Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-11-25

AUTHORS

Euan Watt, Matthew R. Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I. Murray, Emad El-Omar, Georgina L. Hold

ABSTRACT

BackgroundSequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size. We collected paired colonic biopsies and lavage samples from subjects who were attending for colorectal cancer screening colonoscopy.ResultsNext-generation sequencing and qPCR validation were performed with multiple bioinformatics analyses to determine the composition and predict function of the microbiota. Colonic lavage samples contained significantly higher numbers of operational taxonomic units (OTUs) compared to corresponding biopsy samples, however, diversity and evenness between lavage and biopsy samples were similar. The differences seen were driven by the presence of 12 OTUs which were in higher relative abundance in biopsies and were either not present or in low relative abundance in lavage samples, whilst a further 3 OTUs were present in higher amounts in the lavage samples compared to biopsy samples. However, predicted functional community profiling based on 16S ribosomal ribonucleic acid (rRNA) data indicated minimal differences between sample types.ConclusionsWe propose that colonic lavage samples provide a relatively accurate representation of biopsy microbiota composition and should be considered where biopsy size is an issue. More... »

PAGES

61

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s40168-016-0207-9

DOI

http://dx.doi.org/10.1186/s40168-016-0207-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1034631312

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27884202


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/2008/0605", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Microbiology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacteria", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Biopsy", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Colon", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Colonoscopy", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Computational Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Feces", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gastrointestinal Microbiome", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "High-Throughput Nucleotide Sequencing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Intestinal Mucosa", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA, Ribosomal, 16S", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Therapeutic Irrigation", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Watt", 
        "givenName": "Euan", 
        "id": "sg:person.01315553340.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315553340.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Centre for Genome Enabled Biology and Medicine, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Centre for Genome Enabled Biology and Medicine, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gemmell", 
        "givenName": "Matthew R.", 
        "id": "sg:person.07662543371.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07662543371.38"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Berry", 
        "givenName": "Susan", 
        "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, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Glaire", 
        "givenName": "Mark", 
        "id": "sg:person.01313707270.60", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01313707270.60"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Farquharson", 
        "givenName": "Freda", 
        "id": "sg:person.0616671410.60", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0616671410.60"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, 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": "Department of Pathology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Department of Pathology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Murray", 
        "givenName": "Graeme I.", 
        "id": "sg:person.015443324252.23", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015443324252.23"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "St George and Sutherland Clinical School, University of New South Wales, St George Hospital, Short Street, Kogarah, NSW 2217, Sydney, Australia", 
          "id": "http://www.grid.ac/institutes/grid.1005.4", 
          "name": [
            "Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK", 
            "St George and Sutherland Clinical School, University of New South Wales, St George Hospital, Short Street, Kogarah, NSW 2217, Sydney, Australia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "El-Omar", 
        "givenName": "Emad", 
        "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, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK", 
          "id": "http://www.grid.ac/institutes/grid.7107.1", 
          "name": [
            "Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, 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/srep16350", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034137020", 
          "https://doi.org/10.1038/srep16350"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature08821", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050498034", 
          "https://doi.org/10.1038/nature08821"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00248-013-0192-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014903265", 
          "https://doi.org/10.1007/s00248-013-0192-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/2049-2618-1-16", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012507547", 
          "https://doi.org/10.1186/2049-2618-1-16"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro3344", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045936127", 
          "https://doi.org/10.1038/nrmicro3344"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2011-12-6-r60", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000243423", 
          "https://doi.org/10.1186/gb-2011-12-6-r60"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s12915-014-0087-z", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027737035", 
          "https://doi.org/10.1186/s12915-014-0087-z"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ctg.2015.54", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026026372", 
          "https://doi.org/10.1038/ctg.2015.54"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ajg.2012.335", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017259214", 
          "https://doi.org/10.1038/ajg.2012.335"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00248-010-9738-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013941272", 
          "https://doi.org/10.1007/s00248-010-9738-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.2676", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034019934", 
          "https://doi.org/10.1038/nbt.2676"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/163688a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011831556", 
          "https://doi.org/10.1038/163688a0"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2016-11-25", 
    "datePublishedReg": "2016-11-25", 
    "description": "BackgroundSequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size. We collected paired colonic biopsies and lavage samples from subjects who were attending for colorectal cancer screening colonoscopy.ResultsNext-generation sequencing and qPCR validation were performed with multiple bioinformatics analyses to determine the composition and predict function of the microbiota. Colonic lavage samples contained significantly higher numbers of operational taxonomic units (OTUs) compared to corresponding biopsy samples, however, diversity and evenness between lavage and biopsy samples were similar. The differences seen were driven by the presence of 12 OTUs which were in higher relative abundance in biopsies and were either not present or in low relative abundance in lavage samples, whilst a further 3 OTUs were present in higher amounts in the lavage samples compared to biopsy samples. However, predicted functional community profiling based on 16S ribosomal ribonucleic acid (rRNA) data indicated minimal differences between sample types.ConclusionsWe propose that colonic lavage samples provide a relatively accurate representation of biopsy microbiota composition and should be considered where biopsy size is an issue.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/s40168-016-0207-9", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3959411", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.4576161", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1048878", 
        "issn": [
          "2049-2618"
        ], 
        "name": "Microbiome", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "4"
      }
    ], 
    "keywords": [
      "operational taxonomic units", 
      "relative abundance", 
      "multiple bioinformatics analyses", 
      "high relative abundance", 
      "low relative abundance", 
      "taxonomic units", 
      "community profiling", 
      "bioinformatics analysis", 
      "qPCR validation", 
      "diversity composition", 
      "microbial composition", 
      "acid data", 
      "abundance", 
      "gut microbiota", 
      "microbiota composition", 
      "microbiota analysis", 
      "microbiota", 
      "fecal samples", 
      "evenness", 
      "fecal microbiota analysis", 
      "higher number", 
      "endoscopic colonic biopsies", 
      "sequencing", 
      "diversity", 
      "profiling", 
      "sample types", 
      "high amounts", 
      "composition", 
      "sufficient material", 
      "colonic biopsies", 
      "lavage samples", 
      "biopsy samples", 
      "most studies", 
      "colorectal cancer screening colonoscopy", 
      "analysis", 
      "function", 
      "size", 
      "colonic lavage", 
      "screening colonoscopy", 
      "differences", 
      "minimal differences", 
      "biopsy", 
      "presence", 
      "biopsy size", 
      "proxy", 
      "samples", 
      "lavage", 
      "number", 
      "types", 
      "suitability", 
      "amount", 
      "sample size", 
      "study", 
      "colonoscopy", 
      "data", 
      "complexity", 
      "ConclusionsWe", 
      "limitations", 
      "validation", 
      "approach", 
      "subjects", 
      "units", 
      "accurate representation", 
      "materials", 
      "issues", 
      "representation"
    ], 
    "name": "Extending colonic mucosal microbiome analysis\u2014assessment of colonic lavage as a proxy for endoscopic colonic biopsies", 
    "pagination": "61", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1034631312"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/s40168-016-0207-9"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "27884202"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/s40168-016-0207-9", 
      "https://app.dimensions.ai/details/publication/pub.1034631312"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-11-24T21:00", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20221124/entities/gbq_results/article/article_681.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/s40168-016-0207-9"
  }
]
 

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.10.1186/s40168-016-0207-9'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s40168-016-0207-9'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s40168-016-0207-9'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s40168-016-0207-9'


 

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

300 TRIPLES      21 PREDICATES      117 URIs      97 LITERALS      21 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/s40168-016-0207-9 schema:about N14026124978f4a7fb1c2b0ce10553580
2 N1dc0d1a8805544ec8a32da5ded2a8173
3 N3ac5044b54ed405a8ae8ce47c178464c
4 N45b9ac6fdbd84a47aa45cb910f32096a
5 N46defedfe1ff4f7c8fd6d90d990ca5a6
6 N5ac0ac57e3da43da850ddd88532e623c
7 N6409439a429b41f1ad6e7f7387f2618f
8 N686aa1a60db14746a61cbb0328c17691
9 N6c5a0cba3eec4f6b9b603042680e85e9
10 N92c1e1a55a5b4566a4a9fab721292163
11 Naae1383779c74b58b0ab1dad4eadac6a
12 Nb45d0f5510cb4d46af8dd48097394407
13 Nc4fe16921278415393ee4370c94bf4b2
14 Ned9262ecdd184dd68849fdf200e70bd6
15 anzsrc-for:06
16 anzsrc-for:0605
17 schema:author N7f1a95ab5a01465fac40b889552eaafa
18 schema:citation sg:pub.10.1007/s00248-010-9738-y
19 sg:pub.10.1007/s00248-013-0192-5
20 sg:pub.10.1038/163688a0
21 sg:pub.10.1038/ajg.2012.335
22 sg:pub.10.1038/ctg.2015.54
23 sg:pub.10.1038/nature08821
24 sg:pub.10.1038/nbt.2676
25 sg:pub.10.1038/nrmicro3344
26 sg:pub.10.1038/srep16350
27 sg:pub.10.1186/2049-2618-1-16
28 sg:pub.10.1186/gb-2011-12-6-r60
29 sg:pub.10.1186/s12915-014-0087-z
30 schema:datePublished 2016-11-25
31 schema:datePublishedReg 2016-11-25
32 schema:description BackgroundSequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size. We collected paired colonic biopsies and lavage samples from subjects who were attending for colorectal cancer screening colonoscopy.ResultsNext-generation sequencing and qPCR validation were performed with multiple bioinformatics analyses to determine the composition and predict function of the microbiota. Colonic lavage samples contained significantly higher numbers of operational taxonomic units (OTUs) compared to corresponding biopsy samples, however, diversity and evenness between lavage and biopsy samples were similar. The differences seen were driven by the presence of 12 OTUs which were in higher relative abundance in biopsies and were either not present or in low relative abundance in lavage samples, whilst a further 3 OTUs were present in higher amounts in the lavage samples compared to biopsy samples. However, predicted functional community profiling based on 16S ribosomal ribonucleic acid (rRNA) data indicated minimal differences between sample types.ConclusionsWe propose that colonic lavage samples provide a relatively accurate representation of biopsy microbiota composition and should be considered where biopsy size is an issue.
33 schema:genre article
34 schema:isAccessibleForFree true
35 schema:isPartOf N95b7eee0e6024154834a550ccde35b72
36 Nf925fe4aa1284394aa4e5126fff0cb20
37 sg:journal.1048878
38 schema:keywords ConclusionsWe
39 abundance
40 accurate representation
41 acid data
42 amount
43 analysis
44 approach
45 bioinformatics analysis
46 biopsy
47 biopsy samples
48 biopsy size
49 colonic biopsies
50 colonic lavage
51 colonoscopy
52 colorectal cancer screening colonoscopy
53 community profiling
54 complexity
55 composition
56 data
57 differences
58 diversity
59 diversity composition
60 endoscopic colonic biopsies
61 evenness
62 fecal microbiota analysis
63 fecal samples
64 function
65 gut microbiota
66 high amounts
67 high relative abundance
68 higher number
69 issues
70 lavage
71 lavage samples
72 limitations
73 low relative abundance
74 materials
75 microbial composition
76 microbiota
77 microbiota analysis
78 microbiota composition
79 minimal differences
80 most studies
81 multiple bioinformatics analyses
82 number
83 operational taxonomic units
84 presence
85 profiling
86 proxy
87 qPCR validation
88 relative abundance
89 representation
90 sample size
91 sample types
92 samples
93 screening colonoscopy
94 sequencing
95 size
96 study
97 subjects
98 sufficient material
99 suitability
100 taxonomic units
101 types
102 units
103 validation
104 schema:name Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies
105 schema:pagination 61
106 schema:productId N20f0fae93dad43fa85bdfe3544477a91
107 N867d9eea82444053a42412bab76df471
108 Nf743218bb15148c9bb88b76250c52a0d
109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034631312
110 https://doi.org/10.1186/s40168-016-0207-9
111 schema:sdDatePublished 2022-11-24T21:00
112 schema:sdLicense https://scigraph.springernature.com/explorer/license/
113 schema:sdPublisher Nfa8dbbeb8fea4ceebd651cd50cd43de7
114 schema:url https://doi.org/10.1186/s40168-016-0207-9
115 sgo:license sg:explorer/license/
116 sgo:sdDataset articles
117 rdf:type schema:ScholarlyArticle
118 N14026124978f4a7fb1c2b0ce10553580 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
119 schema:name Bacteria
120 rdf:type schema:DefinedTerm
121 N1dc0d1a8805544ec8a32da5ded2a8173 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name RNA, Ribosomal, 16S
123 rdf:type schema:DefinedTerm
124 N20f0fae93dad43fa85bdfe3544477a91 schema:name doi
125 schema:value 10.1186/s40168-016-0207-9
126 rdf:type schema:PropertyValue
127 N3ac5044b54ed405a8ae8ce47c178464c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
128 schema:name Humans
129 rdf:type schema:DefinedTerm
130 N45b9ac6fdbd84a47aa45cb910f32096a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
131 schema:name Therapeutic Irrigation
132 rdf:type schema:DefinedTerm
133 N46defedfe1ff4f7c8fd6d90d990ca5a6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
134 schema:name Sequence Analysis, DNA
135 rdf:type schema:DefinedTerm
136 N4f9d91663f6447d5a99389fac3ea501a rdf:first sg:person.0715265632.22
137 rdf:rest Nd1c0ef91b1dc48c0bedd531a916e515a
138 N5424ea143706459db4f6913c9120fa49 rdf:first sg:person.01015442527.89
139 rdf:rest rdf:nil
140 N5ac0ac57e3da43da850ddd88532e623c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
141 schema:name Colon
142 rdf:type schema:DefinedTerm
143 N6409439a429b41f1ad6e7f7387f2618f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
144 schema:name Colonoscopy
145 rdf:type schema:DefinedTerm
146 N686aa1a60db14746a61cbb0328c17691 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
147 schema:name Intestinal Mucosa
148 rdf:type schema:DefinedTerm
149 N6c5a0cba3eec4f6b9b603042680e85e9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
150 schema:name Base Sequence
151 rdf:type schema:DefinedTerm
152 N7f1a95ab5a01465fac40b889552eaafa rdf:first sg:person.01315553340.33
153 rdf:rest Nd68af6b0cba84bfe9a86b4801830b12b
154 N867d9eea82444053a42412bab76df471 schema:name dimensions_id
155 schema:value pub.1034631312
156 rdf:type schema:PropertyValue
157 N92c1e1a55a5b4566a4a9fab721292163 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
158 schema:name Biopsy
159 rdf:type schema:DefinedTerm
160 N95b7eee0e6024154834a550ccde35b72 schema:issueNumber 1
161 rdf:type schema:PublicationIssue
162 Na91102755f6d4c758e5357f8a468e33c rdf:first sg:person.01313707270.60
163 rdf:rest Nf96374bd042d47519c4aa45d80723c70
164 Naae1383779c74b58b0ab1dad4eadac6a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
165 schema:name Feces
166 rdf:type schema:DefinedTerm
167 Nb45d0f5510cb4d46af8dd48097394407 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
168 schema:name High-Throughput Nucleotide Sequencing
169 rdf:type schema:DefinedTerm
170 Nc4fe16921278415393ee4370c94bf4b2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
171 schema:name Gastrointestinal Microbiome
172 rdf:type schema:DefinedTerm
173 Nd1c0ef91b1dc48c0bedd531a916e515a rdf:first sg:person.015443324252.23
174 rdf:rest Ne5879e58880c4d34a60531b8ad957574
175 Nd68af6b0cba84bfe9a86b4801830b12b rdf:first sg:person.07662543371.38
176 rdf:rest Nfe166c4334814cad8f1bdb4f81f88421
177 Ne5879e58880c4d34a60531b8ad957574 rdf:first sg:person.0700142176.81
178 rdf:rest N5424ea143706459db4f6913c9120fa49
179 Ned9262ecdd184dd68849fdf200e70bd6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
180 schema:name Computational Biology
181 rdf:type schema:DefinedTerm
182 Nf743218bb15148c9bb88b76250c52a0d schema:name pubmed_id
183 schema:value 27884202
184 rdf:type schema:PropertyValue
185 Nf925fe4aa1284394aa4e5126fff0cb20 schema:volumeNumber 4
186 rdf:type schema:PublicationVolume
187 Nf96374bd042d47519c4aa45d80723c70 rdf:first sg:person.0616671410.60
188 rdf:rest N4f9d91663f6447d5a99389fac3ea501a
189 Nfa8dbbeb8fea4ceebd651cd50cd43de7 schema:name Springer Nature - SN SciGraph project
190 rdf:type schema:Organization
191 Nfe166c4334814cad8f1bdb4f81f88421 rdf:first sg:person.01315040754.46
192 rdf:rest Na91102755f6d4c758e5357f8a468e33c
193 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
194 schema:name Biological Sciences
195 rdf:type schema:DefinedTerm
196 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
197 schema:name Microbiology
198 rdf:type schema:DefinedTerm
199 sg:grant.3959411 http://pending.schema.org/fundedItem sg:pub.10.1186/s40168-016-0207-9
200 rdf:type schema:MonetaryGrant
201 sg:grant.4576161 http://pending.schema.org/fundedItem sg:pub.10.1186/s40168-016-0207-9
202 rdf:type schema:MonetaryGrant
203 sg:journal.1048878 schema:issn 2049-2618
204 schema:name Microbiome
205 schema:publisher Springer Nature
206 rdf:type schema:Periodical
207 sg:person.01015442527.89 schema:affiliation grid-institutes:grid.7107.1
208 schema:familyName Hold
209 schema:givenName Georgina L.
210 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01015442527.89
211 rdf:type schema:Person
212 sg:person.01313707270.60 schema:affiliation grid-institutes:grid.7107.1
213 schema:familyName Glaire
214 schema:givenName Mark
215 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01313707270.60
216 rdf:type schema:Person
217 sg:person.01315040754.46 schema:affiliation grid-institutes:grid.7107.1
218 schema:familyName Berry
219 schema:givenName Susan
220 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315040754.46
221 rdf:type schema:Person
222 sg:person.01315553340.33 schema:affiliation grid-institutes:grid.7107.1
223 schema:familyName Watt
224 schema:givenName Euan
225 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315553340.33
226 rdf:type schema:Person
227 sg:person.015443324252.23 schema:affiliation grid-institutes:grid.7107.1
228 schema:familyName Murray
229 schema:givenName Graeme I.
230 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015443324252.23
231 rdf:type schema:Person
232 sg:person.0616671410.60 schema:affiliation grid-institutes:grid.7107.1
233 schema:familyName Farquharson
234 schema:givenName Freda
235 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0616671410.60
236 rdf:type schema:Person
237 sg:person.0700142176.81 schema:affiliation grid-institutes:grid.1005.4
238 schema:familyName El-Omar
239 schema:givenName Emad
240 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700142176.81
241 rdf:type schema:Person
242 sg:person.0715265632.22 schema:affiliation grid-institutes:grid.7107.1
243 schema:familyName Louis
244 schema:givenName Petra
245 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0715265632.22
246 rdf:type schema:Person
247 sg:person.07662543371.38 schema:affiliation grid-institutes:grid.7107.1
248 schema:familyName Gemmell
249 schema:givenName Matthew R.
250 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07662543371.38
251 rdf:type schema:Person
252 sg:pub.10.1007/s00248-010-9738-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1013941272
253 https://doi.org/10.1007/s00248-010-9738-y
254 rdf:type schema:CreativeWork
255 sg:pub.10.1007/s00248-013-0192-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014903265
256 https://doi.org/10.1007/s00248-013-0192-5
257 rdf:type schema:CreativeWork
258 sg:pub.10.1038/163688a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011831556
259 https://doi.org/10.1038/163688a0
260 rdf:type schema:CreativeWork
261 sg:pub.10.1038/ajg.2012.335 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017259214
262 https://doi.org/10.1038/ajg.2012.335
263 rdf:type schema:CreativeWork
264 sg:pub.10.1038/ctg.2015.54 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026026372
265 https://doi.org/10.1038/ctg.2015.54
266 rdf:type schema:CreativeWork
267 sg:pub.10.1038/nature08821 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050498034
268 https://doi.org/10.1038/nature08821
269 rdf:type schema:CreativeWork
270 sg:pub.10.1038/nbt.2676 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034019934
271 https://doi.org/10.1038/nbt.2676
272 rdf:type schema:CreativeWork
273 sg:pub.10.1038/nrmicro3344 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045936127
274 https://doi.org/10.1038/nrmicro3344
275 rdf:type schema:CreativeWork
276 sg:pub.10.1038/srep16350 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034137020
277 https://doi.org/10.1038/srep16350
278 rdf:type schema:CreativeWork
279 sg:pub.10.1186/2049-2618-1-16 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012507547
280 https://doi.org/10.1186/2049-2618-1-16
281 rdf:type schema:CreativeWork
282 sg:pub.10.1186/gb-2011-12-6-r60 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000243423
283 https://doi.org/10.1186/gb-2011-12-6-r60
284 rdf:type schema:CreativeWork
285 sg:pub.10.1186/s12915-014-0087-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1027737035
286 https://doi.org/10.1186/s12915-014-0087-z
287 rdf:type schema:CreativeWork
288 grid-institutes:grid.1005.4 schema:alternateName St George and Sutherland Clinical School, University of New South Wales, St George Hospital, Short Street, Kogarah, NSW 2217, Sydney, Australia
289 schema:name Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK
290 St George and Sutherland Clinical School, University of New South Wales, St George Hospital, Short Street, Kogarah, NSW 2217, Sydney, Australia
291 rdf:type schema:Organization
292 grid-institutes:grid.7107.1 schema:alternateName Centre for Genome Enabled Biology and Medicine, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK
293 Department of Pathology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK
294 Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK
295 Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK
296 schema:name Centre for Genome Enabled Biology and Medicine, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK
297 Department of Pathology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK
298 Gastrointestinal Research Group, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK
299 Rowett Institute of Nutrition and Health, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD, Aberdeen, UK
300 rdf:type schema:Organization
 




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


...