Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2016-10-03

AUTHORS

Yoshiki Vázquez-Baeza, Embriette R. Hyde, Jan S. Suchodolski, Rob Knight

ABSTRACT

Inflammatory bowel disease (IBD) is an autoimmune condition that is difficult to diagnose, and animal models of this disease have questionable human relevance1. Here, we show that the dysbiosis network underlying IBD in dogs differs from that in humans, with some bacteria such as Fusobacterium switching roles between the two species (as Bacteroides fragilis switches roles between humans and mice)2. For example, a dysbiosis index trained on humans fails when applied to dogs, but a dog-specific dysbiosis index achieves high correlations with the overall dog microbial community diversity patterns. In addition, a random forest classifier trained on dog-specific samples achieves high discriminatory power, even when using stool samples rather than the mucosal biopsies required for high discriminatory power in humans2. These relationships were not detected in previously published dog IBD data sets due to their limited sample size and statistical power3. Taken together, these results reveal the need to train host-specific dysbiosis networks and point the way towards a generalized understanding of IBD across different mammalian models. More... »

PAGES

16177

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmicrobiol.2016.177

DOI

http://dx.doi.org/10.1038/nmicrobiol.2016.177

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1034485901

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27694806


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/2008/1107", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Immunology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Dog Diseases", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Dogs", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Dysbiosis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gastrointestinal Microbiome", 
        "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"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Department of Computer Science and Engineering, University of California, San Diego 92093, USA", 
          "id": "http://www.grid.ac/institutes/grid.266100.3", 
          "name": [
            "Department of Computer Science and Engineering, University of California, San Diego 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "V\u00e1zquez-Baeza", 
        "givenName": "Yoshiki", 
        "id": "sg:person.01113460501.49", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01113460501.49"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Pediatrics, University of California, San Diego 92093, USA", 
          "id": "http://www.grid.ac/institutes/grid.266100.3", 
          "name": [
            "Department of Pediatrics, University of California, San Diego 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hyde", 
        "givenName": "Embriette R.", 
        "id": "sg:person.0756335676.60", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756335676.60"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA", 
          "id": "http://www.grid.ac/institutes/grid.264756.4", 
          "name": [
            "Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Suchodolski", 
        "givenName": "Jan S.", 
        "id": "sg:person.0741107142.87", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0741107142.87"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Pediatrics, University of California, San Diego 92093, USA", 
          "id": "http://www.grid.ac/institutes/grid.266100.3", 
          "name": [
            "Department of Computer Science and Engineering, University of California, San Diego 92093, USA", 
            "Department of Pediatrics, University of California, San Diego 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Knight", 
        "givenName": "Rob", 
        "id": "sg:person.016311745377.96", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016311745377.96"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "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.10.1186/2047-217x-2-16", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022546943", 
          "https://doi.org/10.1186/2047-217x-2-16"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ismej.2011.139", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051863807", 
          "https://doi.org/10.1038/ismej.2011.139"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ncomms10460", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037772509", 
          "https://doi.org/10.1038/ncomms10460"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1023/a:1010933404324", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024739340", 
          "https://doi.org/10.1023/a:1010933404324"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.f.303", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009032055", 
          "https://doi.org/10.1038/nmeth.f.303"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf00317345", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039687142", 
          "https://doi.org/10.1007/bf00317345"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2016-10-03", 
    "datePublishedReg": "2016-10-03", 
    "description": "Inflammatory bowel disease (IBD) is an autoimmune condition that is difficult to diagnose, and animal models of this disease have questionable human relevance1. Here, we show that the dysbiosis network underlying IBD in dogs differs from that in humans, with some bacteria such as Fusobacterium switching roles between the two species (as Bacteroides fragilis switches roles between humans and mice)2. For example, a dysbiosis index trained on humans fails when applied to dogs, but a dog-specific dysbiosis index achieves high correlations with the overall dog microbial community diversity patterns. In addition, a random forest classifier trained on dog-specific samples achieves high discriminatory power, even when using stool samples rather than the mucosal biopsies required for high discriminatory power in humans2. These relationships were not detected in previously published dog IBD data sets due to their limited sample size and statistical power3. Taken together, these results reveal the need to train host-specific dysbiosis networks and point the way towards a generalized understanding of IBD across different mammalian models.", 
    "genre": "article", 
    "id": "sg:pub.10.1038/nmicrobiol.2016.177", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1052984", 
        "issn": [
          "2058-5276", 
          "2058-5276"
        ], 
        "name": "Nature Microbiology", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "12", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "1"
      }
    ], 
    "keywords": [
      "inflammatory bowel disease", 
      "bowel disease", 
      "dysbiosis index", 
      "understanding of IBD", 
      "human inflammatory bowel disease", 
      "high discriminatory power", 
      "autoimmune conditions", 
      "mucosal biopsies", 
      "stool samples", 
      "animal models", 
      "discriminatory power", 
      "Bacteroides fragilis", 
      "disease", 
      "dogs", 
      "different mammalian models", 
      "mammalian models", 
      "humans", 
      "community diversity patterns", 
      "sample size", 
      "biopsy", 
      "diversity patterns", 
      "index", 
      "role", 
      "high correlation", 
      "fragilis", 
      "humans2", 
      "samples", 
      "correlation", 
      "bacteria", 
      "need", 
      "species", 
      "patterns", 
      "addition", 
      "relationship", 
      "results", 
      "model", 
      "understanding", 
      "random forest classifier", 
      "conditions", 
      "forest classifier", 
      "size", 
      "data sets", 
      "network", 
      "way", 
      "set", 
      "example", 
      "power", 
      "classifier", 
      "Power3"
    ], 
    "name": "Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks", 
    "pagination": "16177", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1034485901"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nmicrobiol.2016.177"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "27694806"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nmicrobiol.2016.177", 
      "https://app.dimensions.ai/details/publication/pub.1034485901"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-06-01T22:15", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220601/entities/gbq_results/article/article_713.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1038/nmicrobiol.2016.177"
  }
]
 

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/nmicrobiol.2016.177'

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/nmicrobiol.2016.177'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nmicrobiol.2016.177'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nmicrobiol.2016.177'


 

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

192 TRIPLES      22 PREDICATES      89 URIs      74 LITERALS      14 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nmicrobiol.2016.177 schema:about N1d819049158242f0a9e6814185dbbf2d
2 N2f135f47d65a456997361c021c6fe78c
3 N419f73bf9c494694ad264d5f7f5e415f
4 N44de2b0336aa4e51b42535209d5c9d27
5 N607543c240af47dfb497ccf2b1f34fdd
6 Na5988094d39243018d80e944be9dafdb
7 Ncaf08b99a61848ff802d283842ab370e
8 anzsrc-for:11
9 anzsrc-for:1107
10 schema:author Nee966151dd5f4685ac872b5e3bbf3815
11 schema:citation sg:pub.10.1007/bf00317345
12 sg:pub.10.1023/a:1010933404324
13 sg:pub.10.1038/ismej.2011.139
14 sg:pub.10.1038/nbt.2676
15 sg:pub.10.1038/ncomms10460
16 sg:pub.10.1038/nmeth.f.303
17 sg:pub.10.1186/2047-217x-2-16
18 schema:datePublished 2016-10-03
19 schema:datePublishedReg 2016-10-03
20 schema:description Inflammatory bowel disease (IBD) is an autoimmune condition that is difficult to diagnose, and animal models of this disease have questionable human relevance1. Here, we show that the dysbiosis network underlying IBD in dogs differs from that in humans, with some bacteria such as Fusobacterium switching roles between the two species (as Bacteroides fragilis switches roles between humans and mice)2. For example, a dysbiosis index trained on humans fails when applied to dogs, but a dog-specific dysbiosis index achieves high correlations with the overall dog microbial community diversity patterns. In addition, a random forest classifier trained on dog-specific samples achieves high discriminatory power, even when using stool samples rather than the mucosal biopsies required for high discriminatory power in humans2. These relationships were not detected in previously published dog IBD data sets due to their limited sample size and statistical power3. Taken together, these results reveal the need to train host-specific dysbiosis networks and point the way towards a generalized understanding of IBD across different mammalian models.
21 schema:genre article
22 schema:inLanguage en
23 schema:isAccessibleForFree false
24 schema:isPartOf N3e7859142b454f08a4ec23634c30f456
25 N5efb57cad6664391b844fe630cfc5850
26 sg:journal.1052984
27 schema:keywords Bacteroides fragilis
28 Power3
29 addition
30 animal models
31 autoimmune conditions
32 bacteria
33 biopsy
34 bowel disease
35 classifier
36 community diversity patterns
37 conditions
38 correlation
39 data sets
40 different mammalian models
41 discriminatory power
42 disease
43 diversity patterns
44 dogs
45 dysbiosis index
46 example
47 forest classifier
48 fragilis
49 high correlation
50 high discriminatory power
51 human inflammatory bowel disease
52 humans
53 humans2
54 index
55 inflammatory bowel disease
56 mammalian models
57 model
58 mucosal biopsies
59 need
60 network
61 patterns
62 power
63 random forest classifier
64 relationship
65 results
66 role
67 sample size
68 samples
69 set
70 size
71 species
72 stool samples
73 understanding
74 understanding of IBD
75 way
76 schema:name Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks
77 schema:pagination 16177
78 schema:productId N19f1ecdf197b4a0e8bd3996e76a54690
79 N3becd1739c1c4fed85c8c76dfecce7ae
80 N4a03bda6bd904edeadf9eddaa6934d08
81 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034485901
82 https://doi.org/10.1038/nmicrobiol.2016.177
83 schema:sdDatePublished 2022-06-01T22:15
84 schema:sdLicense https://scigraph.springernature.com/explorer/license/
85 schema:sdPublisher Nc823b8b2ce3e4be4992af58b9f2fd1ce
86 schema:url https://doi.org/10.1038/nmicrobiol.2016.177
87 sgo:license sg:explorer/license/
88 sgo:sdDataset articles
89 rdf:type schema:ScholarlyArticle
90 N19f1ecdf197b4a0e8bd3996e76a54690 schema:name doi
91 schema:value 10.1038/nmicrobiol.2016.177
92 rdf:type schema:PropertyValue
93 N1d819049158242f0a9e6814185dbbf2d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
94 schema:name Animals
95 rdf:type schema:DefinedTerm
96 N286683b12d56469aba7f9fc0e6d686dc rdf:first sg:person.0756335676.60
97 rdf:rest N8334955c24fc4bf7b43dba8b05762f48
98 N2f135f47d65a456997361c021c6fe78c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
99 schema:name Inflammatory Bowel Diseases
100 rdf:type schema:DefinedTerm
101 N3becd1739c1c4fed85c8c76dfecce7ae schema:name pubmed_id
102 schema:value 27694806
103 rdf:type schema:PropertyValue
104 N3e7859142b454f08a4ec23634c30f456 schema:issueNumber 12
105 rdf:type schema:PublicationIssue
106 N419f73bf9c494694ad264d5f7f5e415f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
107 schema:name Gastrointestinal Microbiome
108 rdf:type schema:DefinedTerm
109 N44de2b0336aa4e51b42535209d5c9d27 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
110 schema:name Humans
111 rdf:type schema:DefinedTerm
112 N4a03bda6bd904edeadf9eddaa6934d08 schema:name dimensions_id
113 schema:value pub.1034485901
114 rdf:type schema:PropertyValue
115 N4a2a8f586fb543938c403f1bc2ef03d5 rdf:first sg:person.016311745377.96
116 rdf:rest rdf:nil
117 N5efb57cad6664391b844fe630cfc5850 schema:volumeNumber 1
118 rdf:type schema:PublicationVolume
119 N607543c240af47dfb497ccf2b1f34fdd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name Dysbiosis
121 rdf:type schema:DefinedTerm
122 N8334955c24fc4bf7b43dba8b05762f48 rdf:first sg:person.0741107142.87
123 rdf:rest N4a2a8f586fb543938c403f1bc2ef03d5
124 Na5988094d39243018d80e944be9dafdb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Dogs
126 rdf:type schema:DefinedTerm
127 Nc823b8b2ce3e4be4992af58b9f2fd1ce schema:name Springer Nature - SN SciGraph project
128 rdf:type schema:Organization
129 Ncaf08b99a61848ff802d283842ab370e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
130 schema:name Dog Diseases
131 rdf:type schema:DefinedTerm
132 Nee966151dd5f4685ac872b5e3bbf3815 rdf:first sg:person.01113460501.49
133 rdf:rest N286683b12d56469aba7f9fc0e6d686dc
134 anzsrc-for:11 schema:inDefinedTermSet anzsrc-for:
135 schema:name Medical and Health Sciences
136 rdf:type schema:DefinedTerm
137 anzsrc-for:1107 schema:inDefinedTermSet anzsrc-for:
138 schema:name Immunology
139 rdf:type schema:DefinedTerm
140 sg:journal.1052984 schema:issn 2058-5276
141 schema:name Nature Microbiology
142 schema:publisher Springer Nature
143 rdf:type schema:Periodical
144 sg:person.01113460501.49 schema:affiliation grid-institutes:grid.266100.3
145 schema:familyName Vázquez-Baeza
146 schema:givenName Yoshiki
147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01113460501.49
148 rdf:type schema:Person
149 sg:person.016311745377.96 schema:affiliation grid-institutes:grid.266100.3
150 schema:familyName Knight
151 schema:givenName Rob
152 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016311745377.96
153 rdf:type schema:Person
154 sg:person.0741107142.87 schema:affiliation grid-institutes:grid.264756.4
155 schema:familyName Suchodolski
156 schema:givenName Jan S.
157 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0741107142.87
158 rdf:type schema:Person
159 sg:person.0756335676.60 schema:affiliation grid-institutes:grid.266100.3
160 schema:familyName Hyde
161 schema:givenName Embriette R.
162 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756335676.60
163 rdf:type schema:Person
164 sg:pub.10.1007/bf00317345 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039687142
165 https://doi.org/10.1007/bf00317345
166 rdf:type schema:CreativeWork
167 sg:pub.10.1023/a:1010933404324 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024739340
168 https://doi.org/10.1023/a:1010933404324
169 rdf:type schema:CreativeWork
170 sg:pub.10.1038/ismej.2011.139 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051863807
171 https://doi.org/10.1038/ismej.2011.139
172 rdf:type schema:CreativeWork
173 sg:pub.10.1038/nbt.2676 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034019934
174 https://doi.org/10.1038/nbt.2676
175 rdf:type schema:CreativeWork
176 sg:pub.10.1038/ncomms10460 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037772509
177 https://doi.org/10.1038/ncomms10460
178 rdf:type schema:CreativeWork
179 sg:pub.10.1038/nmeth.f.303 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009032055
180 https://doi.org/10.1038/nmeth.f.303
181 rdf:type schema:CreativeWork
182 sg:pub.10.1186/2047-217x-2-16 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022546943
183 https://doi.org/10.1186/2047-217x-2-16
184 rdf:type schema:CreativeWork
185 grid-institutes:grid.264756.4 schema:alternateName Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
186 schema:name Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
187 rdf:type schema:Organization
188 grid-institutes:grid.266100.3 schema:alternateName Department of Computer Science and Engineering, University of California, San Diego 92093, USA
189 Department of Pediatrics, University of California, San Diego 92093, USA
190 schema:name Department of Computer Science and Engineering, University of California, San Diego 92093, USA
191 Department of Pediatrics, University of California, San Diego 92093, USA
192 rdf:type schema:Organization
 




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


...