 
      "chronic diseases", 
      "pathway", 
      "immune response", 
      "potential insights", 
      "expression", 
      "disease", 
      "patients", 
      "metatranscriptomes", 
      "gut", 
      "millions of people", 
      "RNA", 
      "DNA", 
      "insights", 
      "host", 
      "dysbioses", 
      "activity", 
      "colitis", 
      "exacerbation", 
      "study results", 
      "tract", 
      "relatives", 
      "dynamics", 
      "mechanism", 
      "role", 
      "onset", 
      "group", 
      "response", 
      "individuals", 
      "period", 
      "loss", 
      "consequences", 
      "factors", 
      "levels", 
      "presence", 
      "cases", 
      "millions", 
      "results", 
      "measures", 
      "potential", 
      "profile", 
      "changes", 
      "people", 
      "functionality", 
      "time", 
      "characteristics", 
      "biases", 
      "gap", 
      "first results", 
      "strength", 
      "project"
    ], 
    "name": "Dynamics of metatranscription in the inflammatory bowel disease gut microbiome", 
    "pagination": "337-346", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1099939086"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/s41564-017-0089-z"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "29311644"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/s41564-017-0089-z", 
      "https://app.dimensions.ai/details/publication/pub.1099939086"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-08-04T17:06", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220804/entities/gbq_results/article/article_789.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1038/s41564-017-0089-z"
  }
]
 

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/s41564-017-0089-z'

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/s41564-017-0089-z'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41564-017-0089-z'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41564-017-0089-z'


 

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

460 TRIPLES      21 PREDICATES      146 URIs      125 LITERALS      25 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/s41564-017-0089-z schema:about N0aff1365b2d5418da2e02fe6d893907a
2 N10f9a47c75da4f7b95a215d6ed196ba7
3 N14b18ed93f9a4d84a8d3567e4d6c4511
4 N29c7d68ab90c4f15a737d473978d506b
5 N2ce738f75f3c438cb724b4034d15b9ba
6 N31b1d1b283ff459985d311aac777b314
7 N341cae67d8874d0cb13c2f3c5b037fc2
8 N4106f22734994a68aec943141e26ba64
9 N446af7e229ab40aca34789bcda8ea7e6
10 N5e5ec55929b7428d97c1d44c3e5553bf
11 N791247176e854b81be3578f9d9ee3418
12 N820cfc14f36448d3b21c1800d6508c60
13 Na43a3e769c784ae18f7f4bb133e7f8d3
14 Nc039c602ec0d4181bfb237e02f34cda6
15 Nca901a8be4b04551b315cdbe6a9685ff
16 Nd195f1910a974b2ca20d3fce38d9d597
17 Neafa9fa5d9394beba552b909a94069ba
18 Nedaf945aeb334639a992a3433025c6a6
19 anzsrc-for:06
20 anzsrc-for:0604
21 anzsrc-for:0605
22 schema:author N66f7de56e2bc4fc480e69aa36fadb508
23 schema:citation sg:pub.10.1007/978-90-481-9078-2_6
24 sg:pub.10.1007/s11302-015-9475-2
25 sg:pub.10.1038/ismej.2015.127
26 sg:pub.10.1038/nature11209
27 sg:pub.10.1038/ncomms7528
28 sg:pub.10.1038/nmeth.1923
29 sg:pub.10.1038/nmeth.3176
30 sg:pub.10.1038/nmeth.3589
31 sg:pub.10.1038/nmicrobiol.2017.4
32 sg:pub.10.1038/nrc3613
33 sg:pub.10.1038/nrgastro.2015.150
34 sg:pub.10.1186/gb-2012-13-9-r79
35 schema:datePublished 2018-01-08
36 schema:datePublishedReg 2018-01-08
37 schema:description Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes and metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn’s disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study’s results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.
38 schema:genre article
39 schema:isAccessibleForFree true
40 schema:isPartOf N3ad987da45d9450781c89ccd4aaa8b48
41 N701ccedfdf8f4ca3a2b0a006f6526a4e
42 sg:journal.1052984
43 schema:keywords Crohn's disease
44 DNA
45 Human Microbiome Project
46 Integrative Human Microbiome Project
47 Microbiome Project
48 RNA
49 aberrant immune response
50 abundance
51 activity
52 biases
53 bowel disease
54 cases
55 changes
56 characteristics
57 chronic diseases
58 colitis
59 consequences
60 control patients
61 different organisms
62 digestive tract
63 disease
64 dynamics
65 dysbioses
66 exacerbation
67 exacerbation of IBD
68 expression
69 factors
70 fecal metagenomes
71 first results
72 functional potential
73 functionality
74 gap
75 gene expression
76 genomic abundance
77 group
78 gut
79 gut microbiome
80 gut microorganisms
81 host
82 immune response
83 individual microorganisms
84 individuals
85 inflamed gut
86 inflammatory bowel disease
87 informative relative
88 insights
89 levels
90 loss
91 measures
92 mechanism
93 metagenomes
94 metagenomic abundance
95 metagenomic profiles
96 metatranscriptomes
97 microbial characteristics
98 microbial factors
99 microbial gene expression
100 microbial organisms
101 microbiome
102 microbiome functionality
103 microorganisms
104 millions
105 millions of people
106 non-IBD control patients
107 onset
108 organisms
109 pathway
110 patients
111 people
112 period
113 phenotypical changes
114 potential
115 potential insights
116 predominant transcription
117 presence
118 profile
119 project
120 relatives
121 response
122 results
123 role
124 species-specific biases
125 strength
126 study results
127 time
128 tract
129 transcript levels
130 transcription
131 transcriptional activity
132 ulcerative colitis
133 schema:name Dynamics of metatranscription in the inflammatory bowel disease gut microbiome
134 schema:pagination 337-346
135 schema:productId N1ba2ad1475f143ccaf814afc08802ebf
136 N292d9976392345ffbbeb813e2b25d37a
137 N7a375c1bc9d74eabaf9789efdc2f51dc
138 schema:sameAs https://app.dimensions.ai/details/publication/pub.1099939086
139 https://doi.org/10.1038/s41564-017-0089-z
140 schema:sdDatePublished 2022-08-04T17:06
141 schema:sdLicense https://scigraph.springernature.com/explorer/license/
142 schema:sdPublisher N51ce96997ba34ba4811dd3e8d0ab0f92
143 schema:url https://doi.org/10.1038/s41564-017-0089-z
144 sgo:license sg:explorer/license/
145 sgo:sdDataset articles
146 rdf:type schema:ScholarlyArticle
147 N01343bc6867e4975bc54aae47e39a4d6 rdf:first sg:person.0617342215.97
148 rdf:rest N9addd50adf49411e8b14160d6547b89f
149 N06e6fdf9baba4e568320cebe4b2078d3 rdf:first sg:person.01305635227.39
150 rdf:rest N3dc86d7a16fa4a6f8b0d1cda79cfa3b0
151 N0aff1365b2d5418da2e02fe6d893907a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
152 schema:name Adult
153 rdf:type schema:DefinedTerm
154 N0b1fe5ea72e34e6f92b53039ca2c09b4 rdf:first sg:person.012743332661.02
155 rdf:rest N3a8b156f91de411794394b503f647eb3
156 N10f9a47c75da4f7b95a215d6ed196ba7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
157 schema:name Phenotype
158 rdf:type schema:DefinedTerm
159 N13665350e1eb42b5b02342d97d2da2c5 rdf:first sg:person.01120622312.65
160 rdf:rest Nc0727e5dc00f4d98b965c05c23e2a882
161 N14b18ed93f9a4d84a8d3567e4d6c4511 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
162 schema:name Crohn Disease
163 rdf:type schema:DefinedTerm
164 N160bf20c4e1e43baba4623d25874a9c0 rdf:first sg:person.010766323545.03
165 rdf:rest Nbe2951b734e946709eb4d183d4e97ca1
166 N1aa31c869d25467c82b6e0c12ec7f7ab rdf:first sg:person.01147172155.49
167 rdf:rest N0b1fe5ea72e34e6f92b53039ca2c09b4
168 N1ba2ad1475f143ccaf814afc08802ebf schema:name doi
169 schema:value 10.1038/s41564-017-0089-z
170 rdf:type schema:PropertyValue
171 N292d9976392345ffbbeb813e2b25d37a schema:name dimensions_id
172 schema:value pub.1099939086
173 rdf:type schema:PropertyValue
174 N29c7d68ab90c4f15a737d473978d506b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
175 schema:name Longitudinal Studies
176 rdf:type schema:DefinedTerm
177 N2a2e06e169cd46ab885497aac2cf8887 rdf:first sg:person.01066161527.57
178 rdf:rest N1aa31c869d25467c82b6e0c12ec7f7ab
179 N2ce738f75f3c438cb724b4034d15b9ba schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
180 schema:name Dysbiosis
181 rdf:type schema:DefinedTerm
182 N31b1d1b283ff459985d311aac777b314 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
183 schema:name Female
184 rdf:type schema:DefinedTerm
185 N341cae67d8874d0cb13c2f3c5b037fc2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
186 schema:name Adolescent
187 rdf:type schema:DefinedTerm
188 N3a8b156f91de411794394b503f647eb3 rdf:first sg:person.0773476547.34
189 rdf:rest Ndd94f0199f7046d7be6347d0d98db287
190 N3ad987da45d9450781c89ccd4aaa8b48 schema:volumeNumber 3
191 rdf:type schema:PublicationVolume
192 N3dc86d7a16fa4a6f8b0d1cda79cfa3b0 rdf:first sg:person.0735340465.29
193 rdf:rest N678d19fd13be4b96a3f6ef55f8e02af8
194 N3f47b7638c964673bb0e0065eb3f4bfe rdf:first sg:person.01162263474.10
195 rdf:rest N160bf20c4e1e43baba4623d25874a9c0
196 N4106f22734994a68aec943141e26ba64 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
197 schema:name Metagenomics
198 rdf:type schema:DefinedTerm
199 N446af7e229ab40aca34789bcda8ea7e6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
200 schema:name Gene Expression Profiling
201 rdf:type schema:DefinedTerm
202 N51ce96997ba34ba4811dd3e8d0ab0f92 schema:name Springer Nature - SN SciGraph project
203 rdf:type schema:Organization
204 N5e5ec55929b7428d97c1d44c3e5553bf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
205 schema:name Gastrointestinal Microbiome
206 rdf:type schema:DefinedTerm
207 N62ea6df222914a62b87386985ccfa690 rdf:first sg:person.01214462502.85
208 rdf:rest rdf:nil
209 N66f7de56e2bc4fc480e69aa36fadb508 rdf:first sg:person.0735243706.58
210 rdf:rest N8d7895f1221a4cb3b79bf680a1792b62
211 N678d19fd13be4b96a3f6ef55f8e02af8 rdf:first sg:person.015641574201.36
212 rdf:rest N94f8a3b581da4a3e933eee53df88888c
213 N701ccedfdf8f4ca3a2b0a006f6526a4e schema:issueNumber 3
214 rdf:type schema:PublicationIssue
215 N791247176e854b81be3578f9d9ee3418 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
216 schema:name Transcription, Genetic
217 rdf:type schema:DefinedTerm
218 N7a375c1bc9d74eabaf9789efdc2f51dc schema:name pubmed_id
219 schema:value 29311644
220 rdf:type schema:PropertyValue
221 N820cfc14f36448d3b21c1800d6508c60 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
222 schema:name Inflammatory Bowel Diseases
223 rdf:type schema:DefinedTerm
224 N8d7895f1221a4cb3b79bf680a1792b62 rdf:first sg:person.0772302366.11
225 rdf:rest N06e6fdf9baba4e568320cebe4b2078d3
226 N94f8a3b581da4a3e933eee53df88888c rdf:first sg:person.01070777175.16
227 rdf:rest N3f47b7638c964673bb0e0065eb3f4bfe
228 N9addd50adf49411e8b14160d6547b89f rdf:first sg:person.01107263510.81
229 rdf:rest Nd76d69e9513a43938397bb06ad9f9951
230 Na43a3e769c784ae18f7f4bb133e7f8d3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
231 schema:name Humans
232 rdf:type schema:DefinedTerm
233 Nbe2951b734e946709eb4d183d4e97ca1 rdf:first sg:person.0616153736.46
234 rdf:rest N13665350e1eb42b5b02342d97d2da2c5
235 Nc039c602ec0d4181bfb237e02f34cda6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
236 schema:name Young Adult
237 rdf:type schema:DefinedTerm
238 Nc0727e5dc00f4d98b965c05c23e2a882 rdf:first sg:person.01050244072.18
239 rdf:rest Nf782d906bad04121a023b3ff8dcc3953
240 Nca901a8be4b04551b315cdbe6a9685ff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
241 schema:name Male
242 rdf:type schema:DefinedTerm
243 Nd195f1910a974b2ca20d3fce38d9d597 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
244 schema:name Child
245 rdf:type schema:DefinedTerm
246 Nd76d69e9513a43938397bb06ad9f9951 rdf:first sg:person.01157070417.56
247 rdf:rest N2a2e06e169cd46ab885497aac2cf8887
248 Ndd94f0199f7046d7be6347d0d98db287 rdf:first sg:person.0717130066.82
249 rdf:rest N62ea6df222914a62b87386985ccfa690
250 Neafa9fa5d9394beba552b909a94069ba schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
251 schema:name Feces
252 rdf:type schema:DefinedTerm
253 Nedaf945aeb334639a992a3433025c6a6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
254 schema:name Colitis, Ulcerative
255 rdf:type schema:DefinedTerm
256 Nf782d906bad04121a023b3ff8dcc3953 rdf:first sg:person.0734646245.51
257 rdf:rest N01343bc6867e4975bc54aae47e39a4d6
258 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
259 schema:name Biological Sciences
260 rdf:type schema:DefinedTerm
261 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
262 schema:name Genetics
263 rdf:type schema:DefinedTerm
264 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
265 schema:name Microbiology
266 rdf:type schema:DefinedTerm
267 sg:grant.2436126 http://pending.schema.org/fundedItem sg:pub.10.1038/s41564-017-0089-z
268 rdf:type schema:MonetaryGrant
269 sg:grant.2439002 http://pending.schema.org/fundedItem sg:pub.10.1038/s41564-017-0089-z
270 rdf:type schema:MonetaryGrant
271 sg:grant.2439042 http://pending.schema.org/fundedItem sg:pub.10.1038/s41564-017-0089-z
272 rdf:type schema:MonetaryGrant
273 sg:grant.2500444 http://pending.schema.org/fundedItem sg:pub.10.1038/s41564-017-0089-z
274 rdf:type schema:MonetaryGrant
275 sg:grant.2690017 http://pending.schema.org/fundedItem sg:pub.10.1038/s41564-017-0089-z
276 rdf:type schema:MonetaryGrant
277 sg:grant.3806830 http://pending.schema.org/fundedItem sg:pub.10.1038/s41564-017-0089-z
278 rdf:type schema:MonetaryGrant
279 sg:grant.5475480 http://pending.schema.org/fundedItem sg:pub.10.1038/s41564-017-0089-z
280 rdf:type schema:MonetaryGrant
281 sg:journal.1052984 schema:issn 2058-5276
282 schema:name Nature Microbiology
283 schema:publisher Springer Nature
284 rdf:type schema:Periodical
285 sg:person.01050244072.18 schema:affiliation grid-institutes:grid.189967.8
286 schema:familyName Prasad
287 schema:givenName Mahadev
288 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050244072.18
289 rdf:type schema:Person
290 sg:person.01066161527.57 schema:affiliation grid-institutes:grid.239573.9
291 schema:familyName Denson
292 schema:givenName Lee A.
293 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01066161527.57
294 rdf:type schema:Person
295 sg:person.01070777175.16 schema:affiliation grid-institutes:grid.66859.34
296 schema:familyName Poon
297 schema:givenName Tiffany W.
298 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01070777175.16
299 rdf:type schema:Person
300 sg:person.010766323545.03 schema:affiliation grid-institutes:grid.32224.35
301 schema:familyName Andrews
302 schema:givenName Elizabeth
303 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010766323545.03
304 rdf:type schema:Person
305 sg:person.01107263510.81 schema:affiliation grid-institutes:grid.32224.35
306 schema:familyName Wilson
307 schema:givenName Robin G.
308 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01107263510.81
309 rdf:type schema:Person
310 sg:person.01120622312.65 schema:affiliation grid-institutes:grid.239573.9
311 schema:familyName Lake
312 schema:givenName Kathleen
313 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01120622312.65
314 rdf:type schema:Person
315 sg:person.01147172155.49 schema:affiliation grid-institutes:grid.428158.2
316 schema:familyName Kugathasan
317 schema:givenName Subra
318 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01147172155.49
319 rdf:type schema:Person
320 sg:person.01157070417.56 schema:affiliation grid-institutes:grid.19006.3e
321 schema:familyName Braun
322 schema:givenName Jonathan
323 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157070417.56
324 rdf:type schema:Person
325 sg:person.01162263474.10 schema:affiliation grid-institutes:grid.32224.35
326 schema:familyName Ananthakrishnan
327 schema:givenName Ashwin N.
328 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01162263474.10
329 rdf:type schema:Person
330 sg:person.01214462502.85 schema:affiliation grid-institutes:grid.38142.3c
331 schema:familyName Huttenhower
332 schema:givenName Curtis
333 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01214462502.85
334 rdf:type schema:Person
335 sg:person.012743332661.02 schema:affiliation grid-institutes:grid.50956.3f
336 schema:familyName McGovern
337 schema:givenName Dermot P. B.
338 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012743332661.02
339 rdf:type schema:Person
340 sg:person.01305635227.39 schema:affiliation grid-institutes:grid.38142.3c
341 schema:familyName Lloyd-Price
342 schema:givenName Jason
343 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01305635227.39
344 rdf:type schema:Person
345 sg:person.015641574201.36 schema:affiliation grid-institutes:grid.38142.3c
346 schema:familyName Schwager
347 schema:givenName Randall
348 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015641574201.36
349 rdf:type schema:Person
350 sg:person.0616153736.46 schema:affiliation grid-institutes:grid.50956.3f
351 schema:familyName Barron
352 schema:givenName Gildardo
353 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0616153736.46
354 rdf:type schema:Person
355 sg:person.0617342215.97 schema:affiliation grid-institutes:grid.32224.35
356 schema:familyName Stevens
357 schema:givenName Betsy
358 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0617342215.97
359 rdf:type schema:Person
360 sg:person.0717130066.82 schema:affiliation grid-institutes:grid.116068.8
361 schema:familyName Xavier
362 schema:givenName Ramnik J.
363 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717130066.82
364 rdf:type schema:Person
365 sg:person.0734646245.51 schema:affiliation grid-institutes:grid.19006.3e
366 schema:familyName Sauk
367 schema:givenName Jenny
368 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0734646245.51
369 rdf:type schema:Person
370 sg:person.0735243706.58 schema:affiliation grid-institutes:grid.38142.3c
371 schema:familyName Schirmer
372 schema:givenName Melanie
373 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0735243706.58
374 rdf:type schema:Person
375 sg:person.0735340465.29 schema:affiliation grid-institutes:grid.38142.3c
376 schema:familyName McIver
377 schema:givenName Lauren J.
378 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0735340465.29
379 rdf:type schema:Person
380 sg:person.0772302366.11 schema:affiliation grid-institutes:grid.38142.3c
381 schema:familyName Franzosa
382 schema:givenName Eric A.
383 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772302366.11
384 rdf:type schema:Person
385 sg:person.0773476547.34 schema:affiliation grid-institutes:grid.66859.34
386 schema:familyName Vlamakis
387 schema:givenName Hera
388 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773476547.34
389 rdf:type schema:Person
390 sg:pub.10.1007/978-90-481-9078-2_6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005457539
391 https://doi.org/10.1007/978-90-481-9078-2_6
392 rdf:type schema:CreativeWork
393 sg:pub.10.1007/s11302-015-9475-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044492550
394 https://doi.org/10.1007/s11302-015-9475-2
395 rdf:type schema:CreativeWork
396 sg:pub.10.1038/ismej.2015.127 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006611214
397 https://doi.org/10.1038/ismej.2015.127
398 rdf:type schema:CreativeWork
399 sg:pub.10.1038/nature11209 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027248000
400 https://doi.org/10.1038/nature11209
401 rdf:type schema:CreativeWork
402 sg:pub.10.1038/ncomms7528 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047959844
403 https://doi.org/10.1038/ncomms7528
404 rdf:type schema:CreativeWork
405 sg:pub.10.1038/nmeth.1923 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006541515
406 https://doi.org/10.1038/nmeth.1923
407 rdf:type schema:CreativeWork
408 sg:pub.10.1038/nmeth.3176 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023901695
409 https://doi.org/10.1038/nmeth.3176
410 rdf:type schema:CreativeWork
411 sg:pub.10.1038/nmeth.3589 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028162909
412 https://doi.org/10.1038/nmeth.3589
413 rdf:type schema:CreativeWork
414 sg:pub.10.1038/nmicrobiol.2017.4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1083801915
415 https://doi.org/10.1038/nmicrobiol.2017.4
416 rdf:type schema:CreativeWork
417 sg:pub.10.1038/nrc3613 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012572377
418 https://doi.org/10.1038/nrc3613
419 rdf:type schema:CreativeWork
420 sg:pub.10.1038/nrgastro.2015.150 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003936311
421 https://doi.org/10.1038/nrgastro.2015.150
422 rdf:type schema:CreativeWork
423 sg:pub.10.1186/gb-2012-13-9-r79 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029450096
424 https://doi.org/10.1186/gb-2012-13-9-r79
425 rdf:type schema:CreativeWork
426 grid-institutes:grid.116068.8 schema:alternateName Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
427 schema:name Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
428 Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
429 Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
430 The Broad Institute of MIT and Harvard, Cambridge, MA, USA
431 rdf:type schema:Organization
432 grid-institutes:grid.189967.8 schema:alternateName Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
433 schema:name Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
434 rdf:type schema:Organization
435 grid-institutes:grid.19006.3e schema:alternateName Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
436 Vatche and Tamar Manoukian Division of Digestive Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
437 schema:name Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
438 Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
439 Vatche and Tamar Manoukian Division of Digestive Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
440 rdf:type schema:Organization
441 grid-institutes:grid.239573.9 schema:alternateName Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
442 schema:name Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
443 rdf:type schema:Organization
444 grid-institutes:grid.32224.35 schema:alternateName Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
445 schema:name Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
446 rdf:type schema:Organization
447 grid-institutes:grid.38142.3c schema:alternateName Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
448 schema:name Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
449 The Broad Institute of MIT and Harvard, Cambridge, MA, USA
450 rdf:type schema:Organization
451 grid-institutes:grid.428158.2 schema:alternateName Children’s Healthcare of Atlanta, Atlanta, GA, USA
452 schema:name Children’s Healthcare of Atlanta, Atlanta, GA, USA
453 Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
454 rdf:type schema:Organization
455 grid-institutes:grid.50956.3f schema:alternateName The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
456 schema:name The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
457 rdf:type schema:Organization
458 grid-institutes:grid.66859.34 schema:alternateName The Broad Institute of MIT and Harvard, Cambridge, MA, USA
459 schema:name The Broad Institute of MIT and Harvard, Cambridge, MA, USA
460 rdf:type schema:Organization
 




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


...