Microbiota of De-Novo Pediatric IBD: Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-10-09

AUTHORS

Richard Hansen, Richard K Russell, Caroline Reiff, Petra Louis, Freda McIntosh, Susan H Berry, Indrani Mukhopadhya, W Michael Bisset, Andy R Barclay, Jon Bishop, Diana M Flynn, Paraic McGrogan, Sabarinathan Loganathan, Gamal Mahdi, Harry J Flint, Emad M El-Omar, Georgina L Hold

ABSTRACT

OBJECTIVES: The gastrointestinal microbiota is considered important in inflammatory bowel disease (IBD) pathogenesis. Discoveries from established disease cohorts report reduced bacterial diversity, changes in bacterial composition, and a protective role for Faecalibacterium prausnitzii in Crohn's disease (CD). The majority of studies to date are however potentially confounded by the effect of treatment and a reliance on established rather than de-novo disease. METHODS: Microbial changes at diagnosis were examined by biopsying the colonic mucosa of 37 children: 25 with newly presenting, untreated IBD with active colitis (13 CD and 12 ulcerative colitis (UC)), and 12 pediatric controls with a macroscopically and microscopically normal colon. We utilized a dual-methodology approach with pyrosequencing (threshold >10,000 reads) and confirmatory real-time PCR (RT-PCR). RESULTS: Threshold pyrosequencing output was obtained on 34 subjects (11 CD, 11 UC, 12 controls). No significant changes were noted at phylum level among the Bacteroidetes, Firmicutes, or Proteobacteria. A significant reduction in bacterial α-diversity was noted in CD vs. controls by three methods (Shannon, Simpson, and phylogenetic diversity) but not in UC vs. controls. An increase in Faecalibacterium was observed in CD compared with controls by pyrosequencing (mean 16.7% vs. 9.1% of reads, P=0.02) and replicated by specific F. prausnitzii RT-PCR (36.0% vs. 19.0% of total bacteria, P=0.02). No disease-specific clustering was evident on principal components analysis. CONCLUSIONS: Our results offer a comprehensive examination of the IBD mucosal microbiota at diagnosis, unaffected by therapeutic confounders or changes over time. Our results challenge the current model of a protective role for F. prausnitzii in CD, suggesting a more dynamic role for this organism than previously described. More... »

PAGES

1913

Journal

TITLE

The American Journal of Gastroenterology

ISSUE

12

VOLUME

107

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ajg.2012.335

DOI

http://dx.doi.org/10.1038/ajg.2012.335

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1017259214

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/23044767


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/2008/11", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Medical and Health Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/1103", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Clinical Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Adolescent", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Child", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Clostridium", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Colitis, Ulcerative", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Colony Count, Microbial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Crohn Disease", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Female", 
        "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": "Male", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Real-Time Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Child Health, Royal Aberdeen Children's Hospital, University of Aberdeen, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK", 
            "Child Health, Royal Aberdeen Children's Hospital, University of Aberdeen, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hansen", 
        "givenName": "Richard", 
        "id": "sg:person.016336561600.90", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016336561600.90"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK", 
          "id": "http://www.grid.ac/institutes/grid.415571.3", 
          "name": [
            "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Russell", 
        "givenName": "Richard K", 
        "id": "sg:person.014036667402.97", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014036667402.97"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Max Planck Institute, Cologne, Germany", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Max Planck Institute, Cologne, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Reiff", 
        "givenName": "Caroline", 
        "id": "sg:person.01266313660.51", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01266313660.51"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gut Health Programme, Rowett Institute, University of Aberdeen, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gut Health Programme, Rowett Institute, University of Aberdeen, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Louis", 
        "givenName": "Petra", 
        "id": "sg:person.0715265632.22", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0715265632.22"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gut Health Programme, Rowett Institute, University of Aberdeen, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gut Health Programme, Rowett Institute, University of Aberdeen, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "McIntosh", 
        "givenName": "Freda", 
        "id": "sg:person.0714640405.30", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714640405.30"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Berry", 
        "givenName": "Susan H", 
        "id": "sg:person.01315040754.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315040754.46"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mukhopadhya", 
        "givenName": "Indrani", 
        "id": "sg:person.01234470761.11", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01234470761.11"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Paediatric Gastroenterology, Royal Aberdeen Children's Hospital, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.416072.6", 
          "name": [
            "Department of Paediatric Gastroenterology, Royal Aberdeen Children's Hospital, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bisset", 
        "givenName": "W Michael", 
        "id": "sg:person.01056401531.08", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01056401531.08"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK", 
          "id": "http://www.grid.ac/institutes/grid.415571.3", 
          "name": [
            "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Barclay", 
        "givenName": "Andy R", 
        "id": "sg:person.01070225054.99", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01070225054.99"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK", 
          "id": "http://www.grid.ac/institutes/grid.415571.3", 
          "name": [
            "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bishop", 
        "givenName": "Jon", 
        "id": "sg:person.01204453454.42", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01204453454.42"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK", 
          "id": "http://www.grid.ac/institutes/grid.415571.3", 
          "name": [
            "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Flynn", 
        "givenName": "Diana M", 
        "id": "sg:person.01062432661.50", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01062432661.50"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK", 
          "id": "http://www.grid.ac/institutes/grid.415571.3", 
          "name": [
            "Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "McGrogan", 
        "givenName": "Paraic", 
        "id": "sg:person.01246102213.92", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01246102213.92"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Paediatric Gastroenterology, Royal Aberdeen Children's Hospital, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.416072.6", 
          "name": [
            "Department of Paediatric Gastroenterology, Royal Aberdeen Children's Hospital, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Loganathan", 
        "givenName": "Sabarinathan", 
        "id": "sg:person.0757637554.63", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0757637554.63"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Paediatric Gastroenterology, Royal Aberdeen Children's Hospital, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.416072.6", 
          "name": [
            "Department of Paediatric Gastroenterology, Royal Aberdeen Children's Hospital, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mahdi", 
        "givenName": "Gamal", 
        "id": "sg:person.0636724513.94", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0636724513.94"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gut Health Programme, Rowett Institute, University of Aberdeen, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gut Health Programme, Rowett Institute, University of Aberdeen, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Flint", 
        "givenName": "Harry J", 
        "id": "sg:person.01021722152.69", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021722152.69"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "El-Omar", 
        "givenName": "Emad M", 
        "id": "sg:person.0700142176.81", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700142176.81"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hold", 
        "givenName": "Georgina L", 
        "id": "sg:person.01015442527.89", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01015442527.89"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/nri2515", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004447638", 
          "https://doi.org/10.1038/nri2515"
        ], 
        "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": "sg:pub.10.1038/nature07008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006761326", 
          "https://doi.org/10.1038/nature07008"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ni.1823", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033326093", 
          "https://doi.org/10.1038/ni.1823"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.489", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047391697", 
          "https://doi.org/10.1038/ng.489"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2180-11-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004777032", 
          "https://doi.org/10.1186/1471-2180-11-7"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ismej.2012.5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051087848", 
          "https://doi.org/10.1038/ismej.2012.5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nm.2069", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042587063", 
          "https://doi.org/10.1038/nm.2069"
        ], 
        "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.10.1038/nrgastro.2012.14", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032491276", 
          "https://doi.org/10.1038/nrgastro.2012.14"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2012-10-09", 
    "datePublishedReg": "2012-10-09", 
    "description": "OBJECTIVES: The gastrointestinal microbiota is considered important in inflammatory bowel disease (IBD) pathogenesis. Discoveries from established disease cohorts report reduced bacterial diversity, changes in bacterial composition, and a protective role for Faecalibacterium prausnitzii in Crohn's disease (CD). The majority of studies to date are however potentially confounded by the effect of treatment and a reliance on established rather than de-novo disease.\nMETHODS: Microbial changes at diagnosis were examined by biopsying the colonic mucosa of 37 children: 25 with newly presenting, untreated IBD with active colitis (13 CD and 12 ulcerative colitis (UC)), and 12 pediatric controls with a macroscopically and microscopically normal colon. We utilized a dual-methodology approach with pyrosequencing (threshold >10,000 reads) and confirmatory real-time PCR (RT-PCR).\nRESULTS: Threshold pyrosequencing output was obtained on 34 subjects (11 CD, 11 UC, 12 controls). No significant changes were noted at phylum level among the Bacteroidetes, Firmicutes, or Proteobacteria. A significant reduction in bacterial \u03b1-diversity was noted in CD vs. controls by three methods (Shannon, Simpson, and phylogenetic diversity) but not in UC vs. controls. An increase in Faecalibacterium was observed in CD compared with controls by pyrosequencing (mean 16.7% vs. 9.1% of reads, P=0.02) and replicated by specific F. prausnitzii RT-PCR (36.0% vs. 19.0% of total bacteria, P=0.02). No disease-specific clustering was evident on principal components analysis.\nCONCLUSIONS: Our results offer a comprehensive examination of the IBD mucosal microbiota at diagnosis, unaffected by therapeutic confounders or changes over time. Our results challenge the current model of a protective role for F. prausnitzii in CD, suggesting a more dynamic role for this organism than previously described.", 
    "genre": "article", 
    "id": "sg:pub.10.1038/ajg.2012.335", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.5151000", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1412991", 
        "issn": [
          "0002-9270", 
          "1572-0241"
        ], 
        "name": "The American Journal of Gastroenterology", 
        "publisher": "Wolters Kluwer", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "12", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "107"
      }
    ], 
    "keywords": [
      "Crohn's disease", 
      "protective role", 
      "Faecalibacterium prausnitzii", 
      "inflammatory bowel disease (IBD) pathogenesis", 
      "de novo disease", 
      "confirmatory real-time PCR", 
      "effect of treatment", 
      "active colitis", 
      "therapeutic confounders", 
      "pediatric IBD", 
      "ulcerative colitis", 
      "pediatric controls", 
      "colonic mucosa", 
      "real-time PCR", 
      "disease cohort", 
      "mucosal microbiota", 
      "disease pathogenesis", 
      "F. prausnitzii", 
      "majority of studies", 
      "normal colon", 
      "gastrointestinal microbiota", 
      "reduced bacterial diversity", 
      "RT-PCR", 
      "disease", 
      "prausnitzii", 
      "colitis", 
      "significant reduction", 
      "microbiota", 
      "IBD", 
      "diagnosis", 
      "significant changes", 
      "microbial changes", 
      "phylum level", 
      "bacterial composition", 
      "Crohn's", 
      "comprehensive examination", 
      "confounders", 
      "mucosa", 
      "pathogenesis", 
      "cohort", 
      "colon", 
      "Faecalibacterium", 
      "control", 
      "role", 
      "treatment", 
      "children", 
      "changes", 
      "examination", 
      "subjects", 
      "\u03b1-diversity", 
      "PCR", 
      "UC", 
      "majority", 
      "dynamic role", 
      "levels", 
      "bacterial diversity", 
      "study", 
      "increase", 
      "date", 
      "reduction", 
      "effect", 
      "pyrosequencing", 
      "results", 
      "threshold", 
      "bacterial \u03b1-diversity", 
      "Firmicutes", 
      "Bacteroidetes", 
      "discovery", 
      "principal component analysis", 
      "time", 
      "analysis", 
      "current models", 
      "organisms", 
      "component analysis", 
      "method", 
      "reliance", 
      "model", 
      "output", 
      "approach", 
      "Proteobacteria", 
      "diversity", 
      "clustering", 
      "composition"
    ], 
    "name": "Microbiota of De-Novo Pediatric IBD: Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis", 
    "pagination": "1913", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1017259214"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/ajg.2012.335"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "23044767"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/ajg.2012.335", 
      "https://app.dimensions.ai/details/publication/pub.1017259214"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-12-01T06:29", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20221201/entities/gbq_results/article/article_554.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1038/ajg.2012.335"
  }
]
 

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/ajg.2012.335'

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/ajg.2012.335'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/ajg.2012.335'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/ajg.2012.335'


 

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

355 TRIPLES      21 PREDICATES      129 URIs      111 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/ajg.2012.335 schema:about N2150b89041164e0ea03926cadaace7ae
2 N434fa0611f2944e39ecd9f3ec7ae3dbc
3 N4406403dcdfa4b1b8b887b0e4c8494f5
4 N5c671a90d1034cd2a37b9952753dc8d6
5 N6c09d8f27e544a0bb3cb33b770561a6b
6 N9e72fb4a85dd497390e8e6fd7ce5a7db
7 Na329f5274c214070815a6f5eee12f570
8 Naa38b0d290ab482f8aa45c17f7bdfd24
9 Nabc6df1388c0474084c7771b6d2d2f4c
10 Nb69d93423438488fbf02c8aabecec8be
11 Nbd8d6b7b0cba40fda3b4434e2e10dfa1
12 anzsrc-for:11
13 anzsrc-for:1103
14 schema:author N76f3b63d7f2b44b7be46a364ff6fb140
15 schema:citation sg:pub.10.1038/ismej.2012.5
16 sg:pub.10.1038/nature07008
17 sg:pub.10.1038/nature11209
18 sg:pub.10.1038/nature11234
19 sg:pub.10.1038/ng.489
20 sg:pub.10.1038/ni.1823
21 sg:pub.10.1038/nm.2069
22 sg:pub.10.1038/nrgastro.2012.14
23 sg:pub.10.1038/nri2515
24 sg:pub.10.1186/1471-2180-11-7
25 schema:datePublished 2012-10-09
26 schema:datePublishedReg 2012-10-09
27 schema:description OBJECTIVES: The gastrointestinal microbiota is considered important in inflammatory bowel disease (IBD) pathogenesis. Discoveries from established disease cohorts report reduced bacterial diversity, changes in bacterial composition, and a protective role for Faecalibacterium prausnitzii in Crohn's disease (CD). The majority of studies to date are however potentially confounded by the effect of treatment and a reliance on established rather than de-novo disease. METHODS: Microbial changes at diagnosis were examined by biopsying the colonic mucosa of 37 children: 25 with newly presenting, untreated IBD with active colitis (13 CD and 12 ulcerative colitis (UC)), and 12 pediatric controls with a macroscopically and microscopically normal colon. We utilized a dual-methodology approach with pyrosequencing (threshold >10,000 reads) and confirmatory real-time PCR (RT-PCR). RESULTS: Threshold pyrosequencing output was obtained on 34 subjects (11 CD, 11 UC, 12 controls). No significant changes were noted at phylum level among the Bacteroidetes, Firmicutes, or Proteobacteria. A significant reduction in bacterial α-diversity was noted in CD vs. controls by three methods (Shannon, Simpson, and phylogenetic diversity) but not in UC vs. controls. An increase in Faecalibacterium was observed in CD compared with controls by pyrosequencing (mean 16.7% vs. 9.1% of reads, P=0.02) and replicated by specific F. prausnitzii RT-PCR (36.0% vs. 19.0% of total bacteria, P=0.02). No disease-specific clustering was evident on principal components analysis. CONCLUSIONS: Our results offer a comprehensive examination of the IBD mucosal microbiota at diagnosis, unaffected by therapeutic confounders or changes over time. Our results challenge the current model of a protective role for F. prausnitzii in CD, suggesting a more dynamic role for this organism than previously described.
28 schema:genre article
29 schema:isAccessibleForFree true
30 schema:isPartOf N8d42cff9931b435f8474237da4607042
31 Nd3f4cfabae0542e4920a3086686201cf
32 sg:journal.1412991
33 schema:keywords Bacteroidetes
34 Crohn's
35 Crohn's disease
36 F. prausnitzii
37 Faecalibacterium
38 Faecalibacterium prausnitzii
39 Firmicutes
40 IBD
41 PCR
42 Proteobacteria
43 RT-PCR
44 UC
45 active colitis
46 analysis
47 approach
48 bacterial composition
49 bacterial diversity
50 bacterial α-diversity
51 changes
52 children
53 clustering
54 cohort
55 colitis
56 colon
57 colonic mucosa
58 component analysis
59 composition
60 comprehensive examination
61 confirmatory real-time PCR
62 confounders
63 control
64 current models
65 date
66 de novo disease
67 diagnosis
68 discovery
69 disease
70 disease cohort
71 disease pathogenesis
72 diversity
73 dynamic role
74 effect
75 effect of treatment
76 examination
77 gastrointestinal microbiota
78 increase
79 inflammatory bowel disease (IBD) pathogenesis
80 levels
81 majority
82 majority of studies
83 method
84 microbial changes
85 microbiota
86 model
87 mucosa
88 mucosal microbiota
89 normal colon
90 organisms
91 output
92 pathogenesis
93 pediatric IBD
94 pediatric controls
95 phylum level
96 prausnitzii
97 principal component analysis
98 protective role
99 pyrosequencing
100 real-time PCR
101 reduced bacterial diversity
102 reduction
103 reliance
104 results
105 role
106 significant changes
107 significant reduction
108 study
109 subjects
110 therapeutic confounders
111 threshold
112 time
113 treatment
114 ulcerative colitis
115 α-diversity
116 schema:name Microbiota of De-Novo Pediatric IBD: Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis
117 schema:pagination 1913
118 schema:productId N29fb775251974eee9989df6d9cc16f23
119 Nc2d902f67f8e43d38887a3468b754933
120 Ne9a2117b22d54362a63d6b846e9eb5d1
121 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017259214
122 https://doi.org/10.1038/ajg.2012.335
123 schema:sdDatePublished 2022-12-01T06:29
124 schema:sdLicense https://scigraph.springernature.com/explorer/license/
125 schema:sdPublisher N7e1688c351164810a366f7028792c907
126 schema:url https://doi.org/10.1038/ajg.2012.335
127 sgo:license sg:explorer/license/
128 sgo:sdDataset articles
129 rdf:type schema:ScholarlyArticle
130 N0a1fffb72faf471fa63b225cd0932ec1 rdf:first sg:person.01234470761.11
131 rdf:rest N5a074ae226294186995cf92563e18c64
132 N165c9e82245a41e9b187fbea35377ccb rdf:first sg:person.014036667402.97
133 rdf:rest Ndd44a4d6ac56499485b782f042c0b753
134 N1f6640bb181342e1bba211cd48673704 rdf:first sg:person.01204453454.42
135 rdf:rest Nd7bb9f7bc1384e2ba9ea070de136c3d7
136 N2150b89041164e0ea03926cadaace7ae schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
137 schema:name Humans
138 rdf:type schema:DefinedTerm
139 N27b7de5952534493a2466b9132d9857a rdf:first sg:person.0700142176.81
140 rdf:rest Nf93ad94e51a242f99a7205fd9c265b0f
141 N29fb775251974eee9989df6d9cc16f23 schema:name pubmed_id
142 schema:value 23044767
143 rdf:type schema:PropertyValue
144 N434fa0611f2944e39ecd9f3ec7ae3dbc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
145 schema:name Clostridium
146 rdf:type schema:DefinedTerm
147 N4406403dcdfa4b1b8b887b0e4c8494f5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
148 schema:name Female
149 rdf:type schema:DefinedTerm
150 N5a074ae226294186995cf92563e18c64 rdf:first sg:person.01056401531.08
151 rdf:rest N777e8bac252e486a99a5b8f6ce0a0b83
152 N5c671a90d1034cd2a37b9952753dc8d6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
153 schema:name Child
154 rdf:type schema:DefinedTerm
155 N63137406282345fabb017cbff2caa47c rdf:first sg:person.01246102213.92
156 rdf:rest Nb2a99d90937e4506b0fd1ee24f9b8ed9
157 N6c09d8f27e544a0bb3cb33b770561a6b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
158 schema:name Adolescent
159 rdf:type schema:DefinedTerm
160 N76f3b63d7f2b44b7be46a364ff6fb140 rdf:first sg:person.016336561600.90
161 rdf:rest N165c9e82245a41e9b187fbea35377ccb
162 N777e8bac252e486a99a5b8f6ce0a0b83 rdf:first sg:person.01070225054.99
163 rdf:rest N1f6640bb181342e1bba211cd48673704
164 N7e1688c351164810a366f7028792c907 schema:name Springer Nature - SN SciGraph project
165 rdf:type schema:Organization
166 N80665ffa274043c1989d731916921d2d rdf:first sg:person.01315040754.46
167 rdf:rest N0a1fffb72faf471fa63b225cd0932ec1
168 N8d42cff9931b435f8474237da4607042 schema:volumeNumber 107
169 rdf:type schema:PublicationVolume
170 N9435688b50d94124bdba5c0a46d8c125 rdf:first sg:person.0715265632.22
171 rdf:rest Na3628f5cf55e403f984921e0156b458a
172 N9e72fb4a85dd497390e8e6fd7ce5a7db schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
173 schema:name Crohn Disease
174 rdf:type schema:DefinedTerm
175 Na329f5274c214070815a6f5eee12f570 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
176 schema:name Inflammatory Bowel Diseases
177 rdf:type schema:DefinedTerm
178 Na3628f5cf55e403f984921e0156b458a rdf:first sg:person.0714640405.30
179 rdf:rest N80665ffa274043c1989d731916921d2d
180 Naa38b0d290ab482f8aa45c17f7bdfd24 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
181 schema:name Colony Count, Microbial
182 rdf:type schema:DefinedTerm
183 Nabc6df1388c0474084c7771b6d2d2f4c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
184 schema:name Colitis, Ulcerative
185 rdf:type schema:DefinedTerm
186 Nb2a99d90937e4506b0fd1ee24f9b8ed9 rdf:first sg:person.0757637554.63
187 rdf:rest Ne9d4e87dcae14e379558a613bee9cda1
188 Nb69d93423438488fbf02c8aabecec8be schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
189 schema:name Male
190 rdf:type schema:DefinedTerm
191 Nb8228e35fbbc4f6c9cc5ba4192e17dc9 rdf:first sg:person.01021722152.69
192 rdf:rest N27b7de5952534493a2466b9132d9857a
193 Nbd8d6b7b0cba40fda3b4434e2e10dfa1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
194 schema:name Real-Time Polymerase Chain Reaction
195 rdf:type schema:DefinedTerm
196 Nc2d902f67f8e43d38887a3468b754933 schema:name dimensions_id
197 schema:value pub.1017259214
198 rdf:type schema:PropertyValue
199 Nd3f4cfabae0542e4920a3086686201cf schema:issueNumber 12
200 rdf:type schema:PublicationIssue
201 Nd7bb9f7bc1384e2ba9ea070de136c3d7 rdf:first sg:person.01062432661.50
202 rdf:rest N63137406282345fabb017cbff2caa47c
203 Ndd44a4d6ac56499485b782f042c0b753 rdf:first sg:person.01266313660.51
204 rdf:rest N9435688b50d94124bdba5c0a46d8c125
205 Ne9a2117b22d54362a63d6b846e9eb5d1 schema:name doi
206 schema:value 10.1038/ajg.2012.335
207 rdf:type schema:PropertyValue
208 Ne9d4e87dcae14e379558a613bee9cda1 rdf:first sg:person.0636724513.94
209 rdf:rest Nb8228e35fbbc4f6c9cc5ba4192e17dc9
210 Nf93ad94e51a242f99a7205fd9c265b0f rdf:first sg:person.01015442527.89
211 rdf:rest rdf:nil
212 anzsrc-for:11 schema:inDefinedTermSet anzsrc-for:
213 schema:name Medical and Health Sciences
214 rdf:type schema:DefinedTerm
215 anzsrc-for:1103 schema:inDefinedTermSet anzsrc-for:
216 schema:name Clinical Sciences
217 rdf:type schema:DefinedTerm
218 sg:grant.5151000 http://pending.schema.org/fundedItem sg:pub.10.1038/ajg.2012.335
219 rdf:type schema:MonetaryGrant
220 sg:journal.1412991 schema:issn 0002-9270
221 1572-0241
222 schema:name The American Journal of Gastroenterology
223 schema:publisher Wolters Kluwer
224 rdf:type schema:Periodical
225 sg:person.01015442527.89 schema:affiliation grid-institutes:grid.7107.1
226 schema:familyName Hold
227 schema:givenName Georgina L
228 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01015442527.89
229 rdf:type schema:Person
230 sg:person.01021722152.69 schema:affiliation grid-institutes:grid.7107.1
231 schema:familyName Flint
232 schema:givenName Harry J
233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021722152.69
234 rdf:type schema:Person
235 sg:person.01056401531.08 schema:affiliation grid-institutes:grid.416072.6
236 schema:familyName Bisset
237 schema:givenName W Michael
238 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01056401531.08
239 rdf:type schema:Person
240 sg:person.01062432661.50 schema:affiliation grid-institutes:grid.415571.3
241 schema:familyName Flynn
242 schema:givenName Diana M
243 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01062432661.50
244 rdf:type schema:Person
245 sg:person.01070225054.99 schema:affiliation grid-institutes:grid.415571.3
246 schema:familyName Barclay
247 schema:givenName Andy R
248 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01070225054.99
249 rdf:type schema:Person
250 sg:person.01204453454.42 schema:affiliation grid-institutes:grid.415571.3
251 schema:familyName Bishop
252 schema:givenName Jon
253 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01204453454.42
254 rdf:type schema:Person
255 sg:person.01234470761.11 schema:affiliation grid-institutes:grid.7107.1
256 schema:familyName Mukhopadhya
257 schema:givenName Indrani
258 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01234470761.11
259 rdf:type schema:Person
260 sg:person.01246102213.92 schema:affiliation grid-institutes:grid.415571.3
261 schema:familyName McGrogan
262 schema:givenName Paraic
263 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01246102213.92
264 rdf:type schema:Person
265 sg:person.01266313660.51 schema:affiliation grid-institutes:None
266 schema:familyName Reiff
267 schema:givenName Caroline
268 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01266313660.51
269 rdf:type schema:Person
270 sg:person.01315040754.46 schema:affiliation grid-institutes:grid.7107.1
271 schema:familyName Berry
272 schema:givenName Susan H
273 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315040754.46
274 rdf:type schema:Person
275 sg:person.014036667402.97 schema:affiliation grid-institutes:grid.415571.3
276 schema:familyName Russell
277 schema:givenName Richard K
278 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014036667402.97
279 rdf:type schema:Person
280 sg:person.016336561600.90 schema:affiliation grid-institutes:grid.7107.1
281 schema:familyName Hansen
282 schema:givenName Richard
283 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016336561600.90
284 rdf:type schema:Person
285 sg:person.0636724513.94 schema:affiliation grid-institutes:grid.416072.6
286 schema:familyName Mahdi
287 schema:givenName Gamal
288 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0636724513.94
289 rdf:type schema:Person
290 sg:person.0700142176.81 schema:affiliation grid-institutes:grid.7107.1
291 schema:familyName El-Omar
292 schema:givenName Emad M
293 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700142176.81
294 rdf:type schema:Person
295 sg:person.0714640405.30 schema:affiliation grid-institutes:grid.7107.1
296 schema:familyName McIntosh
297 schema:givenName Freda
298 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714640405.30
299 rdf:type schema:Person
300 sg:person.0715265632.22 schema:affiliation grid-institutes:grid.7107.1
301 schema:familyName Louis
302 schema:givenName Petra
303 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0715265632.22
304 rdf:type schema:Person
305 sg:person.0757637554.63 schema:affiliation grid-institutes:grid.416072.6
306 schema:familyName Loganathan
307 schema:givenName Sabarinathan
308 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0757637554.63
309 rdf:type schema:Person
310 sg:pub.10.1038/ismej.2012.5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051087848
311 https://doi.org/10.1038/ismej.2012.5
312 rdf:type schema:CreativeWork
313 sg:pub.10.1038/nature07008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006761326
314 https://doi.org/10.1038/nature07008
315 rdf:type schema:CreativeWork
316 sg:pub.10.1038/nature11209 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027248000
317 https://doi.org/10.1038/nature11209
318 rdf:type schema:CreativeWork
319 sg:pub.10.1038/nature11234 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007740093
320 https://doi.org/10.1038/nature11234
321 rdf:type schema:CreativeWork
322 sg:pub.10.1038/ng.489 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047391697
323 https://doi.org/10.1038/ng.489
324 rdf:type schema:CreativeWork
325 sg:pub.10.1038/ni.1823 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033326093
326 https://doi.org/10.1038/ni.1823
327 rdf:type schema:CreativeWork
328 sg:pub.10.1038/nm.2069 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042587063
329 https://doi.org/10.1038/nm.2069
330 rdf:type schema:CreativeWork
331 sg:pub.10.1038/nrgastro.2012.14 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032491276
332 https://doi.org/10.1038/nrgastro.2012.14
333 rdf:type schema:CreativeWork
334 sg:pub.10.1038/nri2515 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004447638
335 https://doi.org/10.1038/nri2515
336 rdf:type schema:CreativeWork
337 sg:pub.10.1186/1471-2180-11-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004777032
338 https://doi.org/10.1186/1471-2180-11-7
339 rdf:type schema:CreativeWork
340 grid-institutes:None schema:alternateName Max Planck Institute, Cologne, Germany
341 schema:name Max Planck Institute, Cologne, Germany
342 rdf:type schema:Organization
343 grid-institutes:grid.415571.3 schema:alternateName Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK
344 schema:name Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, UK
345 rdf:type schema:Organization
346 grid-institutes:grid.416072.6 schema:alternateName Department of Paediatric Gastroenterology, Royal Aberdeen Children's Hospital, Aberdeen, UK
347 schema:name Department of Paediatric Gastroenterology, Royal Aberdeen Children's Hospital, Aberdeen, UK
348 rdf:type schema:Organization
349 grid-institutes:grid.7107.1 schema:alternateName Child Health, Royal Aberdeen Children's Hospital, University of Aberdeen, Aberdeen, UK
350 Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK
351 Gut Health Programme, Rowett Institute, University of Aberdeen, Aberdeen, UK
352 schema:name Child Health, Royal Aberdeen Children's Hospital, University of Aberdeen, Aberdeen, UK
353 Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK
354 Gut Health Programme, Rowett Institute, University of Aberdeen, Aberdeen, UK
355 rdf:type schema:Organization
 




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


...